@article{davis_angle_ferl_gilbert_grunden_rials_senseman_thompson_toews_2024, title={The scholarship of honorifics}, volume={3}, ISSN={["1435-0653"]}, DOI={10.1002/csc2.21219}, abstractNote={Abstract}, journal={CROP SCIENCE}, author={Davis, John M. and Angle, J. Scott and Ferl, Robert J. and Gilbert, Robert A. and Grunden, Amy M. and Rials, Tim G. and Senseman, Scott A. and Thompson, Gary A. and Toews, Michael D.}, year={2024}, month={Mar} } @article{somalinga_foss_grunden_2023, title={Biochemical characterization of a psychrophilic and halotolerant a-carbonic anhydrase from a deep-sea bacterium, Photobacterium profundum}, volume={9}, ISSN={["2471-1888"]}, DOI={10.3934/microbiol.2023028}, abstractNote={

Prokaryotic α–carbonic anhydrases (α-CA) are metalloenzymes that catalyze the reversible hydration of CO2 to bicarbonate and proton. We had reported the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum SS9. In this manuscript, we report the first biochemical characterization of P. profundum α–CA (PprCA) which revealed several catalytic properties that are atypical for this class of CA's. Purified PprCA exhibited maximal catalytic activity at psychrophilic temperatures with substantial decrease in activity at mesophilic and thermophilic range. Similar to other α–CA's, Ppr9A showed peak activity at alkaline pH (pH 11), although, PprCA retained 88% of its activity even at acidic pH (pH 5). Exposing PprCA to varying concentrations of oxidizing and reducing agents revealed that N-terminal cysteine residues in PprCA may play a role in the structural stability of the enzyme. Although inefficient in CO2 hydration activity under mesophilic and thermophilic temperatures, PprCA exhibited salt-dependent thermotolerance and catalytic activity under extreme halophilic conditions. Similar to other well-characterized α–CA's, PprCA is also inhibited by monovalent anions even at low concentrations. Finally, we demonstrate that PprCA accelerates CO2 biomineralization to calcium carbonate under alkaline conditions.

}, number={3}, journal={AIMS MICROBIOLOGY}, author={Somalinga, Vijayakumar and Foss, Emily and Grunden, Amy M.}, year={2023}, pages={540–553} } @article{ortiz-medina_poole_grunden_call_2023, title={Nitrogen Fixation and Ammonium Assimilation Pathway Expression of Geobacter sulfurreducens Changes in Response to the Anode Potential in Microbial Electrochemical Cells}, volume={3}, ISSN={["1098-5336"]}, DOI={10.1128/aem.02073-22}, abstractNote={Biological nitrogen fixation coupled with ammonium recovery provides a sustainable alternative to the carbon-, water-, and energy-intensive Haber-Bosch process. Aerobic biological nitrogen fixation technologies are hindered by oxygen gas inhibition of the nitrogenase enzyme.}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Ortiz-Medina, Juan F. and Poole, Mark R. and Grunden, Amy M. and Call, Douglas F.}, year={2023}, month={Mar} } @article{cuebas-irizarry_grunden_2023, title={Streptomyces spp. as biocatalyst sources in pulp and paper and textile industries: Biodegradation, bioconversion and valorization of waste}, volume={4}, ISSN={["1751-7915"]}, url={https://doi.org/10.1111/1751-7915.14258}, DOI={10.1111/1751-7915.14258}, abstractNote={Abstract}, journal={MICROBIAL BIOTECHNOLOGY}, author={Cuebas-Irizarry, Mara F. and Grunden, Amy M.}, year={2023}, month={Apr} } @article{zwilling_whitham_zambrano_pifano_grunden_jameel_venditti_gonzalez_2023, title={Survivability of Salmonella Typhimurium (ATCC 14208) and Listeria innocua (ATCC 51742) on lignocellulosic materials for paper packaging}, volume={9}, ISSN={["2405-8440"]}, url={https://doi.org/10.1016/j.heliyon.2023.e14122}, DOI={10.1016/j.heliyon.2023.e14122}, abstractNote={Lignocellulosic materials are widely used for food packaging due to their renewable and biodegradable nature. However, their porous and absorptive properties can lead to the uptake and retention of bacteria during food processing, transportation, and storage, which pose a potential risk for outbreaks of foodborne disease. Thus, it is of great importance to understand how bacteria proliferate and survive on lignocellulosic surfaces. The aim of this research was to compare the growth and survivability of Salmonella Typhimurium and Listeria innocua on bleached and unbleached paper packaging materials. Two different paper materials were fabricated to simulate linerboard from fully bleached and unbleached market pulps and inoculated with each bacterium at high bacterial loads (107 CFU). The bacteria propagated during the first 48 h of incubation and persisted at very high levels (>107 CFU/cm2) for 40 days for all paper and bacterium types. However, the unbleached paper allowed for a greater degree of bacterial growth to occur compared to bleached paper, suspected to be due to the more hydrophobic nature of the unbleached, lignin-containing fibers. Several other considerations may also alter the behavior of bacteria on lignocellulosic materials, such as storage conditions, nutrient availability, and chemical composition of the fibers.}, number={3}, journal={HELIYON}, author={Zwilling, Jacob D. and Whitham, Jason and Zambrano, Franklin and Pifano, Alonzo and Grunden, Amy and Jameel, Hasan and Venditti, Richard and Gonzalez, Ronalds}, year={2023}, month={Mar} } @article{whitham_grunden_2023, title={Trimming and Decontamination of Metagenomic Data can Significantly Impact Assembly and Binning Metrics, Phylogenomic and Functional Analysis}, volume={18}, ISSN={["2212-392X"]}, DOI={10.2174/1574893618666230227145952}, abstractNote={ Background: Investigators using metagenomic sequencing to study microbiomes often trim and decontaminate reads without knowing their effect on downstream analyses. }, number={5}, journal={CURRENT BIOINFORMATICS}, author={Whitham, Jason M. and Grunden, Amy M.}, year={2023}, pages={428–439} } @article{zervas_ellegaard-jensen_hennessy_bak_guan_horn herms_molina zamudio_thybo ganzhorn_muller-stover_ahmad_et al._2022, title={Diversity and Structure of Bacterial Communities in Different Rhizocompartments (Rhizoplane, Rhizosphere, and Bulk) at Flag Leaf Emergence in Four Winter Wheat Varieties}, volume={4}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00222-22}, abstractNote={Understanding basic interactions at the plant-soil interphase is critical if we are to exploit natural microbial communities for improved crop resilience. We report here 16S amplicon sequencing data from 3 rhizocompartments of 4 wheat cultivars grown under controlled greenhouse conditions. We observed that rhizocompartments and cultivar affect the community composition.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Zervas, Athanasios and Ellegaard-Jensen, Lea and Hennessy, Rosanna C. and Bak, Frederik and Guan, Ying and Horn Herms, Courtney and Molina Zamudio, Kitzia Yashvelt and Thybo Ganzhorn, Dorthe and Muller-Stover, Dorette Sophie and Ahmad, Jabeen and et al.}, year={2022}, month={Apr} } @article{ahmad_zervas_ellegaard-jensen_hennessy_carbone_cornish_muller-stover_grunden_jacobsen_nicolaisen_2022, title={Microbial Diversity in Four Rhizocompartments (Bulk Soil, Rhizosphere, Rhizoplane, and Endosphere) of Four Winter Wheat Varieties at the Fully Emerged Flag Leaf Growth Stage}, volume={10}, ISSN={["2576-098X"]}, DOI={10.1128/mra.00663-22}, abstractNote={Community composition and recruitment are important elements of plant-microbe interactions and may provide insights for plant development and resilience. The results of 16S rRNA amplicon sequencing from four rhizocompartments for four wheat cultivars grown under controlled conditions and sampled after flag leaf emergence are provided. Data demonstrate differences in microbial communities according to rhizocompartment.}, journal={MICROBIOLOGY RESOURCE ANNOUNCEMENTS}, author={Ahmad, Jabeen and Zervas, Athanasios and Ellegaard-Jensen, Lea and Hennessy, Rosanna C. and Carbone, Ignazio and Cornish, Vicki and Muller-Stover, Dorette Sophie and Grunden, Amy and Jacobsen, Carsten S. and Nicolaisen, Mette Haubjerg}, year={2022}, month={Oct} } @article{wapshott-stehli_myers_quesada_grunden_stapelmann_2022, title={Plasma-driven biocatalysis: In situ hydrogen peroxide production with an atmospheric pressure plasma jet increases the performance of OleT(JE) when compared to adding the same molar amount of hydrogen peroxide in bolus}, volume={2}, ISSN={["1612-8869"]}, url={https://doi.org/10.1002/ppap.202100160}, DOI={10.1002/ppap.202100160}, abstractNote={Abstract}, journal={PLASMA PROCESSES AND POLYMERS}, author={Wapshott-Stehli, Hannah L. and Myers, Brayden G. and Quesada, Maria J. Herrera and Grunden, Amy and Stapelmann, Katharina}, year={2022}, month={Feb} } @article{sanders_grunden_dunn_2021, title={A review of clothing microbiology: the history of clothing and the role of microbes in textiles}, volume={17}, ISBN={1744-957X}, DOI={10.1098/rsbl.2020.0700}, abstractNote={Humans have worn clothing for thousands of years, and since its invention, clothing has evolved from its simple utilitarian function for survival to become an integral part of society. While much consideration has been given to the broad environmental impacts of the textile and laundering industries, little is known about the impact wearing clothing has had on the human microbiome, particularly that of the skin, despite our long history with clothing. This review discusses the history of clothing and the evolution of textiles, what is and is not known about microbial persistence on and degradation of various fibres, and what opportunities for the industrial and environmental application of clothing microbiology exist for the future.}, number={1}, journal={BIOLOGY LETTERS}, author={Sanders, Deaja and Grunden, Amy and Dunn, Robert R.}, year={2021} } @misc{brown_pawlak_grunden_2021, title={Bacterial valorization of pulp and paper industry process streams and waste}, volume={105}, ISSN={["1432-0614"]}, url={https://doi.org/10.1007/s00253-021-11107-2}, DOI={10.1007/s00253-021-11107-2}, abstractNote={The pulp and paper industry is a major source of lignocellulose-containing streams. The components of lignocellulose material are lignin, hemicellulose, and cellulose that may be hydrolyzed into their smaller components and used as feedstocks for valorization efforts. Much of this material is contained in underutilized streams and waste products, such as black liquor, pulp and paper sludge, and wastewater. Bacterial fermentation strategies have suitable potential to upgrade lignocellulosic biomass contained in these streams to value-added chemicals. Bacterial conversion allows for a sustainable and economically feasible approach to valorizing these streams, which can bolster and expand applications of the pulp and paper industry. This review discusses the composition of pulp and paper streams, bacterial isolates from process streams that can be used for lignocellulose biotransformations, and technological approaches for improving valorization efforts. KEY POINTS: • Reviews the conversion of pulp and paper industry waste by bacterial isolates. • Metabolic pathways for the breakdown of lignocellulose components. • Methods for isolating bacteria, determining value-added products, and increasing product yields.}, number={4}, journal={APPLIED MICROBIOLOGY AND BIOTECHNOLOGY}, publisher={Springer Science and Business Media LLC}, author={Brown, Dylan M. and Pawlak, Joel and Grunden, Amy M.}, year={2021}, month={Feb}, pages={1345–1363} } @article{wapshott-stehli_grunden_2021, title={In situ H2O2 generation methods in the context of enzyme biocatalysis}, volume={145}, ISSN={["1879-0909"]}, DOI={10.1016/j.enzmictec.2021.109744}, abstractNote={Hydrogen peroxide is a versatile oxidant that has use in medical and biotechnology industries. Many enzymes require this oxidant as a reaction mediator in order to undergo their oxygenation chemistries. While there is a reliable method for generating hydrogen peroxide via an anthraquinone cycle, there are several advantages for generating hydrogen in situ. As highlighted in this review, this is particularly beneficial in the case of biocatalysts that require hydrogen peroxide as a reaction mediator because the exogenous addition of hydrogen peroxide can damage their reactive heme centers and render them inactive. In addition, generation of hydrogen peroxide in situ does not dilute the reaction mixture and cause solution parameters to change. The environment would also benefit from a hydrogen peroxide synthesis cycle that does not rely on nonrenewable chemicals obtained from fossil fuels. Generation of hydrogen peroxide in situ for biocatalysis using enzymes, bioelectrocatalyis, photocatalysis, and cold temperature plasmas are addressed. Particular emphasis is given to reaction processes that support high total turnover numbers (TTNs) of the hydrogen peroxide-requiring enzymes. Discussion of innovations in the use of hydrogen peroxide-producing enzyme cascades for antimicrobial activity, wastewater effluent treatment, and biosensors are also included.}, journal={ENZYME AND MICROBIAL TECHNOLOGY}, author={Wapshott-Stehli, Hannah L. and Grunden, Amy M.}, year={2021}, month={Apr} } @misc{craig_johnson_grunden_2021, title={Leveraging Pseudomonas Stress Response Mechanisms for Industrial Applications}, volume={12}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2021.660134}, abstractNote={Members of the genus Pseudomonas are metabolically versatile and capable of adapting to a wide variety of environments. Stress physiology of Pseudomonas strains has been extensively studied because of their biotechnological potential in agriculture as well as their medical importance with regards to pathogenicity and antibiotic resistance. This versatility and scientific relevance led to a substantial amount of information regarding the stress response of a diverse set of species such as Pseudomonas chlororaphis, P. fluorescens, P. putida, P. aeruginosa, and P. syringae. In this review, environmental and industrial stressors including desiccation, heat, and cold stress, are cataloged along with their corresponding mechanisms of survival in Pseudomonas. Mechanisms of survival are grouped by the type of inducing stress with a focus on adaptations such as synthesis of protective substances, biofilm formation, entering a non-culturable state, enlisting chaperones, transcription and translation regulation, and altering membrane composition. The strategies Pseudomonas strains utilize for survival can be leveraged during the development of beneficial strains to increase viability and product efficacy.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Craig, Kelly and Johnson, Brant R. and Grunden, Amy}, year={2021}, month={May} } @article{ranieri_sponsel_kizer_rojas‐pierce_hernández_gatiboni_grunden_stapelmann_2021, title={Plasma agriculture: Review from the perspective of the plant and its ecosystem}, url={https://doi.org/10.1002/ppap.202000162}, DOI={10.1002/ppap.202000162}, abstractNote={Abstract}, journal={Plasma Processes and Polymers}, author={Ranieri, Pietro and Sponsel, Nicholas and Kizer, Jon and Rojas‐Pierce, Marcela and Hernández, Ricardo and Gatiboni, Luciano and Grunden, Amy and Stapelmann, Katharina}, year={2021}, month={Jan} } @article{buhrman_enriquez_dillard_baer_truong_grunden_rose_2021, title={Structure, Function, and Thermal Adaptation of the Biotin Carboxylase Domain Dimer from Hydrogenobacter thermophilus 2-Oxoglutarate Carboxylase}, volume={60}, ISSN={["0006-2960"]}, url={https://doi.org/10.1021/acs.biochem.0c00815}, DOI={10.1021/acs.biochem.0c00815}, abstractNote={2-Oxoglutarate carboxylase (OGC), a unique member of the biotin-dependent carboxylase family from the order Aquificales, captures dissolved CO2 via the reductive tricarboxylic acid (rTCA) cycle. Structure and function studies of OGC may facilitate adaptation of the rTCA cycle to increase the level of carbon fixation for biofuel production. Here we compare the biotin carboxylase (BC) domain of Hydrogenobacter thermophilus OGC with the well-studied mesophilic homologues to identify features that may contribute to thermal stability and activity. We report three OGC BC X-ray structures, each bound to bicarbonate, ADP, or ADP-Mg2+, and propose that substrate binding at high temperatures is facilitated by interactions that stabilize the flexible subdomain B in a partially closed conformation. Kinetic measurements with varying ATP and biotin concentrations distinguish two temperature-dependent steps, consistent with biotin's rate-limiting role in organizing the active site. Transition state thermodynamic values derived from the Eyring equation indicate a larger positive ΔH⧧ and a less negative ΔS⧧ compared to those of a previously reported mesophilic homologue. These thermodynamic values are explained by partially rate limiting product release. Phylogenetic analysis of BC domains suggests that OGC diverged prior to Aquificales evolution. The phylogenetic tree identifies mis-annotations of the Aquificales BC sequences, including the Aquifex aeolicus pyruvate carboxylase structure. Notably, our structural data reveal that the OGC BC dimer comprises a "wet" dimerization interface that is dominated by hydrophilic interactions and structural water molecules common to all BC domains and likely facilitates the conformational changes associated with the catalytic cycle. Mutations in the dimerization domain demonstrate that dimerization contributes to thermal stability.}, number={4}, journal={BIOCHEMISTRY}, publisher={American Chemical Society (ACS)}, author={Buhrman, Greg and Enriquez, Paul and Dillard, Lucas and Baer, Hayden and Truong, Vivian and Grunden, Amy M. and Rose, Robert B.}, year={2021}, month={Feb}, pages={324–345} } @article{wapshott-stehli_grunden_2021, title={Temperature and solvent exposure response of three fatty acid peroxygenase enzymes for application in industrial enzyme processes}, volume={571}, ISSN={["1090-2104"]}, url={https://doi.org/10.1016/j.bbrc.2021.07.052}, DOI={10.1016/j.bbrc.2021.07.052}, abstractNote={Free fatty acids (FFAs) are a useful feedstock for a range of industrial chemical synthesis applications. However, efficiently converting FFAs to molecules for biofuel and other high-value chemicals requires more efficient and cost-effective catalysts. Cytochrome P450 fatty acid peroxygenases (CYP152) have a unique chemistry that allows use of the peroxide shunt pathway for biochemical conversion of FFAs. Known CYP152s are heat labile, however, requiring characterization of more thermotolerant versions for use in industrial applications. A fatty acid peroxygenase from Bacillus methanolicus (CYP152K6) was shown here to have a higher optimal reaction temperature than OleT (CYP152L1). CYP152K6 was stable up to 50 °C and showed great stability in 3% acetone and dimethylformamide. Stability in solvents helps the enzyme's substrates remain soluble in solution for more efficient catalysis, and heat stability allows enzymes to remain active longer during industrial processes.}, journal={BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS}, publisher={Elsevier BV}, author={Wapshott-Stehli, Hannah L. and Grunden, Amy M.}, year={2021}, month={Sep}, pages={60–65} } @article{halawani_dunn_grunden_smith_2020, title={Bacterial exposure leads to variable mortality but not a measurable increase in surface antimicrobials across ant species}, volume={8}, ISSN={["2167-8359"]}, DOI={10.7717/peerj.10412}, abstractNote={Social insects have co-existed with microbial species for millions of years and have evolved a diversity of collective defenses, including the use of antimicrobials. While many studies have revealed strategies that ants use against microbial entomopathogens, and several have shown ant-produced compounds inhibit environmental bacterial growth, few studies have tested whether exposure to environmental bacteria represents a health threat to ants. We compare four ant species’ responses to exposure to Escherichia coli and Staphylococcus epidermidis bacteria in order to broaden our understanding of microbial health-threats to ants and their ability to defend against them. In a first experiment, we measure worker mortality of Solenopsis invicta, Brachymyrmex chinensis, Aphaenogaster rudis, and Dorymyrmex bureni in response to exposure to E. coli and S. epidermidis. We found that exposure to E. coli was lethal for S. invicta and D. bureni, while all other effects of exposure were not different from experimental controls. In a second experiment, we compared the antimicrobial ability of surface extracts from bacteria-exposed and non-exposed S. invicta and B. chinensis worker ants, to see if exposure to E. coli or S. epidermidis led to an increase in antimicrobial compounds. We found no difference in the inhibitory effects from either treatment group in either species. Our results demonstrate the susceptibility to bacteria is varied across ant species. This variation may correlate with an ant species’ use of surface antimicrobials, as we found significant mortality effects in species which also were producing antimicrobials. Further exploration of a wide range of both bacteria and ant species is likely to reveal unique and nuanced antimicrobial strategies and deepen our understanding of how ant societies respond to microbial health threats.}, journal={PEERJ}, author={Halawani, Omar and Dunn, Robert R. and Grunden, Amy M. and Smith, Adrian A.}, year={2020}, month={Dec} } @article{tambalo_raymundo_grunden_2020, title={Thermostable endoglucanase gene derived by amplification from the genomic DNA of a cellulose-enriched mixed culture from mudspring water of Mt. Makiling, Laguna, Philippines}, volume={36}, ISSN={["1573-0972"]}, DOI={10.1007/s11274-020-02825-2}, abstractNote={Culture-independent molecular-based approaches can be used to identify genes of interest from environmental sources that have desirable properties such as thermo activity. For this study, a putative thermo stable endoglucanase gene was identified from a mixed culture resulting from the inoculation of Brock-CMcellulose (1%) broth with mudspring water from Mt. Makiling, Laguna, Philippines that had been incubated at 90 °C. Genomic DNA was extracted from the cellulose-enriched mixed culture and endo1949 forward and reverse primers were used to amplify the endoglucanase gene, which was cloned into pCR-script plasmid vector. Blastn alignment of the sequenced insert revealed 99.69% similarity to the glycosyl hydrolase, sso1354 (CelA1; Q97YG7) from Saccharolobus solfataricus. The endoglucanase gene (GenBank accession number MK984682) was determined to be 1,021 nucleotide bases in length, corresponding to 333 amino acids with a molecular mass of ~ 37 kDa. The endoglucanase gene was inserted into a pET21 vector and transformed in E. coli BL21 for expression. Partially purified recombinant Mt. Makiling endoglucanase (MM-Engl) showed a specific activity of 187.61 U/mg and demonstrated heat stability up to 80 °C. The thermo-acid stable endoglucanase can be used in a supplementary hydrolysis step to further hydrolyze the lignocellulosic materials that were previously treated under high temperature-dilute acid conditions, thereby enhancing the release of more glucose sugars for bioethanol production.}, number={3}, journal={WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY}, author={Tambalo, Richard D. and Raymundo, Asuncion K. and Grunden, Amy M.}, year={2020}, month={Mar} } @article{ortiz-medina_grunden_hyman_call_2019, title={Nitrogen Gas Fixation and Conversion to Ammonium Using Microbial Electrolysis Cells}, volume={7}, ISSN={2168-0485 2168-0485}, url={http://dx.doi.org/10.1021/ACSSUSCHEMENG.8B05763}, DOI={10.1021/ACSSUSCHEMENG.8B05763}, abstractNote={Ammonia (NH3) is an important industrial chemical that is produced using the energy- and carbon-intensive Haber-Bosch process. Recovering NH3 from microorganisms that fix nitrogen gas (N2) may provide a sustainable alternative because their specialized nitrogenase enzymes can reduce N2 to ammonium (NH4+) without the need for high temperature and pressure. This study explored the possibility of converting N2 into NH4+ using anaerobic, single-chamber microbial electrolysis cells (MECs). N2 fixation rates [based on an acetylene gas (C2H2) to ethylene gas (C2H4) conversion assay] of a microbial consortium increased significantly when the applied voltage between the anode and cathode increased from 0.7 to 1.0 V and reached a maximum of ∼40 nmol of C2H4 min–1 mg protein–1, which is comparable to model aerobic N2-fixing bacteria. The presence of NH4+, which can inhibit the activity of the nitrogenase enzyme, did not significantly reduce N2 fixation rates. Upon addition of methionine sulfoximine, an NH4+ uptake i...}, number={3}, journal={ACS Sustainable Chemistry & Engineering}, publisher={American Chemical Society (ACS)}, author={Ortiz-Medina, Juan F. and Grunden, Amy M. and Hyman, Michael R. and Call, Douglas F.}, year={2019}, month={Jan}, pages={3511–3519} } @article{mathews_epps_blackburn_goshe_grunden_dunn_2019, title={Public questions spur the discovery of new bacterial species associated with lignin bioconversion of industrial waste}, volume={6}, ISSN={["2054-5703"]}, url={https://doi.org/10.1098/rsos.180748}, DOI={10.1098/rsos.180748}, abstractNote={ A citizen science project found that the greenhouse camel cricket ( Diestrammena asynamora ) is common in North American homes. Public response was to wonder ‘what good are they anyway?’ and ecology and evolution guided the search for potential benefit. We predicted that camel crickets and similar household species would likely host bacteria with the ability to degrade recalcitrant carbon compounds. Lignocellulose is particularly relevant as it is difficult to degrade yet is an important feedstock for pulp and paper, chemical and biofuel industries. We screened gut bacteria of greenhouse camel crickets and another household insect, the hide beetle ( Dermestes maculatus ) for the ability to grow on and degrade lignocellulose components as well as the lignocellulose-derived industrial waste product black liquor. From three greenhouse camel crickets and three hide beetles, 14 bacterial strains were identified that were capable of growth on lignocellulosic components, including lignin. Cedecea lapagei was selected for further study due to growth on most lignocellulose components. The C. lapagei secretome was identified using LC/MS/MS analysis. This work demonstrates a novel source of lignocellulose-degrading bacteria and introduces an effective workflow to identify bacterial enzymes for transforming industrial waste into value-added products. More generally, our research suggests the value of ecologically guided discovery of novel organisms. }, number={3}, journal={ROYAL SOCIETY OPEN SCIENCE}, publisher={The Royal Society}, author={Mathews, Stephanie L. and Epps, Mary Jane and Blackburn, R. Kevin and Goshe, Michael B. and Grunden, Amy M. and Dunn, Robert R.}, year={2019}, month={Mar} } @misc{smith-moore_grunden_2018, title={Bacteria and archaea as the sources of traits for enhanced plant phenotypes}, volume={36}, ISSN={["1873-1899"]}, DOI={10.1016/j.biotechadv.2018.07.007}, abstractNote={Rising global demand for food and population increases are driving the need for improved crop productivity over the next 30 years. Plants have inherent metabolic limitations on productivity such as inefficiencies in carbon fixation and sensitivity to environmental conditions. Bacteria and archaea inhabit some of the most inhospitable environments on the planet and possess unique metabolic pathways and genes to cope with these conditions. Microbial genes involved in carbon fixation, abiotic stress tolerance, and nutrient acquisition have been utilized in plants to enhance plant phenotypes by increasing yield, photosynthesis, and abiotic stress tolerance. Transgenic plants expressing bacterial and archaeal genes will be discussed along with emerging strategies and tools to increase plant growth and yield.}, number={7}, journal={BIOTECHNOLOGY ADVANCES}, author={Smith-Moore, Caroline M. and Grunden, Amy M.}, year={2018}, month={Nov}, pages={1900–1916} } @article{somalinga_klemmer_arun_mathews_wapshott_grunden_2018, title={Cloning, Over-Expression, and Purification of Carbonic Anhydrase from an Extremophilic Bacterium: An Introduction to Advanced Molecular Biology}, volume={80}, ISSN={["1938-4211"]}, url={http://dx.doi.org/10.1525/abt.2018.80.1.29}, DOI={10.1525/abt.2018.80.1.29}, abstractNote={The photosynthetic bioreactor research program is a training platform appropriate for introducing advanced molecular biology techniques to undergraduate students and advanced high school biology students. For this advanced molecular biology training exercise, the enzyme carbonic anhydrase was cloned, over-expressed, purified, and functionally characterized. Carbonic anhydrases are industrially important enzymes with potential use in carbon sequestration and biofuel production. Alpha and beta carbonic anhydrases from Photobacterium profundum, a psychrophilic, halotolerant bacterium, were characterized in this study. Carbonic anhydrases that can withstand high salinity and are active at low temperatures can be transformed into oleaginous marine microalgae to enhance biofuel production. Our research program started with a three-day boot camp with lectures in relevant topics of molecular biology, microbiology, and research methods. After the boot camp, the lab phase of the project involved training students to perform polymerase chain reaction, DNA gel electrophoresis, DNA ligation, and bacterial transformation. In the final phase of the project, students were trained in recombinant protein over-expression and protein purification techniques. Here we report successful cloning and over-expression by high school students of two novel carbonic anhydrases from a psychrohalophile with application in biofuel production.}, number={1}, journal={AMERICAN BIOLOGY TEACHER}, publisher={University of California Press}, author={Somalinga, Vijayakumar and Klemmer, Hannah and Arun, Ashikha and Mathews, Stephanie and Wapshott, Hannah and Grunden, Amy M.}, year={2018}, month={Jan}, pages={29–34} } @misc{kitchener_grunden_2018, title={Methods for enhancing cyanobacterial stress tolerance to enable improved production of biofuels and industrially relevant chemicals}, volume={102}, ISSN={["1432-0614"]}, url={https://doi.org/10.1007/s00253-018-8755-5}, DOI={10.1007/s00253-018-8755-5}, abstractNote={Cyanobacteria are photosynthetic prokaryotes that can fix atmospheric CO 2 and can be engineered to produce industrially important compounds such as alcohols, free fatty acids, alkanes used in next-generation biofuels, and commodity chemicals such as ethylene or farnesene. They can be easily genetically manipulated, have minimal nutrient requirements, and are quite tolerant to abiotic stress making them an appealing alternative to other biofuel-producing microbes which require additional carbon sources and plants which compete with food crops for arable land. Many of the compounds produced in cyanobacteria are toxic as titers increase which can slow growth, reduce production, and decrease overall biomass. Additionally, many factors associated with outdoor culturing of cyanobacteria such as UV exposure and fluctuations in temperature can also limit the production potential of cyanobacteria. For cyanobacteria to be utilized successfully as biofactories, tolerance to these stressors must be increased and ameliorating stress responses must be enhanced. Genetic manipulation, directed evolution, and supplementation of culture media with antioxidants are all viable strategies for designing more robust cyanobacterial strains that have the potential to meet industrial production goals.}, number={4}, journal={APPLIED MICROBIOLOGY AND BIOTECHNOLOGY}, publisher={Springer Science and Business Media LLC}, author={Kitchener, Rebecca L. and Grunden, Amy M.}, year={2018}, month={Feb}, pages={1617–1628} } @article{karam_mcmillan_lai_reyes_sederoff_grunden_ranjithan_levis_ducoste_2017, title={Construction and setup of a bench-scale algal photosynthetic bioreactor with temperature, light, and ph monitoring for kinetic growth tests}, number={124}, journal={Jove-Journal of Visualized Experiments}, author={Karam, A. L. and McMillan, C. C. and Lai, Y. C. and Reyes, F. L. and Sederoff, H. W. and Grunden, A. M. and Ranjithan, R. S. and Levis, J. W. and Ducoste, J. J.}, year={2017} } @article{kay_breidt_fratamico_baranzoni_kim_grunden_oh_2017, title={Escherichia coli O157:H7 Acid Sensitivity Correlates with Flocculation Phenotype during Nutrient Limitation}, volume={8}, ISSN={["1664-302X"]}, DOI={10.3389/fmicb.2017.01404}, abstractNote={Shiga toxin producing Escherichia coli (STEC) strains vary in acid resistance; however, little is known about the underlying mechanisms that result in strain specific differences. Among 25 STEC O157:H7 strains tested, 7 strains flocculated when grown statically for 18 h in minimal salts medium at 37°C, while 18 strains did not. Interestingly, the flocculation phenotype (cells came out of suspension) was found to correlate with degree of acid sensitivity in an assay with 400 mM acetic acid solution at pH 3.3 targeting acidified foods. Strains exhibiting flocculation were more acid sensitive and were designated FAS, for flocculation acid sensitive, while the acid resistant strain designated PAR for planktonic acid resistant. Flocculation was not observed for any strains during growth in complex medium (Luria Bertani broth). STEC strains B201 and B241 were chosen as representative FAS (2.4 log reduction) and PAR (0.15 log reduction) strains, respectively, due to differences in acid resistance and flocculation phenotype. Results from electron microscopy showed evidence of fimbriae production in B201, whereas fimbriae were not observed in B241.Curli fimbriae production was identified through plating on Congo red differential medium, and all FAS strains showed curli fimbriae production. Surprisingly, 5 PAR strains also had evidence of curli production. Transcriptomic and targeted gene expression data for B201 and B241indicated that csg and hde (curli and acid induced chaperone genes, respectively) expression positively correlated with the phenotypic differences observed for these strains. These data suggest that FAS strains grown in minimal medium express curli, resulting in a flocculation phenotype. This may be regulated by GcvB, which positively regulates curli fimbriae production and represses acid chaperone proteins. RpoS and other regulatory mechanisms may impact curli fimbriae production, as well. These findings may help elucidate mechanisms underlying differences among STEC strains in relating acid resistance and biofilm formation.}, journal={FRONTIERS IN MICROBIOLOGY}, author={Kay, Kathryn L. and Breidt, Frederick and Fratamico, Pina M. and Baranzoni, Gian M. and Kim, Gwang-Hee and Grunden, Amy M. and Oh, Deog-Hwan}, year={2017}, month={Jul} } @article{duckworth_andrews_cubeta_grunden_ojiambo_2017, title={Revisiting Graduate Student Training to Address Agricultural and Environmental Societal Challenges}, volume={2}, ISSN={2471-9625}, url={http://dx.doi.org/10.2134/ael2017.06.0019}, DOI={10.2134/ael2017.06.0019}, abstractNote={Core Ideas Society is faced with daunting environmental and agricultural challenges. There is a pressing need for multidisciplinary teams of collaborative scientists. Novel graduate educational models may be needed to train students to address grand challenges. An example of illustrating the model through microbiome science of plants and soil is presented. }, number={1}, journal={Agricultural & Environmental Letters}, publisher={Wiley}, author={Duckworth, Owen W. and Andrews, Megan Y. and Cubeta, Marc A. and Grunden, Amy M. and Ojiambo, Peter S.}, year={2017}, pages={170019} } @article{somalinga_buhrman_arun_rose_grunden_2016, title={A High-Resolution Crystal Structure of a Psychrohalophilic alpha-Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface}, volume={11}, ISSN={["1932-6203"]}, url={https://europepmc.org/articles/PMC5148590}, DOI={10.1371/journal.pone.0168022}, abstractNote={Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highly conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s.}, number={12}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Somalinga, Vijayakumar and Buhrman, Greg and Arun, Ashikha and Rose, Robert B. and Grunden, Amy M.}, editor={Hofmann, AndreasEditor}, year={2016}, month={Dec} } @article{whitham_schulte_bobay_bruno-barcena_chinn_flickinger_pawlak_grunden_2016, title={Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain}, volume={101}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/S00253-016-7978-6}, DOI={10.1007/s00253-016-7978-6}, abstractNote={A Clostridium ljungdahlii lab-isolated spontaneous-mutant strain, OTA1, has been shown to produce twice as much ethanol as the C. ljungdahlii ATCC 55383 strain when cultured in a mixotrophic medium containing fructose and syngas. Whole-genome sequencing identified four unique single nucleotide polymorphisms (SNPs) in the C. ljungdahlii OTA1 genome. Among these, two SNPs were found in the gene coding for AcsA and HemL, enzymes involved in acetyl-CoA formation from CO/CO 2 . Homology models of the respective mutated enzymes revealed alterations in the size and hydrogen bonding of the amino acids in their active sites. Failed attempts to grow OTA1 autotrophically suggested that one or both of these mutated genes prevented acetyl-CoA synthesis from CO/CO 2 , demonstrating that its activity was required for autotrophic growth by C. ljungdahlii. An inoperable Wood-Ljungdahl pathway resulted in higher CO 2 and ethanol yields and lower biomass and acetate yields compared to WT for multiple growth conditions including heterotrophic and mixotrophic conditions. The two other SNPs identified in the C. ljungdahlii OTA1 genome were in genes coding for transcriptional regulators (CLJU_c09320 and CLJU_c18110) and were found to be responsible for deregulated expression of co-localized arginine catabolism and 2-deoxy-D-ribose catabolism genes. Growth medium supplementation experiments suggested that increased arginine metabolism and 2-deoxy-D-ribose were likely to have minor effects on biomass and fermentation product yields. In addition, in silico flux balance analysis simulating mixotrophic and heterotrophic conditions showed no change in flux to ethanol when flux through HemL was changed whereas limited flux through AcsA increased the ethanol flux for both simulations. In characterizing the effects of the SNPs identified in the C. ljungdahlii OTA1 genome, a non-autotrophic hyper ethanol-producing strain of C. ljungdahlii was identified that has utility for further physiology and strain performance studies and as a biocatalyst for industrial applications.}, number={4}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Nature}, author={Whitham, Jason M. and Schulte, Mark J. and Bobay, Benjamin G. and Bruno-Barcena, Jose M. and Chinn, Mari S. and Flickinger, Michael C. and Pawlak, Joel J. and Grunden, Amy M.}, year={2016}, month={Nov}, pages={1615–1630} } @article{mathews_grunden_pawlak_2016, title={Degradation of lignocellulose and lignin by Paenibacillus glucanolyticus}, volume={110}, ISSN={["1879-0208"]}, url={http://dx.doi.org/10.1016/j.ibiod.2016.02.012}, DOI={10.1016/j.ibiod.2016.02.012}, abstractNote={Lignocellulose is an abundant renewable carbon source that has been used for fuel and chemical production. Lignocellulose refers to the plant cell wall and is composed of cellulose, hemicellulose, and lignin. Lignin is a recalcitrant amorphous aromatic compound. Paenibacillus glucanolyticus SLM1, a facultative anaerobe that grows optimally at pH 9, was isolated from pulp mill waste. Initial characterization showed that this bacterium could degrade cellulose and hemicellulose and also suggested that it may be able to degrade lignin. This work examines the ability of P. glucanolyticus SLM1 and the type strain P. glucanolyticus 5162 to degrade lignocellulose, lignin, and aromatic lignin-related compounds using growth studies, dye degradation assays, GC–MS, and GPC. Our results show that both strains of P. glucanolyticus can degrade aromatic lignin-related compounds under aerobic and anaerobic conditions. These strains can also degrade polymeric lignin under anaerobic conditions. However, only P. glucanolyticus SLM1 can also degrade polymeric lignin under aerobic conditions.}, journal={INTERNATIONAL BIODETERIORATION & BIODEGRADATION}, publisher={Elsevier BV}, author={Mathews, Stephanie L. and Grunden, Amy M. and Pawlak, Joel}, year={2016}, month={May}, pages={79–86} } @article{geng_liu_ji_hoffmann_grunden_xiang_2016, title={Enhancing Heat Tolerance of the Little Dogwood Cornus canadensis L. f. with Introduction of a Superoxide Reductase Gene from the Hyperthermophilic Archaeon Pyrococcus furiosus}, volume={7}, ISSN={1664-462X}, url={http://dx.doi.org/10.3389/fpls.2016.00026}, DOI={10.3389/fpls.2016.00026}, abstractNote={Production of reactive oxygen species (ROS) can be accelerated under various biotic and abiotic stresses causing lipid peroxidation, protein degradation, enzyme inactivation, and DNA damage. Superoxide reductase (SOR) is a novel antioxidant enzyme from Pyrococcus furiosus and is employed by this anaerobic hyperthermophilic archaeon for efficient detoxification of ROS. In this study, SOR was introduced into a flowering plant Cornus canadensis to enhance its heat tolerance and reduce heat induced damage. A fusion construct of the SOR gene and Green Fluorescent Protein gene (GFP) was introduced into C. canadensis using Agrobacterium-mediated transformation. Heat tolerance of the GFP-SOR expressing transgenic plants was investigated by observing morphological symptoms of heat injury and by examining changes in photosynthesis, malondialdehyde (MDA), and proline levels in the plants. Our results indicate that the expression of the P. furiosus SOR gene in the transgenic plants alleviated lipid peroxidation of cell membranes and photoinhibition of PS II, and decreased the accumulation of proline at 40°C. After a series of exposures to increasing temperatures, the SOR transgenic plants remained healthy and green whereas most of the non-transgenic plants dried up and were unable to recover. While it had previously been reported that expression of SOR in Arabidopsis enhanced heat tolerance, this is the first report of the successful demonstration of improved heat tolerance in a non-model plant resulting from the introduction of P. furiosus SOR. The study demonstrates the potential of SOR for crop improvement and that inherent limitations of plant heat tolerance can be ameliorated with P. furiosus SOR.}, journal={Frontiers in Plant Science}, publisher={Frontiers Media SA}, author={Geng, Xing-Min and Liu, Xiang and Ji, Mikyoung and Hoffmann, William A. and Grunden, Amy and Xiang, Qiu-Yun J.}, year={2016}, month={Jan} } @article{savage_hills_driscoll_fergus_grunden_dunn_2016, title={Microbial diversity of extreme habitats in human homes}, volume={4}, ISSN={2167-8359}, url={http://dx.doi.org/10.7717/peerj.2376}, DOI={10.7717/peerj.2376}, abstractNote={High-throughput sequencing techniques have opened up the world of microbial diversity to scientists, and a flurry of studies in the most remote and extreme habitats on earth have begun to elucidate the key roles of microbes in ecosystems with extreme conditions. These same environmental extremes can also be found closer to humans, even in our homes. Here, we used high-throughput sequencing techniques to assess bacterial and archaeal diversity in the extreme environments inside human homes (e.g., dishwashers, hot water heaters, washing machine bleach reservoirs, etc.). We focused on habitats in the home with extreme temperature, pH, and chemical environmental conditions. We found a lower diversity of microbes in these extreme home environments compared to less extreme habitats in the home. However, we were nonetheless able to detect sequences from a relatively diverse array of bacteria and archaea. Habitats with extreme temperatures alone appeared to be able to support a greater diversity of microbes than habitats with extreme pH or extreme chemical environments alone. Microbial diversity was lowest when habitats had both extreme temperature and one of these other extremes. In habitats with both extreme temperatures and extreme pH, taxa with known associations with extreme conditions dominated. Our findings highlight the importance of examining interactive effects of multiple environmental extremes on microbial communities. Inasmuch as taxa from extreme environments can be both beneficial and harmful to humans, our findings also suggest future work to understand both the threats and opportunities posed by the life in these habitats.}, number={9}, journal={PeerJ}, publisher={PeerJ}, author={Savage, Amy M. and Hills, Justin and Driscoll, Katherine and Fergus, Daniel J. and Grunden, Amy M. and Dunn, Robert R.}, year={2016}, month={Sep}, pages={e2376} } @article{mathews_smithson_grunden_2016, title={Purification and characterization of a recombinant laccase-like multi-copper oxidase from Paenibacillus glucanolyticus SLM1}, volume={121}, ISSN={["1365-2672"]}, url={http://dx.doi.org/10.1111/jam.13241}, DOI={10.1111/jam.13241}, abstractNote={The aim of this study was to evaluate the activity of a novel bacterial laccase‐like multi‐copper oxidase (LMCO) from Paenibacillus glucanolyticus SLM1: a bacterium isolated from pulp and paper waste.}, number={5}, journal={JOURNAL OF APPLIED MICROBIOLOGY}, publisher={Wiley}, author={Mathews, S. L. and Smithson, C. E. and Grunden, A. M.}, year={2016}, month={Nov}, pages={1335–1345} } @article{dalal_yalamanchili_hovary_ji_rodriguez-welsh_aslett_ganapathy_grunden_sederoff_qu_et al._2015, title={A novel gateway-compatible binary vector series (PC-GW) for flexible cloning of multiple genes for genetic transformation of plants}, volume={81}, ISSN={["1095-9890"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84938634755&partnerID=MN8TOARS}, DOI={10.1016/j.plasmid.2015.06.003}, abstractNote={The rapidly advancing field of plant synthetic biology requires transforming plants with multiple genes. This has sparked a growing interest in flexible plant transformation vectors, which can be used for multi-gene transformations. We have developed a novel binary vector series, named the PC-GW series (GenBank: KP826769-KP826773), for Agrobacterium-mediated plant transformation. The PC-GW vectors use the pCAMBIA vector backbone, and contain NPTII, hpt, bar, mCherry or egfp genes as selectable markers for plant transformation. In a modified multiple cloning site (MCS) of the T-DNA region, we have placed the attR1, attR2 and ccdB sequences for rapid cloning of one to four genes by Gateway™-assisted recombination. In addition, we have introduced four meganuclease sites, and other restriction sites for multi-gene vector construction. Finally, we have placed a CaMV 35S promoter and a 35S terminator on the 5' and 3' ends of the MCS. The CaMV 35S promoter is flanked by PstI restriction sites that can be used to replace it with another promoter sequence if needed. The PC-GW vectors provide choices for selectable markers, cloning methods, and can accommodate up to eight gene constructs in a single T-DNA, thereby significantly reducing the number of transformations or crosses needed to generate multi-transgene expressing plants.}, journal={PLASMID}, author={Dalal, J. and Yalamanchili, R. and Hovary, C. La and Ji, M. and Rodriguez-Welsh, M. and Aslett, D. and Ganapathy, S. and Grunden, A. and Sederoff, Heike and Qu, R. D. and et al.}, year={2015}, month={Sep}, pages={55–62} } @article{mathews_pawlak_grunden_2015, title={Bacterial biodegradation and bioconversion of industrial lignocellulosic streams}, volume={99}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/S00253-015-6471-Y}, DOI={10.1007/s00253-015-6471-y}, abstractNote={Lignocellulose is a term for plant materials that are composed of matrices of cellulose, hemicellulose, and lignin. Lignocellulose is a renewable feedstock for many industries. Lignocellulosic materials are used for the production of paper, fuels, and chemicals. Typically, industry focuses on transforming the polysaccharides present in lignocellulose into products resulting in the incomplete use of this resource. The materials that are not completely used make up the underutilized streams of materials that contain cellulose, hemicellulose, and lignin. These underutilized streams have potential for conversion into valuable products. Treatment of these lignocellulosic streams with bacteria, which specifically degrade lignocellulose through the action of enzymes, offers a low-energy and low-cost method for biodegradation and bioconversion. This review describes lignocellulosic streams and summarizes different aspects of biological treatments including the bacteria isolated from lignocellulose-containing environments and enzymes which may be used for bioconversion. The chemicals produced during bioconversion can be used for a variety of products including adhesives, plastics, resins, food additives, and petrochemical replacements.}, number={7}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Mathews, Stephanie L. and Pawlak, Joel and Grunden, Amy M.}, year={2015}, month={Feb}, pages={2939–2954} } @article{ji_barnwell_grunden_2015, title={Characterization of recombinant glutathione reductase from the psychrophilic Antarctic bacterium Colwellia psychrerythraea}, volume={19}, ISSN={["1433-4909"]}, DOI={10.1007/s00792-015-0762-1}, abstractNote={Glutathione reductases catalyze the reduction of oxidized glutathione (glutathione disulfide, GSSG) using NADPH as the substrate to produce reduced glutathione (GSH), which is an important antioxidant molecule that helps maintain the proper reducing environment of the cell. A recombinant form of glutathione reductase from Colwellia psychrerythraea, a marine psychrophilic bacterium, has been biochemically characterized to determine its molecular and enzymatic properties. C. psychrerythraea glutathione reductase was shown to be a homodimer with a molecular weight of 48.7 kDa using SDS-PAGE, MALDI-TOF mass spectrometry and gel filtration. The C. psychrerythraea glutathione reductase sequence shows significant homology to that of Escherichia coli glutathione reductase (66 % identity), and it possesses the FAD and NADPH binding motifs, as well as absorption spectrum features which are characteristic of flavoenzymes such as glutathione reductase. The psychrophilic C. psychrerythraea glutathione reductase exhibits higher k cat and k cat/K m at lower temperatures (4 °C) compared to mesophilic Baker's yeast glutathione reductase. However, C. psychrerythraea glutathione reductase was able to complement an E. coli glutathione reductase deletion strain in oxidative stress growth assays, demonstrating the functionality of C. psychrerythraea glutathione reductase over a broad temperature range, which suggests its potential utility as an antioxidant enzyme in heterologous systems.}, number={4}, journal={EXTREMOPHILES}, author={Ji, Mikyoung and Barnwell, Callie V. and Grunden, Amy M.}, year={2015}, month={Jul}, pages={863–874} } @article{whitham_tirado-acevedo_chinn_pawlak_grunden_2015, title={Metabolic Response of Clostridium ljungdahlii to Oxygen Exposure}, volume={81}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/AEM.02491-15}, DOI={10.1128/aem.02491-15}, abstractNote={ABSTRACT}, number={24}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Whitham, Jason M. and Tirado-Acevedo, Oscar and Chinn, Mari S. and Pawlak, Joel J. and Grunden, Amy M.}, editor={Parales, R. E.Editor}, year={2015}, month={Oct}, pages={8379–8391} } @article{utturkar_klingeman_bruno-barcena_chinn_grunden_köpke_brown_2015, title={Sequence data for Clostridium autoethanogenum using three generations of sequencing technologies}, volume={2}, ISSN={2052-4463}, url={http://dx.doi.org/10.1038/SDATA.2015.14}, DOI={10.1038/SDATA.2015.14}, abstractNote={During the past decade, DNA sequencing output has been mostly dominated by the second generation sequencing platforms which are characterized by low cost, high throughput and shorter read lengths for example, Illumina. The emergence and development of so called third generation sequencing platforms such as PacBio has permitted exceptionally long reads (over 20 kb) to be generated. Due to read length increases, algorithm improvements and hybrid assembly approaches, the concept of one chromosome, one contig and automated finishing of microbial genomes is now a realistic and achievable task for many microbial laboratories. In this paper, we describe high quality sequence datasets which span three generations of sequencing technologies, containing six types of data from four NGS platforms and originating from a single microorganism, Clostridium autoethanogenum. The dataset reported here will be useful for the scientific community to evaluate upcoming NGS platforms, enabling comparison of existing and novel bioinformatics approaches and will encourage interest in the development of innovative experimental and computational methods for NGS data.}, number={1}, journal={Scientific Data}, publisher={Springer Science and Business Media LLC}, author={Utturkar, Sagar M and Klingeman, Dawn M and Bruno-Barcena, José M and Chinn, Mari S and Grunden, Amy M and Köpke, Michael and Brown, Steven D}, year={2015}, month={Apr} } @misc{schreck_grunden_2014, title={Biotechnological applications of halophilic lipases and thioesterases}, volume={98}, ISSN={["1432-0614"]}, DOI={10.1007/s00253-013-5417-5}, abstractNote={Lipases and esterases are enzymes which hydrolyze ester bonds between a fatty acid moiety and an esterified conjugate, such as a glycerol or phosphate. These enzymes have a wide spectrum of use in industrial applications where their high activity, broad substrate specificity, and stability under harsh conditions have made them integral in biofuel production, textile processing, waste treatment, and as detergent additives. To date, these industrial applications have mainly leveraged enzymes from mesophilic and thermophilic organisms. However, increasingly, attention has turned to halophilic enzymes as catalysts in environments where high salt stability is desired. This review provides a brief overview of lipases and esterases and examines specific structural motifs and evolutionary adaptations of halophilic lipases. Finally, we examine the state of research involving these enzymes and provide an in-depth look at an exciting algal-based biofuel production system. This system uses a recombinant halophilic lipase to increase oil production efficiency by cleaving algal fatty acids from the acyl carrier protein, which eliminates feedback inhibition of fatty acid synthesis.}, number={3}, journal={APPLIED MICROBIOLOGY AND BIOTECHNOLOGY}, author={Schreck, Steven D. and Grunden, Amy M.}, year={2014}, month={Feb}, pages={1011–1021} } @article{mathews_pawlak_grunden_2014, title={Isolation of Paenibacillus glucanolyticus from pulp mill sources with potential to deconstruct pulping waste}, volume={164}, ISSN={["1873-2976"]}, url={http://dx.doi.org/10.1016/j.biortech.2014.04.093}, DOI={10.1016/j.biortech.2014.04.093}, abstractNote={Black liquor is a pulping waste generated by the kraft process that has potential for downstream bioconversion. A microorganism was isolated from a black liquor sample collected from the Department of Forest Biomaterials at North Carolina State University. The organism was identified as Paenibacillus glucanolyticus using 16S rRNA sequence analysis and was shown to be capable of growth on black liquor as the sole carbon source based on minimal media growth studies. Minimal media growth curves demonstrated that this facultative anaerobic microorganism can degrade black liquor as well as cellulose, hemicellulose, and lignin. Gas chromatography-mass spectrometry was used to identify products generated by P. glucanolyticus when it was grown anaerobically on black liquor. Fermentation products which could be converted into high-value chemicals such as succinic, propanoic, lactic, and malonic acids were detected.}, journal={BIORESOURCE TECHNOLOGY}, publisher={Elsevier BV}, author={Mathews, Stephanie L. and Pawlak, Joel J. and Grunden, Amy M.}, year={2014}, month={Jul}, pages={100–105} } @article{wang_allen_campos_cade_dean_dvora_immer_mixson_srirangan_sauer_et al._2013, title={ASI:Dunaliellamarine microalgae to drop-in replacement liquid transportation fuel}, volume={32}, ISSN={1944-7442}, url={http://dx.doi.org/10.1002/EP.11855}, DOI={10.1002/EP.11855}, abstractNote={Microalgae are a promising biofuels feedstock, theoretically yielding concentrations of triacylglycerides (TAGs) per unit area that are far higher than traditional feedstocks due to their rapid growth. Dunaliella is particularly advantageous as a feedstock because it is currently commercially mass cultured, thrives in salt water, and has no cell wall. Fourteen strains of Dunaliella have been investigated for growth rates and lipid production in mass culture and tested for enhanced lipid production under a range of environmental stressors including salinity, pH, nitrogen and phosphorus limitation, and light regime. The nuclear genome has been sequenced for four of these strains, with the objective of increasing carbon flux through genetic engineering. Electroflocculation followed by osmotic membrane rupturing may be a very energy and cost efficient means of harvesting the lipid bodies from Dunaliella. A technically feasible and scalable thermo‐catalytic process to convert the lipids into replacements for liquid transportation fuels has been developed. The lipids were converted into long‐chain alkanes through continuous thermal hydrolysis followed by fed‐batch thermo‐catalytic decarboxylation. These alkanes can be reformed into renewable diesel via conventional catalytic hydrocarbon isomerization reactions to improve cold flow properties, if desired. © 2013 American Institute of Chemical Engineers Environ Prog, 32: 916–925, 2013}, number={4}, journal={Environmental Progress & Sustainable Energy}, publisher={Wiley}, author={Wang, Wei-Cheng and Allen, Elle and Campos, Andrew A. and Cade, Rushyannah Killens and Dean, Lisa and Dvora, Mia and Immer, Jeremy G. and Mixson, Stephanie and Srirangan, Soundarya and Sauer, Marie-Laure and et al.}, year={2013}, month={Sep}, pages={916–925} } @article{gosse_chinn_grunden_bernal_jenkins_yeager_kosourov_seibert_flickinger_2012, title={A versatile method for preparation of hydrated microbial–latex biocatalytic coatings for gas absorption and gas evolution}, volume={39}, ISSN={1367-5435 1476-5535}, url={http://dx.doi.org/10.1007/S10295-012-1135-8}, DOI={10.1007/s10295-012-1135-8}, abstractNote={Abstract}, number={9}, journal={Journal of Industrial Microbiology & Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Gosse, Jimmy L. and Chinn, Mari S. and Grunden, Amy M. and Bernal, Oscar I. and Jenkins, Jessica S. and Yeager, Chris and Kosourov, Sergey and Seibert, Michael and Flickinger, Michael C.}, year={2012}, month={May}, pages={1269–1278} } @article{mcmahan_grunden_devine_sobsey_2012, title={Evaluation of a quantitative H2S MPN test for fecal microbes analysis of water using biochemical and molecular identification}, volume={46}, ISSN={["0043-1354"]}, DOI={10.1016/j.watres.2011.12.037}, abstractNote={The sensitivity and specificity of the H2S test to detect fecal bacteria in water has been variable and uncertain in previous studies, partly due to its presence–absence results. Furthermore, in groundwater samples false-positive results have been reported, with H2S-positive samples containing no fecal coliforms or Escherichia coli. False-negative results also have been reported in other studies, with H2S-negative samples found to contain E. coli. Using biochemical and molecular methods and a novel quantitative test format, this research identified the types and numbers of microbial community members present in natural water samples, including fecal indicators and pathogens as well as other bacteria. Representative water sources tested in this study included cistern rainwater, a protected lake, and wells in agricultural and forest settings. Samples from quantitative H2S tests of water were further cultured for fecal bacteria by spread plating onto the selective media for detection and isolation of Aeromonas spp., E. coli, Clostridium spp., H2S-producers, and species of Salmonella and Shigella. Isolates were then tested for H2S production, and identified to the genus and species level using biochemical methods. Terminal Restriction Fragment Length Polymorphisms (TRFLP) was the molecular method employed to quantitatively characterize microbial community diversity. Overall, it was shown that water samples testing positive for H2S bacteria also had bacteria of likely fecal origin and waters containing fecal pathogens also were positive for H2S bacteria. Of the microorganisms isolated from natural water, greater than 70 percent were identified using TRFLP analysis to reveal a relatively stable group of organisms whose community composition differed with water source and over time. These results further document the validity of the H2S test for detecting and quantifying fecal contamination of water.}, number={6}, journal={WATER RESEARCH}, author={McMahan, Lanakila and Grunden, Amy M. and Devine, Anthony A. and Sobsey, Mark D.}, year={2012}, month={Apr}, pages={1693–1704} } @misc{kitchener_grunden_2012, title={Prolidase function in proline metabolism and its medical and biotechnological applications}, volume={113}, ISSN={["1365-2672"]}, DOI={10.1111/j.1365-2672.2012.05310.x}, abstractNote={Prolidase is a multifunctional enzyme that possesses the unique ability to degrade imidodipeptides in which a proline or hydroxyproline residue is located at the C‐terminal end. Prolidases have been isolated from archaea and bacteria, where they are thought to participate in proline recycling. In mammalian species, prolidases are found in the cytoplasm and function primarily to liberate proline in the final stage of protein catabolism, particularly during the biosynthesis and degradation of collagen. Collagen comprises nearly one‐third of the total protein in the body, and it is essential in maintaining tissue structure and integrity. Prolidase deficiency (PD), a rare autosomal recessive disorder in which mutations in the PEPD gene affect prolidase functionality, tends to have serious and sometimes life‐threatening clinical symptoms. Recombinant prolidases have many applications and have been investigated not only as a possible treatment for PD, but also as a part of anti‐cancer strategies, a component of biodecontamination cocktails and in the dairy industry. This review will serve to discuss the many in vivo functions of procaryotic and eucaryotic prolidases, as well as the most recent advances in therapeutic and biotechnological application of prolidases.}, number={2}, journal={JOURNAL OF APPLIED MICROBIOLOGY}, author={Kitchener, R. L. and Grunden, A. M.}, year={2012}, month={Aug}, pages={233–247} } @article{theriot_semcer_shah_grunden_2011, title={Improving the Catalytic Activity of Hyperthermophilic Pyrococcus horikoshii Prolidase for Detoxification of Organophosphorus Nerve Agents over a Broad Range of Temperatures}, volume={2011}, ISSN={1472-3646 1472-3654}, url={http://dx.doi.org/10.1155/2011/565127}, DOI={10.1155/2011/565127}, abstractNote={Prolidases hydrolyze Xaa-Pro dipeptides and can also cleave the P-F and P-O bonds found in organophosphorus (OP) compounds, including the nerve agents soman and sarin.Ph1prol (PH0974) has previously been isolated and characterized fromPyrococcus horikoshiiand was shown to have higher catalytic activity over a broader pH range, higher affinity for metal, and increased thermostability compared toP. furiosusprolidase,Pfprol (PF1343). To obtain a better enzyme for OP nerve agent decontamination and to investigate the structural factors that may influence protein thermostability and thermoactivity, randomly mutatedPh1prol enzymes were prepared. FourPh1prol mutants (A195T/G306S-, Y301C/K342N-, E127G/E252D-, and E36V-Ph1prol) were isolated which had greater thermostability and improved activity over a broader range of temperatures against Xaa-Pro dipeptides and OP nerve agents compared to wild typePyrococcusprolidases.}, journal={Archaea}, publisher={Hindawi Limited}, author={Theriot, Casey M. and Semcer, Rebecca L. and Shah, Saumil S. and Grunden, Amy M.}, editor={C.M., B.Semcer and Shah, S.Editors}, year={2011}, pages={1–9} } @article{mcmahan_devine_grunden_sobsey_2011, title={Validation of the H2S method to detect bacteria of fecal origin by cultured and molecular methods}, volume={92}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/S00253-011-3520-Z}, DOI={10.1007/S00253-011-3520-Z}, abstractNote={Using biochemical and molecular methods, this research determined whether or not the H(2)S test did correctly identify sewage-contaminated waters by being the first to use culturing and molecular methods to identify the types and numbers of fecal indicator organisms, pathogens, and other microbes present in sewage samples with positive H(2)S test results. For the culture-based method, samples were analyzed for the presence of fecal bacteria by spread plating the sewage sample onto differential and selective media for Aeromonas spp., Escherichia coli, sulfite-reducing clostridia, H(2)S-producing bacteria, and Salmonella/Shigella spp. The isolates were then: (1) tested to determine whether they were H(2)S-producing organisms and (2) identified to the genus and species level using biochemical methods. The molecular method used to characterize the microbial populations of select samples was terminal restriction fragment length polymorphisms. These experiments on sewage provided evidence that positive H(2)S tests consistently contained fecal bacteria and pathogens. There were strong relationships of agreement between the organisms identified by both methods tested. This study is an important advance in microbial water quality detection since it is focused on the evaluation of a novel, low-cost, water microbiology test that has the potential to provide millions of people worldwide access to water quality detection technology. Of prime consideration in evaluating water quality tests is the determination of the test's accuracy and specificity, and this article is a fundamental step in providing that information.}, number={6}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={McMahan, Lanakila and Devine, Anthony A. and Grunden, Amy M. and Sobsey, Mark D.}, year={2011}, month={Oct}, pages={1287–1295} } @article{boss_sederoff_im_moran_grunden_perera_2010, title={Basal Signaling Regulates Plant Growth and Development}, volume={154}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-77957739073&partnerID=MN8TOARS}, DOI={10.1104/pp.110.161232}, abstractNote={The term signal transduction refers to the classical paradigm where an external stimulus is sensed and initiates an increase in second messengers. Each second messenger transmits and amplifies the signal by activating a subset of downstream pathways. This complex network of interwoven downstream}, number={2}, journal={PLANT PHYSIOLOGY}, author={Boss, Wendy F. and Sederoff, Heike Winter and Im, Yang Ju and Moran, Nava and Grunden, Amy M. and Perera, Imara Y.}, year={2010}, month={Oct}, pages={439–443} } @article{theriot_grunden_2010, title={Hydrolysis of organophosphorus compounds by microbial enzymes}, volume={89}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-010-2807-9}, DOI={10.1007/s00253-010-2807-9}, abstractNote={There are classes of microbial enzymes that have the ability to degrade harmful organophosphorus (OP) compounds that are present in some pesticides and nerve agents. To date, the most studied and potentially important OP-degrading enzymes are organophosphorus hydrolase (OPH) and organophosphorus acid anhydrolase (OPAA), which have both been characterized from a number of organisms. Here we provide an update of what is experimentally known about OPH and OPAA to include their structures, substrate specificity, and catalytic properties. Current and future potential applications of these enzymes in the hydrolysis of OP compounds are also addressed.}, number={1}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Grunden, Amy M.}, year={2010}, month={Oct}, pages={35–43} } @article{theriot_du_tove_grunden_2010, title={Improving the catalytic activity of hyperthermophilic Pyrococcus prolidases for detoxification of organophosphorus nerve agents over a broad range of temperatures}, volume={87}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-010-2614-3}, DOI={10.1007/s00253-010-2614-3}, abstractNote={Prolidase isolated from the hyperthermophilic archaeon Pyrococcus furiosus has potential for application for decontamination of organophosphorus compounds in certain pesticides and chemical warfare agents under harsh conditions. However, current applications that use an enzyme-based cocktail are limited by poor long-term enzyme stability and low reactivity over a broad range of temperatures. To obtain a better enzyme for OP nerve agent decontamination and to investigate structural factors that influence protein thermostability and thermoactivity, randomly mutated P. furiosus prolidases were prepared by using XL1-red-based mutagenesis and error-prone PCR. An Escherichia coli strain JD1 (lambdaDE3) (auxotrophic for proline [DeltaproA] and having deletions in pepQ and pepP dipeptidases with specificity for proline-containing dipeptides) was constructed for screening mutant P. furiosus prolidase expression plasmids. JD1 (lambdaDE3) cells were transformed with mutated prolidase expression plasmids and plated on minimal media supplemented with 50 muM Leu-Pro as the only source of proline. By using this positive selection, Pyrococcus prolidase mutants with improved activity over a broader range of temperatures were isolated. The activities of the mutants over a broad temperature range were measured for both Xaa-Pro dipeptides and OP nerve agents, and the thermoactivity and thermostability of the mutants were determined.}, number={5}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Du, Xuelian and Tove, Sherry R. and Grunden, Amy M.}, year={2010}, month={Apr}, pages={1715–1726} } @misc{tirado-acevedo_chinn_grunden_2010, title={Production of biofuels from synthesis gas using microbial catalysts}, volume={70}, journal={Advances in applied microbiology, vol 70}, author={Tirado-Acevedo, O. and Chinn, M. S. and Grunden, A. M.}, year={2010}, pages={57–92} } @article{theriot_tove_grunden_2009, title={Characterization of two proline dipeptidases (prolidases) from the hyperthermophilic archaeon Pyrococcus horikoshii}, volume={86}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-009-2235-x}, DOI={10.1007/s00253-009-2235-x}, abstractNote={Prolidases hydrolyze the unique bond between X-Pro dipeptides and can also cleave the P-F and P-O bonds found in organophosphorus compounds, including the nerve agents, soman and sarin. The advantages of using hyperthermophilic enzymes in biodetoxification strategies are based on their enzyme stability and efficiency. Therefore, it is advantageous to examine new thermostable prolidases for potential use in biotechnological applications. Two thermostable prolidase homologs, PH1149 and PH0974, were identified in the genome of Pyrococcus horikoshii based on their sequences having conserved metal binding and catalytic amino acid residues that are present in other known prolidases, such as the previously characterized Pyrococcus furiosus prolidase. These P. horikoshii prolidases were expressed recombinantly in the Escherichia coli strain BL21 (lambdaDE3), and both were shown to function as proline dipeptidases. Biochemical characterization of these prolidases shows they have higher catalytic activities over a broader pH range, higher affinity for metal and are more stable compared to P. furiosus prolidase. This study has important implications for the potential use of these enzymes in biotechnological applications and provides further information on the functional traits of hyperthermophilic proteins, specifically metalloenzymes.}, number={1}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Tove, Sherry R. and Grunden, Amy M.}, year={2009}, month={Sep}, pages={177–188} } @article{johnson_devine_ellis_grunden_fellner_2009, title={Effects of antibiotics and oil on microbial profiles and fermentation in mixed cultures of ruminal microorganisms}, volume={92}, ISSN={["1525-3198"]}, DOI={10.3168/jds.2008-1841}, abstractNote={Ionophores and supplemental fat are fed to lactating cows to improve feed efficiency. Their effect on rumen fermentation is similar, but less is known about their impact on rumen microbes. The objective of this study was to determine the effects of monensin (M), bacitracin (B), and soybean oil (O) on microbial populations. Mixed cultures of rumen microbes were incubated in 5 dual-flow continuous fermentors and fed 13.8 g of alfalfa hay pellets daily (DM basis) for 16 d. All fermentors were allowed to stabilize for 4 d. From d 5 to 10, two fermentors received O (5% of diet DM), one fermentor received M (22 mg/kg), and one received B (22 mg/kg). From d 11 to 16, the 2 fermentors receiving O also received either M (OM) or B (OB) and O was included in the fermentors receiving M (MO) and B (BO). One fermentor served as the control and received 100% alfalfa pellets throughout the experiment. Each run was replicated 3 times. Samples were taken at 2 h after the morning feeding on d 4, 10, and 16 and were analyzed for bacterial populations using terminal restriction fragment length polymorphism. Volatile fatty acid concentration, methane production, and pH in the control cultures were not affected by time and remained similar during the entire experiment. The M and O treatments reduced molar concentration of acetate, increased concentration of propionate, and decreased methane production. Bacitracin did not alter acetate or propionate concentration, but reduced methane production. All 3 treatments (M, B, and O) altered the fragment patterns of microbial profiles. In contrast, treatments MO, OM, BO, and OB had little effect on culture fermentation despite differences in the patterns of microbial fragments. The terminal restriction fragment length polymorphism data suggest that microbial adaptation to the in vitro system in the control fermentor occurred within 4 d.}, number={9}, journal={JOURNAL OF DAIRY SCIENCE}, author={Johnson, M. C. and Devine, A. A. and Ellis, J. C. and Grunden, A. M. and Fellner, V.}, year={2009}, month={Sep}, pages={4467–4480} } @article{theriot_tove_grunden_2009, title={Erratum to: Characterization of two proline dipeptidases (prolidases) from the hyperthermophilic archaeon Pyrococcus horikoshii}, volume={86}, ISSN={0175-7598 1432-0614}, url={http://dx.doi.org/10.1007/s00253-009-2300-5}, DOI={10.1007/s00253-009-2300-5}, number={1}, journal={Applied Microbiology and Biotechnology}, publisher={Springer Science and Business Media LLC}, author={Theriot, Casey M. and Tove, Sherry R. and Grunden, Amy M.}, year={2009}, month={Oct}, pages={393–393} } @article{cotter_chinn_grunden_2009, title={Ethanol and acetate production by Clostridium ljungdahlii and Clostridium autoethanogenum using resting cells}, volume={32}, ISSN={["1615-7591"]}, DOI={10.1007/s00449-008-0256-y}, abstractNote={Combined gasification and fermentation technologies can potentially produce biofuels from renewable biomass. Gasification generates synthesis gas consisting primarily of CO, CO(2), H(2), N(2), with smaller amounts of CH(4), NO(x), O(2), C(2) compounds, ash and tars. Several anaerobic bacteria species can ferment bottled mixtures of pure synthesis gas constituents. However, there are challenges to maintaining culture viability of synthesis gas exposed cells. This study was designed to enhance culture stability and improve ethanol-to-acetate ratios using resting (non-growing) cells in synthesis gas fermentation. Resting cell states were induced in autotrophic Clostridium ljungdahlii cultures with minimal ethanol and acetate production due to low metabolic activity compared to growing cell production levels of 5.2 and 40.1 mM of ethanol and acetate. Clostridium autoethanogenum cultures were not induced into true resting states but did show improvement in total ethanol production (from 5.1 mM in growing cultures to 9.4 in one nitrogen-limited medium) as well as increased shifts in ethanol-to-acetate production ratios.}, number={3}, journal={BIOPROCESS AND BIOSYSTEMS ENGINEERING}, author={Cotter, Jacqueline L. and Chinn, Mari S. and Grunden, Amy M.}, year={2009}, month={Apr}, pages={369–380} } @article{im_ji_lee_killens_grunden_boss_2009, title={Expression of Pyrococcus furiosus Superoxide Reductase in Arabidopsis Enhances Heat Tolerance}, volume={151}, ISSN={["1532-2548"]}, DOI={10.1104/pp.109.145409}, abstractNote={Abstract}, number={2}, journal={PLANT PHYSIOLOGY}, author={Im, Yang Ju and Ji, Mikyoung and Lee, Alice and Killens, Rushyannah and Grunden, Amy M. and Boss, Wendy F.}, year={2009}, month={Oct}, pages={893–904} } @article{cotter_chinn_grunden_2009, title={Influence of process parameters on growth of Clostridium ljungdahlii and Clostridium autoethanogenum on synthesis gas}, volume={44}, ISSN={["1879-0909"]}, DOI={10.1016/j.enzmictec.2008.11.002}, abstractNote={Effects of initial medium pH and gas flow rate on Clostridium ljungdahlii and Clostridium autoethanogenum in liquid batch, continuous gas fermentations were investigated. Synthesis gas components were supplied at varying flow rates (5, 7.5 and 10 mL/min) for C. ljungdahlii (pH 6.8 and 5.5) and C. autoethanogenum (pH 6.0). Growth on synthesis gas was slower than growth on sugars. For C. ljungdahlii, higher cell densities were achieved at pH 6.8 (579 mg/L) compared to pH 5.5 (378 mg/L). The ethanol concentration at pH 6.8 was also 110% greater than that at pH 5.5. The interaction of flow rate and pH was statistically significant with the greatest acetate production in the 10 mL/min, pH 6.8 treatment. The ethanol to acetate ratios were smaller at lower pH levels and higher flow rates. In C. autoethanogenum fermentations, higher flow rates resulted in greater end product formation with no significant effect on product ratios.}, number={5}, journal={ENZYME AND MICROBIAL TECHNOLOGY}, author={Cotter, Jacqueline L. and Chinn, Mari S. and Grunden, Amy M.}, year={2009}, month={May}, pages={281–288} } @article{ying_grunden_nie_adams_ma_2009, title={Molecular characterization of the recombinant iron-containing alcohol dehydrogenase from the hyperthermophilic Archaeon, Thermococcus strain ES1}, volume={13}, ISSN={["1433-4909"]}, DOI={10.1007/s00792-008-0217-z}, abstractNote={The gene encoding a thermostable iron-containing alcohol dehydrogenase from Thermococcus Strain ES1 (ES1 ADH) was cloned, sequenced and expressed in Escherichia coli. The recombinant and native ES1 ADHs were purified using multistep column chromatography under anaerobic conditions. Both enzymes appeared to be homotetramers with a subunit size of 45+/-1 kDa as revealed by SDS-PAGE, which was close to the calculated value (44.8 kDa). The recombinant ADH contained 1.0+/-0.1 g-atom iron per subunit. Both enzymes were sensitive to oxygen with a half-life upon exposure to air of about 4 min. The recombinant enzyme exhibited a specific activity of 105+/-2 U mg(-1), which was very similar to that of the native enzyme (110+/-3 U mg(-1)). The optimal pH-values for both enzymes for ethanol oxidation and acetaldehyde reduction were 10.4 and 7.0, respectively. Both enzymes also showed similar temperature-dependent activities, and catalyzed the oxidation of primary alcohols, but there was no activity towards methanol and secondary alcohols. Kinetic parameters of the enzymes showed lower K (m)-values for acetaldehyde and NADPH and higher K (m)-values for ethanol and NADP(+). It is concluded that the gene encoding ES1 ADH was expressed successfully in E. coli. This is the first report of a fully active recombinant version of an iron-containing ADH from a hyperthermophile.}, number={2}, journal={EXTREMOPHILES}, author={Ying, Xiangxian and Grunden, Amy M. and Nie, Lin and Adams, Michael W. W. and Ma, Kesen}, year={2009}, month={Mar}, pages={299–311} } @article{lee_sevinsky_bundy_grunden_stephenson_2009, title={Proteomics of Pyrococcus furiosus, a Hyperthermophilic Archaeon Refractory to Traditional Methods}, volume={8}, ISSN={["1535-3907"]}, DOI={10.1021/pr801119h}, abstractNote={Pyrococcus furiosus is one of the most extensively studied hyperthermophilic archaea. Proteins from this hyperthemophile organism are extremely thermostable and are highly resistant to chemical denaturants, organic solvents and proteolytic digestion. This thermostability makes it difficult to apply traditional methods of enzymatically digesting a complex mixture of proteins, commonly a first step in peptide generation in most shotgun proteomics methods. Here, we have developed a simple shotgun proteomics approach for the global identification of the P. furiosus proteome. This methodology uses a detergent-based microwave assisted acid hydrolysis (MAAH) step coupled with an overnight trypsin digest to obtain peptides. Subsequent peptide fractionation by isoelectric focusing in immobilized pH gradients (IPG-IEF), followed by chromatographic separation with reverse phase nano-HPLC and electrospray ionization tandem mass spectrometry (ESI-MS/MS) of peptides enabled the identification of over 900 proteins representing over 44% of the proteome. In most functional classes, over 50% of the predicted proteins were identified, including a number of membrane proteins. This new sample preparation technique will enable extensive proteomics data to be obtained for this organism, thereby enabling the reconstruction of metabolic pathways and promoting a systems biology based understanding of this important extremophile.}, number={8}, journal={JOURNAL OF PROTEOME RESEARCH}, author={Lee, Alice M. and Sevinsky, Joel R. and Bundy, Jonathan L. and Grunden, Amy M. and Stephenson, James L., Jr.}, year={2009}, month={Aug}, pages={3844–3851} } @misc{theriot_tove_grunden_2009, title={biotechnological applications of recombinant microbial prolidases}, volume={68}, journal={Advances in applied microbiology, vol 68}, author={Theriot, C. M. and Tove, S. R. and Grunden, A. M.}, year={2009}, pages={99-} } @article{du_tove_kast-hutcheson_grunden_2005, title={Characterization of the dinuclear metal center of Pyrococcus furiosus prolidase by analysis of targeted mutants}, volume={579}, ISSN={["1873-3468"]}, DOI={10.1016/j.febslet.2005.09.086}, abstractNote={Prolidases are dipeptidases specific for cleavage of Xaa‐Pro dipeptides. Pyrococcus furiosus prolidase is a homodimer having one Co‐bound dinuclear metal cluster per monomer with one tightly bound Co(II) site and the other loosely bound (K d 0.24 mM). To identify which Co site is tight‐binding and which is loose‐binding, site‐directed mutagenesis was used to modify amino acid residues that participate in binding the Co1 (E‐313 and H‐284), the Co2 site (D‐209) or the bidentate ligand (E‐327). Metal‐content, enzyme activity and CD‐spectra analyses of D209A‐, H284L‐, and E327L‐prolidase mutants show that Co1 is the tight‐binding and Co2 the loose‐binding metal center.}, number={27}, journal={FEBS LETTERS}, author={Du, XL and Tove, S and Kast-Hutcheson, K and Grunden, AM}, year={2005}, month={Nov}, pages={6140–6146} } @article{grunden_jenney_ma_ji_weinberg_adams_2005, title={In vitro reconstitution of an NADPH-dependent superoxide reduction pathway from Pyrococcus furiosus}, volume={71}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.71.3.1522-1530.2005}, abstractNote={ABSTRACT}, number={3}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Grunden, AA and Jenney, FE and Ma, KS and Ji, MY and Weinberg, MV and Adams, MWW}, year={2005}, month={Mar}, pages={1522–1530} } @article{im_ji_lee_boss_grunden_2005, title={Production of a thermostable archaeal superoxide reductase in plant cells}, volume={579}, ISSN={["1873-3468"]}, DOI={10.1016/j.febslet.2005.09.015}, abstractNote={ Pyrococcus furiosus superoxide reductase (SOR) is a thermostable archaeal enzyme that reduces superoxide without producing oxygen. When produced as a fusion protein with the green fluorescent protein in plant cells, P. furiosus SOR is located in the cytosol and nucleus. The recombinant SOR enzyme retains its function and heat stability when assayed in vitro. Importantly, expressing SOR in plant cells enhances their survival at high temperature indicating that it functions in vivo. The archaeal SOR provides a novel mechanism to reduce superoxide and demonstrates the potential for using archaeal genes to alter eukaryotic metabolism.}, number={25}, journal={FEBS LETTERS}, author={Im, YJ and Ji, MK and Lee, AM and Boss, WF and Grunden, AM}, year={2005}, month={Oct}, pages={5521–5526} } @article{maher_ghosh_grunden_menon_adams_freeman_guss_2004, title={Structure of the Prolidase fromPyrococcus furiosus†}, volume={43}, ISSN={0006-2960 1520-4995}, url={http://dx.doi.org/10.1021/bi0356451}, DOI={10.1021/bi0356451}, abstractNote={The structure of prolidase from the hyperthermophilic archaeon Pyrococcus furiosus (Pfprol) has been solved and refined at 2.0 A resolution. This is the first structure of a prolidase, i.e., a peptidase specific for dipeptides having proline as the second residue. The asymmetric unit of the crystals contains a homodimer of the enzyme. Each of the two protein subunits has two domains. The C-terminal domain includes the catalytic site, which is centered on a dinuclear metal cluster. In the as-isolated form of Pfprol, the active-site metal atoms are Co(II) [Ghosh, M., et al. (1998) J. Bacteriol. 180, 4781-9]. An unexpected finding is that in the crystalline enzyme the active-site metal atoms are Zn(II), presumably as a result of metal exchange during crystallization. Both of the Zn(II) atoms are five-coordinate. The ligands include a bridging water molecule or hydroxide ion, which is likely to act as a nucleophile in the catalytic reaction. The two-domain polypeptide fold of Pfprol is similar to the folds of two functionally related enzymes, aminopeptidase P (APPro) and creatinase. In addition, the catalytic C-terminal domain of Pfprol has a polypeptide fold resembling that of the sole domain of a fourth enzyme, methionine aminopeptidase (MetAP). The active sites of APPro and MetAP, like that of Pfprol, include a dinuclear metal center. The metal ligands in the three enzymes are homologous. Comparisons with the molecular structures of APPro and MetAP suggest how Pfprol discriminates against oligopeptides and in favor of Xaa-Pro substrates. The crystal structure of Pfprol was solved by multiple-wavelength anomalous dispersion. The crystals yielded diffraction data of relatively high quality and resolution, despite the fact that one of the two protein subunits in the asymmetric unit was found to be significantly disordered. The final R and R(free) values are 0.24 and 0.28, respectively.}, number={10}, journal={Biochemistry}, publisher={American Chemical Society (ACS)}, author={Maher, Megan J. and Ghosh, Mousumi and Grunden, Amy M. and Menon, Angeli L. and Adams, Michael W. W. and Freeman, Hans C. and Guss, J. Mitchell}, year={2004}, month={Mar}, pages={2771–2783} } @article{cargile_bundy_grunden_stephenson_2004, title={Synthesis/degradation ratio mass spectrometry for measuring relative dynamic protein turnover}, volume={76}, ISSN={["0003-2700"]}, DOI={10.1021/ac034841a}, abstractNote={One of the major unanswered questions in quantitative proteomics is that of dynamic protein turnover in the cell. Here we present a new approach to quantitative proteomics that measures the relative dynamic turnover of proteins in cellular systems. In this approach, termed synthesis/degradation ratio mass spectrometry, stable isotope labeling is employed to calculate a relative synthesis/degradation ratio that reflects the relative rate at which 13C is incorporated into individual proteins in the cell. This synthesis/degradation ratio calculation is based on a Poisson distribution model that is designed to support high-throughput analysis. Protein separation and analysis is accomplished by utilizing one-dimensional SDS-PAGE gel electrophoresis followed by cutting the gel into a series of bands for in-gel digestion. The resulting peptide mixtures are analyzed via solid-phase MALDI LC-MS and LC-MS/MS using a tandem time-of-flight mass spectrometer. A portion of the soluble protein fraction from an E. coli K-12 strain was analyzed with synthesis/degradation ratios varying from approximately 0.1 to 4.4 for a variety of different proteins. Unlike other quantitative techniques, synthesis/degradation ratio mass spectrometry requires only a single cell culture to obtain useful biological information about the processes occurring inside a cell. This technique is highly amenable to shotgun proteomics-based approaches and thus should allow relative turnover measurements for whole proteomes in the future.}, number={1}, journal={ANALYTICAL CHEMISTRY}, author={Cargile, BJ and Bundy, JL and Grunden, AM and Stephenson, JL}, year={2004}, month={Jan}, pages={86–97} } @article{self_grunden_hasona_shanmugam_2001, title={Molybdate transport}, volume={152}, ISSN={["1769-7123"]}, DOI={10.1016/S0923-2508(01)01202-5}, abstractNote={In both bacteria and archaea, molybdate is transported by an ABC-type transporter comprising three proteins, ModA (periplasmic binding protein), ModB (membrane protein) and ModC, the ATPase. The modABC operon expression is controlled by ModE-Mo. In the absence of the high-affinity molybdate transporter, molybdate is also transported by another ABC transporter which transports sulfate/thiosulfate as well as by a nonspecific anion transporter. Comparative analysis of the molybdate transport proteins in various bacteria and archaea is the focus of this review.}, number={3-4}, journal={RESEARCH IN MICROBIOLOGY}, author={Self, WT and Grunden, AM and Hasona, A and Shanmugam, KT}, year={2001}, pages={311–321} } @article{grunden_ghosh_adams_2001, title={Proline dipeptidase from Pyrococcus furiosus}, volume={330}, DOI={10.1016/s0076-6879(01)30395-6}, abstractNote={Prolyl residues are unique among the 20 common amino acid residues in that they confer a conformational constraint on peptide chains due to the cyclic nature of their pyrrolidine side group. This conformational constraint prevents cleavage of bonds adjacent to proline by most proteases; however, several enzymes have been characterized that are capable of hydrolyzing these bonds. Prolidases have been isolated from mammalian, bacterial (Lactobacillus and Xanthomonas), and archaeal (pyrococcus) sources and appear to be ubiquitous in nature. Although the physiological role of the enzyme is unclear in both bacteria and archaea, its absence in humans results in abnormalities of the skin and other collagenous tissues. Prolidases have several potential biotechnological applications. One possible use is in the dairy industry as a cheese-ripening agent, as removal of proline from proline-containing peptides in cheese reduces bitterness. A second application is as an enzyme to degrade organophosphorus acidcontaining compounds present in a number of chemical warfare agents and pesticides. The organophosphorus acid-hydrolyzing capabilities of prolidase have been suggested by the discovery that the protein characterized as an organophosphorus acid anhydrolase (OPAA) and prolidase are one in the same.}, journal={Hyperthermophilic enzymes. Part A}, publisher={San Diego, Calif.: Academic Press}, author={Grunden, Amy and Ghosh, M. and Adams, M. W. W.}, year={2001}, pages={433–445} }