Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae

Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

Benjamini, Y., & Hochberg, Y. (1995) · Journal of the Royal Statistical Society Series B: Statistical Methodology · doi:10.1111/j.2517-6161.1995.tb02031.x · Cited by 109,482 · see citing works

The Sequence Alignment/Map format and SAMtools

Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041 · see citing works

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

<tt>edgeR</tt> : a Bioconductor package for differential expression analysis of digital gene expression data

Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364 · see citing works

SciPy 1.0: fundamental algorithms for scientific computing in Python

Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2020) · Nature Methods · doi:10.1038/s41592-019-0686-2 · Cited by 38,430 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

SciPy 1.0: fundamental algorithms for scientific computing in Python

Virtanen, P., Gommers, R., Oliphant, T. E., Haberland, M., Reddy, T., Cournapeau, D., Burovski, E., Peterson, P., Weckesser, W., Bright, J., et al. (2019) · Apollo - University of Cambridge Repository · doi:10.17863/cam.64134 · Cited by 10,460 · see citing works

Universal sample preparation method for proteome analysis

Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352 · see citing works

A scaling normalization method for differential expression analysis of RNA-seq data

Robinson, M. D., & Oshlack, A. (2010) · Genome Biology · doi:10.1186/gb-2010-11-3-r25 · Cited by 7,876 · see citing works

Global quantification of mammalian gene expression control

Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works

SignalP 5.0 improves signal peptide predictions using deep neural networks

Armenteros, J. J. A., Tsirigos, K. D., Sønderby, C. K., Petersen, T. N., Winther, O., Brunak, S., von HEIJNE, G., & Nielsen, H. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0036-z · Cited by 4,206 · see citing works

2016 update of the PRIDE database and its related tools

Vizcaíno, J. A., Csordás, A., del‐Toro, N., Dianes, J. A., Griss, J., Lavidas, I., Mayer, G., Pérez‐Riverol, Y., Reisinger, F., Ternent, T., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1145 · Cited by 3,466 · see citing works

The FoldX web server: an online force field

Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki387 · Cited by 2,759 · see citing works

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

Huerta-Cepas, J., Forslund, K., Coelho, L. P., Szklarczyk, D., Jensen, L. J., von Mering, C., & Bork, P. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx148 · Cited by 2,709 · see citing works

A hidden Markov model for predicting transmembrane helices in protein sequences.

Sonnhammer, E. L. L., von HEIJNE, G., & Krogh, A. (1998) · PubMed · Cited by 2,483 · see citing works

BEDTools: The Swiss‐Army Tool for Genome Feature Analysis

Quinlan, A. R. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1112s47 · Cited by 2,286 · see citing works

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

Huerta‐Cepas, J., Szklarczyk, D., Forslund, S. K., Cook, H., Heller, D., Walter, M. C., Rattei, T., Mende, D. R., Sunagawa, S., Kuhn, M., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1248 · Cited by 2,062 · see citing works

Complete Sequence Analysis of the Genome of the Bacterium Mycoplasma Pneumoniae

Himmelreich, R., Hilbert, H., Plagens, H., Pirkl, E., Li, B.-C., & Herrmann, R. (1996) · Nucleic Acids Research · doi:10.1093/nar/24.22.4420 · Cited by 1,142 · see citing works

Role of a peptide tagging system in degradation of proteins synthesized from damaged messenger RNA

Keiler, K. C., Waller, P. R. H., & Sauer, R. T. (1996) · Science · doi:10.1126/science.271.5251.990 · Cited by 1,125 · see citing works

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

Robinson, M. D., & Smyth, G. K. (2007) · Biostatistics · doi:10.1093/biostatistics/kxm030 · Cited by 1,073 · see citing works

Moderated statistical tests for assessing differences in tag abundance

Robinson, M. D., & Smyth, G. K. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm453 · Cited by 856 · see citing works

Substrate specificity of the DnaK chaperone determined by screening cellulose‐bound peptide libraries

Rüdiger, S., Germeroth, L., Schneider‐Mergener, J., & Bukau, B. (1997) · The EMBO Journal · doi:10.1093/emboj/16.7.1501 · Cited by 815 · see citing works

2016 update of the PRIDE database and its related tools

Vizcaíno, J. A., Csordás, A., del‐Toro, N., Dianes, J. A., Griss, J., Lavidas, I., Mayer, G., Pérez‐Riverol, Y., Reisinger, F., Ternent, T., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw880 · Cited by 806 · see citing works

AAA+ Proteases: ATP-Fueled Machines of Protein Destruction

Sauer, R. T., & Baker, T. A. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-060408-172623 · Cited by 763 · see citing works

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

Rawlings, N. D., Barrett, A. J., & Finn, R. D. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1118 · Cited by 688 · see citing works

Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense

Vasu, K., & Nagaraja, V. (2013) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.00044-12 · Cited by 606 · see citing works

Proteomic Discovery of Cellular Substrates of the ClpXP Protease Reveals Five Classes of ClpX-Recognition Signals

Flynn, J. M., Neher, S. B., Kim, Y., Sauer, R. T., & Baker, T. A. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00060-1 · Cited by 605 · see citing works

FoldX 5.0: working with RNA, small molecules and a new graphical interface

Delgado, J., Radusky, L., Cianferoni, D., & Serrano, L. G. (2019) · Bioinformatics · doi:10.1093/bioinformatics/btz184 · Cited by 523 · see citing works

Proteome organization in a genome-reduced bacterium

Kühner, S., van Noort, V., Betts, M. J., Leo-Macias, A., Batisse, C., Rode, M., Yamada, T., Maier, T., Bader, S., Beltran-Alvarez, P., et al. (2009) · Science · doi:10.1126/science.1176343 · Cited by 471 · see citing works

Tethering the Z ring to the membrane through a conserved membrane targeting sequence in FtsA

Pichoff, S., & Lutkenhaus, J. (2005) · Molecular Microbiology · doi:10.1111/j.1365-2958.2005.04522.x · Cited by 439 · see citing works

Transcriptome complexity in a genome-reduced bacterium

Güell, M., van Noort, V., Yus, E., Chen, W.-H., Leigh-Bell, J., Michalodimitrakis, K., Yamada, T., Arumugam, M., Doerks, T., Kühner, S., et al. (2009) · Science · doi:10.1126/science.1176951 · Cited by 418 · see citing works

Dynamics of Protein Turnover, a Missing Dimension in Proteomics

Pratt, J. M., Petty, J., Riba‐Garcia, I., Robertson, D. H. L., Gaskell, S. J., Oliver, S. G., & Beynon, R. J. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200046-mcp200 · Cited by 390 · see citing works

Impact of genome reduction on bacterial metabolism and its regulation

Yus, E., Maier, T., Michalodimitrakis, K., van Noort, V., Yamada, T., Chen, W.-H., Wodke, J. A. H., Güell, M., Martínez, S., Bourgeois, R., et al. (2009) · Science · doi:10.1126/science.1177263 · Cited by 327 · see citing works

A Specificity-Enhancing Factor for the ClpXP Degradation Machine

Levchenko, I. V., Seidel, M., Sauer, R. T., & Baker, T. A. (2000) · Science · doi:10.1126/science.289.5488.2354 · Cited by 324 · see citing works

Quantification of mRNA and protein and integration with protein turnover in a bacterium

Maier, T., Schmidt, A., Güell, M., Kühner, S., Gavin, A., Aebersold, R., & Serrano, L. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.38 · Cited by 297 · see citing works

FtsH is required for proteolytic elimination of uncomplexed forms of SecY, an essential protein translocase subunit.

Kihara, A., Akiyama, Y., & Ito, K. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.10.4532 · Cited by 269 · see citing works

Global Proteome Turnover Analyses of the Yeasts S. cerevisiae and S. pombe

Christiano, R., Nagaraj, N., Fröhlich, F., & Walther, T. C. (2014) · Cell Reports · doi:10.1016/j.celrep.2014.10.065 · Cited by 268 · see citing works

Balanced biosynthesis of major membrane components through regulated degradation of the committed enzyme of lipid A biosynthesis by the AAA protease FtsH (HflB) in Escherichia coli

Ogura, T., Inoue, K., Tatsuta, T., Suzaki, T., Karata, K., Young, K., Su, L. J., Fierke, C. A., Jackman, J. E., Raetz, C. R. H., et al. (1999) · Molecular Microbiology · doi:10.1046/j.1365-2958.1999.01221.x · Cited by 265 · see citing works

The N-end rule pathway for regulated proteolysis: prokaryotic and eukaryotic strategies

Mogk, A., Schmidt, R., & Bukau, B. (2007) · Trends in Cell Biology · doi:10.1016/j.tcb.2007.02.001 · Cited by 261 · see citing works

The GroE chaperonin machine is a major modulator of the CIRCE heat shock regulon of Bacillus subtilis

Mogk, A., Homuth, G., Scholz, C., Kim, L., Schmid, F. X., & Schumann, W. (1997) · The EMBO Journal · doi:10.1093/emboj/16.15.4579 · Cited by 256 · see citing works

Genetic and Functional Analyses of the Conserved C-Terminal Core Domain of Escherichia coli FtsZ

Ma, X., & Margolin, W. (1999) · Journal of Bacteriology · doi:10.1128/jb.181.24.7531-7544.1999 · Cited by 251 · see citing works

The Crystal Structure of a GroEL/Peptide Complex

Chen, L., & Sigler, P. B. (1999) · Cell · doi:10.1016/s0092-8674(00)81673-6 · Cited by 242 · see citing works

Recognition of misfolded proteins by Lon, a AAA + proteasePreprint

Gur, E., & Sauer, R. T. (2008) · Genes & Development · doi:10.1101/gad.1670908 · Cited by 232 · see citing works

ClpS is an essential component of the N-end rule pathway in Escherichia coli

Erbse, A. H., Schmidt, R., Bornemann, T., Schneider‐Mergener, J., Mogk, A., Zahn, R., Dougan, D. A., & Bukau, B. (2006) · Nature · doi:10.1038/nature04412 · Cited by 229 · see citing works

Arginine phosphorylation marks proteins for degradation by a Clp protease

Trentini, D. B., Suskiewicz, M. J., Heuck, A., Kurzbauer, R., Deszcz, L., Mechtler, K., & Clausen, T. (2016) · Nature · doi:10.1038/nature20122 · Cited by 228 · see citing works

Regulated Proteolysis in Bacteria

Mahmoud, S. A., & Chien, P. (2018) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062917-012848 · Cited by 214 · see citing works

Biological roles of the Lon ATP-dependent protease

Tsilibaris, V., Maenhaut-Michel, G., & Melderen, L. V. (2006) · Research in Microbiology · doi:10.1016/j.resmic.2006.05.004 · Cited by 207 · see citing works

QCloud: A cloud-based quality control system for mass spectrometry-based proteomics laboratories

Chiva, C., Olivella, R., Borràs, E., Espadas, G., Pastor, O., Solé, A., & Sabidó, E. (2018) · PLoS ONE · doi:10.1371/journal.pone.0189209 · Cited by 196 · see citing works

Binding specificity of Escherichia coli trigger factor

Patzelt, H., Rüdiger, S., Brehmer, D., Krämer, G., Vorderwülbecke, S., Schaffitzel, E., Waitz, A., Hesterkamp, T., Dong, L., Schneider‐Mergener, J., et al. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.261432298 · Cited by 185 · see citing works

Regulation of SOS mutagenesis by proteolysis.

Frank, E. G., Ennis, D. G., Gonzalez, M., Levine, A. S., & Woodgate, R. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.19.10291 · Cited by 164 · see citing works

SeqPurge: highly-sensitive adapter trimming for paired-end NGS data

Sturm, M., Schroeder, C., & Bauer, P. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1069-7 · Cited by 154 · see citing works

Inclusion bodies: Specificity in their aggregation process and amyloid-like structure

Morell, M., Bravo, R., Espargaró, A., Sisquella, X., Avilés, F. X., Fernàndez‐Busquets, X., & Ventura, S. (2008) · Biochimica et Biophysica Acta (BBA) - Molecular Cell Research · doi:10.1016/j.bbamcr.2008.06.007 · Cited by 150 · see citing works

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome‐reduced bacterium

Lluch‐Senar, M., Delgado, J., Chen, W., Lloréns‐Rico, V., O’Reilly, F. J., Wodke, J. A. H., Unal, E. B., Yus, E., Martínez, S., Nichols, R. J., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145558 · Cited by 135 · 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

The ftsH gene of Bacillus subtilis is involved in major cellular processes such as sporulation, stress adaptation and secretion

Deuerling, E., Mogk, A., Richter, C. G., Purucker, M., & Schumann, W. (1997) · Molecular Microbiology · doi:10.1046/j.1365-2958.1997.2721636.x · Cited by 127 · see citing works

Trapping and Proteomic Identification of Cellular Substrates of the ClpP Protease in Staphylococcus aureus

Feng, J., Michalik, S., Varming, A. N., Andersen, J. H., Albrecht, D., Jelsbak, L., Krieger, S., Ohlsen, K., Hecker, M., Gerth, U., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr300394r · Cited by 126 · see citing works

Structure, function, and assembly of the terminal organelle of Mycoplasma pneumoniae

Krause, D. C., & Balish, M. F. (2001) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(01)00126-4 · Cited by 123 · see citing works

Regulation and quality control by Lon-dependent proteolysis

Melderen, L. V., & Aertsen, A. (2009) · Research in Microbiology · doi:10.1016/j.resmic.2009.08.021 · Cited by 121 · see citing works

A microtiter trypan blue absorbance assay for the quantitative determination of excitotoxic neuronal injury in cell culture

Uliasz, T. F., & Hewett, S. J. (2000) · Journal of Neuroscience Methods · doi:10.1016/s0165-0270(00)00248-x · Cited by 118 · see citing works

A Conserved Residue at the Extreme C-Terminus of FtsZ Is Critical for the FtsA-FtsZ Interaction in Staphylococcus aureus

Yan, K., Pearce, K. H., & Payne, D. J. (2000) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.2000.2439 · Cited by 116 · see citing works

Defined chromosome structure in the genome-reduced bacterium Mycoplasma pneumoniae

Trussart, M., Yus, E., Martinez, S., Baù, D., Tahara, Y. O., Pengo, T., Widjaja, M., Kretschmer, S., Swoger, J., Djordjevic, S., et al. (2017) · Nature Communications · doi:10.1038/ncomms14665 · Cited by 114 · see citing works

Protein Aggregates: an Aging Factor Involved in Cell Death

Maisonneuve, E., Ezraty, B., & Dukan, S. (2008) · Journal of Bacteriology · doi:10.1128/jb.00736-08 · Cited by 108 · see citing works

Phase-variable methylation and epigenetic regulation by type I restriction–modification systems

Croix, M. D. S., Vacca, I., Kwun, M. J., Ralph, J. D., Bentley, S. D., Haigh, R., Croucher, N. J., & Oggioni, M. R. (2017) · FEMS Microbiology Reviews · doi:10.1093/femsre/fux025 · Cited by 107 · see citing works

Integrating Protein Homeostasis Strategies in ProkaryotesPreprint

Mogk, A., Huber, D., & Bukau, B. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a004366 · Cited by 105 · see citing works

When, how and why? Regulated proteolysis by the essential FtsH protease in Escherichia coli

Bittner, L., Arends, J., & Narberhaus, F. (2017) · Biological Chemistry · doi:10.1515/hsz-2016-0302 · Cited by 100 · see citing works

Turnover of Endogenous SsrA-tagged Proteins Mediated by ATP-dependent Proteases in Escherichia coli

Lies, M., & Maurizi, M. R. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m801692200 · Cited by 97 · see citing works

Modification of PATase by L/F‐transferase generates a ClpS‐dependent N‐end rule substrate in Escherichia coli

Ninnis, R. L., Spall, S. K., Talbo, G. H., Truscott, K. N., & Dougan, D. A. (2009) · The EMBO Journal · doi:10.1038/emboj.2009.134 · Cited by 96 · see citing works

Control of DNA replication initiation by recruitment of an essential initiation protein to the membrane of Bacillus subtilis

Rokop, M. E., Auchtung, J. M., & Grossman, A. D. (2004) · Molecular Microbiology · doi:10.1111/j.1365-2958.2004.04091.x · Cited by 89 · see citing works

Defining the mycoplasma ‘cytoskeleton’: the protein composition of the Triton X-100 insoluble fraction of the bacterium Mycoplasma pneumoniae determined by 2-D gel electrophoresis and mass spectrometry

Regula, J. T., Boguth, G., Görg, A., Hegermann, J., Mayer, F., Frank, R. W., & Herrmann, R. (2001) · Microbiology · doi:10.1099/00221287-147-4-1045 · Cited by 88 · see citing works

ClpS is the recognition component for Escherichia coli substrates of the N‐end rule degradation pathway

Schmidt, R., Zahn, R., Bukau, B., & Mogk, A. (2009) · Molecular Microbiology · doi:10.1111/j.1365-2958.2009.06666.x · Cited by 86 · see citing works

Identification of ClpP substrates in C aulobacter crescentus reveals a role for regulated proteolysis in bacterial development

Bhat, N. H., Vass, R. H., Stoddard, P. R., Shin, D. K., & Chien, P. (2013) · Molecular Microbiology · doi:10.1111/mmi.12241 · Cited by 78 · see citing works

Membrane Protein Degradation by FtsH Can Be Initiated from Either End

Chiba, S., Akiyama, Y., & Ito, K. (2002) · Journal of Bacteriology · doi:10.1128/jb.184.17.4775-4782.2002 · Cited by 76 · see citing works

Comparison of two-dimensional electrophoresis patterns of heat shock protein Hsp27 species in normal and cardiomyopathic hearts

Scheler, C., Li, X., Salnikow, J., Dunn, M. J., & Jungblut, P. R. (1999) · Electrophoresis · doi:10.1002/(sici)1522-2683(19991201)20:18 · Cited by 72 · see citing works

Comparative analysis of antibiotic resistance gene markers in Mycoplasma genitalium: application to studies of the minimal gene complement

Pich, Ò. Q., Burgos, R., Planell, R., Querol, E., & Piñol, J. (2006) · Microbiology · doi:10.1099/mic.0.28287-0 · Cited by 64 · see citing works

A high-efficiency recombineering system with PCR-based ssDNA in Bacillus subtilis mediated by the native phage recombinase GP35

Sun, Z., Deng, A., Hu, T., Wu, J., Sun, Q., Bai, H., Zhang, G., & Wen, T. (2015) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-6485-5 · Cited by 63 · see citing works

Involvement of the Lon Protease in the SOS Response Triggered by Ciprofloxacin in Pseudomonas aeruginosa PAO1

Breidenstein, E. B. M., Bains, M., & Hancock, R. E. W. (2012) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.06014-11 · Cited by 61 · see citing works

The Interplay of ClpXP with the Cell Division Machinery in Escherichia coli

Camberg, J. L., Hoskins, J. R., & Wickner, S. (2011) · Journal of Bacteriology · doi:10.1128/jb.01317-10 · Cited by 59 · see citing works

Systematic Structural Analyses of Attachment Organelle in Mycoplasma pneumoniae

Nakane, D., Kenri, T., Matsuo, L., & Miyata, M. (2015) · PLoS Pathogens · doi:10.1371/journal.ppat.1005299 · Cited by 59 · see citing works

MS-EmpiRe Utilizes Peptide-level Noise Distributions for Ultra-sensitive Detection of Differentially Expressed Proteins

Ammar, C., Gruber, M., Csaba, G., & Zimmer, R. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra119.001509 · Cited by 56 · see citing works

Proteolysis of the replication checkpoint protein Sda is necessary for the efficient initiation of sporulation after transient replication stress in Bacillus subtilis

Ruvolo, M., Mach, K. E., & Burkholder, W. F. (2006) · Molecular Microbiology · doi:10.1111/j.1365-2958.2006.05167.x · Cited by 55 · see citing works

Selective adaptor dependent protein degradation in bacteria

Kuhlmann, N. J., & Chien, P. (2017) · Current Opinion in Microbiology · doi:10.1016/j.mib.2017.03.013 · Cited by 54 · see citing works

Impact of C‐terminal amino acid composition on protein expression in bacteria

Weber, M. L., Burgos, R., Yus, E., Yang, J., Lluch‐Senar, M., & Serrano, L. G. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199208 · Cited by 54 · see citing works

ClpXP and ClpAP proteolytic activity on divisome substrates is differentially regulated following the C aulobacter asymmetric cell division

Williams, B., Bhat, N. H., Chien, P., & Shapiro, L. (2014) · Molecular Microbiology · doi:10.1111/mmi.12698 · Cited by 54 · see citing works

Length recognition at the N‐terminal tail for the initiation of FtsH‐mediated proteolysis

Chiba, S., Akiyama, Y., Mori, H., Matsuo, E., & Ito, K. (2000) · EMBO Reports · doi:10.1093/embo-reports/kvd005 · Cited by 54 · see citing works

Loading and activation of DNA replicative helicases: the key step of initiation of DNA replication

Li, Y., & Araki, H. (2013) · Genes to Cells · doi:10.1111/gtc.12040 · Cited by 52 · see citing works

Mini review: ATP‐dependent proteases in bacteria

Bittner, L., Arends, J., & Narberhaus, F. (2016) · Biopolymers · doi:10.1002/bip.22831 · Cited by 49 · see citing works

Determination of the Gene Regulatory Network of a Genome-Reduced Bacterium Highlights Alternative Regulation Independent of Transcription Factors

Yus, E., Lloréns‐Rico, V., Martínez, S., Gallo, C., Eilers, H., Blötz, C., Stülke, J., Lluch‐Senar, M., & Serrano, L. G. (2019) · Cell Systems · doi:10.1016/j.cels.2019.07.001 · Cited by 48 · see citing works

Experimental proof for a signal peptidase I like activity in Mycoplasma pneumoniae, but absence of a gene encoding a conserved bacterial type I SPase

Catrein, I., Herrmann, R., Bosserhoff, A., & Ruppert, T. (2005) · FEBS Journal · doi:10.1111/j.1742-4658.2005.04710.x · Cited by 46 · see citing works

Summarization vs Peptide-Based Models in Label-Free Quantitative Proteomics: Performance, Pitfalls, and Data Analysis Guidelines

Goeminne, L. J. E., Argentini, A., Martens, L., & Clement, L. (2015) · Journal of Proteome Research · doi:10.1021/pr501223t · Cited by 44 · see citing works

Discovery of AAA+ Protease Substrates through Trapping Approaches

Liao, J. R., & van Wijk, K. J. (2019) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2018.12.006 · Cited by 42 · see citing works

Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances

Chen, W.-H., van Noort, V., Lluch‐Senar, M., Hennrich, M. L., Wodke, J. A. H., Yus, E., Alibés, A., Roma, G., Mende, D. R., Pesavento, C., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw004 · Cited by 40 · see citing works

Mycoplasma pneumoniae Genome Editing Based on Oligo Recombineering and Cas9-Mediated Counterselection

Piñero‐Lambea, C., García-Ramallo, E., Martínez, S., Delgado, J., Serrano, L. G., & Lluch‐Senar, M. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00022 · Cited by 37 · see citing works

RecA mediates MgpB and MgpC phase and antigenic variation in Mycoplasma genitalium, but plays a minor role in DNA repair

Burgos, R., Wood, G. E., Young, L., Glass, J. I., & Totten, P. A. (2012) · Molecular Microbiology · doi:10.1111/j.1365-2958.2012.08130.x · Cited by 36 · see citing works

Large-scale metabolome analysis and quantitative integration with genomics and proteomics data in Mycoplasma pneumoniae

Maier, T., Marcos, J., Wodke, J. A. H., Paetzold, B., Liebeke, M., Gallego, R. G., & Serrano, L. G. (2013) · Molecular BioSystems · doi:10.1039/c3mb70113a · Cited by 34 · see citing works

In vivo trapping of FtsH substrates by label‐free quantitative proteomics

Arends, J., Thomanek, N., Kuhlmann, K., Marcus, K., & Narberhaus, F. (2016) · PROTEOMICS · doi:10.1002/pmic.201600316 · Cited by 33 · see citing works

Regulation of RcsA by the ClpYQ (HslUV) protease in Escherichia coli

Kuo, M.-S., Chen, K.-P., & Wu, W.-F. (2004) · Microbiology · doi:10.1099/mic.0.26446-0 · Cited by 31 · see citing works

Activation of σ20-dependent recombination and horizontal gene transfer in Mycoplasma genitalium

Torres-Puig, S., Martínez-Torró, C., Granero-Moya, I., Querol, E., Piñol, J., & Pich, Ò. Q. (2018) · DNA Research · doi:10.1093/dnares/dsy011 · Cited by 26 · see citing works

An Integrated Proteomic Approach Uncovers Novel Substrates and Functions of the Lon Protease in Escherichia coli

Arends, J., Griego, M., Thomanek, N., Lindemann, C., Kutscher, B., Meyer, H. E., & Narberhaus, F. (2018) · PROTEOMICS · doi:10.1002/pmic.201800080 · Cited by 26 · see citing works

All-in-one construct for genome engineering using Cre-lox technology

Mariscal, A. M., González‐González, L., Querol, E., & Piñol, J. (2016) · DNA Research · doi:10.1093/dnares/dsw015 · Cited by 21 · see citing works

MG 428 is a novel positive regulator of recombination that triggers mgpB and mgpC gene variation in M ycoplasma genitalium

Burgos, R., & Totten, P. A. (2014) · Molecular Microbiology · doi:10.1111/mmi.12760 · Cited by 21 · see citing works

Reconstitution of an Active Arginine Deiminase Pathway in Mycoplasma pneumoniae M129

Rechnitzer, H., Rottem, S., & Herrmann, R. (2013) · Infection and Immunity · doi:10.1128/iai.00441-13 · Cited by 11 · see citing works

Engineered live bacteria suppress Pseudomonas aeruginosa infection in mouse lung and dissolve endotracheal-tube biofilms

Mazzolini, R., Rodríguez-Arce, I., Fernández‐Barat, L., Piñero‐Lambea, C., Garrido, V., Rebollada‐Merino, A., Motos, A., Torres, A., Grilló, M. J., Serrano, L. G., et al. (2023) · Nature Biotechnology · doi:10.1038/s41587-022-01584-9 · Cited by 89 · see citing works

Engineering a genome‐reduced bacterium to eliminate Staphylococcus aureus biofilms in vivo

Garrido, V., Piñero‐Lambea, C., Rodríguez-Arce, I., Paetzold, B., Ferrar, T. S., Weber, M. L., García-Ramallo, E., Gallo, C., Collantes, M., Peñuelas, I., et al. (2021) · Molecular Systems Biology · doi:10.15252/msb.202010145 · Cited by 50 · see citing works

A model industrial workhorse: Bacillus subtilis strain 168 and its genome after a quarter of a century

Bremer, E., Calteau, A., Danchin, A., Harwood, C. R., Helmann, J. D., Médigue, C., Palsson, B. Ø., Sekowska, A., Vallenet, D., Zuniga, A., et al. (2023) · Microbial Biotechnology · doi:10.1111/1751-7915.14257 · Cited by 41 · see citing works

Bacterial expression of a designed single‐chain IL‐10 prevents severe lung inflammation

Montero‐Blay, A., Delgado, J., Rodríguez-Arce, I., Lastrucci, C., Piñero‐Lambea, C., Lluch‐Senar, M., & Serrano, L. G. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211037 · Cited by 32 · see citing works

The role of plant proteases in the response of plants to abiotic stress factors

Luciński, R., & Adamiec, M. (2023) · Frontiers in Plant Physiology · doi:10.3389/fphgy.2023.1330216 · Cited by 26 · see citing works

Toward the Complete Functional Characterization of a Minimal Bacterial Proteome

Bianchi, D. M., Pelletier, J. F., Hutchison, C. A., Glass, J. I., & Luthey-Schulten, Z. (2022) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.2c04188 · Cited by 22 · see citing works

Functional Characterization of the Cell Division Gene Cluster of the Wall-less Bacterium Mycoplasma genitalium

Martínez-Torró, C., Torres-Puig, S., Marcos-Silva, M., Huguet-Ramón, M., Muñoz-Navarro, C., Lluch‐Senar, M., Serrano, L. G., Querol, E., Piñol, J., & Pich, Ò. Q. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.695572 · Cited by 23 · see citing works

The Lon protease temporally restricts polar cell differentiation events during the Caulobacter cell cycle

Omnus, D. J., Fink, M. J., Szwedo, K., & Jonas, K. (2021) · eLife · doi:10.7554/elife.73875 · Cited by 20 · see citing works

SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome

Piñero‐Lambea, C., García-Ramallo, E., Miravet‐Verde, S., Burgos, R., Scarpa, M., Serrano, L. G., & Lluch‐Senar, M. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac836 · Cited by 18 · see citing works

Isolation, whole genome sequencing and application of a broad-spectrum Salmonella phage

Zheng, X., Wang, X., Yu, Z., Liu, M., Li, P., Gao, L., Wang, H., Ma, X., Wang, L., Huo, X., et al. (2024) · Archives of Microbiology · doi:10.1007/s00203-024-04061-w · Cited by 13 · see citing works

Comprehensive quantitative modeling of translation efficiency in a genome‐reduced bacterium

Weber, M. L., Sogues, A., Yus, E., Burgos, R., Gallo, C., Martínez, S., Lluch‐Senar, M., & Serrano, L. G. (2023) · Molecular Systems Biology · doi:10.15252/msb.202211301 · Cited by 11 · see citing works

Cellular mechanics during division of a genomically minimal cell

Pelletier, J. F., Glass, J. I., & Strychalski, E. A. (2022) · Trends in Cell Biology · doi:10.1016/j.tcb.2022.06.009 · Cited by 11 · see citing works

ProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs

Miravet‐Verde, S., Mazzolini, R., Segura-Morales, C., Broto, A., Lluch‐Senar, M., & Serrano, L. G. (2024) · Nature Communications · doi:10.1038/s41467-024-46112-2 · Cited by 10 · see citing works

Development of a Serum-Free Medium To Aid Large-Scale Production of Mycoplasma -Based Therapies

Burgos, R., García-Ramallo, E., Shaw, D. J., Lluch‐Senar, M., & Serrano, L. G. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.04859-22 · Cited by 10 · see citing works

MycoWiki: Functional annotation of the minimal model organism Mycoplasma pneumoniae

Elfmann, C., Zhu, B., Pedreira, T., Hoßbach, B. M., Lluch‐Senar, M., Serrano, L., & Stülke, J. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.935066 · Cited by 7 · see citing works

Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging

Tower, J. (2024) · Frontiers in Aging · doi:10.3389/fragi.2024.1376060 · Cited by 9 · see citing works

Unraveling developmental gene regulation in holometabolous insects through comparative transcriptomics and proteomics

Wilkens, M., Zimbelmann, S., Roth, F., Cartano, J., Sayols, S., Dejung, M., Levin, M., & Butter, F. (2025) · Communications Biology · doi:10.1038/s42003-025-08414-z · Cited by 8 · see citing works

Widespread ribosome stalling in a genome-reduced bacterium and the need for translational quality control

Burgos, R., Weber, M. L., Gallo, C., Lluch‐Senar, M., & Serrano, L. G. (2021) · iScience · doi:10.1016/j.isci.2021.102985 · Cited by 6 · see citing works

In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex

Jensen, R. K., Xue, L., Marotta, F., Somody, J. C., Selkrig, J., Lenz, S., Rappsilber, J., Savitski, M. M., Kosiński, J., Typas, A., et al. (2026) · Cell · doi:10.1016/j.cell.2026.08.055 · Cited by 5 · see citing works

Living Microbial Drugs

Özçelik, C. E., Tunç, N., Şen, S., & Şeker, U. Ö. Ş. (2026) · Chemistry - A European Journal · doi:10.1002/chem.202503523 · Cited by 4 · see citing works

Dual mode of delivery of Mycoplasma pneumoniae CARDS toxin determines the toxin trafficking pathway and cytotoxicity in host cells

Sreenath, K., Li, L., Molotsky, D., ., J. A. A., Baseman, J. B., & Kannan, T. R. (2025) · mBio · doi:10.1128/mbio.02640-25 · Cited by 3 · see citing works

Heterologous protein exposure and secretion optimization in Mycoplasma pneumoniae

Ana, Y., Gerngross, D., & Serrano, L. G. (2024) · Microbial Cell Factories · doi:10.1186/s12934-024-02574-z · Cited by 3 · see citing works

Survival strategies of mycoplasmas: the critical role of post-translational modifications

Li, T., Yuan, H., Zhang, W., & Guo, F. (2025) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2025.1688880 · Cited by 2 · see citing works

Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell

Fu, E., Thornburg, Z. R., Brier, T. A., Wei, R., Yuan, B., Gilbert, B. R., Wang, S., & Luthey-Schulten, Z. A. (2025) · The Journal of Physical Chemistry B · doi:10.1021/acs.jpcb.5c04532 · Cited by 2 · see citing works

Systematic analysis of structural disorder in the minimal proteome of Mycoplasma pneumoniae

Pozzoli, U., Forni, D., Arrigoni, F., Mozzi, A., Cagliani, R., GIOIA, L. D., & Sironi, M. (2025) · Microbiology Spectrum · doi:10.1128/spectrum.00968-25 · Cited by 1 · see citing works

Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map

Miravet‐Verde, S., Burgos, R., García-Ramallo, E., Weber, M. L., & Serrano, L. G. (2025) · Molecular Systems Biology · doi:10.1038/s44320-025-00133-1 · Cited by 1 · see citing works

Fucoidan-active enzymes: Recent progress in their heterologous expression and future prospects for applications

Abdelrahman, S., Zahran, R., & Zayed, A. (2026) · Journal of Applied Phycology · doi:10.1007/s10811-026-03834-8 · Cited by 1 · see citing works

Proteomic Analysis of Unicellular Cyanobacterium Crocosphaera subtropica ATCC 51142 under Extended Light or Dark Growth

Panda, P., Giri, S. J., Sherman, L. A., Kihara, D., & Aryal, U. K. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00439 · Cited by 1 · see citing works

DYNAMICS OF ARG-X PROTEOLYTIC ACTIVITY IN POSITIVELY CHARGED PROTEIN FRACTIONS DURING ESCHERICHIA COLI GROWTH IN CULTURE

Stupak, E. E., & Vafina, G. H. (2022) · ÈKOBIOTEH · doi:10.31163/2618-964x-2022-5-3-130-137 · Cited by 1 · see citing works

Isolation, Whole Genome Sequencing and Preliminary Application of a Broad-Spectrum Salmonella PhagePreprint

Zheng, X., Wang, X., Yu, Z., Liu, M., Ma, X., Wang, L., Huo, X., & Zhang, W. (2023) · SSRN Electronic Journal · doi:10.2139/ssrn.4617617

Direct and indirect pathways linking the Lon protease to motility behaviors in the pathogen Pseudomonas aeruginosa

Kallazhi, A., Rahman, A., Römling, U., & Jonas, K. (2025) · PLoS Pathogens · doi:10.1371/journal.ppat.1013288

Molecular mechanisms of gene expression regulation in Mycoplasma spp.: insights into virulence-related genes

Paes, J. A., & Ferreira, H. B. (2025) · Gene · doi:10.1016/j.gene.2025.149709

Function and transcription of the lon gene in Xanthomonas campestris pv. campestris

Chang, H., Yeh, J.-H., Lo, H., Liao, C., & Hsiao, Y. (2025) · Antonie van Leeuwenhoek · doi:10.1007/s10482-025-02177-7

A versatile plug and play bacterial chassis based on a fast-growing Mycoplasma species

Inäbnit, J., Démoulins, T., Pramateftaki, P. V., Bourgeon, M., Labroussaa, F., Jores, J., & Torres-Puig, S. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1134

Synthetic Biology. Morality and Reason

Matyushkina, D. S., Gorbunov, K. S., Fisunov, G. Y., & Govorun, V. M. (2025) · Russian Journal of Genetics · doi:10.1134/s1022795425700942

Bortezomib exhibited bacteriostatic activity and pro-inflammatory effect against Mycoplasma pneumoniae

Zhang, Z., Mao, Y., Wang, X., Ji, H., & Li, Y.-Y. (2026) · The Journal of Antibiotics · doi:10.1038/s41429-026-00942-y

From decline to resurgence: current perspectives on Mycoplasma pneumoniae

Liu, Y., & Ye, Q. (2026) · Clinical Microbiology Reviews · doi:10.1128/cmr.00051-26

Visualizing Mycoplasma with Nanometer Resolution without Compromising Viability

Kumar, A., Perry, N., Paul, A., Özdoğan, M., Joseph, J., Ringnalda, J., Murkute, P., & Timp, G. L. (2026) · ACS Nano · doi:10.1021/acsnano.6c08047

Degradation Mechanism of AAA+ Proteases and Regulation of Streptomyces Metabolism

Xu, W., Gao, W., Bu, Q., & Li, Y. (2022) · Biomolecules · doi:10.3390/biom12121848 · Cited by 7 · see citing works

The Lon AAA+ Protease

Gur, E. (2013) · Sub-cellular biochemistry/Subcellular biochemistry · doi:10.1007/978-94-007-5940-4_2 · Cited by 62 · see citing works

Regulation and quality control by Lon-dependent proteolysis

Melderen, L. V., & Aertsen, A. (2009) · Research in Microbiology · doi:10.1016/j.resmic.2009.08.021 · Cited by 121 · see citing works

Reconstitution of FtsH-Mediated Membrane Protein Degradation in Bicelles

Yang, Y., Kim, M., Guo, R., Gaffney, K. A., & Hong, H. (2017) · Biophysical Journal · doi:10.1016/j.bpj.2016.11.508

Chaperone networks in bacteria: analysis of protein homeostasis in minimal cells

Wong, P., & Houry, W. A. (2003) · Journal of Structural Biology · doi:10.1016/j.jsb.2003.11.006 · Cited by 84 · see citing works