@article{khatibi_chou_loder_zurawski_adams_kelly_2017, title={Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus}, volume={114}, ISSN={["1097-0290"]}, DOI={10.1002/bit.26408}, abstractNote={Abstract}, number={12}, journal={BIOTECHNOLOGY AND BIOENGINEERING}, author={Khatibi, Piyum A. and Chou, Chung-jung and Loder, Andrew J. and Zurawski, Jeffrey V. and Adams, Michael W. W. and Kelly, Robert M.}, year={2017}, month={Dec}, pages={2947–2954} }
 @article{engelke_chou_uprety_jess_deiters_2014, title={Control of Protein Function through Optochemical Translocation}, volume={3}, ISSN={["2161-5063"]}, DOI={10.1021/sb400192a}, abstractNote={Controlled manipulation of proteins and their function is important in almost all biological disciplines. Here, we demonstrate control of protein activity with light. We present two different applications—light-triggered transcription and light-triggered protease cleavage—both based on the same concept of protein mislocation, followed by optochemically triggered translocation to an active cellular compartment. In our approach, we genetically encode a photocaged lysine into the nuclear localization signal (NLS) of the transcription factor SATB1. This blocks nuclear import of the protein until illumination induces caging group removal and release of the protein into the nucleus. In the first application, prepending this NLS to the transcription factor FOXO3 allows us to optochemically switch on its transcription activity. The second application uses the developed light-activated NLS to control nuclear import of TEV protease and subsequent cleavage of nuclear proteins containing TEV cleavage sites. The small size of the light-controlled NLS (only 20 amino acids) minimizes impact of its insertion on protein function and promises a general approach to a wide range of optochemical applications. Since the light-activated NLS is genetically encoded and optically triggered, it will prove useful to address a variety of problems requiring spatial and temporal control of protein function, for example, in stem-cell, developmental, and cancer biology.}, number={10}, journal={ACS SYNTHETIC BIOLOGY}, author={Engelke, Hanna and Chou, Chungjung and Uprety, Rajendra and Jess, Phillip and Deiters, Alexander}, year={2014}, month={Oct}, pages={731–736} }
 @article{luo_uprety_naro_chou_nguyen_chin_deiters_2014, title={Genetically Encoded Optochemical Probes for Simultaneous Fluorescence Reporting and Light Activation of Protein Function with Two-Photon Excitation}, volume={136}, ISSN={["1520-5126"]}, DOI={10.1021/ja5055862}, abstractNote={The site-specific incorporation of three new coumarin lysine analogues into proteins was achieved in bacterial and mammalian cells using an engineered pyrrolysyl-tRNA synthetase system. The genetically encoded coumarin lysines were successfully applied as fluorescent cellular probes for protein localization and for the optical activation of protein function. As a proof-of-principle, photoregulation of firefly luciferase was achieved in live cells by caging a key lysine residue, and excellent OFF to ON light-switching ratios were observed. Furthermore, two-photon and single-photon optochemical control of EGFP maturation was demonstrated, enabling the use of different, potentially orthogonal excitation wavelengths (365, 405, and 760 nm) for the sequential activation of protein function in live cells. These results demonstrate that coumarin lysines are a new and valuable class of optical probes that can be used for the investigation and regulation of protein structure, dynamics, function, and localization in live cells. The small size of coumarin, the site-specific incorporation, the application as both a light-activated caging group and as a fluorescent probe, and the broad range of excitation wavelengths are advantageous over other genetically encoded photocontrol systems and provide a precise and multifunctional tool for cellular biology.}, number={44}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Luo, Ji and Uprety, Rajendra and Naro, Yuta and Chou, Chungjung and Nguyen, Duy P. and Chin, Jason W. and Deiters, Alexander}, year={2014}, month={Nov}, pages={15551–15558} }
 @article{torres-kolbus_chou_liu_deiters_2014, title={Synthesis of Non-linear Protein Dimers through a Genetically Encoded Thiol-ene Reaction}, volume={9}, ISSN={["1932-6203"]}, DOI={10.1371/journal.pone.0105467}, abstractNote={Site-specific incorporation of bioorthogonal unnatural amino acids into proteins provides a useful tool for the installation of specific functionalities that will allow for the labeling of proteins with virtually any probe. We demonstrate the genetic encoding of a set of alkene lysines using the orthogonal PylRS/PylTCUA pair in Escherichia coli. The installed double bond functionality was then applied in a photoinitiated thiol-ene reaction of the protein with a fluorescent thiol-bearing probe, as well as a cysteine residue of a second protein, showing the applicability of this approach in the formation of heterogeneous non-linear fused proteins.}, number={9}, journal={PLOS ONE}, author={Torres-Kolbus, Jessica and Chou, Chungjung and Liu, Jihe and Deiters, Alexander}, year={2014}, month={Sep} }
 @article{hemphill_chou_chin_deiters_2013, title={Genetically encoded light-activated transcription for spatiotemporal control of gene expression and gene silencing in mammalian cells}, volume={135}, DOI={10.1021/ja4051026}, abstractNote={Photocaging provides a method to spatially and temporally control biological function and gene expression with high resolution. Proteins can be photochemically controlled through the site-specific installation of caging groups on amino acid side chains that are essential for protein function. The photocaging of a synthetic gene network using unnatural amino acid mutagenesis in mammalian cells was demonstrated with an engineered bacteriophage RNA polymerase. A caged T7 RNA polymerase was expressed in cells with an expanded genetic code and used in the photochemical activation of genes under control of an orthogonal T7 promoter, demonstrating tight spatial and temporal control. The synthetic gene expression system was validated with two reporter genes (luciferase and EGFP) and applied to the light-triggered transcription of short hairpin RNA constructs for the induction of RNA interference.}, number={36}, journal={Journal of the American Chemical Society}, author={Hemphill, J. and Chou, C. J. and Chin, J. W. and Deiters, A.}, year={2013}, pages={13433–13439} }
 @article{lang_davis_torres-kolbus_chou_deiters_chin_2012, title={Genetically encoded norbornene directs site-specific cellular protein labelling via a rapid bioorthogonal reaction}, volume={4}, ISSN={["1755-4330"]}, DOI={10.1038/nchem.1250}, abstractNote={The site-specific incorporation of bioorthogonal groups via genetic code expansion provides a powerful general strategy for site-specifically labelling proteins with any probe. However, the slow reactivity of the bioorthogonal functional groups that can be encoded genetically limits the utility of this strategy. We demonstrate the genetic encoding of a norbornene amino acid using the pyrrolysyl tRNA synthetase/tRNACUA pair in Escherichia coli and mammalian cells. We developed a series of tetrazine-based probes that exhibit ‘turn-on’ fluorescence on their rapid reaction with norbornenes. We demonstrate that the labelling of an encoded norbornene is specific with respect to the entire soluble E. coli proteome and thousands of times faster than established encodable bioorthogonal reactions. We show explicitly the advantages of this approach over state-of-the-art bioorthogonal reactions for protein labelling in vitro and on mammalian cells, and demonstrate the rapid bioorthogonal site-specific labelling of a protein on the mammalian cell surface. The site-specific incorporation of a norbornene amino acid into proteins via genetic code expansion, together with the synthesis of a series of tetrazine-based probes that exhibit turn-on fluorescence on their fast cycloaddition with norbornene, enables rapid protein labelling on mammalian cells.}, number={4}, journal={NATURE CHEMISTRY}, author={Lang, Kathrin and Davis, Lloyd and Torres-Kolbus, Jessica and Chou, Chungjung and Deiters, Alexander and Chin, Jason W.}, year={2012}, month={Apr}, pages={298–304} }
 @article{chou_uprety_davis_chin_deiters_2011, title={Genetically encoding an aliphatic diazirine for protein photocrosslinking}, volume={2}, ISSN={["2041-6539"]}, DOI={10.1039/c0sc00373e}, abstractNote={Photocrosslinking is an important approach that allows discovery and detailed investigation of protein–protein, protein–oligonucleotide, and protein–small molecule interactions with high temporal and spatial resolution. A major limitation to the universal application of this methodology is the site-specific introduction of efficient aliphatic photocrosslinking probes into proteins of interest. Here, we report a novel aliphatic diazirine amino acid and its genetically encoded, site-specific incorporation into proteins in bacterial and mammalian cells. Furthermore, we demonstrate efficient photocrosslinking of a test proteinin vitro and in vivo.}, number={3}, journal={CHEMICAL SCIENCE}, author={Chou, Chungjung and Uprety, Rajendra and Davis, Lloyd and Chin, Jason W. and Deiters, Alexander}, year={2011}, pages={480–483} }
 @article{chou_deiters_2011, title={Light-Activated Gene Editing with a Photocaged Zinc-Finger Nuclease}, volume={50}, ISSN={["1433-7851"]}, DOI={10.1002/anie.201101157}, abstractNote={A general approach for targeted gene modification with precise external control and high spatial and temporal resolution will greatly advance investigations in genetics, gene therapy, and developmental biology. However, traditional methods such as homologous recombination[1] and nonhomologous end joining[2] for the introduction and deletion of genomic DNA sequences usually display very low efficiency in vivo, thus limiting their applicability. Recently, the efficiency of these processes has been greatly improved by the ability to site-specifically introduce doublestrand breaks (DSBs) into genomic DNA.[3,4] A family of artificial restriction enzymes, namely zinc-finger nucleases (ZFN), has been developed to sequence-selectively achieve dsDNA scission. ZFNs have since emerged as important and widely recognized tools for the genetic modification of cells, model organisms, and possibly humans to investigate gene function and to treat genetic disorders.[5–9]}, number={30}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Chou, Chungjung and Deiters, Alexander}, year={2011}, pages={6839–6842} }
 @article{chou_young_deiters_2010, title={Photocaged T7 RNA Polymerase for the Light Activation of Transcription and Gene Function in Pro- and Eukaryotic Cells}, volume={11}, ISSN={["1439-7633"]}, DOI={10.1002/cbic.201000041}, abstractNote={Abstract}, number={7}, journal={CHEMBIOCHEM}, author={Chou, Chungjung and Young, Douglas D. and Deiters, Alexander}, year={2010}, month={May}, pages={972–977} }
 @article{chou_young_deiters_2009, title={A Light-Activated DNA Polymerase}, volume={48}, ISSN={["1521-3773"]}, DOI={10.1002/anie.200901115}, abstractNote={When the time is right: The widely applied Thermus aquaticus DNA polymerase was rendered light-activatable by incorporation of the photocaged amino acid ortho-nitrobenzyl tyrosine in place of a key tyrosine residue in the active site (see picture). As the modified enzyme was completely inactive until irradiated with UV light, temporal regulation of polymerase activity was possible.}, number={32}, journal={ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, author={Chou, Chungjung and Young, Douglas D. and Deiters, Alexander}, year={2009}, pages={5950–5953} }
 @article{santa-maria_chou_yencho_haigler_thompson_kelly_sosinski_2009, title={Plant cell calcium-rich environment enhances thermostability of recombinantly produced α-amylase from the hyperthermophilic bacterium Thermotoga maritime}, volume={104}, ISSN={0006-3592 1097-0290}, url={http://dx.doi.org/10.1002/bit.22468}, DOI={10.1002/bit.22468}, abstractNote={Abstract}, number={5}, journal={Biotechnology and Bioengineering}, publisher={Wiley}, author={Santa-Maria, Monica C. and Chou, Chung-Jung and Yencho, G. Craig and Haigler, Candace H. and Thompson, William F. and Kelly, Robert M. and Sosinski, Bryon}, year={2009}, month={Dec}, pages={947–956} }
 @article{nichols_johnson_chou_kelly_2009, title={Temperature, not LuxS, mediates AI-2 formation in hydrothermal habitats}, volume={68}, ISSN={["1574-6941"]}, DOI={10.1111/j.1574-6941.2009.00662.x}, abstractNote={Quorum sensing provides the basis for coordinating community-wide, microbial behaviors in many mesophilic bacteria. However, little attention has been directed toward the possibility that such phenomena occur in extremely thermal microbial environments. Despite the absence of luxS in hyperthermophile genomes, autoinducer-2 (AI-2), a boronated furanone and proposed 'universal' interspecies mesophilic bacterial communication signal, could be formed by Thermotoga maritima and Pyrococcus furiosus through a combination of biotic and abiotic reaction steps. AI-2 did not, however, induce any detectable quorum-sensing phenotypes in these organisms, although transcriptome-based evidence of an AI-2-induced stress response was observed in T. maritima. The significance, if any, of AI-2 in hydrothermal habitats is not yet clear. Nevertheless, these results show the importance of considering environmental factors, in this case high temperatures, as abiotic causative agents of biochemical and microbiological phenomena.}, number={2}, journal={FEMS MICROBIOLOGY ECOLOGY}, author={Nichols, Jason D. and Johnson, Matthew R. and Chou, Chung-Jung and Kelly, Robert M.}, year={2009}, month={Apr}, pages={173–181} }
 @article{comfort_chou_conners_vanfossen_kelly_2008, title={Functional-genomics-based identification and characterization of open reading frames encoding alpha-glucoside-processing enzymes in the hyperthermophilic archaeon Pyrococcus furiosus}, volume={74}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.01920-07}, abstractNote={ABSTRACT}, number={4}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Comfort, Donald A. and Chou, Chung-Jung and Conners, Shannon B. and VanFossen, Amy L. and Kelly, Robert M.}, year={2008}, month={Feb}, pages={1281–1283} }
 @misc{chou_jenney_adams_kelly_2008, title={Hydrogenesis in hyperthermophilic microorganisms: Implications for biofuels}, volume={10}, ISSN={["1096-7184"]}, DOI={10.1016/j.ymben.2008.06.007}, abstractNote={Hydrothermal microbiotopes are characterized by the consumption and production of molecular hydrogen. Heterotrophic hyperthermophilic microorganisms (growth T(opt)> or =80 degrees C) actively participate in the production of H(2) in these environments through the fermentation of peptides and carbohydrates. Hyperthermophiles have been shown to approach the theoretical (Thauer) limit of 4 mol of H(2) produced per mole of glucose equivalent consumed, albeit at lower volumetric productivities than observed for mesophilic bacteria, especially enterics and clostridia. Potential advantages for biohydrogen production at elevated temperatures include fewer metabolic byproducts formed, absence of catabolic repression for growth on heterogeneous biomass substrates, and reduced loss of H(2) through conversion to H(2)S and CH(4) by mesophilic consortia containing sulfate reducers and methanogens. To fully exploit the use of these novel microorganisms and their constituent hydrogenases for biohydrogen production, development of versatile genetic systems and improvements in current understanding of electron flux from fermentable substrates to H(2) in hyperthermophiles are needed.}, number={6}, journal={METABOLIC ENGINEERING}, author={Chou, Chung-Jung and Jenney, Francis E., Jr. and Adams, Michael W. W. and Kelly, Robert M.}, year={2008}, month={Nov}, pages={394–404} }
 @article{chou_shockley_conners_lewis_comfort_adams_kelly_2007, title={Impact of substrate glycoside linkage. and elemental sulfur on bioenergetics, of and hydrogen production by the hyperthermophilic Archaeon Pyrococcus furiosus}, volume={73}, ISSN={["1098-5336"]}, DOI={10.1128/AEM.00597-07}, abstractNote={ABSTRACT}, number={21}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Chou, Chung-Jung and Shockley, Keith R. and Conners, Shannon B. and Lewis, Derrick L. and Comfort, Donald A. and Adams, Michael W. W. and Kelly, Robert M.}, year={2007}, month={Nov}, pages={6842–6853} }
 @article{montero_johnson_chou_conners_geouge_tachdjian_nichols_kelly_2007, title={Responses of wild-type and resistant strains of the hyperthermophilic bacterium Thermotoga maritima to chloramphenicol challenge}, volume={73}, ISSN={["0099-2240"]}, DOI={10.1128/AEM.00453-07}, abstractNote={ABSTRACT}, number={15}, journal={APPLIED AND ENVIRONMENTAL MICROBIOLOGY}, author={Montero, Clemente I. and Johnson, Matthew R. and Chou, Chung-Jung and Conners, Shannon B. and Geouge, Sarah G. and Tachdjian, Sabrina and Nichols, Jason D. and Kelly, Robert M.}, year={2007}, month={Aug}, pages={5058–5065} }
 @article{lee_shockley_schut_conners_montero_johnson_chou_bridger_wigner_brehm_et al._2006, title={Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus}, volume={188}, ISSN={["1098-5530"]}, DOI={10.1128/JB.188.6.2115-2125.2006}, abstractNote={ABSTRACT}, number={6}, journal={JOURNAL OF BACTERIOLOGY}, author={Lee, HS and Shockley, KR and Schut, GJ and Conners, SB and Montero, CI and Johnson, MR and Chou, CJ and Bridger, SL and Wigner, N and Brehm, SD and et al.}, year={2006}, month={Mar}, pages={2115–2125} }