Escherichia coli Small Proteome

The complete genome sequence of Escherichia coli K-12.

Blattner, F., Plunkett, G., Bloch, C., Perna, N., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C., Mayhew, G., et al. (1997) · Science · doi:10.1126/science.277.5331.1453 · Cited by 7,996 · see citing works

NCBI prokaryotic genome annotation pipeline

Tatusova, T. A., DiCuccio, M. N., Badretdin, A. J., Chetvernin, V., Nawrocki, E. P., Zaslavsky, L. Y., Lomsadze, A., Pruitt, K. D., Borodovsky, M. Y., & Ostell, J. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw569 · Cited by 7,065 · see citing works

Sequence logos: a new way to display consensus sequences

Schneider, T. D., & Stephens, R. M. (1990) · Nucleic Acids Research · doi:10.1093/nar/18.20.6097 · Cited by 3,396 · see citing works

Ciprofloxacin Causes Persister Formation by Inducing the TisB toxin in Escherichia coli

Dörr, T., Vulić, M., & Lewis, K. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000317 · Cited by 781 · see citing works

EcoCyc: a comprehensive database resource for Escherichia coli

Keseler, I. M. (2004) · Nucleic Acids Research · doi:10.1093/nar/gki108 · Cited by 737 · see citing works

IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions

Mann, M., Wright, P. R., & Backofen, R. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx279 · Cited by 725 · see citing works

Structure of the AcrAB–TolC multidrug efflux pump

Du, D., Wang, Z., James, N. R., Voss, J. E., Klimont, E., Ohene‐Agyei, T., Venter, H., Chiu, W., & Luisi, B. F. (2014) · Nature · doi:10.1038/nature13205 · Cited by 664 · see citing works

Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides

Gevaert, K., Goethals, M., Martens, L., Damme, J. V., Staes, A., Thomas, G. R., & Vandekerckhove, J. S. (2003) · Nature Biotechnology · doi:10.1038/nbt810 · Cited by 594 · see citing works

Phage as agents of lateral gene transfer

Canchaya, C. A., Fournous, G., Chibani-Chennoufi, S., Dillmann, M.-L., & Brüssow, H. (2003) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(03)00086-9 · Cited by 503 · see citing works

EcoCyc: a comprehensive database of Escherichia coli biology

Keseler, I. M., Collado‐Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama‐Castro, S., Muñiz-Rascado, L., Bonavides-Martínez, C., Paley, S., Krummenacker, M., Altman, T., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq1143 · Cited by 498 · 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

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 dual function for a bacterial small RNA: SgrS performs base pairing-dependent regulation and encodes a functional polypeptide

Wadler, C. S., & Vanderpool, C. K. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0708102104 · Cited by 313 · see citing works

Small Toxic Proteins and the Antisense RNAs That Repress Them

Fozo, E. M., Hemm, M. R., & Storz, G. (2008) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00025-08 · Cited by 263 · see citing works

Toxins Hha and CspD and small RNA regulator Hfq are involved in persister cell formation through MqsR in Escherichia coli

Kim, Y., & Wood, T. K. (2009) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2009.11.033 · Cited by 243 · see citing works

Small Open Reading Frames: Beautiful Needles in the HaystackPreprint

Basrai, M. A., Hieter, P., & Boeke, J. D. (1997) · Genome Research · doi:10.1101/gr.7.8.768 · Cited by 240 · see citing works

Feedback Inhibition in the PhoQ/PhoP Signaling System by a Membrane Peptide

Lippa, A. M., & Goulian, M. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000788 · Cited by 240 · see citing works

Detection of 5'- and 3'-UTR-derived small RNAs and cis-encoded antisense RNAs in Escherichia coli

Kawano, M. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki256 · Cited by 237 · 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

Conserved small protein associates with the multidrug efflux pump AcrB and differentially affects antibiotic resistance

Hobbs, E. C., Yin, X., Paul, B. J., Astarita, J. L., & Storz, G. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1210093109 · Cited by 220 · see citing works

ATTENUATION IN AMINO ACID BIOSYNTHETIC OPERONS

Kolter, R., & Yanofsky, C. (1982) · Annual Review of Genetics · doi:10.1146/annurev.ge.16.120182.000553 · Cited by 220 · see citing works

The purification and characterization of the cytochrome d terminal oxidase complex of the Escherichia coli aerobic respiratory chain.

Miller, M. J., & Gennis, R. B. (1983) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)44645-x · Cited by 205 · see citing works

Control of Fur synthesis by the non‐coding RNA RyhB and iron‐responsive decoding

Večerek, B., Moll, I., & Bläsi, U. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601553 · Cited by 188 · 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

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

Fozo, E. M., Kawano, M., Fontaine, F., Kaya, Y., Mendieta, K. S., Jones, K. L., Ocampo, A., Rudd, K. E., & Storz, G. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06394.x · Cited by 174 · see citing works

Multiple hok genes on the chromosome of Escherichia coli

Pedersen, K. B., & Gerdes, K. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01431.x · Cited by 172 · 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

Recognizing the pseudogenes in bacterial genomes

Lerat, E. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki631 · Cited by 164 · see citing works

Structure of a bd oxidase indicates similar mechanisms for membrane-integrated oxygen reductases

Safarian, S., Rajendran, C., Müller, H., Preu, J., Langer, J. D., Ovchinnikov, S., Hirose, T., Kusumoto, T., Sakamoto, J., & Michel, H. (2016) · Science · doi:10.1126/science.aaf2477 · Cited by 163 · see citing works

The Escherichia coli MntR Miniregulon Includes Genes Encoding a Small Protein and an Efflux Pump Required for Manganese Homeostasis

Waters, L. S., Sandoval, M., & Storz, G. (2011) · Journal of Bacteriology · doi:10.1128/jb.05872-11 · Cited by 157 · see citing works

The EcoCyc Database

Karp, P. D., Weaver, D. S., Paley, S., Fulcher, C. A., Kubo, A., Kothari, A., Krummenacker, M., Subhraveti, P., Weerasinghe, D., Gama‐Castro, S., et al. (2014) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0009-2013 · Cited by 150 · see citing works

The Escherichia coli Small Protein MntS and Exporter MntP Optimize the Intracellular Concentration of Manganese

Martin, J. E., Waters, L. S., Storz, G., & Imlay, J. A. (2015) · PLoS Genetics · doi:10.1371/journal.pgen.1004977 · Cited by 129 · see citing works

Unraveling the hidden universe of small proteins in bacterial genomes

Miravet‐Verde, S., Ferrar, T. S., Espadas, G., Mazzolini, R., Gharrab, A., Sabidó, E., Serrano, L. G., & Lluch‐Senar, M. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188290 · Cited by 127 · see citing works

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases

Safarian, S., Hahn, A. S., Mills, D. J., Radloff, M., Eisinger, M., Nikolaev, A., Meier‐Credo, J., Melin, F., Miyoshi, H., Gennis, R. B., et al. (2019) · Science · doi:10.1126/science.aay0967 · Cited by 127 · see citing works

The KdpF Subunit Is Part of the K+-translocating Kdp Complex of Escherichia coli and Is Responsible for Stabilization of the Complex in Vitro

Gaßel, M., Möllenkamp, T., Puppe, W., & Altendorf, K. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.53.37901 · Cited by 118 · see citing works

The nucleotide sequence of the dnaA gene promoter and of the adjacent rpmH gene, coding for the ribosomal protein L34, of Escherichia coli.

Hansen, F. G., Hansen, E. B., & Atlung, T. (1982) · The EMBO Journal · doi:10.1002/j.1460-2075.1982.tb01294.x · Cited by 116 · see citing works

Missing genes in the annotation of prokaryotic genomes

Warren, A. S., Archuleta, J., Feng, W.-C., & Setúbal, J. C. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-131 · Cited by 109 · see citing works

Small RNAs and Small Proteins Involved in Resistance to Cell Envelope Stress and Acid Shock in Escherichia coli : Analysis of a Bar-Coded Mutant Collection

Hobbs, E. C., Astarita, J. L., & Storz, G. (2009) · Journal of Bacteriology · doi:10.1128/jb.00873-09 · Cited by 108 · see citing works

The EcoCyc Database

Karp, P. D., Ong, W. K., Paley, S., Billington, R., Caspi, R., Fulcher, C. A., Kothari, A., Krummenacker, M., Latendresse, M., Midford, P. E., et al. (2018) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0006-2018 · Cited by 108 · see citing works

The Escherichia coli CydX Protein Is a Member of the CydAB Cytochrome bd Oxidase Complex and Is Required for Cytochrome bd Oxidase Activity

VanOrsdel, C. E., Bhatt, S., Allen, R. J., Brenner, E. P., Hobson, J. J., Jamil, A., Haynes, B. M., Genson, A. M., & Hemm, M. R. (2013) · Journal of Bacteriology · doi:10.1128/jb.00324-13 · Cited by 107 · see citing works

Autogenous regulation of the gene for transcription termination factor rho in Escherichia coli: localization and function of its attenuators

Matsumoto, Y., Shigesada, K., Hirano, M., & Imai, M. (1986) · Journal of Bacteriology · doi:10.1128/jb.166.3.945-958.1986 · Cited by 101 · see citing works

The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death

Bishop, R. E., Leskiw, B. K., Hodges, R. S., Kay, C. M., & Weiner, J. H. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.1894 · Cited by 99 · see citing works

The Persistence-Inducing Toxin HokB Forms Dynamic Pores That Cause ATP Leakage

Wilmaerts, D., Bayoumi, M., Dewachter, L., Knapen, W., Mika, J. T., Hofkens, J., Dedecker, P., Maglia, G., Verstraeten, N., & Michiels, J. J. (2018) · mBio · doi:10.1128/mbio.00744-18 · Cited by 98 · see citing works

Analysis of Escherichia coli Ribosomal Proteins by an Improved Two Dimensional Gel Electrophoresis. I. Detection of Four New Proteins

Wada, A. (1986) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a121866 · Cited by 93 · see citing works

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

The Small Protein SgrT Controls Transport Activity of the Glucose-Specific Phosphotransferase System

Lloyd, C. R., Park, S.-J., Fei, J., & Vanderpool, C. K. (2017) · Journal of Bacteriology · doi:10.1128/jb.00869-16 · Cited by 89 · see citing works

Escherichia coli Ribosome-Associated Protein SRA, Whose Copy Number Increases during Stationary Phase

Izutsu, K., Wada, C., Komine, Y., Sako, T., Ueguchi, C., Nakura, S., & Wada, A. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.9.2765-2773.2001 · Cited by 88 · see citing works

A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation

Ivanov, I. P., Atkins, J. F., & Michael, A. J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1037 · Cited by 87 · see citing works

Subunit CydX of Escherichia coli cytochrome bd ubiquinol oxidase is essential for assembly and stability of the di‐heme active site

Hoeser, J., Hong, S., Gehmann, G., Gennis, R. B., & Friedrich, T. (2014) · FEBS Letters · doi:10.1016/j.febslet.2014.03.036 · Cited by 86 · see citing works

Homologous bd oxidases share the same architecture but differ in mechanism

Thesseling, A., Rasmussen, T., Burschel, S., Wohlwend, D., Kägi, J. P., Müller, R., Böttcher, B., & Friedrich, T. (2019) · Nature Communications · doi:10.1038/s41467-019-13122-4 · Cited by 86 · see citing works

Hydrophobic peptides: novel regulators within bacterial membrane

Alix, E., & Blanc‐Potard, A. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06626.x · Cited by 85 · see citing works

Intrinsic Ribosome Destabilization Underlies Translation and Provides an Organism with a Strategy of Environmental Sensing

Chadani, Y., Niwa, T., Izumi, T., Sugata, N., Nagao, A., Suzuki, T., Chiba, S., Ito, K., & Taguchi, H. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.10.020 · Cited by 85 · see citing works

A fail‐safe system for the ribosome under zinc‐limiting conditions in Bacillus subtilis

Natori, Y., Nanamiya, H., Akanuma, G., Kosono, S., Kudo, T., Ochi, K., & Kawamura, F. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05513.x · Cited by 83 · see citing works

Membrane Localization of Small Proteins in Escherichia coli

Fontaine, F., Fuchs, R. T., & Storz, G. (2011) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.245696 · Cited by 80 · see citing works

Structural features of transmembrane helices

Hildebrand, P. W., Preißner, R., & Frömmel, C. (2004) · FEBS Letters · doi:10.1016/s0014-5793(04)00061-4 · Cited by 80 · see citing works

Increasing intracellular magnesium levels with the 31-amino acid MgtS protein

Wang, H., Yin, X., Orr, M. W., Dambach, M., Curtis, R., & Storz, G. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1703415114 · Cited by 80 · see citing works

Distinguishing the ORFs from the ELFs: short bacterial genes and the annotation of genomes

Ochman, H. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02668-9 · Cited by 78 · see citing works

Crystal structure of the potassium-importing KdpFABC membrane complex

Huang, C.-S., Pedersen, B. P., & Stokes, D. L. (2017) · Nature · doi:10.1038/nature22970 · Cited by 77 · see citing works

HokB Monomerization and Membrane Repolarization Control Persister Awakening

Wilmaerts, D., Dewachter, L., Loose, P.-J. D., Bollen, C., Verstraeten, N., & Michiels, J. J. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.06.015 · Cited by 77 · 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

Primary Structures of and Genes for New Ribosomal Proteins A and B in Escherichia coli

Wada, A., & SAKO, T. (1987) · The Journal of Biochemistry · doi:10.1093/jb/101.3.817 · Cited by 73 · see citing works

Ornithine capture by a translating ribosome controls bacterial polyamine synthesis

del Valle, A. H., Seip, B., Cervera-Marzal, I., Sacheau, G., Seefeldt, A. C., & Innis, C. A. (2020) · Nature Microbiology · doi:10.1038/s41564-020-0669-1 · Cited by 68 · see citing works

A review of COFRADIC techniques targeting protein N-terminal acetylation

Damme, P. V., Damme, J. V., Demol, H., Staes, A., Vandekerckhove, J. S., & Gevaert, K. (2009) · BMC Proceedings · doi:10.1186/1753-6561-3-s6-s6 · Cited by 66 · see citing works

The small membrane protein MgrB regulates PhoQ bifunctionality to control PhoP target gene expression dynamics

Salazar, M. E., Podgornaia, A., & Laub, M. T. (2016) · Molecular Microbiology · doi:10.1111/mmi.13471 · 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

Translational Regulation of the JunD Messenger RNA

Short, J. D., & Pfarr, C. M. (2002) · Journal of Biological Chemistry · doi:10.1074/jbc.m204553200 · Cited by 62 · see citing works

Identifying New Small Proteins in Escherichia coli

VanOrsdel, C. E., Kelly, J. P., Burke, B. N., Lein, C. D., Oufiero, C. E., Sanchez, J. F., Wimmers, L. E., Hearn, D. J., Abuikhdair, F. J., Barnhart, K. R., et al. (2018) · PROTEOMICS · doi:10.1002/pmic.201700064 · Cited by 61 · see citing works

The small protein CydX is required for function of cytochrome bd oxidase in Brucella abortus

Sun, Y.-H., de Jong, M. F., den Hartigh, A. B., Roux, C. M., Rolán, H. G., & Tsolis, R. M. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00047 · Cited by 60 · see citing works

Low molecular weight proteins: A challenge for post‐genomic research

Rudd, K. E., Humphery‐Smith, I., Wasinger, V. C., & Bairoch, A. (1998) · Electrophoresis · doi:10.1002/elps.1150190413 · Cited by 60 · see citing works

Optimization of parameters for coverage of low molecular weight proteins

Müller, S. A., Kohajda, T., Findeiß, S., Stadler, P. F., Stefan Washietl, A., Kellis, M., von Bergen�, M., & Kalkhof, S. (2010) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-010-4093-x · Cited by 54 · see citing works

The small protein MgtS and small RNA MgrR modulate the PitA phosphate symporter to boost intracellular magnesium levels

Yin, X., Orr, M. W., Wang, H., Hobbs, E. C., Shabalina, S. A., & Storz, G. (2018) · Molecular Microbiology · doi:10.1111/mmi.14143 · Cited by 49 · see citing works

Cryo-EM structures of KdpFABC suggest a K+ transport mechanism via two inter-subunit half-channels

Stock, C., Hielkema, L., Tascón, I., Wunnicke, D., Oostergetel, G. T., Azkargorta, M., Paulino, C., & Hänelt, I. (2018) · Nature Communications · doi:10.1038/s41467-018-07319-2 · Cited by 49 · see citing works

Conservation analysis of the CydX protein yields insights into small protein identification and evolution

Allen, R. J., Brenner, E. P., VanOrsdel, C. E., Hobson, J. J., Hearn, D. J., & Hemm, M. R. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-946 · Cited by 43 · see citing works

Viral Miniproteins

DiMaio, D. (2014) · Annual Review of Microbiology · doi:10.1146/annurev-micro-091313-103727 · Cited by 40 · see citing works

Identification of prokaryotic small proteins using a comparative genomic approach

Samayoa, J. A., Yildiz, F. H., & Karplus, K. J. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr275 · Cited by 39 · see citing works

Translational Repression of the RpoS Antiadapter IraD by CsrA Is Mediated via Translational Coupling to a Short Upstream Open Reading Frame

Park, H., McGibbon, L. C., Potts, A. H., Yakhnin, H., Romeo, T., & Babitzke, P. (2017) · mBio · doi:10.1128/mbio.01355-17 · Cited by 36 · see citing works

Analysis of Escherichia coli Ribosomal Proteins by an Improved Two Dimensional Gel Electrophoresis. II. Characterization of Fonr New Proteins

Wada, A. (1986) · The Journal of Biochemistry · doi:10.1093/oxfordjournals.jbchem.a121867 · Cited by 36 · see citing works

Translatomics combined with transcriptomics and proteomics reveals novel functional, recently evolved orphan genes in Escherichia coli O157:H7 (EHEC)

Neuhaus, K., Landstorfer, R., Fellner, L., Simon, S., Schafferhans, A., Goldberg, T., Marx, H., Ozoline, O. N., Rost, B., Küster, B., et al. (2016) · BMC Genomics · doi:10.1186/s12864-016-2456-1 · Cited by 33 · see citing works

Characterization of the tol-pal and cyd region of Escherichia coli K-12: transcript analysis and identification of two new proteins encoded by the cyd operon

Müller, M. M., & Webster, R. E. (1997) · Journal of Bacteriology · doi:10.1128/jb.179.6.2077-2080.1997 · Cited by 30 · see citing works

Thousands of missed genes found in bacterial genomes and their analysis with COMBREX

Wood, D. E., Lin, H., Levy‐Moonshine, A., Swaminathan, R., Chang, Y.-C., Anton, B. P., Osmani, L., Steffen, M. A., Kasif, S., & Salzberg, S. L. (2012) · Biology Direct · doi:10.1186/1745-6150-7-37 · Cited by 30 · see citing works

Comparative Proteomics Enables Identification of Nonannotated Cold Shock Proteins in E. coli

D’Lima, N. G., Khitun, A., Rosenbloom, A. D., Yuan, P., Gassaway, B. M., Barber, K. W., Rinehart, J., & Slavoff, S. A. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00419 · Cited by 30 · 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

Regulation of aspartate transcarbamoylase synthesis in Escherichia coli: analysis of deletion mutations in the promoter region of the pyrBI operon.

Levin, H. L., & Schachman, H. K. (1985) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.82.14.4643 · Cited by 29 · see citing works

Proteome-wide Alterations in Escherichia coli Translation Rates upon Anaerobiosis

Kramer, G., Sprenger, R. R., Nessen, M. A., Roseboom, W., Speijer, D., de Jong, L., de Mattos, M. J. T., Back, J. W., & de Koster, C. G. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.001826 · Cited by 29 · see citing works

Comparison of the basic Escherichia coli antizyme 1 and antizyme 2 with the ribosomal proteins S20/L26 and L34.

Panagiotidis, C. Α., & Canellakis, E. S. (1984) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(17)42508-7 · Cited by 28 · see citing works

mRNA dynamics and alternative conformations adopted under low and high arginine concentrations control polyamine biosynthesis in Salmonella

Ben-Zvi, T., Pushkarev, A., Seri, H., Elgrably‐Weiss, M., Papenfort, K., & Altuvia, S. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1007646 · Cited by 27 · see citing works

The Novel Anaerobiosis-Responsive Overlapping Gene ano Is Overlapping Antisense to the Annotated Gene ECs2385 of Escherichia coli O157:H7 Sakai

Hücker, S. M., Vanderhaeghen, S., Abellan-Schneyder, I., Scherer, S., & Neuhaus, K. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.00931 · Cited by 20 · see citing works

A novel short L-arginine responsive protein-coding gene (laoB) antiparallel overlapping to a CadC-like transcriptional regulator in Escherichia coli O157:H7 Sakai originated by overprinting

Hücker, S. M., Vanderhaeghen, S., Abellan-Schneyder, I., Wecko, R., Simon, S., Scherer, S., & Neuhaus, K. (2018) · BMC Evolutionary Biology · doi:10.1186/s12862-018-1134-0 · Cited by 19 · see citing works

YshB Promotes Intracellular Replication and Is Required for Salmonella Virulence

Bomjan, R., Zhang, M., & Zhou, D. (2019) · Journal of Bacteriology · doi:10.1128/jb.00314-19 · Cited by 18 · see citing works

The Small Protein CydX Is Required for Cytochrome bd Quinol Oxidase Stability and Function in Salmonella enterica Serovar Typhimurium: a Phenotypic Study

Duc, K. M., Kang, B. G., Lee, C., Park, H. J., Park, Y. M., Joung, Y. H., & Bang, I. S. (2019) · Journal of Bacteriology · doi:10.1128/jb.00348-19 · Cited by 17 · see citing works

SearchDOGS Bacteria, Software That Provides Automated Identification of Potentially Missed Genes in Annotated Bacterial Genomes

hÉigeartaigh, S. Ó., Armisén, D., Byrne, K. P., & Wolfe, K. H. (2014) · Journal of Bacteriology · doi:10.1128/jb.01368-13 · Cited by 12 · see citing works

The elusive short gene – an ensemble method for recognition for prokaryotic genome

Goli, B., & Nair, A. S. (2012) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2012.04.090 · Cited by 11 · see citing works

A Method for High-Performance Sequence Analysis Using Polyvinylidene Difluoride Membranes with a Biphasic Reaction Column Sequencer

Reim, D. F., & Speicher, D. W. (1994) · Analytical Biochemistry · doi:10.1006/abio.1994.1027 · Cited by 11 · see citing works

Investigation of amino acid specificity in the CydX small protein shows sequence plasticity at the functional level

Hobson, J. J., Gallegos, A. S., Atha, B. W., Kelly, J. P., Lein, C. D., VanOrsdel, C. E., Weldon, J. E., & Hemm, M. R. (2018) · PLoS ONE · doi:10.1371/journal.pone.0198699 · Cited by 11 · see citing works

Identification of a chloroform-soluble membrane miniprotein in Escherichia coli and its homolog in Salmonella typhimurium

Guan, Z., Wang, X., & Raetz, C. R. H. (2010) · Analytical Biochemistry · doi:10.1016/j.ab.2010.10.035 · Cited by 9 · 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

Active site rearrangement and structural divergence in prokaryotic respiratory oxidases

Safarian, S., Hahn, A. S., Mills, D. J., Radloff, M., Eisinger, M., Nikolaev, A., Meier‐Credo, J., Melin, F., Miyoshi, H., Gennis, R. B., et al. (2019) · Science · doi:10.1126/science.aay0967 · Cited by 127 · see citing works

Revisiting sORFs: overcoming challenges to identify and characterize functional microproteins

Schlesinger, D., & Elsässer, S. J. (2021) · FEBS Journal · doi:10.1111/febs.15769 · Cited by 111 · see citing works

Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides

Cassidy, L., Kaulich, P. T., Maaß, S., Bartel, J., Becher, D., & Tholey, A. (2021) · Proteomics · doi:10.1002/pmic.202100008 · Cited by 61 · 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

The largely unexplored biology of small proteins in pro‐ and eukaryotes

Steinberg, R., & Koch, H. (2021) · FEBS Journal · doi:10.1111/febs.15845 · Cited by 71 · see citing works

An RNA-centric global view of Clostridioides difficile reveals broad activity of Hfq in a clinically important gram-positive bacterium

Fuchs, M., Lamm‐Schmidt, V., Sulzer, J., Ponath, F., Jenniches, L., Kirk, J. A., Fagan, R. P., Barquist, L., Vogel, J., & Faber, F. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2103579118 · Cited by 65 · see citing works

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

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

Escherichia coli: An Overview of Main Characteristics

Basavaraju, M., & Gunashree, B. S. (2022) · IntechOpen eBooks · doi:10.5772/intechopen.105508 · Cited by 53 · 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

Uncovering small membrane proteins in pathogenic bacteria: Regulatory functions and therapeutic potential

Garai, P., & Blanc‐Potard, A. (2020) · Molecular Microbiology · doi:10.1111/mmi.14564 · Cited by 51 · 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

Bacterial Small Membrane Proteins: the Swiss Army Knife of Regulators at the Lipid Bilayer

Yadavalli, S. S., & Yuan, J. (2021) · Journal of Bacteriology · doi:10.1128/jb.00344-21 · Cited by 49 · 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

Small Open Reading Frame-Encoded Micro-Peptides: An Emerging Protein World

Dong, X., Zhang, K., Xun, C., Chu, T., Liang, S., Zeng, Y., & Liu, Z. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241310562 · Cited by 35 · 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

Dual-function AzuCR RNA modulates carbon metabolism

Raina, M., Aoyama, J. J., Bhatt, S., Paul, B. J., Zhang, A., Updegrove, T. B., Miranda‐Ríos, J., & Storz, G. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2117930119 · Cited by 33 · see citing works

The Small Toxic Salmonella Protein TimP Targets the Cytoplasmic Membrane and Is Repressed by the Small RNA TimR

Andresen, L., Martínez-Burgo, Y., Zangelin, J. N., Rizvanovic, A., & Holmqvist, E. (2020) · mBio · doi:10.1128/mbio.01659-20 · Cited by 32 · see citing works

Revealing the small proteome ofHaloferax volcaniiby combining ribosome profiling and small-protein optimized mass spectrometry

Hadjeras, L., Bartel, J., Maier, L., Maaß, S., Vogel, V., Svensson, S. L., Eggenhofer, F., Gelhausen, R., Müller, T., Alkhnbashi, O. S., et al. (2023) · microLife · doi:10.1093/femsml/uqad001 · 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

Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions

Tufail, M. A., Jordan, B., Hadjeras, L., Gelhausen, R., Cassidy, L., Habenicht, T., Gutt, M., Hellwig, L., Backofen, R., Tholey, A., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-53008-8 · Cited by 26 · 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

Rescue of Escherichia coli auxotrophy by de novo small proteins

Babina, A. M., Surkov, S., Ye, W., Jerlström-Hultqvist, J., Larsson, M., Holmqvist, E., Jemth, P., Andersson, D. I., & Knopp, M. (2023) · eLife · doi:10.7554/elife.78299 · Cited by 24 · see citing works

Type I toxin-antitoxin systems in bacteria: from regulation to biological functions

Shore, S. F. H., Leinberger, F. H., Fozo, E. M., & Berghoff, B. A. (2024) · EcoSal Plus · doi:10.1128/ecosalplus.esp-0025-2022 · Cited by 25 · 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

σ28-dependent small RNA regulation of flagella biosynthesis

Melamed, S., Zhang, A., Jarník, M., Mills, J., Silverman, A., Zhang, H., & Storz, G. (2023) · eLife · doi:10.7554/elife.87151 · Cited by 22 · 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

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

The small protein MntS evolved from a signal peptide and acquired a novel function regulating manganese homeostasis in Escherichia coli

Wright, Z., Seymour, M., Paszczak, K., Truttmann, T., Senn, K. A., Stilp, S., Jansen, N., Gosz, M., Goeden, L., Anantharaman, V., et al. (2023) · Molecular Microbiology · doi:10.1111/mmi.15206 · 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

The inhibitory mechanism of a small protein reveals its role in antimicrobial peptide sensing

Jiang, S., Steup, L. C., Kippnich, C., Lazaridi, S., Malengo, G., Lemmin, T., & Yuan, J. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2309607120 · Cited by 16 · see citing works

Community benchmarking and evaluation of human unannotated microprotein detection by mass spectrometry based proteomics

Wacholder, A. C., Deutsch, E. W., Kok, L. W., van Dinter, J. T., Lee, J., Wright, J. C., Leblanc, S., Jayatissa, A. H., Jiang, K., Arefiev, I., et al. (2026) · Nature Communications · doi:10.1038/s41467-025-68002-x · Cited by 14 · see citing works

High-throughput discovery of inhibitory protein fragments with AlphaFold

Savinov, A., Swanson, S., Keating, A. E., & Li, G.-W. (2025) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2322412122 · Cited by 18 · see citing works

The Small Open Reading Frame‐Encoded Peptides: Advances in Methodologies and Functional Studies

Chen, L., Yang, Y., Zhang, Y., Li, K., Cai, H., Wang, H., & Zhao, Q. C. (2021) · ChemBioChem · doi:10.1002/cbic.202100534 · Cited by 12 · see citing works

sORFdb – a database for sORFs, small proteins, and small protein families in bacteria

Hahnfeld, J. M., Schwengers, O., Jelonek, L., Diedrich, S., Cemič, F., & Goesmann, A. (2025) · BMC Genomics · doi:10.1186/s12864-025-11301-w · Cited by 11 · see citing works

Detection and Quantitation of Small Proteins Using Mass Spectrometry

Franco, P., Zeinert, R., Meier-Credo, J., Storz, G., & Langer, J. D. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.101052 · Cited by 10 · see citing works

Prediction of protein-coding small ORFs in multi-species using integrated sequence-derived features and the random forest model

Yu, J., Jiang, W., Zhu, S.-B., Liao, Z., Dou, X., Liu, J., Guo, F., & Dong, C. (2023) · Methods · doi:10.1016/j.ymeth.2022.12.003 · Cited by 10 · see citing works

Differential synthesis of novel small protein times Salmonella virulence program

Salvail, H., Choi, J., & Groisman, E. A. (2022) · PLoS Genetics · doi:10.1371/journal.pgen.1010074 · Cited by 10 · see citing works

Small but mighty: the rise of microprotein biology in neuroscience

Duffy, E. E., Assad, E. G., Kalish, B. T., & Greenberg, M. E. (2024) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2024.1386219 · Cited by 9 · see citing works

The contribution of mRNA targeting to spatial protein localization in bacteria

Shang, W., Lichtenberg, E., Mlesnita, A.-M., Wilde, A., & Koch, H. (2024) · FEBS Journal · doi:10.1111/febs.17054 · Cited by 10 · see citing works

S2P intramembrane protease RseP degrades small membrane proteins and suppresses the cytotoxicity of intrinsic toxin HokB

Yokoyama, T., Yamagata, Y., Honna, S., Mizuno, S., Katagiri, S., Oi, R., Nogi, T., Hizukuri, Y., & Akiyama, Y. (2023) · mBio · doi:10.1128/mbio.01086-23 · Cited by 8 · see citing works

Comprehensive evaluation of protein-coding sORFs prediction based on a random sequence strategy

Yu, J., Guo, L., Dou, X., Jiang, W., Qian, B., Liu, J., Wang, J., Wang, C., & Xu, C. (2021) · Frontiers in Bioscience-Landmark · doi:10.52586/4943 · Cited by 8 · see citing works

Small protein mediates inhibition of ammonium transport in <i>Methanosarcina mazei</i> —an ancient mechanism?

Habenicht, T., Weidenbach, K., Velazquez-Campoy, A., Buey, R. M., Balsera, M., & Schmitz, R. A. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.02811-23 · Cited by 8 · see citing works

OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques

Cerqueira, F. R., & de Vasconcelos, A. T. R. (2020) · Database · doi:10.1093/database/baaa067 · Cited by 8 · see citing works

Mapping functional regions of essential bacterial proteins with dominant-negative protein fragments

Savinov, A., Fernandez, A., & Fields, S. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2200124119 · Cited by 8 · see citing works

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessmentPreprint

Wacholder, A. C., Deutsch, E. W., Kok, L. W., van Dinter, J. T., Lee, J., Wright, J. C., Leblanc, S., Jayatissa, A. H., Jiang, K., Arefiev, I., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.02.19.639069 · Cited by 6 · see citing works

Identifying new small proteins through a molecular biology course‐based undergraduate research experience laboratory class

Miranda, R. J., Warren, C., Mcdougal, K., Kimble, S. J. A., Sanchez, J., Norman, L. L., Anderson, V., & Hemm, M. R. (2023) · Biochemistry and Molecular Biology Education · doi:10.1002/bmb.21764 · Cited by 5 · see citing works

Initiation at AUGUG and GUGUG sequences can lead to translation of overlapping reading frames in E. coli

Kohl, M. P., Kompatscher, M., Clementi, N., Holl, L., & Erlacher, M. D. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac1175 · Cited by 5 · see citing works

Analysis of stress-induced small proteins in Escherichia coli reveals that YoaI mediates cross-talk between distinct signaling systems

Vellappan, S., Sun, J., Favate, J. S., Jagadeesan, P., Cerda, D., Shah, P., & Yadavalli, S. S. (2025) · Science Signaling · doi:10.1126/scisignal.adu7253 · Cited by 4 · see citing works

Profiling a Community-Specific Function Landscape for Bacterial Peptides Through Protein-Level Meta-Assembly and Machine Learning

Vajjala, M., Johnson, B., Kasparek, L., Leuze, M. R., & Yao, Q. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.935351 · Cited by 4 · see citing works

Rise of Bacterial Small Proteins and Peptides in Therapeutic Applications

Meenakshi, S., & Shelin, R. (2023) · Protein and Peptide Letters · doi:10.2174/0929866530666230118144723 · Cited by 4 · see citing works

Complementary Ribo-seq approaches map the translatome and provide a small protein census in the foodborne pathogen Campylobacter jejuniPreprint

Froschauer, K., Svensson, S. L., Gelhausen, R., Fiore, E., Kible, P., Klaude, A., Kucklick, M., Fuchs, S., Eggenhofer, F., Engelmann, S., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.09.515450 · Cited by 4 · see citing works

One transcript, two functions: the emerging roles of dual-function RNAs

Luke, L. M., & Papenfort, K. (2025) · microLife · doi:10.1093/femsml/uqaf034 · Cited by 3 · see citing works

σ28-dependent small RNA regulation of flagella biosynthesis

Melamed, S., Zhang, A., Jarník, M., Mills, J., Silverman, A., Zhang, H., & Storz, G. (2023) · eLife · doi:10.7554/elife.87151.3 · Cited by 3 · see citing works

Staphylococcus aureus SigS Induces Expression of a Regulatory Protein Pair That Modulates Its mRNA Stability

Ali, A. A., Alsulami, J., Aubee, J. I., Idowu, A., Tomlinson, B. R., Felton, E. A., Jackson, J. K., Kennedy, S. J., Torres, N. J., Shaw, L. N., et al. (2023) · Journal of Bacteriology · doi:10.1128/jb.00392-22 · Cited by 3 · see citing works

Short, Rich, and Powerful: a New Family of Arginine-Rich Small Proteins Have Outsized Impact in Agrobacterium tumefaciens

Alakavuklar, M. A., & Fuqua, C. (2020) · Journal of Bacteriology · doi:10.1128/jb.00450-20 · Cited by 3 · see citing works

The Cryptic Bacterial MicroproteomePreprint

Fesenko, I. A., Sahakyan, H., Shabalina, S. A., & Koonin, E. V. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.02.17.580829 · Cited by 3 · see citing works

A revised genome annotation of the model cyanobacterium Synechocystis based on start and stop codon-enriched ribosome profiling and proteogenomicsPreprint

Hadjeras, L., Krauspe, V., Gelhausen, R., Heiniger, B., Spät, P., Reimann, V., Jaques, G., Minges, P., Bilger, R., Gerstner, M., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.20.695498 · Cited by 3 · see citing works

Exploring the transcription start sites and other genomic features facilitates the accurate identification and annotation of small RNAs across multiple stress conditions in Mycobacterium tuberculosis

Cheah, H.-L., Citartan, M., Lee, L.-P., Ahmed, S. A., Salleh, M. Z., Teh, L. K., & Tang, T. (2024) · Functional & Integrative Genomics · doi:10.1007/s10142-024-01437-5 · Cited by 2 · see citing works

Metabolic silencing induced by the small bacterial membrane protein YohP

Natriashvili, A., Mohammadsadeghi, N., Milanov, M., Smudde, E., Prucker, I., Jessen, H. J., Carabadjac, I., Heerklotz, H. H., Franco, P. H. C., Langer, J. D., et al. (2025) · iScience · doi:10.1016/j.isci.2025.114123 · Cited by 2 · see citing works

Proteome characterization of single gene deletion mutants lacking zinc finger µ-proteins in Haloferax volcanii

Franco, P. H. C., Üresin, D., Borst, A., Rusling, L. A., Soppa, J., & Langer, J. D. (2026) · microLife · doi:10.1093/femsml/uqag005 · Cited by 2 · see citing works

Microproteins: emerging roles as antibiotics

Galeota-Sprung, B., Bhatt, A. S., & de la Fuente‐Núñez, C. (2025) · Trends in Genetics · doi:10.1016/j.tig.2024.12.004 · Cited by 2 · see citing works

A highly conserved sRNA downregulates multiple genes, including a σ 54 transcriptional activator, in the virulence mode of Bordetella pertussis

Sim, M., Nguyen, J., Škopová, K., Yoo, K., Tai, C., Knipling, L., Chen, Q., Kim, D. D., Nolan, S., Elaksher, R. A., et al. (2025) · mBio · doi:10.1128/mbio.01356-25 · Cited by 2 · see citing works

The small bacterial membrane protein YohP induces nucleoid condensation in E. coli and inhibits oligomerization of antimicrobial peptides

Natriashvili, A., Mohammadsadeghi, N., Smudde, E., Berghoff, B. A., Ulbrich, M. H., & Koch, H. (2025) · microLife · doi:10.1093/femsml/uqaf030 · Cited by 2 · see citing works

The continuing evolution of barcode applications: Functional toxicology to cell lineage

Fasullo, M., & Dolan, M. (2022) · Experimental Biology and Medicine · doi:10.1177/15353702221121600 · Cited by 3 · see citing works

Phycobilisome breakdown effector NblD is required to maintain the cellular amino acid composition during nitrogen starvationPreprint

Krauspe, V., Timm, S., Hagemann, M., & Hess, W. R. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.03.18.436103 · Cited by 2 · see citing works

The GndA microprotein promotes cell growth during heat shock in Escherichia coliPreprint

Mohsen, J. J., Bertolotti, N. R., Jiang, K., Mohsen, M. G., DeRosa, C. M., Dewani, N., Quinto, L. B., Dabdoub, G., Erkalo, B., Landajuela, A., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.06.29.601336 · Cited by 2 · see citing works

In silico identification and characterization of micropeptides with potential therapeutic properties from non-coding DNA of E. coli

Raj, N., Lashari, S. A., Revikumar, A., & Tahir, M. (2025) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2025.111213 · Cited by 1 · see citing works

Functional diversity and molecular interactions of small membrane proteins in bacteria

Yuan, J., Koch, H., & Berghoff, B. A. (2025) · microLife · doi:10.1093/femsml/uqaf035 · 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

Integrative transcriptomic and network analysis reveals small open reading frames associated with cellular adaptive responsees and methylation-linked pathogenicity in Leptospira interrogans

Khew, C., Mohd-Fowzi, N., Zaifulzaman, N. N., Harun, S., Razak, S. A., Mohamed‐Hussein, Z., & Mohd‐Assaad, N. (2026) · Functional & Integrative Genomics · doi:10.1007/s10142-026-01882-4 · Cited by 1 · see citing works

Pro-SMP finder–A systematic approach for discovering small membrane proteins in prokaryotes

Hoffman, T., Kinne, J., & Cho, K. H. (2024) · PLoS ONE · doi:10.1371/journal.pone.0299169 · Cited by 1 · see citing works

Prediction of Protein-Coding Small ORFs Based on Supervised Contrastive Learning

Xie, D., Bian, X., Wang, Z., & Qu, Z. (2024) · IEEE Access · doi:10.1109/access.2024.3419766 · Cited by 1 · see citing works

AzuCR RNA modulates carbon metabolism as a dual-function RNA in Escherichia coliPreprint

Raina, M., Aoyama, J. J., Bhatt, S., Paul, B. J., & Storz, G. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.04.27.441574 · Cited by 1 · see citing works

Genome scale identification of new genes using saturated reporter transposon mutagenesisPreprint

Goodall, E. C. A., Hodges, F. J., Kok, W., Permana, B., Cuddihy, T., Yang, Z., Kahler, N., Shires, K., Pullela, K., Torres, V. V. L., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.06.611592 · Cited by 1 · see citing works

“ Staphylococcus aureus SigS induces expression of a regulatory protein pair that modulate its mRNA stability”Preprint

Ali, A. A., Alsulami, J., Aubee, J. I., Idowu, A., Tomlinson, B. R., Felton, E. A., Jackson, J. K., Shaw, L. N., & Thompson, K. M. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.10.19.512975

Small proteome of the nitrogen-fixing plant symbiont Sinorhizobium melilotiPreprint

Hadjeras, L., Heiniger, B., Maaß, S., Scheuer, R., Gelhausen, R., Azarderakhsh, S., Barth-Weber, S., Backofen, R., Becher, D., Ahrens, C. H., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.11.12.516264

The inhibitory mechanism of a small protein reveals its role in antimicrobial peptide sensingPreprint

Jiang, S., Steup, L. C., Kippnich, C., Lazaridi, S., Malengo, G., Lemmin, T., & Yuan, J. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.12.22.521624

Mind the gap: Intergenic regions in bacteria encode numerous small proteins

Lin, J. D., & Bhatt, A. S. (2025) · Molecular Cell · doi:10.1016/j.molcel.2025.02.018

Popcorn: prediction of short coding and noncoding genomic sequences in prokaryotes

Kyrouz, A., Liu, L., Qin, L., & Tjaden, B. C. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf250

Transcription profiling and functional analysis of spRNAs and their corresponding asRNAs in Methanosarcina mazeiPreprint

Jordan, B., Gohil, R., Prasse, D., Hellwig, L., Repnik, U., Jiang, S., Yuan, J., & Schmitz, R. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.10.28.685009

Small subunits MttS and MttQ of the MttP transporter regulate trimethylamine transport in Methanosarcina mazeiPreprint

Habenicht, T., Hellwig, L., Kießling, C., Elling, F. J., & Schmitz, R. A. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.02.691841

Integrative Transcriptomic and Network Analysis Reveals Small Open Reading Frames as Regulators of DNA Methylation-Linked Pathogenicity and Adaptability in Leptospira interrogansPreprint

Khew, C., Fowzi, N. S. M., Zaifulzaman, N. N., Harun, S., Razak, S. A., Mohamed‐Hussein, Z., & Mohd‐Assaad, N. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2025.12.08.692996

Small Open Reading Frames in Bacteria: A Narrative Review of AI-Driven Challenges and Prospects

Babalola, A., Hamdani, H. Y., Ahmad, A., Damiri, N., Firdaus‐Raih, M., & Mat-Sharani, S. (2025) · IPSJ Transactions on Bioinformatics · doi:10.2197/ipsjtbio.18.39

Stringent proteogenomic discovery of novel small proteins in Mycobacterium tuberculosis clinical reference strainsPreprint

Heiniger, B., Schori, C., Arefian, M., Banaei‐Esfahani, A., Schuler, M., Borrell, S., Loiseau, C., Brites, D., Comas, I., Aebersold, R. H., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.01.27.701740

Characterization of a family of small proteins regulated by second messenger-binding riboswitches in Clostridioides difficile

Badilla-Lobo, A. (2024) · doi:10.70675/475e57d1z425ez4861z88dfz82af7e51d93e

A family of small proteins links c-di-GMP riboswitch signaling with sporulation in Clostridioides difficilePreprint

Badilla-Lobo, A., Waligora‐Dupriet, A., Penven, L., Seifert, R., Rodríguez, C., Barbut, F., Soutourina, O. A., & Johann, P. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.10.731418

The Ascent of Miniproteins

Yoo, Y., & Nanda, V. (2026) · Biochemistry · doi:10.1021/acs.biochem.6c00311

The GndA Microprotein Promotes Cell Growth during Heat Shock in Escherichia coli

Mohsen, J. J., Bertolotti, N. R., Jiang, K., Mohsen, M. G., DeRosa, C. M., Dewani, N., Quinto, L. B., Dabdoub, G., Erkalo, B., Landajuela, A., et al. (2026) · Biochemistry · doi:10.1021/acs.biochem.6c00391

Identifying New Small Proteins in Escherichia coli

VanOrsdel, C. E., Kelly, J. P., Burke, B. N., Lein, C. D., Oufiero, C. E., Sanchez, J. F., Wimmers, L. E., Hearn, D. J., Abuikhdair, F. J., Barnhart, K. R., et al. (2018) · PROTEOMICS · doi:10.1002/pmic.201700064 · Cited by 61 · see citing works

The small protein floodgates are opening; now the functional analysis begins

Ramamurthi, K. S., & Storz, G. (2014) · BMC Biology · doi:10.1186/s12915-014-0096-y · Cited by 37 · see citing works

A survey of small RNA-encoding genes in Escherichia coli

Hershberg, R. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg297 · Cited by 251 · see citing works

SURVEY AND SUMMARY A survey of small RNA-encoding genes in Escherichia coli

Hershberg, R., Altuvia, S., & Margalit, H. (2002) · Europe PMC (PubMed Central)

Global Functional Atlas of Escherichia coli Encompassing Previously Uncharacterized Proteins

Hu, P., Janga, S. C., Babu, M., Díaz-Mejía, J. J., Butland, G., Yang, W., Pogoutse, O., Guo, X., Phanse, S., Wong, P., et al. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000096 · Cited by 387 · see citing works