Polycysteine‐encoding leaderless short ORFs function as cysteine‐responsive attenuators of operonic gene expression in mycobacteria
Open accessPublished version of a preprint
Abstract
Genome‐wide transcriptomic analyses have revealed abundant expressed short open reading frames (ORFs) in bacteria. Whether these short ORFs, or the small proteins they encode, are functional remains an open question. One quarter of mycobacterial mRNAs are leaderless, beginning with a 5′‐AUG or GUG initiation codon. Leaderless mRNAs often encode unannotated short ORFs as the first gene of a polycistronic transcript. Here, we show that polycysteine‐encoding leaderless short ORFs function as cysteine‐responsive attenuators of operonic gene expression. Detailed mutational analysis shows that one polycysteine short ORF controls expression of the downstream genes. Our data indicate that ribosomes stalled in the polycysteine tract block mRNA structures that otherwise sequester the ribosome‐binding site of the 3′gene. We assessed endogenous proteomic responses to cysteine limitation in Mycobacterium smegmatis using mass spectrometry. Six cysteine metabolic loci having unannotated polycysteine‐encoding leaderless short ORF architectures responded to cysteine limitation, revealing widespread cysteine‐responsive attenuation in mycobacteria. Individual leaderless short ORFs confer independent operon‐level control, while their shared dependence on cysteine ensures a collective response mediated by ribosome pausing. We propose the term ribulon to classify ribosome‐directed regulons. Regulon‐level coordination by ribosomes on sensory short ORFs illustrates one utility of the many unannotated short ORFs expressed in bacterial genomes.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Poly-cysteine sORFs act as cis-acting attenuators of downstream genes required for cysteine uptake and biosynthesis.
“These poly-cysteine sORFs act as cis-acting attenuators of downstream genes required for cysteine uptake and biosynthesis (76).”
From Mycobacterium smegmatis: The Vanguard of Mycobacterial Research (2023) · cites this paper as [76]
The Results section reports that polycysteine leaderless sORFs regulate downstream operonic genes in response to cysteine, and the Discussion describes attenuation of a cysteine-biosynthesis pathway locus. The passages identify the other regulated operons as having cysteine-associated activities, but do not establish the claim that they include genes required for cysteine uptake. (LLM, conf=0.84)
Experimental — accuracy not yet measured
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works
MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets
Kumar, S., Stecher, G., & Tamura, K. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw054 · Cited by 43,923 · see citing works
MEGA6: Molecular Evolutionary Genetics Analysis version 6.0.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., & Kumar, S. (2013) · Molecular biology and evolution · doi:10.1093/molbev/mst197 · Cited by 41,174 · see citing works
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
Nguyen, L.-T., Schmidt, H. A., von Haeseler, A., & Minh, B. Q. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msu300 · Cited by 26,046 · see citing works
Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works
EMBOSS: the European molecular biology open software suite.
Rice, P., Longden, I., & Bleasby, A. (2000) · Trends in Genetics · doi:10.1016/s0168-9525(00)02024-2 · Cited by 9,466 · see citing works
Ultrafast Approximation for Phylogenetic Bootstrap
Minh, B. Q., Nguyen, M. A. T., & von Haeseler, A. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst024 · Cited by 4,844 · see citing works
The EMBL-EBI search and sequence analysis tools APIs in 2019
Madeira, F., Park, Y. M., Lee, J., Buso, N., Gur, T., Madhusoodanan, N., Basutkar, P., Tivey, A. R. N., Potter, S. C., Finn, R. D., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz268 · Cited by 4,167 · see citing works
Elias, J. E., & Gygi, S. P. (2007) · Nature Methods · doi:10.1038/nmeth1019 · Cited by 3,925 · see citing works
An Improved General Amino Acid Replacement Matrix
Le, S. Q., & Gascuel, O. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn067 · Cited by 3,127 · see citing works
Rappsilber, J., Ishihama, Y., & Mann, M. (2002) · Analytical Chemistry · doi:10.1021/ac026117i · Cited by 2,589 · see citing works
Translational control by 5′-untranslated regions of eukaryotic mRNAs
Hinnebusch, A. G., Ivanov, I. P., & Sonenberg, N. (2016) · Science · doi:10.1126/science.aad9868 · Cited by 1,079 · see citing works
Deutsch, E. W., Csordás, A., Sun, Z., Jarnuczak, A. F., Pérez‐Riverol, Y., Ternent, T., Campbell, D. S., Llinares, M. B., Okuda, S., Kawano, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw936 · Cited by 864 · see citing works
Attenuation in the control of expression of bacterial operons
Yanofsky, C. (1981) · Nature · doi:10.1038/289751a0 · Cited by 759 · see citing works
A space-time process model for the evolution of DNA sequences.
Yang, Z. (1995) · Genetics · doi:10.1093/genetics/139.2.993 · Cited by 432 · see citing works
Suspension trapping (STrap) sample preparation method for bottom‐up proteomics analysis
Zougman, A., Selby, P. J., & Banks, R. E. (2014) · PROTEOMICS · doi:10.1002/pmic.201300553 · Cited by 419 · see citing works
TRANSLATIONAL COUPLING DURING EXPRESSION OF THE TRYPTOPHAN OPERON OF ESCHERICHIA COLI
Oppenheim, D. S., & Yanofsky, C. (1980) · Genetics · doi:10.1093/genetics/95.4.785 · Cited by 382 · see citing works
Mismatch amplification mutation assay (MAMA): application to the c-H-ras gene.Preprint
Cha, R. S., Zarbl, H., Keohavong, P., & Thilly, W. G. (1992) · Genome Research · doi:10.1101/gr.2.1.14 · Cited by 375 · see citing works
Fur Regulon in Gram-negative Bacteria
Stojiljković, I., Bäumler, A. J., & Hantke, K. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1163 · Cited by 371 · see citing works
Classification and function of small open reading frames
Couso, J. P., & Patraquim, P. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.58 · Cited by 335 · see citing works
The Influence of Rate Heterogeneity among Sites on the Time Dependence of Molecular Rates
Soubrier, J., Steel, M., Lee, M. S. Y., Sarkissian, C. S. I. D., Guindon, S., Ho, S. Y. W., & Cooper, A. (2012) · Molecular Biology and Evolution · doi:10.1093/molbev/mss140 · Cited by 316 · see citing works
Cortes, T., Schubert, O. T., Rose, G., Arnvig, K. B., Comas, I., Aebersold, R., & Young, D. B. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.10.031 · Cited by 310 · see citing works
Lost in translation: the influence of ribosomes on bacterial mRNA decay: Figure 1.Preprint
Deana, A., & Belasco, J. G. (2005) · Genes & Development · doi:10.1101/gad.1348805 · Cited by 309 · see citing works
Bacterial Transcription Terminators: The RNA 3′-End Chronicles
Peters, J. M., Vangeloff, A. D., & Landick, R. C. (2011) · Journal of Molecular Biology · doi:10.1016/j.jmb.2011.03.036 · Cited by 307 · see citing works
Arrest Peptides: Cis -Acting Modulators of Translation
Ito, K., & Chiba, S. (2013) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-080211-105026 · Cited by 265 · see citing works
Henkin, T. M., & Yanofsky, C. (2002) · BioEssays · doi:10.1002/bies.10125 · Cited by 244 · see citing works
Shell, S. S., Wang, J., Lapierre, P., Mir, M., Chase, M. R., Pyle, M. M., Gawande, R., Ahmad, R., Sarracino, D. A., Ioerger, T. R., et al. (2015) · PLOS Genetics · doi:10.1371/journal.pgen.1005641 · Cited by 238 · see citing works
Self-citationLarge-Scale Analyses of Human Microbiomes Reveal Thousands of Small, Novel Genes
Sberro, H., Fremin, B. J., Zlitni, S., Edfors, F., Greenfield, N., Snyder, M. P., Pavlopoulos, G. A., Kyrpides, N. C., & Bhatt, A. S. (2019) · Cell · doi:10.1016/j.cell.2019.07.016 · Cited by 237 · see citing works
Ohnishi, K., Kutsukake, K., Suzuki, H., & Tetsuo, L. (1992) · Molecular Microbiology · doi:10.1111/j.1365-2958.1992.tb01771.x · Cited by 235 · see citing works
The Abundance of Short Proteins in the Mammalian Proteome
Frith, M. C., Forrest, A. R. R., Nourbakhsh, E., Pang, K. C., Kai, C., Kawai, J., Carninci, P., Hayashizaki, Y., Bailey, T. L., & Grimmond, S. M. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020052 · Cited by 225 · see citing works
Small membrane proteins found by comparative genomics and ribosome binding site models
Hemm, M. R., Paul, B. J., Schneider, T. D., Storz, G., & Rudd, K. E. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06495.x · Cited by 223 · see citing works
Triple post‐transcriptional control
Bechhofer, D. H. (1990) · Molecular Microbiology · doi:10.1111/j.1365-2958.1990.tb02051.x · Cited by 204 · see citing works
Ribosome regulation by the nascent peptide
Lovett, S. T., & Rogers, E. J. (1996) · Microbiological Reviews · doi:10.1128/mr.60.2.366-385.1996 · Cited by 204 · see citing works
Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome
Meydan, S., Marks, J., Klepacki, D., Sharma, V., Baranov, P. V., Firth, A. E., Margus, T., Kefi, A., Vázquez-Laslop, N., & Mankin, A. S. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.02.017 · Cited by 184 · see citing works
Identifying Small Proteins by Ribosome Profiling with Stalled Initiation Complexes
Weaver, J., Mohammad, F., Buskirk, A. R., & Storz, G. (2019) · mBio · doi:10.1128/mbio.02819-18 · Cited by 180 · see citing works
Duval, M., Korepanov, A. P., Fuchsbauer, O., Fechter, P., Haller, A., Fabbretti, A., Choulier, L., Micura, R., Klaholz, B. P., Romby, P., et al. (2013) · PLoS Biology · doi:10.1371/journal.pbio.1001731 · Cited by 177 · see citing works
Model for regulation of the histidine operon of Salmonella.
Johnston, M., Barnes, W. M., Chumley, F. G., Bossi, L., & Roth, J. (1980) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.77.1.508 · Cited by 175 · see citing works
Redox regulation by reversible protein S-thiolation in bacteria
Vu, L. V., Rossius, M., & Antelmann, H. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00187 · Cited by 173 · see citing works
Small Stress Response Proteins in Escherichia coli : Proteins Missed by Classical Proteomic Studies
Hemm, M. R., Paul, B. J., Miranda‐Ríos, J., Zhang, A., Soltanzad, N., & Storz, G. (2009) · Journal of Bacteriology · doi:10.1128/jb.00872-09 · Cited by 170 · see citing works
Rapid engineering of bacterial artificial chromosomes using oligonucleotides
Swaminathan, S., Ellis, H. M., Waters, L. S., Yu, D., Lee, E.-C., Court, D. L., & Sharan, S. K. (2000) · genesis · doi:10.1002/1526-968x(200101)29:1 · Cited by 154 · see citing works
van Kessel, J. C., & Hatfull, G. F. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06109.x · Cited by 150 · see citing works
Zheng, X., Hu, G., She, Z.-S., & Zhu, H. (2011) · BMC Genomics · doi:10.1186/1471-2164-12-361 · Cited by 117 · see citing works
Drug Sensing by the Ribosome Induces Translational Arrest via Active Site Perturbation
Arenz, S., Meydan, S., Starosta, A. L., Berninghausen, O., Beckmann, R., Vázquez‐Laslop, N., & Wilson, D. N. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.09.014 · Cited by 110 · see citing works
An expanding universe of small proteins
Hobbs, E. C., Fontaine, F., Yin, X., & Storz, G. (2011) · Current Opinion in Microbiology · doi:10.1016/j.mib.2011.01.007 · Cited by 106 · see citing works
Crappé, J., Criekinge, W. V., Trooskens, G., Hayakawa, E., Luyten, W. H. M. L., Baggerman, G., & Menschaert, G. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-648 · Cited by 93 · see citing works
Miranda-CasoLuengo, A. A., Staunton, P. M., Dinan, A. M., Lohan, A. J., & Loftus, B. J. (2016) · BMC Genomics · doi:10.1186/s12864-016-2868-y · Cited by 81 · see citing works
Regulation of Bacterial Gene Expression by Transcription Attenuation
Turnbough, C. L. (2019) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00019-19 · Cited by 79 · see citing works
Pervasive translation in Mycobacterium tuberculosis
Smith, C., Canestrari, J. G., Wang, A. J., Champion, M. M., Derbyshire, K. M., Gray, T. A., & Wade, J. T. (2022) · eLife · doi:10.7554/elife.73980 · Cited by 71 · see citing works
Self-citationRibosome regulation by the nascent peptide.
Lovett, P. S., & Rogers, E. J. (1996) · Microbiological Reviews · doi:10.1128/mmbr.60.2.366-385.1996 · Cited by 69 · see citing works
Martini, M. C., Zhou, Y., Sun, H., & Shell, S. S. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00591 · Cited by 65 · see citing works
Evolution and the universality of the mechanism of initiation of protein synthesis
Nakamoto, T. (2008) · Gene · doi:10.1016/j.gene.2008.11.001 · Cited by 63 · see citing works
Anti-peptidyl transferase leader peptides of attenuation-regulated chloramphenicol-resistance genes.
Gu, Z., Harrod, R., Rogers, E. J., & Lovett, S. T. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.12.5612 · Cited by 57 · see citing works
Leaderless mRNAs in the Spotlight: Ancient but Not Outdated!
Beck, H. J., & Moll, I. (2018) · Microbiology Spectrum · doi:10.1128/microbiolspec.rwr-0016-2017 · Cited by 55 · see citing works
Xu, X., Vilchèze, C., Av‐Gay, Y., Gómez-Velasco, A., & Jacobs, W. R. (2011) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00020-11 · Cited by 50 · see citing works
Barkan, D., Stallings, C. L., & Glickman, M. S. (2010) · Gene · doi:10.1016/j.gene.2010.09.005 · Cited by 47 · see citing works
Zhao, G., Weatherspoon‐Griffin, N., Kong, W., Curtiss, R., & Shi, Y. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0807071106 · Cited by 45 · see citing works
Bosserman, R. E., Nguyen, T. T. M., Sanchez, K. G., Chirakos, A. E., Ferrell, M. J., Thompson, C. R., Champion, M. M., Abramovitch, R. B., & Champion, P. A. D. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1710167114 · Cited by 44 · see citing works
Self-citationProteoSign: an end-user online differential proteomics statistical analysis platform
Efstathiou, G., Antonakis, A., Pavlopoulos, G. A., Θεοδοσίου, Θ., Divanach, P., Trudgian, D. C., Thomas, B., Papanikolaou, N., Aivaliotis, M., Acuto, O., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx444 · Cited by 40 · see citing works
Bosserman, R. E., Nicholson, K. R., Champion, M. M., & Champion, P. A. D. (2019) · Journal of Bacteriology · doi:10.1128/jb.00760-18 · Cited by 36 · see citing works
Self-citationBurian, J., & Thompson, C. (2018) · Molecular Microbiology · doi:10.1111/mmi.13890 · Cited by 22 · see citing works
Pervasive Translation in Mycobacterium tuberculosisPreprint
Smith, C., Canestrari, J. G., Wang, A. J., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/665208 · Cited by 21 · see citing works
Self-citation
Flagged first, then by citations
Cited by
Sorted by citations
Mycobacterium smegmatis: The Vanguard of Mycobacterial Research
Sparks, I. L., Derbyshire, K. M., Jacobs, W. R., & Morita, Y. S. (2023) · Journal of Bacteriology · doi:10.1128/jb.00337-22 · Cited by 149 · see citing works
Self-citationPervasive translation in Mycobacterium tuberculosis
Smith, C., Canestrari, J. G., Wang, A. J., Champion, M. M., Derbyshire, K. M., Gray, T. A., & Wade, J. T. (2022) · eLife · doi:10.7554/elife.73980 · Cited by 71 · see citing works
Self-citationVenturini, E., Svensson, S. L., Maaß, S., Gelhausen, R., Eggenhofer, F., Li, L., Cain, A. K., Parkhill, J., Becher, D., Backofen, R., et al. (2020) · microLife · doi:10.1093/femsml/uqaa002 · Cited by 57 · see citing works
Proteo-genetic analysis reveals clear hierarchy of ESX-1 secretion in Mycobacterium marinum
Cronin, R. M., Ferrell, M. J., Cahir, C. W., Champion, M. M., & Champion, P. A. D. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2123100119 · Cited by 40 · see citing works
Self-citationBarth, V. C., Chauhan, U., Zeng, J., Su, X., Zheng, H., Husson, R. N., & Woychik, N. A. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2022136118 · Cited by 44 · see citing works
Sawyer, E. B., Phelan, J. E., Clark, T. G., & Cortes, T. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108695 · Cited by 25 · see citing works
The BR-body proteome contains a complex network of protein-protein and protein-RNA interactions
Nandana, V., Rathnayaka-Mudiyanselage, I. W., Muthunayake, N. S., Hatami, A., Mousseau, C. B., Ortiz‐Rodríguez, L. A., Vaishnav, J., Collins, M., Gega, A., Mallikaarachchi, K. S., et al. (2023) · Cell Reports · doi:10.1016/j.celrep.2023.113229 · Cited by 27 · see citing works
Self-citationRegulation of Leaderless mRNA Translation in Bacteria
Leiva, L. E., & Katz, A. (2022) · Microorganisms · doi:10.3390/microorganisms10040723 · Cited by 27 · see citing works
Small Proteins in Archaea, a Mainly Unexplored World
Weidenbach, K., Gutt, M., Cassidy, L., Chibani, C. M., & Schmitz, R. A. (2021) · Journal of Bacteriology · doi:10.1128/jb.00313-21 · Cited by 24 · see citing works
D’Halluin, A., Polgar, P., Kipkorir, T., Patel, Z., Cortes, T., & Arnvig, K. B. (2023) · iScience · doi:10.1016/j.isci.2023.106465 · Cited by 22 · see citing works
Miniprep assisted proteomics (MAP) for rapid proteomics sample preparation
Mousseau, C. B., Pierre, C., Hu, D. D., & Champion, M. M. (2022) · Analytical Methods · doi:10.1039/d2ay01549h · Cited by 17 · see citing works
Self-citationAvila‐Cobian, L. F., Benedetti, S. D., Kim, C. K., Feltzer, R. E., Champion, M. M., Fisher, J. F., & Mobashery, S. (2022) · Communications Biology · doi:10.1038/s42003-022-04230-x · Cited by 16 · see citing works
Self-citationD’Halluin, A., Polgar, P., Kipkorir, T., Patel, Z., Cortes, T., & Arnvig, K. B. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.01.494293 · Cited by 11 · see citing works
Stiens, J., Tan, Y. Y., Joyce, R., Arnvig, K. B., Kendall, S. L., & Nobeli, I. (2023) · Molecular Microbiology · doi:10.1111/mmi.15055 · Cited by 10 · see citing works
The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens
Nicholson, K. R., Mousseau, C. B., Champion, M. M., & Champion, P. A. D. (2021) · PLoS Pathogens · doi:10.1371/journal.ppat.1009124 · Cited by 9 · see citing works
Self-citationCanestrari, J. G., Gordon, E. C., Bruce, S. A., Lasek‐Nesselquist, E., Schultz, S. R., Marietta, H. A., Biegas, K. J., Swarts, B. M., Champion, M. M., Derbyshire, K. M., et al. (2025) · Molecular Microbiology · doi:10.1111/mmi.70030 · Cited by 3 · see citing works
Self-citationRibosome profiling in Mycobacterium tuberculosis reveals robust leaderless translationPreprint
Sawyer, E. B., Phelan, J. E., Clark, T. G., & Cortes, T. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.04.22.055855 · Cited by 2 · see citing works
Fred Goldberg machines in the pathogenesis of Mycobacterium tuberculosis
Darwin, K. H. (2026) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2026.111373 · Cited by 1 · see citing works
Harnessing toxin-mediated ribosome stalling as a complementary tool to annotate bacterial ORFs
Troian, E. A., Barth, V. C., Chauhan, U., Zheng, H., Zhao, C., Zeng, J., Husson, R. N., & Woychik, N. A. (2026) · Nucleic Acids Research · doi:10.1093/nar/gkag252 · Cited by 1 · see citing works
Bokolia, N. P., & Khan, I. A. (2021) · The Journal of Biochemistry · doi:10.1093/jb/mvab080
Eckartt, K. A., Munsamy, V., Quiñones-García, S., DeJesus, M. A., Ju, X., Liu, S., & Rock, J. M. (2026) · Nature Microbiology · doi:10.1038/s41564-026-02357-9
Mycobacteria Emerge as Leaders in Leaderless Translation
Canestrari, J. G., & Gray, T. A. (2026) · Annual Review of Microbiology · doi:10.1146/annurev-micro-042424-051945
Self-citationSain, S., Chauhan, U., Barth, V. C., Jr., Troian, E. A., Abbadi, B. L., Malakar, B., Husson, R. N., & Woychik, N. A. (2026) · PLoS Pathogens · doi:10.1371/journal.ppat.1014679
- Authors
- Canestrari, J. G., Lasek‐Nesselquist, E., Upadhyay, A., Rofaeil, M., Champion, M. M., Wade, J. T., Derbyshire, K. M., & Gray, T. A.
- Affiliations
- New York State Department of Health (US)
- University of Notre Dame (US)
- Corresponding author
- Gray, Todd A.
- Venue
- Molecular Microbiology
- Publisher
- Wiley
- Published
- 2020-04-09
- Volume
- 114
- Issue
- 1
- Pages
- 93-108
- ISSN
- 0950-382X (ISSN-L)
- 1365-2958
- PMC
- PMC8764745
- OpenAlex
- W3010808916
- Cited by
- 25
- References
- 59
- Citations by year
- 2026: 5 · 2025: 2 · 2023: 4 · 2022: 6 · 2021: 6 · 2020: 2
- FWCI
- 2.63
- Type
- journal article
- Language
- en
- Open access
- green
- doi.org
- Locations
- Molecular Microbiology (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (R21AI147608, R21AI119427, R01AI097191, R21AI117158)
- New York State Department of Health - Wadsworth Center
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- ribosome stalling, ribosome pausing, Mycobacterium smegmatis, polycistronic transcripts, cysteine metabolism
- MeSH terms
- Cysteine, Mycobacterium tuberculosis, Peptides, RNA, Messenger, Gene Expression Regulation, Bacterial, Open Reading Frames, Mycobacterium smegmatis, Response Elements, Transcription Initiation Site
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
