Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

Meydan, Sezen; Marks, James; Klepacki, Dorota; Sharma, Virag; Baranov, Pavel V.; Firth, Andrew E.; Margus, Tōnu; Kefi, Amira; Vázquez-Laslop, Nora; Mankin, Alexander S.

doi:10.1016/j.molcel.2019.02.017

Cited by 185RNA and protein synthesis mechanismsBacterial Genetics and BiotechnologyGenomics and Phylogenetic Studies

Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

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Meydan, Sezen, Marks, James, Klepacki, Dorota, Sharma, Virag, Baranov, Pavel V., Firth, Andrew E., Margus, Tōnu, Kefi, Amira +2 more·2019·Molecular Cell

DOI 10.1016/j.molcel.2019.02.017PMC PMC7115971

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Abstract

The use of alternative translation initiation sites enables production of more than one protein from a single gene, thereby expanding the cellular proteome. Although several such examples have been serendipitously found in bacteria, genome-wide mapping of alternative translation start sites has been unattainable. We found that the antibiotic retapamulin specifically arrests initiating ribosomes at start codons of the genes. Retapamulin-enhanced Ribo-seq analysis (Ribo-RET) not only allowed mapping of conventional initiation sites at the beginning of the genes, but strikingly, it also revealed putative internal start sites in a number of Escherichia coli genes. Experiments demonstrated that the internal start codons can be recognized by the ribosomes and direct translation initiation in vitro and in vivo. Proteins, whose synthesis is initiated at internal in-frame and out-of-frame start sites, can be functionally important and contribute to the "alternative" bacterial proteome. The internal start sites may also play regulatory roles in gene expression.

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Growing experimental evidence in mycobacteria and other prokaryotes has shown that many sproteins are functional, requiring a rethinking of gene definitions.
“However, growing experimental evidence in mycobacteria and other prokaryotes has shown that many sproteins are functional, requiring a rethinking of gene definitions (71–75).”
From Mycobacterium smegmatis: The Vanguard of Mycobacterial Research (2023) · cites this paper as [72]
The Results report an E. coli alternative protein, ArcB-C, whose translation was experimentally confirmed and whose start site gave cells a growth advantage under low-oxygen conditions. The Discussion says many additional translation starts were found, but their protein products’ functions are largely unknown; the experiments were confined to E. coli, not mycobacteria. The paper supports reconsidering some gene annotations, but not the broader claim that many small proteins have been shown to be functional. (LLM, conf=0.88)
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Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products.
Datsenko, K., & Wanner, B. (2000) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.120163297 · Cited by 15,902 · see citing works
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Sievers, F., Wilm, A., Dineen, D., Gibson, T., Karplus, K., Li, W.-Z., Lopez, R., McWilliam, H., Remmert, M., Söding, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.75 · Cited by 15,576 · see citing works
WebLogo: A Sequence Logo Generator: Figure 1Preprint
Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,433 · see citing works
Enzymatic assembly of DNA molecules up to several hundred kilobases
Gibson, D. G., Young, L., Chuang, R.-Y., Venter, J. C., Hutchison, C. A., & Smith, H. O. (2009) · Nature Methods · doi:10.1038/nmeth.1318 · Cited by 9,742 · see citing works
Construction of Escherichia coli K‐12 in‐frame, single‐gene knockout mutants: the Keio collection
Baba, T., Ara, T., Hasegawa, M., Takai, Y., Okumura, Y., Baba, M., Datsenko, K. A., Tomita, M., Wanner, B. L., & Mori, H. (2006) · Molecular Systems Biology · doi:10.1038/msb4100050 · Cited by 7,858 · see citing works
T-Coffee: A novel method for fast and accurate multiple sequence alignment.
Notredame, C., Higgins, D., & Heringa, J. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4042 · Cited by 7,321 · see citing works
Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, N. T., Ghaemmaghami, S., Newman, J. R. S., & Weissman, J. S. (2009) · Science · doi:10.1126/science.1168978 · Cited by 3,853 · see citing works
ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
Huerta‐Cepas, J., Serra, F., & Peer Bork, B. (2016) · Molecular Biology and Evolution · doi:10.1093/molbev/msw046 · Cited by 2,239 · see citing works
Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes
Ingolia, N. T., Lareau, L. F., & Weissman, J. S. (2011) · Cell · doi:10.1016/j.cell.2011.10.002 · Cited by 2,187 · see citing works
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update
Afgan, E., Baker, D., van den Beek, M., Blankenberg, D. J., Bouvier, D., Čech, M., Chilton, J. M., Clements, D., Coraor, N., Eberhard, C., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw343 · Cited by 2,150 · see citing works
Cell-free translation reconstituted with purified components
Shimizu, Y., Inoue, A., Tomari, Y., Suzuki, T., Yokogawa, T., Nishikawa, K., & Ueda, T. (2001) · Nature Biotechnology · doi:10.1038/90802 · Cited by 1,826 · see citing works
RNAhybrid: microRNA target prediction easy, fast and flexible
Kruger, J., & Rehmsmeier, M. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl243 · Cited by 1,716 · see citing works
Determinant of cistron specificity in bacterial ribosomes
Shine, J., & Dalgarno, L. (1975) · Nature · doi:10.1038/254034a0 · Cited by 1,365 · see citing works
Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources
Li, G., Burkhardt, D. H., Gross, C. A., & Weissman, J. S. (2014) · Cell · doi:10.1016/j.cell.2014.02.033 · Cited by 1,218 · see citing works
The Molecular Basis of Antibiotic Action
Gale, E. F. (1981) · Medical Entomology and Zoology · Cited by 1,217 · see citing works
Tightly regulated tac promoter vectors useful for the expression of unfused and fused proteins in Escherichia coli
Amann, E. P., Ochs, B., & Kj, A. (1988) · Gene · doi:10.1016/0378-1119(88)90440-4 · Cited by 1,045 · see citing works
Microbial gene identification using interpolated Markov models
Salzberg, S. L., Delcher, A. L., Kasif, S., & White, O. R. (1998) · Nucleic Acids Research · doi:10.1093/nar/26.2.544 · Cited by 989 · see citing works
The Structural Basis for the Action of the Antibiotics Tetracycline, Pactamycin, and Hygromycin B on the 30S Ribosomal Subunit
Brodersen, D. E., Clemons, W. M., Carter, A. P., Morgan-Warren, R. J., Wimberly, B. T., & Ramakrishnan, V. (2000) · Cell · doi:10.1016/s0092-8674(00)00216-6 · Cited by 950 · see citing works
Regulation of translation via mRNA structure in prokaryotes and eukaryotes
Kozak, M. (2005) · Gene · doi:10.1016/j.gene.2005.06.037 · Cited by 747 · see citing works
Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution
Lee, S., Liu, B., Lee, S., Huang, S., Shen, B., & Qian, S. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1207846109 · Cited by 595 · see citing works
The Ribosomal Exit Tunnel Functions as a Discriminating Gate
Nakatogawa, H., & Ito, K. (2002) · Cell · doi:10.1016/s0092-8674(02)00649-9 · Cited by 534 · see citing works
Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3
Pioletti, M., Schlünzen, F., Harms, J., Zarivach, R., Glühmann, M., Avila, H., Bashan, A., Bartels, H., Auerbach, T., Jacobi, C., et al. (2001) · The EMBO Journal · doi:10.1093/emboj/20.8.1829 · Cited by 527 · see citing works
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny
Wilson, D. A., Pethica, R., Zhou, Y., Talbot, C. C., Vogel, C., Madera, M., Chothia, C., & Gough, J. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn762 · Cited by 488 · see citing works
tRNA selection and kinetic proofreading in translation
Blanchard, S. C., Gonzalez, R. L., Kim, H. D., Chu, S., & Puglisi, J. D. (2004) · Nature Structural & Molecular Biology · doi:10.1038/nsmb831 · Cited by 466 · see citing works
Selective Ribosome Profiling Reveals the Cotranslational Chaperone Action of Trigger Factor In Vivo
Oh, E., Becker, A. H., Sandikci, A., Huber, D., Chaba, R., Gloge, F., Nichols, R. J., Typas, A., Gross, C. A., Krämer, G., et al. (2011) · Cell · doi:10.1016/j.cell.2011.10.044 · Cited by 445 · see citing works
Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites
Borujeni, A. E., Channarasappa, A. S., & Salis, H. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1139 · Cited by 445 · see citing works
[27] Extension inhibition analysis of translation initiation complexes
Hartz, D., McPheeters, D. S., Traut, R. R., & Gold, L. (1988) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(88)64058-4 · Cited by 397 · see citing works
Global Gene Expression Profiling in Escherichia coli K12
Salmon, K. A., Hung, S., Steffen, N. R., Krupp, R., Baldi, P., Hatfield, G. W., & Gunsalus, R. P. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m414030200 · Cited by 365 · see citing works
Small Proteins Can No Longer Be Ignored
Storz, G., Wolf, Y. I., & Ramamurthi, K. S. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-070611-102400 · Cited by 359 · see citing works
Global transcriptional start site mapping using differential RNA sequencing reveals novel antisense RNAs in Escherichia coli
Thomason, M. K., Bischler, T., Eisenbart, S. K., Förstner, K. U., Zhang, A., Herbig, A., Nieselt, K., Sharma, C. M., & Storz, G. (2015) · Journal of Bacteriology · doi:10.1128/jb.02096-14 · Cited by 335 · see citing works
The A-Z of bacterial translation inhibitors
Wilson, D. N. (2009) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.3109/10409230903307311 · Cited by 322 · see citing works
Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use
Atkins, J. F., Loughran, G., Bhatt, P. R., Firth, A. E., & Baranov, P. V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw530 · Cited by 320 · see citing works
Self-citation
Translation in ProkaryotesPreprint
Rodnina, M. V. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a032664 · Cited by 279 · 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
Inhibition of peptide bond formation by pleuromutilins: the structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with tiamulin
Schlünzen, F., Pyetan, E., Fucini, P., Yonath, A., & Harms, J. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04346.x · Cited by 240 · see citing works
Quantitative profiling of initiating ribosomes in vivo
Gao, X., Wan, J., Liu, B., Ma, M., Shen, B., & Qian, S. (2014) · Nature Methods · doi:10.1038/nmeth.3208 · Cited by 238 · see citing works
A proton wire to couple aminoacyl-tRNA accommodation and peptide-bond formation on the ribosome
Polikanov, Y. S., Steitz, T. A., & Innis, C. A. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2871 · Cited by 231 · see citing works
Mechanism and Function of the Outer Membrane Channel TolC in Multidrug Resistance and Physiology of Enterobacteria
Zgurskaya, H. I., Krishnamoorthy, G., Ntreh, A. T., & Lu, S. (2011) · Frontiers in Microbiology · doi:10.3389/fmicb.2011.00189 · Cited by 224 · see citing works
High-Precision Analysis of Translational Pausing by Ribosome Profiling in Bacteria Lacking EFP
Woolstenhulme, C. J., Guydosh, N. R., Green, R., & Buskirk, A. R. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.03.014 · Cited by 221 · see citing works
Alternative translation start sites and hidden coding potential of eukaryotic mRNAs
Kochetov, A. V. (2008) · BioEssays · doi:10.1002/bies.20771 · Cited by 218 · see citing works
Protein Complexes of the Escherichia coli Cell Envelope
Stenberg, F., Chovanec, P., Maslen, S., Robinson, C. V., Ilag, L. L., von HEIJNE, G., & Daley, D. O. (2005) · Journal of Biological Chemistry · doi:10.1074/jbc.m506479200 · Cited by 217 · see citing works
Widespread Antisense Transcription in Escherichia coli
Dornenburg, J. E., DeVita, A. M., Palumbo, M. J., & Wade, J. T. (2010) · mBio · doi:10.1128/mbio.00024-10 · Cited by 215 · see citing works
Pleuromutilins: Potent Drugs for Resistant Bugs—Mode of Action and ResistancePreprint
Paukner, S., & Riedl, R. (2016) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a027110 · Cited by 214 · see citing works
Leaderless mRNAs in bacteria: surprises in ribosomal recruitment and translational control
Moll, I., Grill, S., Gualerzi, C. O., & Bläsi, U. (2002) · Molecular Microbiology · doi:10.1046/j.1365-2958.2002.02739.x · Cited by 210 · see citing works
Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprintingPreprint
Fritsch, C., Herrmann, A., Nothnagel, M., Szafranski, K., Huse, K., Schumann, F. H., Schreiber, S., Platzer, M., Krawczak, M., Hampe, J., et al. (2012) · Genome Research · doi:10.1101/gr.139568.112 · Cited by 204 · see citing works
Understanding the Differences between Genome Sequences of Escherichia coli B Strains REL606 and BL21(DE3) and Comparison of the E. coli B and K-12 Genomes
Studier, F. W., Daegelen, P., Lenski, R. E., Maslov, S., & Kim, J. F. (2009) · Journal of Molecular Biology · doi:10.1016/j.jmb.2009.09.021 · Cited by 200 · see citing works
Complete Genome Sequence of Escherichia coli BW25113
Grenier, F., Matteau, D., Baby, V., & Rodrigue, S. (2014) · Genome Announcements · doi:10.1128/genomea.01038-14 · Cited by 198 · see citing works
EcoGene 3.0
Zhou, J., & Rudd, K. E. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1235 · Cited by 195 · see citing works
Measurements of translation initiation from all 64 codons in E. coli
Hecht, A., Glasgow, J. E., Jaschke, P. R., Bawazer, L. A., Munson, M. S., Cochran, J. R., Endy, D., & Salit, M. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx070 · Cited by 194 · see citing works
An antimicrobial peptide that inhibits translation by trapping release factors on the ribosome
Florin, T., Maracci, C., Graf, M., Karki, P., Klepacki, D., Berninghausen, O., Beckmann, R., Vázquez‐Laslop, N., Wilson, D. N., Rodnina, M. V., et al. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3439 · Cited by 192 · see citing works
Self-citation
Induced-fit tightens pleuromutilins binding to ribosomes and remote interactions enable their selectivity
Davidovich, C., Bashan, A., Auerbach-Nevo, T., Yaggie, R. D., Gontarek, R. R., & Yonath, A. (2007) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0700041104 · Cited by 186 · see citing works
Initiation of mRNA translation in bacteria: structural and dynamic aspects
Gualerzi, C. O., & Pon, C. L. (2015) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-015-2010-3 · Cited by 185 · see citing works
The pleuromutilin drugs tiamulin and valnemulin bind to the RNA at the peptidyl transferase centre on the ribosome
Poulsen, S. M., Karlsson, M., Johansson, L. B., & Vester, B. (2001) · Molecular Microbiology · doi:10.1046/j.1365-2958.2001.02595.x · Cited by 180 · see citing works
Biosynthesis of polyamines and polyamine-containing molecules
Michael, A. J. (2016) · Biochemical Journal · doi:10.1042/bcj20160185 · Cited by 180 · 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
The general mode of translation inhibition by macrolide antibiotics
Kannan, K., Kanabar, P. N., Schryer, D. W., Florin, T., Oh, E., Bahroos, N., Tenson, T., Weissman, J. S., & Mankin, A. S. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1417334111 · Cited by 176 · see citing works
Self-citation
A small gene, designated comS, located within the coding region of the fourth amino acid‐activation domain of srfA, is required for competence development in Bacillus subtilis
Hamoen, L. W., Eshuis, H., Jongbloed, J. D. H., Venema, G., & van Sinderen, D. (1995) · Molecular Microbiology · doi:10.1111/j.1365-2958.1995.tb02220.x · Cited by 171 · see citing works
Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center
Marks, J., Kannan, K., Roncase, E. J., Klepacki, D., Kefi, A., Orelle, C., Vázquez-Laslop, N., & Mankin, A. S. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1613055113 · Cited by 159 · see citing works
Self-citation
Identification of comS, a gene of the srfA operon that regulates the establishment of genetic competence in Bacillus subtilis.
D’Souza, C. A., NAKANO, M. M., & Zuber, P. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.20.9397 · Cited by 155 · see citing works
Selective Protein Synthesis by Ribosomes with a Drug-Obstructed Exit Tunnel
Kannan, K., Vázquez‐Laslop, N., & Mankin, A. S. (2012) · Cell · doi:10.1016/j.cell.2012.09.018 · Cited by 154 · see citing works
Self-citation
Comparison of mRNA features affecting translation initiation and reinitiation
Osterman, I. А., Evfratov, S. A., Владимирович, С. П., & Dontsova, O. А. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks989 · Cited by 135 · see citing works
The Minimum Open Reading Frame, AUG-Stop, Induces Boron-Dependent Ribosome Stalling and mRNA Degradation
Tanaka, M., Sotta, N., Yamazumi, Y., Yamashita, Y., Miwa, K., Murota, K., Chiba, Y., Hirai, M. Y., Akiyama, T., Onouchi, H., et al. (2016) · The Plant Cell · doi:10.1105/tpc.16.00481 · Cited by 130 · see citing works
Selective ribosome profiling as a tool for studying the interaction of chaperones and targeting factors with nascent polypeptide chains and ribosomes
Becker, A. H., Oh, E., Weissman, J. S., Krämer, G., & Bukau, B. (2013) · Nature Protocols · doi:10.1038/nprot.2013.133 · Cited by 128 · see citing works
Tools for Characterizing Bacterial Protein Synthesis Inhibitors
Orelle, C., Carlson, S., Kaushal, B., Almutairi, M. M., Liu, H., Ochabowicz, A., Quan, S., Pham, V. C., Squires, C. L., Murphy, B. T., et al. (2013) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01673-13 · Cited by 126 · see citing works
Self-citation
Activity of Retapamulin (SB-275833), a Novel Pleuromutilin, against Selected Resistant Gram-Positive Cocci
Jones, R. N., Fritsche, T. R., Sader, H. S., & Ross, J. E. (2006) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01432-05 · Cited by 125 · see citing works
The Mechanisms of Action of Ribosome-Targeting Peptide Antibiotics
Polikanov, Y. S., Aleksashin, N. A., Beckert, B., & Wilson, D. N. (2018) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2018.00048 · Cited by 124 · see citing works
The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli
Onesti, S., Miller, A. D., & Brick, P. (1995) · Structure · doi:10.1016/s0969-2126(01)00147-2 · Cited by 123 · see citing works
Biochemical Characterization of the Interactions of the Novel Pleuromutilin Derivative Retapamulin with Bacterial Ribosomes
Yan, K., Madden, L., Choudhry, A. E., Voigt, C. S., Copeland, R. A., & Gontarek, R. R. (2006) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00184-06 · Cited by 120 · see citing works
Translation initiation region sequence preferences in Escherichia coli
Vimberg, V., Brauer, A., Remm, M., & Tenson, T. (2007) · BMC Molecular Biology · doi:10.1186/1471-2199-8-100 · Cited by 118 · see citing works
Biosynthetic Arginine Decarboxylase from Escherichia coli
Wu, W. H., & Morris, D. R. (1973) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)44245-2 · Cited by 115 · see citing works
A combined cryo-EM and molecular dynamics approach reveals the mechanism of ErmBL-mediated translation arrest
Arenz, S., Bock, L. V., Graf, M., Innis, C. A., Beckmann, R., Grubmüller, H., Vaiana, A. C., & Wilson, D. N. (2016) · Nature Communications · doi:10.1038/ncomms12026 · Cited by 114 · see citing works
The nucleotide sequences of the ponA and ponB genes encoding penicillin‐binding proteins 1A and 1B of Escherichia coli K12
Broome‐Smith, J. K., Edelman, A., Yousif, S., & Spratt, B. G. (1985) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1985.tb08768.x · Cited by 111 · see citing works
The bacterial N-end rule pathway: expect the unexpected
Dougan, D. A., Truscott, K. N., & Zeth, K. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2010.07120.x · Cited by 105 · see citing works
Initiation Factor IF2, Thiostrepton and Micrococcin Prevent the Binding of Elongation Factor G to the Escherichia coli Ribosome
Cameron, D. M., Thompson, J., March, P. E., & Dahlberg, A. E. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00235-8 · Cited by 99 · see citing works
Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning
Baranov, P. V., Atkins, J. F., & Yordanova, M. M. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3963 · Cited by 95 · see citing works
Self-citation
Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses
Firth, A. E. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku981 · Cited by 93 · see citing works
Self-citation
N-terminomics identifies Prli42 as a membrane miniprotein conserved in Firmicutes and critical for stressosome activation in Listeria monocytogenes
Impens, F., Rolhion, N., Radoshevich, L., Bécavin, C., Duval, M., Mellin, J. R., del Portillo, F. G., Pucciarelli, M. G., Williams, A. H., & Cossart, P. (2017) · Nature Microbiology · doi:10.1038/nmicrobiol.2017.5 · Cited by 93 · see citing works
Distinct tRNA Accommodation Intermediates Observed on the Ribosome with the Antibiotics Hygromycin A and A201A
Polikanov, Y. S., Starosta, A. L., Juette, M. F., Altman, R. B., Terry, D. S., Lu, W., Burnett, B. J., Dinos, G. P., Reynolds, K. A., Blanchard, S. C., et al. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.04.014 · Cited by 91 · see citing works
OrtholugeDB: a bacterial and archaeal orthology resource for improved comparative genomic analysis
Whiteside, M. D., Winsor, G. L., Laird, M. R., & Brinkman, F. S. L. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1241 · Cited by 78 · see citing works
Purification and properties of the biotin repressor. A bifunctional protein.
Eisenberg, M. A., Prakash, O., & Hsiung, S. C. (1982) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)33408-2 · Cited by 75 · see citing works
Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling
Nakahigashi, K., Takai, Y., Kimura, M., Abe, N., Nakayashiki, T., Shiwa, Y., Yoshikawa, H., Wanner, B. L., Ishihama, Y., & Mori, H. (2016) · DNA Research · doi:10.1093/dnares/dsw008 · Cited by 74 · see citing works
Systematic Analysis of Native Membrane Protein Complexes inEscherichia coli
Maddalo, G., Bruzell, F. S., Götzke, H., Toddo, S., Björkholm, P., Eriksson, H., Chovanec, P., Genevaux, P., Lehtiö, J., Ilag, L. L., et al. (2011) · Journal of Proteome Research · doi:10.1021/pr101105c · Cited by 74 · see citing works
Site-directed mutagenesis of the dual translational initiation sites of the clpB gene of Escherichia coli and characterization of its gene products.
Park, S., Kim, K. I., Woo, K. M., Seol, J. H., Tanaka, K., Ichihara, A., Ha, D. B., & Chung, C. H. (1993) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(20)80709-1 · Cited by 70 · see citing works
Improved profile HMM performance by assessment of critical algorithmic features in SAM and HMMER
Wistrand, M., & Sonnhammer, E. L. L. (2005) · BMC Bioinformatics · doi:10.1186/1471-2105-6-99 · Cited by 70 · see citing works
Proteome‐wide analysis of the amino terminal status of Escherichia coli proteins at the steady‐state and upon deformylation inhibition
Bienvenut, W. V., Giglione, C., & Meinnel, T. (2015) · PROTEOMICS · doi:10.1002/pmic.201500027 · Cited by 66 · see citing works
Identification of Unannotated Small Genes in Salmonella
Baek, J., Lee, J., Yoon, K., & Lee, H.-W. (2017) · G3 Genes Genomes Genetics · doi:10.1534/g3.116.036939 · Cited by 63 · see citing works
An analysis of initiation codon utilization in the Domain Bacteria – concerns about the quality of bacterial genome annotation
Villegas, A., & Kropinski, A. M. (2008) · Microbiology · doi:10.1099/mic.0.2008/021360-0 · Cited by 60 · see citing works
Two translational initiation sites in the infB gene are used to express initiation factor IF2 alpha and IF2 beta in Escherichia coli.
PLUMBRIDGE, J. A., Deville, F., Sacerdot, C., Petersen, H. U., Cenatiempo, Y., Cozzone, A. J., GRUNBERG‐MANAGO, M., & Hershey, J. W. B. (1985) · The EMBO Journal · doi:10.1002/j.1460-2075.1985.tb02339.x · Cited by 59 · see citing works
Characterization of Pores Formed by YaeT (Omp85) from Escherichia coli
Stegmeier, J. F., & Andersen, C. (2006) · The Journal of Biochemistry · doi:10.1093/jb/mvj147 · Cited by 59 · see citing works
Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes
Pavesi, A., Vianelli, A., Chirico, N., Bào, Y., Blinkova, O., Belshaw, R. D., Firth, A. E., & Karlin, D. (2018) · PLoS ONE · doi:10.1371/journal.pone.0202513 · Cited by 56 · see citing works
Self-citation
Adenosine diphosphate sugar pyrophosphatase prevents glycogen biosynthesis in Escherichia coli
Moreno-Bruna, B., Baroja‐Fernández, E., Muñoz, F. J., Bastarrica-Berasategui, A., Zandueta-Criado, A., Rodríguez-López, M., Lasa, Í., Akazawa, T., & Pozueta‐Romero, J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.131214098 · Cited by 56 · see citing works
Biosynthetic arginine decarboxylase in Escherichia coli is synthesized as a precursor and located in the cell envelope
Buch, J.-M., & Boyle, S. M. (1985) · Journal of Bacteriology · doi:10.1128/jb.163.2.522-527.1985 · Cited by 49 · see citing works
Chain Initiation Factor 2
Miller, M. J., & Wahba, A. J. (1973) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)44374-3 · Cited by 49 · see citing works
A minimal uORF within the HIV-1 vpu leader allows efficient translation initiation at the downstream env AUG
Krummheuer, J., Johnson, A. T., Hauber, I., Kammler, S., Anderson, J. L., Hauber, J., Purcell, D. F. J., & Schaal, H. (2007) · Virology · doi:10.1016/j.virol.2007.01.022 · Cited by 49 · see citing works
Both forms of translational initiation factor IF2 (α and β) are required for maximal growth of Escherichia coli
Sacerdot, C., Vachon, G., Laalami, S., MOREL‐DEVILLE, F., Cenatiempo, Y., & GRUNBERG‐MANAGO, M. (1992) · Journal of Molecular Biology · doi:10.1016/0022-2836(92)91026-l · Cited by 49 · see citing works
The ArcB Sensor Kinase of Escherichia coli Autophosphorylates by an Intramolecular Reaction
Peña-Sandoval, G. R., & Georgellis, D. (2010) · Journal of Bacteriology · doi:10.1128/jb.01401-09 · Cited by 49 · see citing works
The Translation Initiation Functions of IF2: Targets for Thiostrepton Inhibition
Brandi, L., Marzi, S., Fabbretti, A., Fleischer, C., Hill, W. E., Gualerzi, C. O., & Lodmell, J. S. (2003) · Journal of Molecular Biology · doi:10.1016/j.jmb.2003.10.067 · Cited by 48 · see citing works
YghG (GspS β ) Is a Novel Pilot Protein Required for Localization of the GspS β Type II Secretion System Secretin of Enterotoxigenic Escherichia coli
Strozen, T. G., Li, G., & Howard, S. P. (2012) · Infection and Immunity · doi:10.1128/iai.06394-11 · Cited by 47 · see citing works
Small genes/gene-products inEscherichia coliK-12
Wasinger, V. C., & Humphery‐Smith, I. (1998) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.1998.tb13343.x · Cited by 43 · see citing works
Organization and mode of action of two component system signaling circuits from the various kingdoms of life
Álvarez, A. F., Barba‐Ostria, C., Silva‐Jiménez, H., & Georgellis, D. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13397 · Cited by 42 · see citing works
In Vitro and In Vivo Analysis of the ArcB/A Redox Signaling Pathway
Álvarez, A. F., & Georgellis, D. (2010) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/s0076-6879(10)71012-0 · Cited by 41 · see citing works
Hygromycin A, a Novel Inhibitor of Ribosomal Peptidyltransferase
Guerrero, M. D. C., & Modolell, J. (1980) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1980.tb06044.x · Cited by 40 · see citing works
Genes within Genes in Bacterial Genomes
Meydan, S., Vázquez‐Laslop, N., & Mankin, A. S. (2018) · Microbiology Spectrum · doi:10.1128/microbiolspec.rwr-0020-2018 · Cited by 39 · see citing works
Self-citation
Chromosomal deletion and rearrangement in Streptomyces glaucescens
Birch, A., Häusler, A., Rüttener, C., & Hütter, R. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.11.3531-3538.1991 · Cited by 36 · see citing works
Ribosome signatures aid bacterial translation initiation site identification
Giess, A. P., Jonckheere, V., Ndah, E., Chyżyńska, K., Damme, P. V., & Valen, E. (2017) · BMC Biology · doi:10.1186/s12915-017-0416-0 · Cited by 34 · see citing works
Rapid and Inexpensive Evaluation of Nonstandard Amino Acid Incorporation in Escherichia coli
Monk, J. W., Leonard, S. P., Brown, C. W., Hammerling, M. J., Mortensen, C., Gutierrez, A. E., Shin, N. Y., Watkins‐Dulaney, E. J., Mishler, D. M., & Barrick, J. E. (2016) · ACS Synthetic Biology · doi:10.1021/acssynbio.6b00192 · Cited by 33 · see citing works
The Effects of Tiamulin, a Semisynthetic Pleuromutilin Derivative, on Bacterial Polypeptide Chain Initiation
DORNHELM, P., & Högenauer, G. (1978) · European Journal of Biochemistry · doi:10.1111/j.1432-1033.1978.tb12699.x · Cited by 32 · see citing works
Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer
Kingston, A. W., Ponkratz, C., & Raleigh, E. A. (2017) · Journal of Bacteriology · doi:10.1128/jb.00787-16 · Cited by 31 · see citing works
Comparative Membrane Proteomics Reveals a Nonannotated E. coli Heat Shock Protein
Yuan, P., D’Lima, N. G., & Slavoff, S. A. (2017) · Biochemistry · doi:10.1021/acs.biochem.7b00864 · Cited by 30 · see citing works
Nucleotide sequence and characterization of the sfs1 gene: sfs1 is involved in CRP*-dependent mal gene expression in Escherichia coli
Kawamukai, M., Utsumi, R., Takeda, K., Higashi, A., Matsuda, H., Choi, Y., & Komano, T. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.8.2644-2648.1991 · Cited by 30 · see citing works
An unusual mechanism of bacterial gene expression revealed for the RNase P protein of Thermus strains
Feltens, R., Gößringer, M., Willkomm, D. K., Urlaub, H., & Hartmann, R. K. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0931462100 · Cited by 28 · see citing works
Tandem translation of E.coli initiation factor IF2β: Purification and characterization in vitro of two active forms
Nyengaard, N. R., Mortensen, K. K., Lassen, S. F., Hershey, J. W. B., & Petersen, H. U. (1991) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(91)92118-4 · Cited by 28 · see citing works
Interaction between the CheY response regulator and the histidine‐containing phosphotransfer (HPt) domain of the ArcB sensory kinase in Escherichia coli
Yaku, H., Kato, M., Hakoshima, T., Tsuzuki, M., & Mizuno, T. (1997) · FEBS Letters · doi:10.1016/s0014-5793(97)00459-6 · Cited by 27 · see citing works
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes
Makita, Y., de Hoon, M., & Danchin, A. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-47 · Cited by 26 · see citing works
Regulating with RNA in Bacteria and Archaea
Storz, G., & Papenfort, K. 1. (2018) · doi:10.1128/9781683670247 · Cited by 26 · see citing works
The application of terminomics for the identification of protein start sites and proteoforms in bacteria
Berry, I. J., Steele, J. R., Padula, M. P., & Djordjevic, S. P. (2015) · PROTEOMICS · doi:10.1002/pmic.201500319 · Cited by 26 · see citing works
A New Role for Translation Initiation Factor 2 in Maintaining Genome Integrity
Madison, K. E., Abdelmeguid, M. R., Jones‐Foster, E. N., & Nakai, H. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002648 · Cited by 21 · see citing works
Identifying small proteins by ribosome profiling with stalled initiation complexesPreprint
Weaver, J., Mohammad, F., Buskirk, A. R., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/511675 · Cited by 15 · see citing works
Characterization of Species-Specific Repeats in 613 Prokaryotic Species
Kõressaar, T., & Remm, M. (2012) · DNA Research · doi:10.1093/dnares/dss006 · Cited by 11 · see citing works
Identifying translation initiation sites in prokaryotes using support vector machine
Gao, T., Yang, Z., Wang, Y., & Jing, L. (2009) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2009.10.023 · Cited by 8 · see citing works
Genes within Genes in Bacterial Genomes
Meydan, S., Vázquez‐Laslop, N., & Mankin, A. S. (2018) · ASM Press eBooks · doi:10.1128/9781683670247.ch9 · Cited by 8 · see citing works
Self-citation
Triggering Peptide-Dependent Translation Arrest by Small Molecules: Ribosome Stalling Modulated by Antibiotics
Vázquez‐Laslop, N., & Mankin, A. S. (2014) · Springer eBooks · doi:10.1007/978-4-431-55052-5_10 · Cited by 8 · see citing works
Self-citation
Ribosomal selection of mRNAs with degenerate initiation triplets
He, C., Sabatini, P., Brandi, L., Giuliodori, A. M., Pon, C. L., & Gualerzi, C. O. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx472 · Cited by 6 · see citing works

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Alternative ORFs and small ORFs: shedding light on the dark proteome
Orr, M. W., Mao, Y., Storz, G., & Qian, S. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz734 · Cited by 320 · see citing works
A synthetic antibiotic class overcoming bacterial multidrug resistance
Mitcheltree, M. J., Pisipati, A., Syroegin, E. A., Silvestre, K. J., Klepacki, D., Mason, J. D., Terwilliger, D. W., Testolin, G., Pote, A. R., Wu, K. J. Y., et al. (2021) · Nature · doi:10.1038/s41586-021-04045-6 · Cited by 238 · see citing works
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RNA-RNA Interactomes of ProQ and Hfq Reveal Overlapping and Competing Roles
Melamed, S., Adams, P. P., Zhang, A., Zhang, H., & Storz, G. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.022 · Cited by 231 · 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
Sense codon reassignment enables viral resistance and encoded polymer synthesis
Robertson, W. E., Funke, L. F. H., de la Torre, D., Fredens, J., Elliott, T. S., Spinck, M., Christova, Y., Cervettini, D., Böge, F. L., Liu, K. C., et al. (2021) · Science · doi:10.1126/science.abg3029 · Cited by 192 · see citing works
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
Overlapping genes in natural and engineered genomes
Wright, B. W., Molloy, M. P., & Jaschke, P. R. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00417-w · Cited by 137 · see citing works
A Practical Guide to Small Protein Discovery and Characterization Using Mass Spectrometry
Ahrens, C. H., Wade, J. T., Champion, M. M., & Langer, J. D. (2021) · Journal of Bacteriology · doi:10.1128/jb.00353-21 · Cited by 97 · see citing works
Translational initiation in E. coli occurs at the correct sites genome-wide in the absence of mRNA-rRNA base-pairing
Saito, K., Green, R., & Buskirk, A. R. (2020) · eLife · doi:10.7554/elife.55002 · Cited by 99 · see citing works
<i>Escherichia coli</i> Small Proteome
Hemm, M. R., Weaver, J., & Storz, G. (2020) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0031-2019 · Cited by 91 · see citing works
Structural basis of ABCF-mediated resistance to pleuromutilin, lincosamide, and streptogramin A antibiotics in Gram-positive pathogens
Crowe‐McAuliffe, C., Murina, V., Turnbull, K. J., Kasari, M., Mohamad, M., Polte, C., Takada, H., Vaitkevicius, K., Johansson, J., Ignatova, Z., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-23753-1 · Cited by 84 · see citing works
Ribosome profiling in archaea reveals leaderless translation, novel translational initiation sites, and ribosome pausing at single codon resolution
Gelsinger, D. R., Dallon, E., Reddy, R., Mohammad, F., Buskirk, A. R., & DiRuggiero, J. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa304 · Cited by 77 · see citing works
Prevalence of small base-pairing RNAs derived from diverse genomic loci
Adams, P. P., & Storz, G. (2020) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2020.194524 · Cited by 79 · see citing works
Non-AUG start codons: Expanding and regulating the small and alternative ORFeome
Cao, X., & Slavoff, S. A. (2020) · Experimental Cell Research · doi:10.1016/j.yexcr.2020.111973 · 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
Small Proteins; Big Questions
Gray, T., Storz, G., & Papenfort, K. (2022) · Journal of Bacteriology · doi:10.1128/jb.00341-21 · Cited by 71 · see citing works
Structural basis for context-specific inhibition of translation by oxazolidinone antibiotics
Tsai, K., Stojković, V., Lee, D. J., Young, I. D., Szal, T., Klepacki, D., Vázquez‐Laslop, N., Mankin, A. S., Fraser, J. S., & Fujimori, D. G. (2022) · Nature Structural & Molecular Biology · doi:10.1038/s41594-022-00723-9 · Cited by 70 · see citing works
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Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling
Vázquez‐Laslop, N., Sharma, C. M., Mankin, A. S., & Buskirk, A. R. (2021) · Journal of Bacteriology · doi:10.1128/jb.00294-21 · Cited by 62 · see citing works
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A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence
Venturini, 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
Tetracyclines promote survival and fitness in mitochondrial disease models
Perry, E. A., Bennett, C. F., Luo, C., Balsa, E., Jedrychowski, M. P., O’Malley, K. E., Latorre‐Muro, P., Ladley, R. P., Reda, K., Wright, P. M., et al. (2021) · Nature Metabolism · doi:10.1038/s42255-020-00334-y · Cited by 60 · see citing works
Discovery of a small protein factor involved in the coordinated degradation of phycobilisomes in cyanobacteria
Krauspe, V., Fahrner, M., Spät, P., Steglich, C., Frankenberg-Dinkel, N., Maček, B., Schilling, O., & Hess, W. R. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2012277118 · Cited by 54 · see citing works
No one tool to rule them all: prokaryotic gene prediction tool annotations are highly dependent on the organism of study
Dimonaco, N. J., Aubrey, W., Kenobi, K., Clare, A. J., & Creevey, C. J. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab827 · Cited by 54 · see citing works
Microproteins—Discovery, structure, and function
Mohsen, J. J., Martel, A. A., & Slavoff, S. A. (2023) · PROTEOMICS · doi:10.1002/pmic.202100211 · Cited by 51 · see citing works
Sarecycline interferes with tRNA accommodation and tethers mRNA to the 70S ribosome
Batool, Z., Lomakin, I. B., Polikanov, Y. S., & Bunick, C. G. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2008671117 · Cited by 50 · see citing works
Dual-function Spot 42 RNA encodes a 15–amino acid protein that regulates the CRP transcription factor
Aoyama, J. J., Raina, M., Zhong, A., & Storz, G. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2119866119 · Cited by 50 · see citing works
Diverse CRISPR-Cas Complexes Require Independent Translation of Small and Large Subunits from a Single Gene
McBride, T. M., Schwartz, E. A., Kumar, A., Taylor, D. W., Fineran, P. C., & Fagerlund, R. D. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.11.003 · Cited by 50 · see citing works
ABC‐F translation factors: from antibiotic resistance to immune response
Fostier, C. R., Monlezun, L., Ousalem, F., Singh, S., Hunt, J. F., & Boël, G. (2020) · FEBS Letters · doi:10.1002/1873-3468.13984 · Cited by 46 · see citing works
Activation of the Mitochondrial Unfolded Protein Response: A New Therapeutic Target?
Suarez-Rivero, J. M., Pastor‐Maldonado, C. J., Povea-Cabello, S., Álvarez-Córdoba, M., Villalón-García, I., Talaverón-Rey, M., Suárez-Carrillo, A., Munuera-Cabeza, M., Reche-López, D., Cilleros-Holgado, P., et al. (2022) · Biomedicines · doi:10.3390/biomedicines10071611 · Cited by 47 · see citing works
Genome-wide effects of the antimicrobial peptide apidaecin on translation termination in bacteria
Mangano, K., Florin, T., Shao, X., Klepacki, D., Chelysheva, I., Ignatova, Z., Gao, Y., Mankin, A. S., & Vázquez‐Laslop, N. (2020) · eLife · doi:10.7554/elife.62655 · Cited by 38 · see citing works
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Identification of Novel Translated Small Open Reading Frames in Escherichia coli Using Complementary Ribosome Profiling Approaches
Stringer, A. M., Smith, C., Mangano, K., & Wade, J. T. (2021) · Journal of Bacteriology · doi:10.1128/jb.00352-21 · Cited by 42 · see citing works
Towards the characterization of the hidden world of small proteins in Staphylococcus aureus, a proteogenomics approach
Fuchs, S., Kucklick, M., Lehmann, E., Beckmann, A., Wilkens, M., Kolte, B. S., Mustafayeva, A., Ludwig, T., Diwo, M., Wissing, J. B., et al. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009585 · Cited by 41 · see citing works
The hidden bacterial microproteome
Fesenko, I. A., Sahakyan, H., Dhyani, R., Shabalina, S. A., Storz, G., & Koonin, E. V. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.01.025 · Cited by 41 · see citing works
Large Roles of Small Proteins
Burton, A. T., Zeinert, R., & Storz, G. (2024) · Annual Review of Microbiology · doi:10.1146/annurev-micro-112723-083001 · Cited by 37 · see citing works
smORFer: a modular algorithm to detect small ORFs in prokaryotes
Bartholomäus, A., Kolte, B., Mustafayeva, A., Goebel, I., Fuchs, S., Benndorf, D., Engelmann, S., & Ignatova, Z. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab477 · Cited by 36 · see citing works
Are Antisense Proteins in Prokaryotes Functional?
Ardern, Z., Neuhaus, K., & Scherer, S. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00187 · Cited by 35 · see citing works
Expression of Bacillus subtilis ABCF antibiotic resistance factor VmlR is regulated by RNA polymerase pausing, transcription attenuation, translation attenuation and (p)ppGpp
Takada, H., Mandell, Z. F., Yakhnin, H., Glazyrina, A., Chiba, S., Kurata, T., Wu, K. J. Y., Tresco, B. I. C., Myers, A. G., Atkinson, G. C., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac497 · Cited by 35 · see citing works
Prolonging genetic circuit stability through adaptive evolution of overlapping genes
Chlebek, J. L., Leonard, S. P., Kang-Yun, C. S., Yung, M. C., Ricci, D. P., Jiao, Y., & Park, D. M. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad484 · Cited by 33 · see citing works
Small proteins in bacteria – Big challenges in prediction and identification
Fuchs, S., & Engelmann, S. (2023) · Proteomics · doi:10.1002/pmic.202200421 · Cited by 29 · see citing works
Hidden in plain sight: challenges in proteomics detection of small ORF-encoded polypeptides
Fijałkowski, I., Willems, P. J., Jonckheere, V., Simoens, L., & Damme, P. V. (2022) · microLife · doi:10.1093/femsml/uqac005 · Cited by 33 · see citing works
Engineered multiple translation initiation sites: a novel tool to enhance protein production in Bacillus licheniformis and other industrially relevant bacteria
Zhang, M., Song, J., Xiao, J., Jin, J., Nomura, C. T., Chen, S., & Wang, Q. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1039 · Cited by 32 · see citing works
The context of the ribosome binding site in mRNAs defines specificity of action of kasugamycin, an inhibitor of translation initiation
Zhang, Y., Aleksashin, N. A., Klepacki, D., Anderson, C. M., Vázquez‐Laslop, N., Gross, C. A., & Mankin, A. S. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2118553119 · Cited by 30 · see citing works
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Regulation of the macrolide resistance ABC-F translation factor MsrD
Fostier, C. R., Ousalem, F., Leroy, E., Ngo, S., Soufari, H., Innis, C. A., Hashem, Y., & Boël, G. (2023) · Nature Communications · doi:10.1038/s41467-023-39553-8 · Cited by 30 · see citing works
Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea
Kubatova, N., Pyper, D. J., Jonker, H. R. A., Saxena, K., Remmel, L., Richter, C. P., Brantl, S., Evguenieva‐Hackenberg, E., Hess, W. R., Klug, G., et al. (2019) · ChemBioChem · doi:10.1002/cbic.201900677 · Cited by 29 · see citing works
Ribosome Protection Proteins—“New” Players in the Global Arms Race with Antibiotic-Resistant Pathogens
Ero, R., Yan, X., & Gao, Y. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22105356 · Cited by 29 · see citing works
High complexity of Glutamine synthetase regulation in Methanosarcina mazei : Small protein 26 interacts and enhances glutamine synthetase activity
Gutt, M., Jordan, B., Weidenbach, K., Gudzuhn, M., Kießling, C., Cassidy, L., Helbig, A. O., Tholey, A., Pyper, D. J., Kubatova, N., et al. (2021) · FEBS Journal · doi:10.1111/febs.15799 · Cited by 28 · see citing works
Discovery of Unannotated Small Open Reading Frames in Streptococcus pneumoniae D39 Involved in Quorum Sensing and Virulence Using Ribosome Profiling
Laczkovich, I., Mangano, K., Shao, X., Hockenberry, A. J., Gao, Y., Mankin, A. S., Vázquez‐Laslop, N., & Federle, M. J. (2022) · mBio · doi:10.1128/mbio.01247-22 · Cited by 27 · see citing works
Self-citation
Deciphering the molecular and cellular atlas of immune cells in septic patients with different bacterial infections
Sun, P., Cui, M., Jing, J., Kong, F., Wang, S., Tang, L., Leng, J., & Chen, K. (2023) · Journal of Translational Medicine · doi:10.1186/s12967-023-04631-4 · Cited by 28 · see citing works
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria
Gelhausen, R., Müller, T., Svensson, S. L., Alkhnbashi, O. S., Sharma, C. M., Eggenhofer, F., & Backofen, R. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab549 · Cited by 22 · see citing works
Unraveling the small proteome of the plant symbiont Sinorhizobium meliloti by ribosome profiling and proteogenomics
Hadjeras, L., Heiniger, B., Maaß, S., Scheuer, R., Gelhausen, R., Azarderakhsh, S., Barth-Weber, S., Backofen, R., Becher, D., Ahrens, C. H., et al. (2023) · microLife · doi:10.1093/femsml/uqad012 · Cited by 26 · see citing works
Extensive diversity in RNA termination and regulation revealed by transcriptome mapping for the Lyme pathogen Borrelia burgdorferi
Petroni, E., Esnault, C., Tetreault, D. D., Dale, R., Storz, G., & Adams, P. P. (2023) · Nature Communications · doi:10.1038/s41467-023-39576-1 · Cited by 26 · see citing works
Polycysteine‐encoding leaderless short ORFs function as cysteine‐responsive attenuators of operonic gene expression in mycobacteria
Canestrari, J. G., Lasek‐Nesselquist, E., Upadhyay, A., Rofaeil, M., Champion, M. M., Wade, J. T., Derbyshire, K. M., & Gray, T. A. (2020) · Molecular Microbiology · doi:10.1111/mmi.14498 · Cited by 25 · see citing works
OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes
Nelson, C. W., Ardern, Z., & Wei, X. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa087 · Cited by 25 · see citing works
Small Protein Enrichment Improves Proteomics Detection of sORF Encoded Polypeptides
Fijałkowski, I., Peeters, M. K. R., & Damme, P. V. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.713400 · Cited by 23 · see citing works
Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data
Glaub, A., Huptas, C., Neuhaus, K., & Ardern, Z. (2020) · Journal of Biological Chemistry · doi:10.1074/jbc.ra119.012161 · Cited by 23 · see citing works
Improvement of putrescine production through the arginine decarboxylase pathway in Escherichia coli K-12
Thongbhubate, K., Irie, K., Sakai, Y., Itoh, A., & Suzuki, H. (2021) · AMB Express · doi:10.1186/s13568-021-01330-5 · Cited by 23 · see citing works
Expanding the Vocabulary of Peptide Signals in Streptococcus mutans
Kaspar, J. R., & Walker, A. R. (2019) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2019.00194 · Cited by 23 · see citing works
RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization
Tierney, J. A. S., Świrski, M. I., Tjeldnes, H., Kiran, A. M., Carancini, G., Kiniry, S. J., Michel, A. M., Kufel, J., Valen, E., & Baranov, P. V. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1020 · Cited by 22 · see citing works
Self-citation
Protocol for Ribosome Profiling in Bacteria
Mohammad, F., & Buskirk, A. (2019) · BIO-PROTOCOL · doi:10.21769/bioprotoc.3468 · Cited by 22 · see citing works
Spotlight on alternative frame coding: Two long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection
Kreitmeier, M., Ardern, Z., Abele, M., Ludwig, C., Scherer, S., & Neuhaus, K. (2022) · iScience · doi:10.1016/j.isci.2022.103844 · Cited by 22 · see citing works
Ribosome profiling reveals the fine-tuned response of Escherichia coli to mild and severe acid stress
Schumacher, K., Gelhausen, R., Kion-Crosby, W., Barquist, L., Backofen, R., & Jung, K. (2023) · mSystems · doi:10.1128/msystems.01037-23 · Cited by 22 · see citing works
Lost and Found: Re-searching and Re-scoring Proteomics Data Aids Genome Annotation and Improves Proteome Coverage
Willems, P. J., Fijałkowski, I., & Damme, P. V. (2020) · mSystems · doi:10.1128/msystems.00833-20 · Cited by 22 · see citing works
Regulation outside the box: New mechanisms for small RNAs
Fröhlich, K. S., & Papenfort, K. (2020) · Molecular Microbiology · doi:10.1111/mmi.14523 · Cited by 21 · see citing works
Transcriptional and translational landscape fine-tune genome annotation and explores translation control in cotton
Qanmber, G., You, Q., Yang, Z., Fan, L., Zhang, Z., Chai, M., Gao, B., Li, F., & Yang, Z. (2023) · Journal of Advanced Research · doi:10.1016/j.jare.2023.05.004 · Cited by 21 · see citing works
Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuni
Froschauer, K., Svensson, S. L., Gelhausen, R., Fiore, E., Kible, P., Klaude, A., Kucklick, M., Fuchs, S., Eggenhofer, F., Yang, C., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-58329-w · Cited by 19 · see citing works
Tetracyclines activate mitoribosome quality control and reduce ER stress to promote cell survival
Ronayne, C. T., Jackson, T. D., Bennett, C. F., Perry, E. A., Kantorovic, N., & Puigserver, P. (2023) · EMBO Reports · doi:10.15252/embr.202357228 · Cited by 18 · see citing works
Exposing the small protein load of bacterial life
Simoens, L., Fijałkowski, I., & Damme, P. V. (2023) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuad063 · Cited by 17 · see citing works
A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding Gene pop Is Encoded Antisense to ompA in Escherichia coli O157:H7 (EHEC)
Zehentner, B., Ardern, Z., Kreitmeier, M., Scherer, S., & Neuhaus, K. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.00377 · Cited by 18 · see citing works
Emerging Mechanisms of Human Mitochondrial Translation Regulation
Brischigliaro, M., Ahn, A., Hong, S.-W., Fontanesi, F., & Barrientos, A. (2025) · TIBS -Trends in Biochemical Sciences. Regular ed · doi:10.1016/j.tibs.2025.03.007 · Cited by 19 · see citing works
Non-model bacteria as platforms for endogenous gene expression in synthetic biology
Poppeliers, J., Boon, M., Mey, M. D., Masschelein, J., & Lavigne, R. (2025) · Nature Reviews Bioengineering · doi:10.1038/s44222-025-00354-x · Cited by 18 · see citing works
Mechanism of translation inhibition by type II GNAT toxin AtaT2
Ovchinnikov, S. V., Bikmetov, D., Livenskyi, A., Serebryakova, M. V., Wilcox, B., Mangano, K., Shiriaev, D. I., Osterman, I. А., Владимирович, С. П., Borukhov, S. I., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa551 · Cited by 17 · see citing works
Self-citation
HRIBO: high-throughput analysis of bacterial ribosome profiling data
Gelhausen, R., Svensson, S. L., Froschauer, K., Heyl, F., Hadjeras, L., Sharma, C. M., Eggenhofer, F., & Backofen, R. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btaa959 · Cited by 17 · see citing works
Synthetic genomes unveil the effects of synonymous recodingPreprint
Nyerges, Á., Chiappino-Pepe, A., Budnik, B., Baas-Thomas, M. S., Flynn, R., Yan, S., Ostrov, N., Liu, M., Wang, M., Zheng, Q., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.16.599206 · Cited by 17 · see citing works
Phycobilisome Breakdown Effector NblD Is Required To Maintain Cellular Amino Acid Composition during Nitrogen Starvation
Krauspe, V., Timm, S., Hagemann, M., & Hess, W. R. (2021) · Journal of Bacteriology · doi:10.1128/jb.00158-21 · Cited by 16 · see citing works
Context-based sensing of orthosomycin antibiotics by the translating ribosome
Mangano, K., Marks, J., Klepacki, D., Saha, C. K., Atkinson, G. C., Vázquez‐Laslop, N., & Mankin, A. S. (2022) · Nature Chemical Biology · doi:10.1038/s41589-022-01138-9 · Cited by 16 · see citing works
Self-citation
AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions
Korandla, D. R., Wozniak, J. M., Campeau, A., Gonzalez, D. J., & Wright, E. S. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz714 · Cited by 16 · see citing works
Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells
Shirokikh, N. E. (2021) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2021.2006599 · Cited by 14 · see citing works
The complexity and dynamics of in organello translation assessed by high-resolution mitochondrial ribosome profilingPreprint
Wakigawa, T., Mito, M., Yamashiro, H., Tomuro, K., Tani, H., Tomizawa, K., Chujo, T., Nagao, A., Suzuki, T., Wei, F., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.07.19.549812 · Cited by 16 · see citing works
Bacterial riboproteogenomics: the era of N-terminal proteoform existence revealed.
Fijałkowska, D., Fijalkowski, I., Willems, P., & Damme, P. V. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa013 · Cited by 15 · see citing works
Simultaneous ribosome profiling of hundreds of microbes from the human microbiome
Fremin, B. J., Nicolaou, C., & Bhatt, A. S. (2021) · Nature Protocols · doi:10.1038/s41596-021-00592-4 · Cited by 15 · see citing works
Nucleotide-induced hyper-oligomerization inactivates transcription termination factor ρ
Wang, B., Said, N., Hilal, T., Finazzo, M., Wahl, M. C., & Artsimovitch, I. (2025) · Nature Communications · doi:10.1038/s41467-025-56824-8 · Cited by 14 · see citing works
Global profiling of the RNA and protein complexes of Escherichia coli by size exclusion chromatography followed by RNA sequencing and mass spectrometry (SEC-seq)
Chihara, K., Gerovac, M., Hör, J., & Vogel, J. (2022) · RNA · doi:10.1261/rna.079439.122 · Cited by 14 · see citing works
Monitoring the complexity and dynamics of mitochondrial translation
Wakigawa, T., Mito, M., Ando, Y., Yamashiro, H., Tomuro, K., Tani, H., Tomizawa, K., Chujo, T., Nagao, A., Suzuki, T., et al. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.10.022 · Cited by 13 · see citing works
Agmatine production by Escherichia coli cells expressing SpeA on the extracellular surface
Suzuki, H., Thongbhubate, K., Muraoka, M., & Sasabu, A. (2022) · Enzyme and Microbial Technology · doi:10.1016/j.enzmictec.2022.110139 · Cited by 13 · see citing works
A natural depsipeptide antibiotic binds the E-site of the bacterial ribosome
Kaur, M., Travin, D. Y., Berger, M. J., Jangra, M., Morici, M., Safdari, H. A., Klepacki, D., Wang, W., Cook, M. A., Chou, S., et al. (2026) · Nature · doi:10.1038/s41586-026-10589-2 · Cited by 12 · see citing works
Self-citation
Paenilamicins are context-specific translocation inhibitors of protein synthesis
Koller, T. O., Berger, M. J., Morici, M., Paternoga, H., Bulatov, T. M., Stasi, A. D., Dang, T., Mainz, A., Raulf, K., Crowe‐McAuliffe, C., et al. (2024) · Nature Chemical Biology · doi:10.1038/s41589-024-01752-9 · Cited by 13 · see citing works
Self-citation
Insights into the molecular mechanism of translation inhibition by the ribosome-targeting antibiotic thermorubin
Paranjpe, M. N., Marina, V. I., Grachev, A. A., Maviza, T. P., Tolicheva, O. A., Paleskava, A., Osterman, I. А., Владимирович, С. П., Konevega, A. L., Polikanov, Y. S., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1189 · Cited by 12 · see citing works
Chemical labeling and proteomics for characterization of unannotated small and alternative open reading frame-encoded polypeptides
Chen, Y., Cao, X., Loh, K. H., & Slavoff, S. A. (2023) · Biochemical Society Transactions · doi:10.1042/bst20221074 · Cited by 12 · see citing works
Toxic antiphage defense proteins inhibited by intragenic antitoxin proteins
Zhong, A., Jiang, X., Hickman, A. B., Klier, K., Teodoro, G. I. C., Dyda, F., Laub, M. T., & Storz, G. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2307382120 · Cited by 12 · see citing works
INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors
Hör, J., Jung, J., Ðurica-Mitić, S., Barquist, L., & Vogel, J. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac838 · Cited by 11 · see citing works
ProsmORF-pred: a machine learning-based method for the identification of small ORFs in prokaryotic genomes
Khanduja, A., Kumar, M., & Mohanty, D. (2023) · Briefings in Bioinformatics · doi:10.1093/bib/bbad101 · Cited by 11 · see citing works
Discovery of Novel Pleuromutilin Derivatives as Potent Antibacterial Agents for the Treatment of MRSA Infection
Fang, H.-Q., Zeng, J., Wang, S., Xiao, W., Chen, F., Li, B., Liu, J., Jin, Z., Liu, Y., & Tang, Y. (2022) · Molecules · doi:10.3390/molecules27030931 · Cited by 11 · see citing works
Evidence for Numerous Embedded Antisense Overlapping Genes in Diverse E. coli StrainsPreprint
Zehentner, B., Ardern, Z., Kreitmeier, M., Scherer, S., & Neuhaus, K. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.11.18.388249 · Cited by 10 · see citing works
Readthrough events in plants reveal plasticity of stop codons
Zhang, Y., Li, H., Shen, Y., Wang, S., Tian, L., Yin, H., Shi, J., Xing, A., Zhang, J., Ali, U., et al. (2024) · Cell Reports · doi:10.1016/j.celrep.2024.113723 · Cited by 9 · see citing works
How Small Proteins Adjust the Metabolism of Cyanobacteria Under Stress
Kraus, A., & Hess, W. R. (2024) · BioEssays · doi:10.1002/bies.202400245 · Cited by 9 · see citing works
Identification of Translation Start Sites in Bacterial Genomes
Meydan, S., Klepacki, D., Mankin, A. S., & Vázquez‐Laslop, N. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1150-0_2 · Cited by 9 · see citing works
Self-citation
Structural insights into context-specific inhibition of bacterial translation by macrolides
Syroegin, E. A., Aleksandrova, E. V., Kruglov, A. A., Paranjpe, M. N., Svetlov, M. S., & Polikanov, Y. S. (2025) · Nature Communications · doi:10.1038/s41467-025-64692-5 · Cited by 8 · see citing works
Macrolide, lincosamide, glycopeptide, and other antibacterial antibiotics
Qian, Y., Mobashery, S., & Fisher, J. F. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-90575-6.00008-9 · Cited by 8 · see citing works
Berberine analog of chloramphenicol exhibits a distinct mode of action and unveils ribosome plasticity
Batool, Z., Pavlova, J. A., Paranjpe, M. N., Tereshchenkov, A. G., Lukianov, D. A., Osterman, I. А., Bogdanov, A. A., Sumbatyan, N. V., & Polikanov, Y. S. (2024) · Structure · doi:10.1016/j.str.2024.06.013 · Cited by 8 · see citing works
Frameshift mutations in the mmpR5 gene can have a bedaquiline-susceptible phenotype by retaining a protein structure and function similar to wild-type Mycobacterium tuberculosis
Snobre, J., Meehan, C. J., Mulders, W., Rigouts, L., Buyl, R., de Jong, B. C., Rie, A. V., & Tzfadia, O. (2024) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.00854-24 · Cited by 8 · see citing works
Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications in Mycolicibacterium smegmatis MC2 155 by proteogenomic analysis
Jiang, S., Shi, J., Li, Y., Zhang, Z., Chang, L., Wang, G., Wu, W., Yu, L., Dai, E., Zhang, L., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1015140 · Cited by 8 · see citing works

Identification of Translation Start Sites in Bacterial Genomes
Meydan, S., Klepacki, D., Mankin, A. S., & Vázquez‐Laslop, N. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1150-0_2 · Cited by 9 · see citing works
Self-citation
Genes within Genes in Bacterial Genomes
Meydan, S., Vázquez‐Laslop, N., & Mankin, A. S. (2018) · Microbiology Spectrum · doi:10.1128/microbiolspec.rwr-0020-2018 · Cited by 39 · see citing works
Self-citation
Genome-Wide Profiling of Alternative Translation Initiation Sites
Gao, X., Wan, J., & Qian, S. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3067-8_19 · Cited by 7 · see citing works
Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling
Nakahigashi, K., Takai, Y., Kimura, M., Abe, N., Nakayashiki, T., Shiwa, Y., Yoshikawa, H., Wanner, B. L., Ishihama, Y., & Mori, H. (2016) · DNA Research · doi:10.1093/dnares/dsw008 · Cited by 74 · see citing works
Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression
Fijałkowski, I., Snauwaert, V., & Damme, P. V. (2024) · mBio · doi:10.1128/mbio.00333-24 · Cited by 6 · see citing works

Authors: Meydan, S., Marks, J., Klepacki, D., Sharma, V., Baranov, P. V., Firth, A. E., Margus, T., Kefi, A., Vázquez-Laslop, N., & Mankin, A. S.
Affiliations: University of Illinois Chicago (US)
German Center for Diabetes Research (DE)
University College Cork (IE)
University of Cambridge (GB)
Corresponding author: Mankin, Alexander S.
ORCID: Meydan, Sezen
Marks, James
Sharma, Virag
Baranov, Pavel V.
Firth, Andrew E.
Kefi, Amira
Mankin, Alexander S.
Venue: Molecular Cell
Publisher: Elsevier BV
Published: 2019-05
Volume: 74
Issue: 3
Pages: 481-493.e6
ISSN: 1097-2765 (ISSN-L)
DOI: 10.1016/j.molcel.2019.02.017
PMC: PMC7115971
OpenAlex: W2908521178
Cited by: 184
References: 123
Citations by year: 2026: 20 · 2025: 22 · 2024: 26 · 2023: 28 · 2022: 22 · 2021: 34 · 2020: 23 · 2019: 9
FWCI: 7.28
Type: journal article
Language: en
Open access: bronze
doi.org
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
www.elsevier.com/open-access/userlicense/1.0/ (vor, 367 d)
Locations: Molecular Cell (publishedVersion)
bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
PubMed (publishedVersion)
PubMed Central (acceptedVersion)
Arrow@dit (Dublin Institute of Technology) (submittedVersion, cc-by-nc-nd)
Cork Open Research Archive (University College Cork, Ireland) (submittedVersion, cc-by-nc-nd)
Site cant be reached (submittedVersion, other-oa)
PuSH - Publication Server of Helmholtz Zentrum München (submittedVersion)
Funders: National Science Foundation (MCB 1615851)
SFI-HRB-Wellcome Trust Biomedical Research Partnership (210692/Z/18/Z)
Wellcome Trust (106207)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: retapamulin, ribosome profiling, alternative translation initiation sites, Escherichia coli, gene expression regulation
MeSH terms: Diterpenes, Escherichia coli, Peptide Chain Initiation, Translational, Ribosomes, RNA, Messenger, Gene Expression Regulation, Bacterial, Genome, Bacterial, Codon, Initiator, Bridged Bicyclo Compounds, Heterocyclic, Proteome, Proteomics

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Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome

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