@misc{nguyen_zhang_liu_zhang_jin_taniguchi_miller_lindsey_2023, title={Tolyporphins-Exotic Tetrapyrrole Pigments in a Cyanobacterium-A Review}, volume={28}, ISSN={["1420-3049"]}, url={https://doi.org/10.3390/molecules28166132}, DOI={10.3390/molecules28166132}, abstractNote={Tolyporphins were discovered some 30 years ago as part of a global search for antineoplastic compounds from cyanobacteria. To date, the culture HT-58-2, comprised of a cyanobacterium–microbial consortium, is the sole known producer of tolyporphins. Eighteen tolyporphins are now known—each is a free base tetrapyrrole macrocycle with a dioxobacteriochlorin (14), oxochlorin (3), or porphyrin (1) chromophore. Each compound displays two, three, or four open β-pyrrole positions and two, one, or zero appended C-glycoside (or –OH or –OAc) groups, respectively; the appended groups form part of a geminal disubstitution motif flanking the oxo moiety in the pyrroline ring. The distinct structures and repertoire of tolyporphins stand alone in the large pigments-of-life family. Efforts to understand the cyanobacterial origin, biosynthetic pathways, structural diversity, physiological roles, and potential pharmacological properties of tolyporphins have attracted a broad spectrum of researchers from diverse scientific areas. The identification of putative biosynthetic gene clusters in the HT-58-2 cyanobacterial genome and accompanying studies suggest a new biosynthetic paradigm in the tetrapyrrole arena. The present review provides a comprehensive treatment of the rich science concerning tolyporphins.}, number={16}, journal={MOLECULES}, author={Nguyen, Kathy-Uyen and Zhang, Yunlong and Liu, Qihui and Zhang, Ran and Jin, Xiaohe and Taniguchi, Masahiko and Miller, Eric S. and Lindsey, Jonathan S.}, year={2023}, month={Aug} }
 @article{jin_zhang_zhang_nguyen_lindsey_miller_2021, title={Identification of Putative Biosynthetic Gene Clusters for Tolyporphins in Multiple Filamentous Cyanobacteria}, volume={11}, ISSN={["2075-1729"]}, DOI={10.3390/life11080758}, abstractNote={Tolyporphins A–R are unusual tetrapyrrole macrocycles produced by the non-axenic filamentous cyanobacterium HT-58-2. A putative biosynthetic gene cluster for biosynthesis of tolyporphins (here termed BGC-1) was previously identified in the genome of HT-58-2. Here, homology searching of BGC-1 in HT-58-2 led to identification of similar BGCs in seven other filamentous cyanobacteria, including strains Nostoc sp. 106C, Nostoc sp. RF31YmG, Nostoc sp. FACHB-892, Brasilonema octagenarum UFV-OR1, Brasilonema octagenarum UFV-E1, Brasilonema sennae CENA114 and Oculatella sp. LEGE 06141, suggesting their potential for tolyporphins production. A similar gene cluster (BGC-2) also was identified unexpectedly in HT-58-2. Tolyporphins BGCs were not identified in unicellular cyanobacteria. Phylogenetic analysis based on 16S rRNA and a common component of the BGCs, TolD, points to a close evolutionary history between each strain and their respective tolyporphins BGC. Though identified with putative tolyporphins BGCs, examination of pigments extracted from three cyanobacteria has not revealed the presence of tolyporphins. Overall, the identification of BGCs and potential producers of tolyporphins presents a collection of candidate cyanobacteria for genetic and biochemical analysis pertaining to these unusual tetrapyrrole macrocycles.}, number={8}, journal={LIFE-BASEL}, author={Jin, Xiaohe and Zhang, Yunlong and Zhang, Ran and Nguyen, Kathy-Uyen and Lindsey, Jonathan S. and Miller, Eric S.}, year={2021}, month={Aug} }
 @article{jin_miller_lindsey_2021, title={Natural Product Gene Clusters in the Filamentous Nostocales Cyanobacterium HT-58-2}, volume={11}, ISSN={["2075-1729"]}, DOI={10.3390/life11040356}, abstractNote={Cyanobacteria are known as rich repositories of natural products. One cyanobacterial-microbial consortium (isolate HT-58-2) is known to produce two fundamentally new classes of natural products: the tetrapyrrole pigments tolyporphins A–R, and the diterpenoid compounds tolypodiol, 6-deoxytolypodiol, and 11-hydroxytolypodiol. The genome (7.85 Mbp) of the Nostocales cyanobacterium HT-58-2 was annotated previously for tetrapyrrole biosynthesis genes, which led to the identification of a putative biosynthetic gene cluster (BGC) for tolyporphins. Here, bioinformatics tools have been employed to annotate the genome more broadly in an effort to identify pathways for the biosynthesis of tolypodiols as well as other natural products. A putative BGC (15 genes) for tolypodiols has been identified. Four BGCs have been identified for the biosynthesis of other natural products. Two BGCs related to nitrogen fixation may be relevant, given the association of nitrogen stress with production of tolyporphins. The results point to the rich biosynthetic capacity of the HT-58-2 cyanobacterium beyond the production of tolyporphins and tolypodiols.}, number={4}, journal={LIFE-BASEL}, author={Jin, Xiaohe and Miller, Eric S. and Lindsey, Jonathan S.}, year={2021}, month={Apr} }
 @article{barnhart-dailey_zhang_zhang_anthony_aaron_miller_lindsey_timlin_2019, title={Cellular localization of tolyporphins, unusual tetrapyrroles, in a microbial photosynthetic community determined using hyperspectral confocal fluorescence microscopy}, volume={141}, ISSN={0166-8595 1573-5079}, url={http://dx.doi.org/10.1007/s11120-019-00625-w}, DOI={10.1007/s11120-019-00625-w}, abstractNote={["The cyanobacterial culture HT-58-2, composed of a filamentous cyanobacterium and accompanying community bacteria, produces chlorophyll a as well as the tetrapyrrole macrocycles known as tolyporphins. Almost all known tolyporphins (A-M except K) contain a dioxobacteriochlorin chromophore and exhibit an absorption spectrum somewhat similar to that of chlorophyll a. Here, hyperspectral confocal fluorescence microscopy was employed to noninvasively probe the locale of tolyporphins within live cells under various growth conditions (media, illumination, culture age). Cultures grown in nitrate-depleted media (BG-11", {:sub=>"0"}, " vs. nitrate-rich, BG-11) are known to increase the production of tolyporphins by orders of magnitude (rivaling that of chlorophyll a) over a period of 30-45 days. Multivariate curve resolution (MCR) was applied to an image set containing images from each condition to obtain pure component spectra of the endogenous pigments. The relative abundances of these components were then calculated for individual pixels in each image in the entire set, and 3D-volume renderings were obtained. At 30 days in media with or without nitrate, the chlorophyll a and phycobilisomes (combined phycocyanin and phycobilin components) co-localize in the filament outer cytoplasmic region. Tolyporphins localize in a distinct peripheral pattern in cells grown in BG-11", {:sub=>"0"}, " versus a diffuse pattern (mimicking the chlorophyll a localization) upon growth in BG-11. In BG-11", {:sub=>"0"}, ", distinct puncta of tolyporphins were commonly found at the septa between cells and at the end of filaments. This work quantifies the relative abundance and envelope localization of tolyporphins in single cells, and illustrates the ability to identify novel tetrapyrroles in the presence of chlorophyll a in a photosynthetic microorganism within a non-axenic culture."]}, number={3}, journal={Photosynthesis Research}, publisher={Springer Science and Business Media LLC}, author={Barnhart-Dailey, Meghan and Zhang, Yunlong and Zhang, Ran and Anthony, Stephen M. and Aaron, Jesse S. and Miller, Eric S. and Lindsey, Jonathan S. and Timlin, Jerilyn A.}, year={2019}, month={Mar}, pages={259–271} }
 @article{hughes_jin_zhang_zhang_tran_williams_lindsey_miller_2018, title={Genome sequence, metabolic properties and cyanobacterial attachment of Porphyrobacter sp. HT-58-2 isolated from a filamentous cyanobacterium–microbial consortium}, volume={164}, ISSN={1350-0872 1465-2080}, url={http://dx.doi.org/10.1099/mic.0.000706}, DOI={10.1099/mic.0.000706}, abstractNote={Tolyporphins are structurally diverse tetrapyrrole macrocycles produced by the cyanobacterial culture HT-58-2. Although tolyporphins were discovered over 25 years ago, little was known about the microbiology of the culture. The studies reported herein expand the description of the community of predominantly alphaproteobacteria associated with the filamentous HT-58-2 cyanobacterium and isolate a dominant bacterium, Porphyrobacter sp. HT-58-2, for which the complete genome is established and growth properties are examined. Fluorescence in situ hybridization (FISH) analysis of the cyanobacterium-microbial community with a probe targeting the 16S rRNA of Porphyrobacter sp. HT-58-2 showed fluorescence emanating from the cyanobacterial sheath. Although genes for the biosynthesis of bacteriochlorophyll a (BChl a) are present in the Porphyrobacter sp. HT-58-2 genome, the pigment was not detected under the conditions examined, implying the absence of phototrophic growth. Comparative analysis of four Porphyrobacter spp. genomes from worldwide collection sites showed significant collinear gene blocks, with two inversions and three deletion regions. Taken together, the results enrich our understanding of the HT-58-2 cyanobacterium-microbial culture.}, number={10}, journal={Microbiology}, publisher={Microbiology Society}, author={Hughes, Rebecca-Ayme and Jin, Xiaohe and Zhang, Yunlong and Zhang, Ran and Tran, Sabrina and Williams, Philip G. and Lindsey, Jonathan S. and Miller, Eric S.}, year={2018}, month={Oct}, pages={1229–1239} }
 @article{hanauer_graham_betancur_bobrownicki_cresawn_garlena_jacobs-sera_kaufmann_pope_russell_et al._2017, title={An inclusive Research Education Community (iREC): Impact of the SEA-PHAGES program on research outcomes and student learning}, volume={114}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.1718188115}, DOI={10.1073/pnas.1718188115}, abstractNote={Significance The Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science program is an inclusive Research Education Community with centralized programmatic and scientific support, in which broad student engagement in authentic science is linked to increased accessibility to research experiences for students; increased persistence of these students in science, technology, engineering, and mathematics; and increased scientific productivity for students and faculty alike. Engaging undergraduate students in scientific research promises substantial benefits, but it is not accessible to all students and is rarely implemented early in college education, when it will have the greatest impact. An inclusive Research Education Community (iREC) provides a centralized scientific and administrative infrastructure enabling engagement of large numbers of students at different types of institutions. The Science Education Alliance–Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) is an iREC that promotes engagement and continued involvement in science among beginning undergraduate students. The SEA-PHAGES students show strong gains correlated with persistence relative to those in traditional laboratory courses regardless of academic, ethnic, gender, and socioeconomic profiles. This persistent involvement in science is reflected in key measures, including project ownership, scientific community values, science identity, and scientific networking.}, number={51}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Hanauer, David I. and Graham, Mark J. and Betancur, Laura and Bobrownicki, Aiyana and Cresawn, Steven G. and Garlena, Rebecca A. and Jacobs-Sera, Deborah and Kaufmann, Nancy and Pope, Welkin H. and Russell, Daniel A. and et al.}, year={2017}, month={Dec}, pages={13531–13536} }
 @article{hughes_zhang_zhang_williams_lindsey_miller_2017, title={Genome Sequence and Composition of a Tolyporphin-Producing Cyanobacterium-Microbial Community}, volume={83}, ISSN={["1098-5336"]}, DOI={10.1128/aem.01068-17}, abstractNote={ABSTRACT The cyanobacterial culture HT-58-2 was originally described as a strain of Tolypothrix nodosa with the ability to produce tolyporphins, which comprise a family of distinct tetrapyrrole macrocycles with reported efflux pump inhibition properties. Upon reviving the culture from what was thought to be a nonextant collection, studies of culture conditions, strain characterization, phylogeny, and genomics have been undertaken. Here, HT-58-2 was shown by 16S rRNA analysis to closely align with Brasilonema strains and not with Tolypothrix isolates. Light, fluorescence, and scanning electron microscopy revealed cyanobacterium filaments that are decorated with attached bacteria and associated with free bacteria. Metagenomic surveys of HT-58-2 cultures revealed a diversity of bacteria dominated by Erythrobacteraceae, 97% of which are Porphyrobacter species. A dimethyl sulfoxide washing procedure was found to yield enriched cyanobacterial DNA (presumably by removing community bacteria) and sequence data sufficient for genome assembly. The finished, closed HT-58-2Cyano genome consists of 7.85 Mbp (42.6% G+C) and contains 6,581 genes. All genes for biosynthesis of tetrapyrroles (e.g., heme, chlorophyll a, and phycocyanobilin) and almost all for cobalamin were identified dispersed throughout the chromosome. Among the 6,177 protein-encoding genes, coding sequences (CDSs) for all but two of the eight enzymes for conversion of glutamic acid to protoporphyrinogen IX also were found within one major gene cluster. The cluster also includes 10 putative genes (and one hypothetical gene) encoding proteins with domains for a glycosyltransferase, two cytochrome P450 enzymes, and a flavin adenine dinucleotide (FAD)-binding protein. The composition of the gene cluster suggests a possible role in tolyporphin biosynthesis. IMPORTANCE A worldwide search more than 25 years ago for cyanobacterial natural products with anticancer activity identified a culture (HT-58-2) from Micronesia that produces tolyporphins. Tolyporphins are tetrapyrroles, like chlorophylls, but have several profound structural differences that reside outside the bounds of known biosynthetic pathways. To begin probing the biosynthetic origin and biological function of tolyporphins, our research has focused on studying the cyanobacterial strain, about which almost nothing has been previously reported. We find that the HT-58-2 culture is composed of the cyanobacterium and a community of associated bacteria, complicating the question of which organisms make tolyporphins. Elucidation of the cyanobacterial genome revealed an intriguing gene cluster that contains tetrapyrrole biosynthesis genes and a collection of unknown genes, suggesting that the cluster may be responsible for tolyporphin production. Knowledge of the genome and the gene cluster sharply focuses research to identify related cyanobacterial producers of tolyporphins and delineate the tolyporphin biosynthetic pathway.}, number={19}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Hughes, Rebecca-Ayme and Zhang, Yunlong and Zhang, Ran and Williams, Philip G. and Lindsey, Jonathan S. and Miller, Eric S.}, year={2017}, month={Oct} }
 @article{zhang_zhang_nazari_bagley_miller_williams_muddiman_lindsey_2017, title={Mass spectrometric detection of chlorophyll a and the tetrapyrrole secondary metabolite tolyporphin A in the filamentous cyanobacterium HT-58-2. Approaches to high-throughput screening of intact cyanobacteria}, volume={21}, ISSN={["1099-1409"]}, DOI={10.1142/s108842461750078x}, abstractNote={Tolyporphins are unusual tetrapyrrole macrocycles produced by the filamentous cyanobacterium–microbial community HT-58-2, the only known source to date. Numerous cyanobacterial samples have been collected worldwide but most have not been screened for secondary metabolites. Identification of tolyporphins typically has entailed lipophilic extraction followed by chromatographic fractionation and spectroscopic and/or mass spectrometric analysis. For quantitation, lengthy lipophilic extraction, sample processing and HPLC separation are needed. Examination by MALDI-TOF-MS (with the matrix 1,5-diaminonaphthalene) of lipophilic crude extracts of small-scale HT-58-2 samples (2 mL) without chromatographic fractionation enabled semi-quantitation of tolyporphin A over a 41-day growth period. Screening for tolyporphin A in intact or slightly sheared and vortexed HT-58-2 samples (no lipophilic extraction), and confirmation of identity by tandem MS, were carried out by IR-MALDESI-FTMS. Tolyporphin A was identified by th...}, number={11}, journal={JOURNAL OF PORPHYRINS AND PHTHALOCYANINES}, author={Zhang, Yunlong and Zhang, Ran and Nazari, Milad and Bagley, Michael C. and Miller, Eric S. and Williams, Philip G. and Muddiman, David C. and Lindsey, Jonathan S.}, year={2017}, month={Nov}, pages={759–768} }
 @article{hood_niedzwiedzki_zhang_zhang_dai_miller_bocian_williams_lindsey_holten_2017, title={Photophysical Characterization of the Naturally Occurring Dioxobacteriochlorin Tolyporphin A and Synthetic Oxobacteriochlorin Analogues}, volume={93}, ISSN={["1751-1097"]}, DOI={10.1111/php.12781}, abstractNote={Tolyporphins are tetrapyrrole macrocycles produced by a cyanobacterium‐containing culture known as HT‐58‐2. Tolyporphins A–J are free base dioxobacteriochlorins, whereas tolyporphin K is an oxochlorin. Here, the photophysical characterization is reported of tolyporphin A and two synthetic analogues, an oxobacteriochlorin and a dioxobacteriochlorin. The characterization (in toluene, diethyl ether, ethyl acetate, dichloromethane, 1‐pentanol, 2‐butanone, ethanol, methanol, N,N‐dimethylformamide and dimethylsulfoxide) includes static absorption and fluorescence spectra, fluorescence quantum yields and time‐resolved data. The data afford the lifetime of the lowest singlet excited state and the yields of the nonradiative decay pathways (intersystem crossing and internal conversion). The three macrocycles exhibit only modest variation in spectroscopic and excited‐state photophysical parameters across the solvents. The long‐wavelength (Qy) absorption band of tolyporphin A appears at ~680 nm and is remarkably narrow (full‐width‐at‐half‐maximum ~7 nm). The position of the long‐wavelength (Qy) absorption band of tolyporphin A (~680 nm) more closely resembles that of chlorophyll a (662 nm) than bacteriochlorophyll a (772 nm). The absorption spectra of tolyporphins B–I, K (which were available in minute quantities) are also reported in methanol; the spectra of B–I closely resemble that of tolyporphin A. Taken together, tolyporphin A generally exhibits spectral and photophysical features resembling those of chlorophyll a.}, number={5}, journal={PHOTOCHEMISTRY AND PHOTOBIOLOGY}, author={Hood, Don and Niedzwiedzki, Dariusz M. and Zhang, Ran and Zhang, Yunlong and Dai, Jingqiu and Miller, Eric S. and Bocian, David F. and Williams, Philip G. and Lindsey, Jonathan S. and Holten, Dewey}, year={2017}, month={Oct}, pages={1204–1215} }
 @article{zhang_zhang_hughes_dai_gurr_williams_miller_lindsey_2017, title={Quantitation of Tolyporphins, Diverse Tetrapyrrole Secondary Metabolites with Chlorophyll-Like Absorption, from a Filamentous Cyanobacterium-Microbial Community}, volume={29}, ISSN={0958-0344}, url={http://dx.doi.org/10.1002/pca.2735}, DOI={10.1002/pca.2735}, abstractNote={INTRODUCTION
Tolyporphins are unusual tetrapyrrole macrocycles produced by a non-axenic filamentous cyanobacterium (HT-58-2). Tolyporphins A-J, L, and M share a common dioxobacteriochlorin core, differ in peripheral substituents, and exhibit absorption spectra that overlap that of the dominant cyanobacterial pigment, chlorophyll a. Identification and accurate quantitation of the various tolyporphins in these chlorophyll-rich samples presents challenges.


OBJECTIVE
To develop methods for the quantitative determination of tolyporphins produced under various growth conditions relative to that of chlorophyll a.


METHODOLOGY
Chromatographic fractionation of large-scale (440 L) cultures afforded isolated individual tolyporphins. Lipophilic extraction of small-scale (25 mL) cultures, HPLC separation with an internal standard, and absorption detection enabled quantitation of tolyporphin A and chlorophyll a, and by inference the amounts of tolyporphins A-M. Absorption spectroscopy with multicomponent analysis of lipophilic extracts (2 mL cultures) afforded the ratio of all tolyporphins to chlorophyll a. The reported absorption spectral data for the various tolyporphins required re-evaluation for quantitative purposes.


RESULTS AND DISCUSSION
The amount of tolyporphin A after 50 days of illumination ranged from 0.13 nmol/mg dry cells (media containing nitrate) to 1.12 nmol/mg (without nitrate), with maximum 0.23 times that of chlorophyll a. Under soluble-nitrogen deprivation after 35-50 days, tolyporphin A represents 1/3-1/2 of the total tolyporphins, and the total amount of tolyporphins is up to 1.8-fold that of chlorophyll a.


CONCLUSIONS
The quantitative methods developed herein should facilitate investigation of the biosynthesis of tolyporphins (and other tetrapyrroles) as well as examination of other strains for production of tolyporphins. Copyright © 2017 John Wiley & Sons, Ltd.}, number={2}, journal={Phytochemical Analysis}, publisher={Wiley}, author={Zhang, Yunlong and Zhang, Ran and Hughes, Rebecca-Ayme and Dai, Jingqiu and Gurr, Joshua R. and Williams, Philip G. and Miller, Eric S. and Lindsey, Jonathan S.}, year={2017}, month={Nov}, pages={205–216} }
 @article{lee_li_miller_2017, title={Vibrio Phage KVP40 Encodes a Functional NAD(+) Salvage Pathway}, volume={199}, ISSN={["1098-5530"]}, DOI={10.1128/jb.00855-16}, abstractNote={ABSTRACT The genome of T4-type Vibrio bacteriophage KVP40 has five genes predicted to encode proteins of pyridine nucleotide metabolism, of which two, nadV and natV, would suffice for an NAD+ salvage pathway. NadV is an apparent nicotinamide phosphoribosyltransferase (NAmPRTase), and NatV is an apparent bifunctional nicotinamide mononucleotide adenylyltransferase (NMNATase) and nicotinamide-adenine dinucleotide pyrophosphatase (Nudix hydrolase). Genes encoding the predicted salvage pathway were cloned and expressed in Escherichia coli, the proteins were purified, and their enzymatic properties were examined. KVP40 NadV NAmPRTase is active in vitro, and a clone complements a Salmonella mutant defective in both the bacterial de novo and salvage pathways. Similar to other NAmPRTases, the KVP40 enzyme displayed ATPase activity indicative of energy coupling in the reaction mechanism. The NatV NMNATase activity was measured in a coupled reaction system demonstrating NAD+ biosynthesis from nicotinamide, phosphoribosyl pyrophosphate, and ATP. The NatV Nudix hydrolase domain was also shown to be active, with preferred substrates of ADP-ribose, NAD+, and NADH. Expression analysis using reverse transcription-quantitative PCR (qRT-PCR) and enzyme assays of infected Vibrio parahaemolyticus cells demonstrated nadV and natV transcription during the early and delayed-early periods of infection when other KVP40 genes of nucleotide precursor metabolism are expressed. The distribution and phylogeny of NadV and NatV proteins among several large double-stranded DNA (dsDNA) myophages, and also those from some very large siphophages, suggest broad relevance of pyridine nucleotide scavenging in virus-infected cells. NAD+ biosynthesis presents another important metabolic resource control point by large, rapidly replicating dsDNA bacteriophages. IMPORTANCE T4-type bacteriophages enhance DNA precursor synthesis through reductive reactions that use NADH/NADPH as the electron donor and NAD+ for ADP-ribosylation of proteins involved in transcribing and translating the phage genome. We show here that phage KVP40 encodes a functional pyridine nucleotide scavenging pathway that is expressed during the metabolic period of the infection cycle. The pathway is conserved in other large, dsDNA phages in which the two genes, nadV and natV, share an evolutionary history in their respective phage-host group.}, number={9}, journal={JOURNAL OF BACTERIOLOGY}, author={Lee, Jae Yun and Li, Zhiqun and Miller, Eric S.}, year={2017}, month={May} }
 @article{harrell_miller_2016, title={Genome Sequence of
                    Aeromicrobium erythreum
                    NRRL B-3381, an Erythromycin-Producing Bacterium of the
                    Nocardioidaceae}, volume={4}, ISSN={2169-8287}, url={http://dx.doi.org/10.1128/genomea.00300-16}, DOI={10.1128/genomea.00300-16}, abstractNote={ABSTRACT Aeromicrobium erythreum NRRL B-3381 has a 3,629,239-bp circular genome that has 72% G+C content. There are at least 3,121 coding sequences (CDSs), two rRNA gene operons, and 47 tRNAs. The genome and erythromycin (ery) biosynthetic gene sequences provide resources for metabolic and combinatorial engineering of polyketides.}, number={2}, journal={Genome Announcements}, publisher={American Society for Microbiology}, author={Harrell, Erin A. and Miller, Eric S.}, year={2016}, month={Apr} }
 @article{abraham_bousquet_bruff_carson_clark_connell_davis_dums_everington_groth_et al._2016, title={Paenibacillus larvae
                    Phage Tripp Genome Has 378-Base-Pair Terminal Repeats}, volume={4}, ISSN={2169-8287}, url={http://dx.doi.org/10.1128/genomea.01498-15}, DOI={10.1128/genomea.01498-15}, abstractNote={ABSTRACT Paenibacillus larvae bacteriophage Tripp was isolated from an American foulbrood diseased honey bee hive in North Carolina, USA. The 54,439-bp genome is 48.3% G+C, encodes 92 proteins, no tRNAs, and has 378-bp direct terminal repeats. It is currently unique in Genbank.}, number={1}, journal={Genome Announcements}, publisher={American Society for Microbiology}, author={Abraham, J. and Bousquet, A.-C. and Bruff, E. and Carson, N. and Clark, A. and Connell, A. and Davis, Z. and Dums, J. and Everington, C. and Groth, A. and et al.}, year={2016}, month={Jan} }
 @book{miller_whittman_kropinski_areaenssesn_2015, title={Divavirus taxonomic bacteriophage group infecting Paenibacillus larvae}, institution={International Committee on the Taxonomy of Viruses}, author={Miller, E.S. and Whittman, J. and Kropinski, A.M. and Areaenssesn, E.M.}, year={2015} }
 @article{carson_bruff_defoor_dums_groth_hatfield_iyer_joshi_mcadams_miles_et al._2015, title={Genome Sequences of Six Paenibacillus larvae Siphoviridae Phages}, volume={3}, ISSN={2169-8287}, url={http://dx.doi.org/10.1128/genomea.00101-15}, DOI={10.1128/genomea.00101-15}, abstractNote={ABSTRACT Six sequenced and annotated genomes of Paenibacillus larvae phages isolated from the combs of American foulbrood-diseased beehives are 37 to 45 kbp and have approximately 42% G+C content and 60 to 74 protein-coding genes. Phage Lily is most divergent from Diva, Rani, Redbud, Shelly, and Sitara.}, number={3}, journal={Genome Announcements}, publisher={American Society for Microbiology}, author={Carson, Susan and Bruff, Emily and DeFoor, William and Dums, Jacob and Groth, Adam and Hatfield, Taylor and Iyer, Aruna and Joshi, Kalyani and McAdams, Sarah and Miles, Devon and et al.}, year={2015}, month={Jun} }
 @article{pope_bowman_russell_jacobs-sera_asai_cresawn_jacobs_hendrix_lawrence_hatfull_2015, title={Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity}, volume={4}, ISSN={2050-084X}, url={http://dx.doi.org/10.7554/eLife.06416}, DOI={10.7554/eLife.06416}, abstractNote={The bacteriophage population is large, dynamic, ancient, and genetically diverse. Limited genomic information shows that phage genomes are mosaic, and the genetic architecture of phage populations remains ill-defined. To understand the population structure of phages infecting a single host strain, we isolated, sequenced, and compared 627 phages of Mycobacterium smegmatis. Their genetic diversity is considerable, and there are 28 distinct genomic types (clusters) with related nucleotide sequences. However, amino acid sequence comparisons show pervasive genomic mosaicism, and quantification of inter-cluster and intra-cluster relatedness reveals a continuum of genetic diversity, albeit with uneven representation of different phages. Furthermore, rarefaction analysis shows that the mycobacteriophage population is not closed, and there is a constant influx of genes from other sources. Phage isolation and analysis was performed by a large consortium of academic institutions, illustrating the substantial benefits of a disseminated, structured program involving large numbers of freshman undergraduates in scientific discovery. DOI: http://dx.doi.org/10.7554/eLife.06416.001}, journal={eLife}, publisher={eLife Sciences Publications, Ltd}, author={Pope, Welkin H and Bowman, Charles A and Russell, Daniel A and Jacobs-Sera, Deborah and Asai, David J and Cresawn, Steven G and Jacobs, William R, Jr and Hendrix, Roger W and Lawrence, Jeffrey G and Hatfull, Graham F}, year={2015}, month={Apr} }
 @inproceedings{vu_belloti_gabriel_brochu_miller_bitzer_vouk_2014, title={Modeling ribosome dynamics to optimize heterologous protein production in escherichia coli}, ISBN={9781479970889}, url={http://dx.doi.org/10.1109/GlobalSIP.2014.7032363}, DOI={10.1109/GlobalSIP.2014.7032363}, abstractNote={Ineffective heterologous protein synthesis has often been ascribed to codon bias and rare codons. New experimental evidence suggests that codon bias alone may not be the sole cause of poor translation. In this paper we present a free-energy based model of translation elongation to predict and optimize genes for expression in E. coli. The model takes into account second order free energy effects from the binding between the anti-Shine-Dalgarno sequence of the 3' terminal 16S rRNA tail and the mRNA, tRNA abundance, and ribosome displacement. The model and software allow optimization of genes for increased (or decreased) protein yield. The model's predictive and optimization accuracy was assessed by optimizing and expressing three model genes and multiple mRNA variants coding for GST (26 kDa Glutathion S-Transferase from Schistosomajaponicum). Protein yield of optimized genes showed increase from their wildtype levels. Optimization of Glutathion S-Transferase from Schistosoma japonicum and Alcohol Dehydrogenase from Clostridium ljungdahlii DSM 13528 are discussed as examples. Corresponding author, S. K Vu, can be reached at skvu@ncsu.edu.}, booktitle={2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP)}, publisher={IEEE}, author={Vu, S. K. and Belloti, A. A. and Gabriel, C. J. and Brochu, H. N. and Miller, E. S. and Bitzer, D. L. and Vouk, M. A.}, year={2014}, month={Dec} }
 @article{carson_miller_2013, title={Introducing primary scientific literature to first-year undergraduate researchers}, volume={34}, number={4}, journal={Council on Undergraduate Research on the Web}, author={Carson, S and Miller, Es}, year={2013}, pages={17–22} }
 @article{karam_miller_2010, title={Bacteriophage T4 and its relatives}, volume={7}, ISSN={["1743-422X"]}, DOI={10.1186/1743-422x-7-293}, abstractNote={Bacteriophage T4 and its relatives (A series of critical reviews) Jim Karam & Eric Miller In the coming months Virology Journal will publish a number of authoritative reviews about the biochemistry, structural biology and genomics of the bacteriophage T4 and the T4-related phages. Phage T4 is one of the most extensively investigated viruses and has been the central focus of several monographs and reviews over the last 25 years. Its popularity among experimental biologists is related to the ease with which this phage and some of its relatives can be propagated in widely available nonpathogenic laboratory strains of Escherichia coli and the diversity of experimental approaches that can be used to analyze its DNA genome and the RNA and protein products it encodes. The T4 biological system is amenable to investigation by genetic, phylogenetic, biochemical, biophysical, structural, computational and other tools. Advances in T4 science have paralleled advances in Molecular Biology since the birth of this interdisciplinary field around the middle of the 20 Century [1,2]. Such seminal discoveries as the chemical nature of the gene, the existence of messenger RNA, how the genetic code is read, how genes determine protein structure, how DNA is replicated by multicomponent protein machines and many other findings that have become integral to our current understanding of basic molecular mechanism in biology have typically involved important contributions from the T4 and T4-related experimental systems. The last monograph to comprehensively review all aspects of the molecular biosciences of the T4 virus was published in 1994 [3]. Since that time, the field of Molecular Biology has undergone considerable transformation, particularly as a consequence of advancements in the methods for sequencing microbial and eukaryotic genomes and using DNA sequence data for novel experimental designs that have yielded numerous rewards in resolving biological mysteries and stimulating the growth of biotechnology. The review series to be published in Virology Journal will emphasize advances and seminal discoveries in four major areas of T4 research: Genomics, Gene Expression, DNA Replication and Phage Morphogenesis.}, journal={VIROLOGY JOURNAL}, author={Karam, Jim D. and Miller, Eric S.}, year={2010}, month={Oct} }
 @misc{petrov_ratnayaka_nolan_miller_karam_2010, title={Genomes of the T4-related bacteriophages as windows on microbial genome evolution}, volume={7}, ISSN={["1743-422X"]}, DOI={10.1186/1743-422x-7-292}, abstractNote={Abstract}, journal={VIROLOGY JOURNAL}, author={Petrov, Vasiliy M. and Ratnayaka, Swarnamala and Nolan, James M. and Miller, Eric S. and Karam, Jim D.}, year={2010}, month={Oct} }
 @misc{uzan_miller_2010, title={Post-transcriptional control by bacteriophage T4: mRNA decay and inhibition of translation initiation}, volume={7}, ISSN={["1743-422X"]}, DOI={10.1186/1743-422x-7-360}, abstractNote={Over 50 years of biological research with bacteriophage T4 includes notable discoveries in post-transcriptional control, including the genetic code, mRNA, and tRNA; the very foundations of molecular biology. In this review we compile the past 10 - 15 year literature on RNA-protein interactions with T4 and some of its related phages, with particular focus on advances in mRNA decay and processing, and on translational repression. Binding of T4 proteins RegB, RegA, gp32 and gp43 to their cognate target RNAs has been characterized. For several of these, further study is needed for an atomic-level perspective, where resolved structures of RNA-protein complexes are awaiting investigation. Other features of post-transcriptional control are also summarized. These include: RNA structure at translation initiation regions that either inhibit or promote translation initiation; programmed translational bypassing, where T4 orchestrates ribosome bypass of a 50 nucleotide mRNA sequence; phage exclusion systems that involve T4-mediated activation of a latent endoribonuclease (PrrC) and cofactor-assisted activation of EF-Tu proteolysis (Gol-Lit); and potentially important findings on ADP-ribosylation (by Alt and Mod enzymes) of ribosome-associated proteins that might broadly impact protein synthesis in the infected cell. Many of these problems can continue to be addressed with T4, whereas the growing database of T4-related phage genome sequences provides new resources and potentially new phage-host systems to extend the work into a broader biological, evolutionary context.}, journal={VIROLOGY JOURNAL}, author={Uzan, Marc and Miller, Eric S.}, year={2010}, month={Dec} }
 @article{dong_shew_tredway_lu_sivamani_miller_qu_2008, title={Expression of the bacteriophage T4 lysozyme gene in tall fescue confers resistance to gray leaf spot and brown patch diseases}, volume={17}, ISSN={["1573-9368"]}, DOI={10.1007/s11248-007-9073-3}, abstractNote={Tall fescue (Festuca arundinacea Schreb.) is an important turf and forage grass species worldwide. Fungal diseases present a major limitation in the maintenance of tall fescue lawns, landscapes, and forage fields. Two severe fungal diseases of tall fescue are brown patch, caused by Rhizoctonia solani, and gray leaf spot, caused by Magnaporthe grisea. These diseases are often major problems of other turfgrass species as well. In efforts to obtain tall fescue plants resistant to these diseases, we introduced the bacteriophage T4 lysozyme gene into tall fescue through Agrobacterium-mediated genetic transformation. In replicated experiments under controlled environments conducive to disease development, 6 of 13 transgenic events showed high resistance to inoculation of a mixture of two M. grisea isolates from tall fescue. Three of these six resistant plants also displayed significant resistance to an R. solani isolate from tall fescue. Thus, we have demonstrated that the bacteriophage T4 lysozyme gene confers resistance to both gray leaf spot and brown patch diseases in transgenic tall fescue plants. The gene may have wide applications in engineered fungal disease resistance in various crops.}, number={1}, journal={TRANSGENIC RESEARCH}, author={Dong, Shujie and Shew, H. David and Tredway, Lane P. and Lu, Jianli and Sivamani, Elumalai and Miller, Eric S. and Qu, Rongda}, year={2008}, month={Feb}, pages={47–57} }
 @article{dean_allen_miller_2005, title={In vitro selection of phage RB69 RegA RNA binding sites yields UAA repeats}, volume={336}, ISSN={["0042-6822"]}, DOI={10.1016/j.virol.2005.03.002}, abstractNote={The SELEX method of in vitro selection was used to isolate RNAs that bind the RB69 RegA translational repressor protein immobilized on Ni-NTA agarose. After five rounds of SELEX, the pool of selected RNA displayed striking sequence uniformity: UAAUAAUAAUAAUA was clearly enriched in the 14 nucleotides that underwent selection. Individual, cloned molecules displayed a repeating (UAA) sequence, with only two RNAs having a 3' AUG. Removing the 3' AUG slightly reduced binding in gel shift assays, moving the AUG 5' proximal of the (UAA) slightly improved binding, but (UAA)4 alone still bound the purified protein. Dissociation constants showed that RNA shortened to (UAA)3 and (UAA)2 also retained binding, whereas cytosine clearly prevented binding by RB69 RegA. Scanning of RB69 gene starts and ends with an RB69 RegA SELEX information weight matrix yielded 21 sequences as potential RegA sites. One site, on the mRNA for the pentameric (4:1) phage gp44/62 DNA polymerase clamp loader complex, has the RB69 gene 44 stop codon and 3'-adjacent gene 62 initiation codon in a sequence (GAAAUAAUAUG) that is similar to in vitro selected RNA and was shown to bind RB69 RegA. Sequences between the Shine-Dalgarno and initiation codon, which frequently contain a UAA stop codon of a 5'-adjacent gene, appear to be preferred RB69 RegA binding sites.}, number={1}, journal={VIROLOGY}, author={Dean, TR and Allen, SV and Miller, ES}, year={2005}, month={May}, pages={26–36} }
 @article{pineda_gregory_szczypinski_baxter_hochschild_miller_hinton_2004, title={A family of anti-sigma(70) proteins in T4-type phages and bacteria that are similar to AsiA, a transcription inhibitor and co-activator of bacteriophage T4}, volume={344}, ISSN={["1089-8638"]}, DOI={10.1016/j.jmb.2004.10.003}, abstractNote={Anti-σ70 factors interact with σ70 proteins, the specificity subunits of prokaryotic RNA polymerase. The bacteriophage T4 anti-σ70 protein, AsiA, binds tightly to regions 4.1 and 4.2 of the σ70 subunit of Escherichia coli RNA polymerase and inhibits transcription from σ70 promoters that require recognition of the canonical σ70 −35 DNA sequence. In the presence of the T4 transcription activator MotA, AsiA also functions as a co-activator of transcription from T4 middle promoters, which retain the canonical σ70 −10 consensus sequence but have a MotA box sequence centered at −30 rather than the σ70 −35 sequence. The E. coli anti-σ70 protein Rsd also interacts with region 4.2 of σ70 and inhibits transcription from σ70 promoters. Our sequence comparisons of T4 AsiA with Rsd, with the predicted AsiA orthologs of the T4-type phages RB69, 44RR, KVP40, and Aeh1, and with AlgQ, a regulator of alginate production in Pseudomonas aeruginosa indicate that these proteins share conserved amino acid residues at positions known to be important for the binding of T4 AsiA to σ70 region 4. We show that, like T4 AsiA, Rsd binds to σ70 in a native protein gel and, as with T4 AsiA, a L18S substitution in Rsd disrupts this complex. Previous work has assigned σ70 amino acid F563, within region 4.1, as a critical determinant for AsiA binding. This residue is also involved in the binding of σ70 to the β-flap of core, suggesting that AsiA inhibits transcription by disrupting the interaction between σ70 region 4.1 and the β-flap. We find that as with T4 AsiA, the interaction of KVP40 AsiA, Rsd, or AlgQ with σ70 region 4 is diminished by the substitution F563Y. We also demonstrate that like T4 AsiA and Rsd, KVP40 AsiA inhibits transcription from σ70-dependent promoters. We speculate that the phage AsiA orthologs, Rsd, and AlgQ are members of a related family in T4-type phage and bacteria, which interact similarly with primary σ factors. In addition, we show that even though a clear MotA ortholog has not been identified in the KVP40 genome and the phage genome appears to lack typical middle promoter sequences, KVP40 AsiA activates transcription from T4 middle promoters in the presence of T4 MotA. We speculate that KVP40 encodes a protein that is dissimilar in sequence, but functionally equivalent, to T4 MotA.}, number={5}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Pineda, M and Gregory, BD and Szczypinski, B and Baxter, KR and Hochschild, A and Miller, ES and Hinton, DM}, year={2004}, month={Dec}, pages={1183–1197} }
 @article{yin_ho_miller_shuman_2004, title={Characterization of bacteriophage KVP40 and T4 RNA ligase 2}, volume={319}, ISSN={["0042-6822"]}, DOI={10.1016/j.virol.2003.10.037}, abstractNote={Bacteriophage T4 RNA ligase 2 (Rnl2) exemplifies a subfamily of RNA strand-joining enzymes that includes the trypanosome RNA editing ligases. A homolog of T4 Rnl2 is encoded in the 244-kbp DNA genome of vibriophage KVP40. We show that the 335-amino acid KVP40 Rnl2 is a monomeric protein that catalyzes RNA end-joining through ligase-adenylate and RNA-adenylate (AppRNA) intermediates. In the absence of ATP, pre-adenylated KVP40 Rnl2 reacts with an 18-mer 5'-PO(4) single-strand RNA (pRNA) to form an 18-mer RNA circle. In the presence of ATP, Rnl2 generates predominantly AppRNA. Isolated AppRNA can be circularized by KVP40 Rnl2 in the absence of ATP. The reactivity of phage Rnl2 and the distribution of the products are affected by the length of the pRNA substrate. Whereas 18-mer and 15-mer pRNAs undergo intramolecular sealing by T4 Rnl2 to form monomer circles, a 12-mer pRNA is ligated intermolecularly to form dimers, and a 9-mer pRNA is unreactive. In the presence of ATP, the 15-mer and 12-mer pRNAs are converted to AppRNAs, but the 9-mer pRNA is not. A single 5' deoxynucleotide substitution of an 18-mer pRNA substrate has no apparent effect on the 5' adenylation or circularization reactions of T4 Rnl2. In contrast, a single deoxyribonucleoside at the 3' terminus strongly and selectively suppresses the sealing step, thereby resulting in accumulation of high levels of AppRNA in the absence of ATP. The ATP-dependent "capping" of RNA with AMP by Rnl2 is reminiscent of the capping of eukaryotic mRNA with GMP by GTP:RNA guanylyltransferase and suggests an evolutionary connection between bacteriophage Rnl2 and eukaryotic RNA capping enzymes.}, number={1}, journal={VIROLOGY}, author={Yin, SM and Ho, CK and Miller, ES and Shuman, S}, year={2004}, month={Feb}, pages={141–151} }
 @misc{miller_kutter_mosig_arisaka_kunisawa_ruger_2003, title={Bacteriophage T4 genome}, volume={67}, ISSN={["1098-5557"]}, DOI={10.1128/MMBR.67.1.86-156.2003}, abstractNote={SUMMARYPhage T4 has provided countless contributions to the paradigms of genetics and biochemistry. Its complete genome sequence of 168,903 bp encodes about 300 gene products. T4 biology and its genomic sequence provide the best-understood model for modern functional genomics and proteomics. Variations on gene expression, including overlapping genes, internal translation initiation, spliced genes, translational bypassing, and RNA processing, alert us to the caveats of purely computational methods. The T4 transcriptional pattern reflects its dependence on the host RNA polymerase and the use of phage-encoded proteins that sequentially modify RNA polymerase; transcriptional activator proteins, a phage sigma factor, anti-sigma, and sigma decoy proteins also act to specify early, middle, and late promoter recognition. Posttranscriptional controls by T4 provide excellent systems for the study of RNA-dependent processes, particularly at the structural level. The redundancy of DNA replication and recombination systems of T4 reveals how phage and other genomes are stably replicated and repaired in different environments, providing insight into genome evolution and adaptations to new hosts and growth environments. Moreover, genomic sequence analysis has provided new insights into tail fiber variation, lysis, gene duplications, and membrane localization of proteins, while high-resolution structural determination of the “cell-puncturing device,” combined with the three-dimensional image reconstruction of the baseplate, has revealed the mechanism of penetration during infection. Despite these advances, nearly 130 potential T4 genes remain uncharacterized. Current phage-sequencing initiatives are now revealing the similarities and differences among members of the T4 family, including those that infect bacteria other than Escherichia coli. T4 functional genomics will aid in the interpretation of these newly sequenced T4-related genomes and in broadening our understanding of the complex evolution and ecology of phages—the most abundant and among the most ancient biological entities on Earth.}, number={1}, journal={MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS}, author={Miller, ES and Kutter, E and Mosig, G and Arisaka, F and Kunisawa, T and Ruger, W}, year={2003}, month={Mar}, pages={86-+} }
 @article{miller_heidelberg_eisen_nelson_durkin_ciecko_feldblyum_white_paulsen_nierman_et al._2003, title={Complete genome sequence of the broad-host-range vibriophage KVP40: Comparative genomics of a T4-related bacteriophage}, volume={185}, ISSN={["0021-9193"]}, DOI={10.1128/JB.185.17.5220-5233.2003}, abstractNote={ABSTRACT}, number={17}, journal={JOURNAL OF BACTERIOLOGY}, author={Miller, ES and Heidelberg, JF and Eisen, JA and Nelson, WC and Durkin, AS and Ciecko, A and Feldblyum, TV and White, O and Paulsen, IT and Nierman, WC and et al.}, year={2003}, month={Sep}, pages={5220–5233} }
 @article{evans_crowder_miller_2000, title={Subtilisins of Bacillus spp. hydrolyze keratin and allow growth on feathers}, volume={46}, ISSN={["0008-4166"]}, DOI={10.1139/cjm-46-11-1004}, number={11}, journal={CANADIAN JOURNAL OF MICROBIOLOGY}, author={Evans, KL and Crowder, J and Miller, ES}, year={2000}, month={Nov}, pages={1004–1011} }
 @article{allen_miller_1999, title={RNA-binding properties of in vitro expressed histidine-tagged RB69 RegA translational repressor protein}, volume={269}, ISSN={["1096-0309"]}, DOI={10.1006/abio.1999.4025}, abstractNote={To facilitate RNA-binding studies of the phage RB69 RegA translational repressor protein, regA was configured to add six histidines to the carboxyl end of the protein. In vitro transcription-translation from the T7 promoter on plasmid pSA1 yielded a RegA69-His6 protein that binds nickel-Sepharose and elutes with 0.5 M imidazole. The system was further modified to avoid cloning and the toxic effects of RegA on Escherichia coli by the polymerase chain reaction (PCR), producing linear templates with the configuration T7 promoter-TIR-regA-His6. A translation initiation region was used that conforms to consensus E. coli and eukaryotic initiation sites and eliminates the target for RegA autogenous repression. RegA69-His6 synthesized in E. coli S30 or wheat germ extracts displayed RNA-binding properties similar to wild-type RB69 RegA. Specificity of RNA binding was demonstrated by in vitro repression of T4 gp44 and gp45 but not beta-lactamase, by differential binding to poly(U)- and poly(C)-agarose, and by site-specific binding to a 23-base gene 44 target RNA but not to mutant 44 RNA. Therefore, addition of the His6 tag to the C-terminus of RB69 RegA does not dramatically alter RNA binding, indicating that this region is not directly involved in site recognition. With access to several T4-like phage genomes and regA mutant sequences, in vitro synthesis of His-tagged proteins directly from linear PCR products provides a convenient and efficient system to study RegA and other interesting RNA-binding proteins.}, number={1}, journal={ANALYTICAL BIOCHEMISTRY}, author={Allen, SV and Miller, ES}, year={1999}, month={Apr}, pages={32–37} }
 @misc{shih_lin_miller_1998, title={DNA encoding Bacillus lichenformis PWD-1 keratinase}, volume={5,712,147}, number={1998 Jan. 27}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Shih, J. C. H. and Lin, X. and Miller, E. S.}, year={1998} }
 @article{miller_shih_chang_ballard_1997, title={An E-coli B mutation, rpoB5081, that prevents growth of phage T4 strains defective in host DNA degradation}, volume={157}, DOI={10.1111/j.1574-6968.1997.tb12760.x}, abstractNote={An E. coli B Tab strain, EM121, was isolated that restricts T4 denA (DNA endonuclease II) mutants at 37 degrees C and above, but is permissive for wild-type T4 at all temperatures examined. At 42 degrees C, other mutants affected in nucleic acid metabolism (T4 dexA, regA and uvsW strains) are also restricted. Genetic analysis revealed that one mutation (rpoB5081) in the RNA polymerase beta subunit gene is sufficient for restricting all denA mutants. rpoB5081, together with a second linked mutation, is also required for restricting the other T4 mutants, rpoB5081 (P806S), previously shown to increase transcription termination in E. coli K-12, causes delayed synthesis of T4 late proteins and reduced DNA synthesis in denA infections. Thus, T4 DNA synthesis and gene expression are impaired by the rpoB5081 beta subunit when degradation of host DNA is reduced. Because the restricted T4 mutants are not readily distinguished from wild-type phage under typical plating conditions, EM121 is an important host for screening and mapping T4 denA mutations.}, number={1}, journal={FEMS Microbiology Letters}, author={Miller, Eric and Shih, G. C. and Chang, S. K. and Ballard, D. N.}, year={1997}, pages={109–116} }
 @article{lin_wong_miller_shih_1997, title={Expression of the Bacillus licheniformis PWD-1 keratinase gene in B-subtilis}, volume={19}, ISSN={["0169-4146"]}, DOI={10.1038/sj.jim.2900440}, abstractNote={The kerA gene which encodes the enzyme keratinase was isolated from the feather-degrading bacterium Bacillus licheniformis PWD-1. The entire gene, including pre-, pro- and mature protein regions, was cloned with Pker, its own promoter, P43, the vegetative growth promoter, or the combination of P43-Pker into plasmid pUB18. Transformation of the protease-deficient strain B. subtilis DB104 with these plasmids generated transformant strains FDB-3, FDB-108 and FDB-29 respectively. All transformants expressed active keratinase in both feather and LB media, in contrast to PWD-1, in which kerA was repressed when grown in LB medium. With P43-Pker upstream of kerA, FDB-29 displayed the highest activity in feather medium. Production of keratinase in PWD-1 and transformants was further characterized when glucose or casamino acids were supplemented into the feather medium. These studies help understand the regulation of kerA expression and, in the long run, can help strain development and medium conditioning for the production of this industrially important keratinase.}, number={2}, journal={JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY}, author={Lin, X and Wong, SL and Miller, ES and Shih, JCH}, year={1997}, month={Aug}, pages={134–138} }
 @article{lin_kelemen_miller_shih_1995, title={Nucleotide sequence and expression of kerA, the gene encoding a keratinolytic protease of Bacillus licheniformis PWD-1.}, volume={61}, ISSN={0099-2240}, url={http://dx.doi.org/10.1128/aem.61.4.1469-1474.1995}, DOI={10.1128/aem.61.4.1469-1474.1995}, abstractNote={Bacillus licheniformis PWD-1 (ATCC 53757) secretes keratinase, a proteolytic enzyme which is active on whole feathers. By amino acid sequence similarity and phenylmethylsulfonyl fluoride inhibition, the keratinase was demonstrated to be a serine protease. The entire nucleotide sequence of the coding and flanking regions of the keratinase structure gene, kerA, was determined. A fixed oligonucleotide primer derived from the N-terminal sequence of the purified enzyme and a second random oligonucleotide primer were used in a procedure called PCR walking, which was developed to amplify and sequence the upstream and downstream regions of kerA. Another method, PCR screening, was conducted with a lambda phage vector with inserted PWD-1 genomic DNA fragments as templates and with the known sequences of the vector arms and the N-terminal sequence of the enzyme as primers. PCR amplification and sequence analysis of the lambda library completed the entire kerA sequence and established a set of gene deletions. The kerA gene shares a 97% sequence identity with the gene encoding subtilisin Carlsberg from B. licheniformis NCIMB 6816. The putative promoters, ribosome binding sites, and transcriptional terminators are also similar in these two bacteria. The deduced amino acid sequences indicate only three amino acid differences between the two mature proteases. Northern (RNA) analysis demonstrates that transcriptional regulation controls kerA expression on different growth media.}, number={4}, journal={Applied and environmental microbiology}, publisher={American Society for Microbiology}, author={Lin, X and Kelemen, D W and Miller, E S and Shih, J C}, year={1995}, pages={1469–1474} }
 @article{jozwik_miller_1995, title={RNA-protein interactions of the bacteriophage RB69 RegA translational repressor protein}, volume={33}, journal={Nucleic Acids Symposium Series}, author={Jozwik, C.E. and Miller, E.S.}, year={1995}, pages={256–257} }
 @inbook{miller_karam_spicer_1994, place={Washington, D.C}, title={Control of translation initiation: mRNA structure and protein repressors}, booktitle={Molecular Biology of Bacteriophage T4}, publisher={ASM Press}, author={Miller, E.S. and Karam, J.D. and Spicer, E.}, editor={Karam, J.D. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994}, pages={193–205} }
 @inbook{miller_karam_1994, place={Washington, D.C.}, title={Detection of plasmid encoded T4 proteins: radiolabeling and biological activity}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Miller, E.S. and Karam, J.D.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994} }
 @inbook{carlson_miller_karam_1994, place={Washington, D.C}, title={Experiments in T4 genetics}, booktitle={Molecular Biology of Bacteriophage T4}, publisher={ASM Press}, author={Carlson, K. and Miller, E.S. and Karam, J.D.}, editor={Karam, J.D. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994}, pages={421–483} }
 @inbook{carlson_miller_1994, place={Washington, D.C.}, title={General considerations for strain construction}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Carlson, K. and Miller, E.S.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994}, pages={438–441} }
 @inbook{carlson_miller_1994, place={Washington, D.C.}, title={General procedures for manipulating bacteriophage T4}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Carlson, K. and Miller, E.S.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994} }
 @inbook{karam_hsu_miller_1994, place={Washington, D.C.}, title={Large scale isolation of mRNA from T4-infected cells}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Karam, J.D. and Hsu, T. and Miller, E.S.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994} }
 @book{karam_drake_kreuzer_mosig_hall_eiserling_black_spicer_kutter_carlson_et al._1994, place={Washington, D.C}, title={Molecular Biology of Bacteriophage T4}, publisher={ASM Press}, author={Karam, J.D. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.}, year={1994} }
 @inbook{jozwik_miller_1994, place={Washington, D.C.}, title={PCR amplification of DNA from T4 plaques}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Jozwik, C.E. and Miller, E.S.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994} }
 @inbook{miller_1994, place={Washington, D.C.}, title={Quantitation of T4 DNA synthesis by radiolabelling}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Miller, E.S.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994} }
 @inbook{miller_1994, place={Washington, D.C.}, title={Radiolabelling of T4 proteins and their analysis by gel electrophoresis}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Miller, E.S.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hall, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994} }
 @inbook{kreuzer_miller_1994, place={Washington, D.C.}, title={Rapid screening of phage progeny from multiple-factor crosses}, booktitle={Molecular biology of bacteriophage T4}, publisher={ASM Press}, author={Kreuzer, H. and Miller, E.S.}, editor={Karam, J. and Drake, J.W. and Kreuzer, K.N. and Mosig, G. and Hill, D.H. and Eiserling, F.A. and Black, L.W. and Spicer, E.K. and Kutter, E. and Carlson, K. and et al.Editors}, year={1994}, pages={442–443} }
 @article{jozwik_miller_1992, title={Regions of bacteriophage T4 and RB69 RegA translational repressor proteins that determine RNA-binding specificity.}, volume={89}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/pnas.89.11.5053}, DOI={10.1073/pnas.89.11.5053}, abstractNote={RegA protein of T4 and related bacteriophages is a highly conserved RNA-binding protein that represses the translation of many phage mRNAs that encode enzymes involved in DNA metabolism. RB69, a T4-related bacteriophage, has a unique regA gene, which we have cloned, sequenced, and expressed. The predicted amino acid sequence of RB69 RegA is 78% identical to that of T4 RegA. Plasmid-encoded RB69 RegA expressed in vivo represses the translation of T4 early mRNAs, including those of rIIA, rIIB, 44, 45, rpbA, and regA. Nucleotide sequences were determined for several T4 and RB69 regA mutations, and their corresponding repressor properties were characterized. All of the 10 missense mutations affect residues conserved between RB69 and T4 RegA. Two regions of RegA are especially sensitive to mutation: one between Val-15 and Ala-25 and another between Arg-70 and Ser-73. Sequence alignments and mutational data suggest that the region from Val-15 to Ala-25 is similar to helix-turn-helix domains of DNA-binding proteins and confers RNA-binding specificity upon RegA. The RegA691 protein (Ile-24----Thr) has an in vivo phenotype that appears to distinguish site-specific and cooperative binding modes of hierarchical RegA-mediated translational repression.}, number={11}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Jozwik, C. E. and Miller, E. S.}, year={1992}, month={Jun}, pages={5053–5057} }
 @article{miller_1991, title={Cloning vectors, mutagenesis, and gene disruption (ermR) for the erythromycin-producing bacterium Aeromicrobium erythreum.}, volume={57}, ISSN={0099-2240 1098-5336}, url={http://dx.doi.org/10.1128/aem.57.9.2758-2761.1991}, DOI={10.1128/aem.57.9.2758-2761.1991}, abstractNote={Genetic systems for study of Aeromicrobium erythreum, a gram-positive, G + C-rich (72%) bacterium with the capacity for erythromycin biosynthesis, are described. High-copy-number plasmids suitable as gene cloning vectors include derivatives of the Streptomyces plasmids pIJ101, pVE1, and pJV1. pIJ101 derivatives with missense substitutions at the rep gene BamHI site do not replicate in A. erythreum. Ethyl methanesulfonate treatment generated several amino acid auxotrophs and non-erythromycin-producing (Ery-) strains. Using the Ery- strain AR1807 as a recipient for plasmid-directed integrative recombination, the chromosomal ermR gene (encoding 23S rRNA methyltransferase) was disrupted. Phenotypic characterizations demonstrated that ermR is the sole determinant of macrolide antibiotic resistance in A. erythreum.}, number={9}, journal={Applied and Environmental Microbiology}, publisher={American Society for Microbiology}, author={Miller, E S}, year={1991}, pages={2758–2761} }
 @article{miller_woese_brenner_1991, title={Description of the Erythromycin-Producing Bacterium Arthrobacter sp. Strain NRRL B-3381 as Aeromicrobium erythreum gen. nov., sp. nov.}, volume={41}, ISSN={0020-7713 1465-2102}, url={http://dx.doi.org/10.1099/00207713-41-3-363}, DOI={10.1099/00207713-41-3-363}, abstractNote={Arthrobacter sp. strain NRRL B-3381T (T = type strain) is a nonmycelial, nonsporulating actinomycete that produces the macrolide antibiotic erythromycin. This bacterium differs in many ways from the type species of the genus Arthrobacter (Arthrobacter globiformis), suggesting that a taxonomic revision is appropriate. The G + C content of strain NRRL B-3381T DNA is 71 to 73 mol%, and the peptidoglycan of this organism contains LL-diaminopimelic acid. Evolutionary distance data obtained from 16S rRNA sequences identified NRRL B-3381T as the deepest branching member of the Nocardioides group of actinomycetes. The principal long-chain fatty acids which we identified that distinguished strain NRRL B-3381T from related G + C-rich bacteria were 10-methyloctadecanoic (tuberculosteric), octadecenoic, and hexadecanoic acids. These characteristics, together with phage typing and biochemical characteristics, form the basis for our recommendation that strain NRRL B-3381 should be the type strain of a new taxon, for which we propose the name Aeromicrobium erythreum.}, number={3}, journal={International Journal of Systematic Bacteriology}, publisher={Microbiology Society}, author={Miller, E. S. and Woese, C. R. and Brenner, S.}, year={1991}, month={Jul}, pages={363–368} }
 @article{miller_jozwik_1990, title={Sequence analysis of conserved regA and variable orf43.1 genes in T4-like bacteriophages.}, volume={172}, ISSN={0021-9193 1098-5530}, url={http://dx.doi.org/10.1128/jb.172.9.5180-5186.1990}, DOI={10.1128/jb.172.9.5180-5186.1990}, abstractNote={Bacteriophage T4 RegA protein is a translational repressor of several phage mRNAs. In the T4-related phages examined, regA nucleotide sequences are highly conserved and the inferred amino acid sequences are identical. The exceptional phage, RB69, did not produce a RegA protein reproducibly identifiable by Western blots (immunoblots) nor did it produce mRNA that hybridized to T4 regA primers. Nucleotide sequences of either 223 or 250 base pairs were identified immediately 3' to regA in RB18 and RB51 that were absent in T-even phages. Open reading frames in these regions, designated orf43.1RB18 and orf43.1RB51, potentially encode related proteins of 8.5 and 9.2 kilodaltons, respectively. orf43.1 sequences, detected in 13 of 27 RB bacteriophage chromosomes analyzed by polymerase chain reaction, are either RB18- or RB51-like and have flanking repeat sequences that may promote orf43.1 deletion.}, number={9}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Miller, E S and Jozwik, C E}, year={1990}, pages={5180–5186} }
 @article{miller_karam_dawson_trojanowska_gauss_gold_1987, title={Translational repression: Biological activity of plasmid-encoded bacteriophage T4 RegA protein}, volume={194}, ISSN={0022-2836}, url={http://dx.doi.org/10.1016/0022-2836(87)90670-x}, DOI={10.1016/0022-2836(87)90670-x}, abstractNote={The RegA protein of bacteriophage T4 is a translational repressor that regulates expression of several phage early mRNAs. We have cloned wild-type and mutant alleles of the T4 regA gene under control of the heat-inducible, plasmid-borne leftward promoter (PL) of phage lambda. Expression of the cloned regA+ gene resulted in the synthesis of a protein that closely resembled phage-encoded RegA protein in biological properties. It repressed its own synthesis (autogenous translational control) as well as the synthesis of specific T4-encoded proteins that are known from other studies to be under RegA-mediated translational control. Cloned mutant alleles of regA exhibited derepressed synthesis of the mutant regA gene products and were ineffective in trans against RegA-sensitive mRNA targets. The effects of plasmid-encoded RegA proteins were also demonstrated in experiments using two compatible plasmids in uninfected Escherichia coli. The two-plasmid assays confirm the sensitivities of several cloned T4 genes to RegA-mediated translational repression and are well-suited for genetic analysis of RegA target sites. Repression specificity in this system was demonstrated by using wild-type and operator-constitutive translational initiation sites of T4 rIIB fused to lacZ. The results show that no additional T4 products are required for RegA-mediated translational repression. Additional evidence is provided for the proposal that uridine-rich mRNA sequences are preferred targets for the repressor. Surprisingly, plasmid-generated RegA protein represses the synthesis of some E. coli proteins and appears to enhance selectively the synthesis of others. The RegA protein may have multiple functions, and its binding sites are not restricted to phage mRNAs.}, number={3}, journal={Journal of Molecular Biology}, publisher={Elsevier BV}, author={Miller, Eric S. and Karam, Jim and Dawson, Myra and Trojanowska, Maria and Gauss, Peter and Gold, Larry}, year={1987}, month={Apr}, pages={397–410} }
 @article{miller_winter_campbell_power_gold_1985, title={Bacteriophage T4 RegA protein. Purification of a translational repressor}, volume={260}, DOI={10.1016/S0021-9258(17)38837-3}, abstractNote={The bacteriophage T4 regA protein translationally regulates its own synthesis and the synthesis of several other T4 early proteins.In order to study the mechanism of translational regulation, we have purified the regA protein.Initially a mutant protein, incapable of autogenous repression, was placed under h p , transcriptional control and amplified to approximately 10% of total cell protein.The membrane-associated mutant protein was extracted with organic solvent mixtures and purified by reverse phase-high performance liquid chromatography.Polyclonal antibodies prepared against the mutant protein were used in Western blot assays to monitor purification of the wildtype protein from T4-infected cells.Phosphocellulose and poly(U)-agarose chromatography were important steps in its purification.The binding properties of regA protein to polyribonucleotides are discussed in relation to the mechanism by which the protein recognizes its mRNA targets.After the bacteriophage T4 infects Escherichia coli, gene expression is controlled at the levels of transcription (1, 2) and translation (3, 4).The T4 regA product is one of two phage-encoded translational regulatory proteins (the other is the gene 32 helix-destabilizing protein) that have been identified.Expression of the regA gene, which is controlled by translational autoregulation, affects translation of several early T4 genes (5-7).Analogous tc: other prokaryotic translational repressors, regA protein appears to function by occluding ribosomes and preventing formation of a productive translational initiation complex (8).Although genetic analysis of one regA-repressible mRNA, that of the rIIB gene, has shown that the rIIB translational operator overlaps the ribosome binding site, comparisons with other regA-controlled translation initiation sites have not revealed a consensus sequence or conserved secondary structure (8-10).In addition, among the translational repressor proteins identified to date, the regA protein is uniquely able to recognize the mRNAs from several unlinked transcriptional units.We describe here the purification of the 'wild-type regA protein from T4-infected cells.The approach used was to}, number={24}, journal={Journal of Biological Chemistry}, author={Miller, E.S. and Winter, R. and Campbell, K.M. and Power, S. and Gold, L.}, year={1985}, month={Oct}, pages={13053–13059} }
 @article{miller_brenchley_1984, title={Cloning and characterization of gdhA, the structural gene for glutamate dehydrogenase of Salmonella typhimurium.}, volume={157}, ISSN={0021-9193 1098-5530}, url={http://dx.doi.org/10.1128/jb.157.1.171-178.1984}, DOI={10.1128/jb.157.1.171-178.1984}, abstractNote={Glutamic acid is synthesized in enteric bacteria by either glutamate dehydrogenase or by the coupled activities of glutamate synthase and glutamine synthetase. A hybrid plasmid containing a fragment of the Salmonella typhimurium chromosome cloned into pBR328 restores growth of glutamate auxotrophs of S. typhimurium and Escherichia coli strains which have mutations in the genes for glutamate dehydrogenase and glutamate synthase. A 2.2-kilobase pair region was shown by complementation analysis, enzyme activity measurements, and the maxicell protein synthesizing system to carry the entire glutamate dehydrogenase structural gene, gdhA. Glutamate dehydrogenase encoded by gdhA carried on recombinant plasmids was elevated 5- to over 100-fold in S. typhimurium or E. coli cells and was regulated in both organisms. The gdhA promoter was located by recombination studies and by the in vitro fusion to, and activation of, a promoter-deficient galK gene. Additionally, S. typhimurium gdhA DNA was shown to hybridize to single restriction fragments of chromosomes from other enteric bacteria and from Saccharomyces cerevisiae.}, number={1}, journal={Journal of Bacteriology}, publisher={American Society for Microbiology}, author={Miller, E S and Brenchley, J E}, year={1984}, pages={171–178} }
 @article{trojanowska_miller_karam_stormo_gold_1984, title={The bacteriophage T4regAgene: primary sequence of a translational repressor}, volume={12}, ISSN={0305-1048 1362-4962}, url={http://dx.doi.org/10.1093/nar/12.15.5979}, DOI={10.1093/nar/12.15.5979}, abstractNote={The regA gene product of bacteriophage T4 is an autogenously controlled translational regulatory protein that plays a role in differential inhibition (translational repression) of a subpopulation of T4-encoded "early" mRNA species. The structural gene for this polypeptide maps within a cluster of phage DNA replication genes, (genes 45-44-62-regA-43-42), all but one of which (gene 43) are under regA-mediated translational control. We have cloned the T4 regA gene, determined its nucleotide sequence, and identified the amino-terminal residues of a plasmid-encoded, hyperproduced regA protein. The results suggest that the T4 regA gene product is a 122 amino acid polypeptide that is mildly basic and hydrophilic in character; these features are consistent with known properties of regA protein derived from T4-infected cells. Computer-assisted analyses of the nucleotide sequences of the regA gene and its three upstream neighbors (genes 45, 44, and 62) suggest the existence of three translational initiation units in this four-gene cluster; one for gene 45, one for genes 44, 62 and regA, and one that serves only the regA gene. The analyses also suggest that the gene 44-62 translational unit harbors a stable RNA structure that obligates translational coupling of these two genes.}, number={15}, journal={Nucleic Acids Research}, publisher={Oxford University Press (OUP)}, author={Trojanowska, Maria and Miller, Eric S. and Karam, Jim and Stormo, Gary and Gold, Larry}, year={1984}, pages={5979–5993} }
 @inproceedings{gold_inman_miller_pribnow_schneider_shinedling_stormo_1984, place={Copenhagen}, title={Translational regulation during bacteriophage T4 development}, ISBN={9788716095619}, booktitle={Gene expression : the translation step and its control : proceedings of the Alfred Benzon Symposium 19 held at the premises of the Royal Danish Academy of Sciences and Letters, Copenhagen, 19-23 June 1983}, publisher={Munskgaard}, author={Gold, L. and Inman, M. and Miller, E. and Pribnow, D. and Schneider, T.D. and Shinedling, S. and Stormo, G.}, editor={Clark, B.F.C. and Petersen, H.U.Editors}, year={1984} }
 @article{miller_brenchley_1981, title={L-Methionine SR-sulfoximine resistant glutamine synthetase from mutants of Salmonella typhimurium}, volume={256}, DOI={10.1016/S0021-9258(19)68592-3}, abstractNote={Two mutants of Salmonella typhimurium resistant to growth inhibition by the glutamine synthetase transition state analog, L-methionine SR-sulfoximine, were isolated and characterized. These mutants are glutamine bradytrophs and cannot use growth rate-limiting nitrogen sources. Although this phenotype resembles that of mutants with lesions in the regulatory gene for glutamine synthetase, glnG, these mutations do not lie in the glnG gene. Purification and characterization of the glutamine synthetase from one of the mutants and a control strain demonstrated that the mutant enzyme is defective in the reverse gamma-glutamyltransferase activity but has biosynthetic activity that is resistant to inhibition by L-methionine SR-sulfoximine. The mutant enzyme also has a 4.4-fold higher apparent Km for glutamate (0.2 mM versus 2.1 mM, respectively) and a 13.8-fold higher Km for NH3 (6.4 mM versus 0.46 mM) than the enzyme from the control. These data show that the glutamine synthetase protein has been altered by this mutation, designated as glnA982, and suggest that the L-methionine SR-sulfoximine resistance is conferred by a change in the NH3 binding domain of the enzyme.}, number={21}, journal={Journal of Biological Chemistry}, author={Miller, E.S. and Brenchley, J.E.}, year={1981}, month={Nov}, pages={11307–11312} }
 @article{miller_demaree_tinling_1978, title={Hematozoa of passeriform birds from Eagle Lake, California}, volume={45}, number={2}, journal={Proceedings of the Helminthological Society of Washington}, author={Miller, E.S. and Demaree, R.S. and Tinling, S.P.}, year={1978}, pages={266–268} }