Cited by 306Bacterial Genetics and BiotechnologyBiochemical and Molecular ResearchMicrobial Metabolic Engineering and Bioproduction

The DOI matches its Crossref record; 96 of the 96 references it cites were found in a registry or an index.

Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis

Open access

Eymann, Christine, Homuth, Georg, Scharf, Christian, Hecker, Michael·2002·Journal of Bacteriology

DOI 10.1128/jb.184.9.2500-2520.2002PMC PMC134987

Open this paper in CoChat — free account

Abstract

The stringent response in Bacillus subtilis was characterized by using proteome and transcriptome approaches. Comparison of protein synthesis patterns of wild-type and relA mutant cells cultivated under conditions which provoke the stringent response revealed significant differences. According to their altered synthesis patterns in response to dl-norvaline, proteins were assigned to four distinct classes: (i) negative stringent control, i.e., strongly decreased protein synthesis in the wild type but not in the relA mutant (e.g., r-proteins); (ii) positive stringent control, i.e., induction of protein synthesis in the wild type only (e.g., YvyD and LeuD); (iii) proteins that were induced independently of RelA (e.g., YjcI); and (iv) proteins downregulated independently of RelA (e.g., glycolytic enzymes). Transcriptome studies based on DNA macroarray techniques were used to complement the proteome data, resulting in comparable induction and repression patterns of almost all corresponding genes. However, a comparison of both approaches revealed that only a subset of RelA-dependent genes or proteins was detectable by proteomics, demonstrating that the transcriptome approach allows a more comprehensive global gene expression profile analysis. The present study presents the first comprehensive description of the stringent response of a bacterial species and an almost complete map of protein-encoding genes affected by (p)ppGpp. The negative stringent control concerns reactions typical of growth and reproduction (ribosome synthesis, DNA synthesis, cell wall synthesis, etc.). Negatively controlled unknown y-genes may also code for proteins with a specific function during growth and reproduction (e.g., YlaG). On the other hand, many genes are induced in a RelA-dependent manner, including genes coding for already-known and as-yet-unknown proteins. A passive model is preferred to explain this positive control relying on the redistribution of the RNA polymerase under the influence of (p)ppGpp.

Integrity signals

Registry

Crossref · 10.1128/jb.184.9.2500-2520.2002

Cites

96 of 96 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Escherichia coli and Salmonella :cellular and molecular biology
Neidhardt, F. C. (1996) · ASM Press eBooks · Cited by 8,197
The complete genome sequence of the gram-positive bacterium Bacillus subtilis.
Kunst, F., Ogasawara, N., Moszer, I., Albertini, A. M., Alloni, G., Azevedo, V., Bertero, M. G., Bessières, P., Bolotin, A., Borchert, S., et al. (1997) · Nature · doi:10.1038/36786 · Cited by 3,679
Bacterial Stress Responses
Storz, G., & Hengge, R. (2010) · ASM Press eBooks · doi:10.1128/9781555816841 · Cited by 1,107
The stringent response
Cashel, M. (1996) · Medical Entomology and Zoology · Cited by 860
Residual guanosine 3‘,5‘-bispyrophosphate synthetic activity of relA null mutants can be eliminated by spoT null mutations.
Xiao, H., Kálmán, M., Ikehara, K., Zemel, S., Glaser, G., & Cashel, M. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(19)67694-5 · Cited by 721
Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp
Gentry, D. R., Hernandez, V. J., Nguyen, L. H., Jensen, D. B., & Cashel, M. (1993) · Journal of Bacteriology · doi:10.1128/jb.175.24.7982-7989.1993 · Cited by 448
Global Analysis of the General Stress Response of Bacillus subtilis
Petersohn, A., Brigulla, M., Haas, S. A., Hoheisel, J. D., Völker, U., & Hecker, M. (2001) · Journal of Bacteriology · doi:10.1128/jb.183.19.5617-5631.2001 · Cited by 433
Self-citation
Getting Newly Synthesized Proteins into Shape
Bukau, B., Deuerling, E., Pfund, C., & Craig, E. A. (2000) · Cell · doi:10.1016/s0092-8674(00)80806-5 · Cited by 428
Transcription Regulation by Initiating NTP Concentration: rRNA Synthesis in Bacteria
Gaál, T., Bartlett, M. S., Ross, W., Turnbough, C. L., & Gourse, R. L. (1997) · Science · doi:10.1126/science.278.5346.2092 · Cited by 367
Revisiting the stringent response, ppGpp and starvation signaling
Chatterji, D., & Ojha, A. K. (2001) · Current Opinion in Microbiology · doi:10.1016/s1369-5274(00)00182-x · Cited by 366

Show all 96 references

Research works printed but not linked: 1

Lopez, J., C. Marks, and E. Freese. 1981. The decrease in guanosine nucleotides initiates the sporulation in Bacillus subtilis.Biochim. Biophys. Acta587:238-252.

Sorted by citations

Items 101–200 of 306

Role of RelA of Streptococcus mutans in Global Control of Gene Expression
Nascimento, M. M., Lemos, J. A. C., Abranches, J., Lin, V. K., & Burne, R. A. (2007) · Journal of Bacteriology · doi:10.1128/jb.01395-07 · Cited by 65
Global gene expression during stringent response in Corynebacterium glutamicum in presence and absence of the rel gene encoding (p)ppGpp synthase
Brockmann-Gretza, O., & Kalinowski, J. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-230 · Cited by 64
Genetically modified lactic acid bacteria: applications to food or health and risk assessment
Renault, P. (2002) · Biochimie · doi:10.1016/s0300-9084(02)00029-9 · Cited by 63
13C-flux Analysis Reveals NADPH-balancing Transhydrogenation Cycles in Stationary Phase of Nitrogen-starving Bacillus subtilis
Rühl, M., Coq, D. L., Aymerich, S., & Sauer, U. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.366492 · Cited by 63
ICAT-based comparative proteomic analysis of non-replicating persistent Mycobacterium tuberculosis
Cho, S., Goodlett, D. R., & Franzblau, S. G. (2005) · Tuberculosis · doi:10.1016/j.tube.2005.10.002 · Cited by 62
The relA Homolog of Mycobacterium smegmatis Affects Cell Appearance, Viability, and Gene Expression
Dahl, J. L., Arora, K., Boshoff, H. I., Whiteford, D. C., Pacheco, S. A., Walsh, O. J., Lau-Bonilla, D., Davis, W. B., & Garza, A. G. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.7.2439-2447.2005 · Cited by 64
The role of thiol oxidative stress response in heat‐induced protein aggregate formation during thermotolerance in B acillus subtilis
Runde, S., Molière, N., Heinz, A., Maisonneuve, E., Janczikowski, A., Elsholz, A. K. W., Gerth, U., Hecker, M., & Turgay, K. (2014) · Molecular Microbiology · doi:10.1111/mmi.12521 · Cited by 61
Self-citation
The proteome and transcriptome analysis of Bacillus subtilis in response to salicylic acid
Nguyễn, V. D., Mäder, U., Tran, N. P., Cavin, J., Tam, L. T., Albrecht, D., Hecker, M., & Antelmann, H. (2007) · PROTEOMICS · doi:10.1002/pmic.200600706 · Cited by 61
Self-citation
Monitoring of changes in the membrane proteome during stationary phase adaptation of Bacillus subtilis using in vivo labeling techniques
Dreisbach, A., Otto, A., Becher, D., Hammer, E., Teumer, A., Gouw, J. W., Hecker, M., & Völker, U. (2008) · PROTEOMICS · doi:10.1002/pmic.200701081 · Cited by 60
Self-citation
Correlation of proteomic and transcriptomic profiles of Staphylococcus aureus during the post-exponential phase of growth
Scherl, A., François, P., Bento, M., Deshusses, J., Charbonnier, Y., Converset, V., Huyghe, A., Walter, N., Hoogland, C., Appel, R. D., et al. (2004) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2004.09.017 · Cited by 59
Cold atmospheric pressure plasma-antibiotic synergy in Pseudomonas aeruginosa biofilms is mediated via oxidative stress response
Maybin, J., Thompson, T. P., Flynn, P. B., Skvortsov, T., Hickok, N. J., Freeman, T. A., & Gilmore, B. (2023) · Biofilm · doi:10.1016/j.bioflm.2023.100122 · Cited by 60
Global transcriptional analysis of the stringent response in Enterococcus faecalis
Gaca, A. O., Abranches, J., Kajfasz, J. K., & Lemos, J. A. C. (2012) · Microbiology · doi:10.1099/mic.0.060236-0 · Cited by 58
Understanding Microbial Metabolism
Downs, D. M. (2006) · Annual Review of Microbiology · doi:10.1146/annurev.micro.60.080805.142308 · Cited by 56
ppGpp in Sinorhizobium meliloti: biosynthesis in response to sudden nutritional downshifts and modulation of the transcriptome
Krol, E., & Becker, A. (2011) · Molecular Microbiology · doi:10.1111/j.1365-2958.2011.07752.x · Cited by 54
Stationary Phase Mutagenesis inB. subtilis: A Paradigm to Study Genetic Diversity Programs in Cells Under Stress
Robleto, E. A., Yasbin, R. E., Ross, C. A., & Pedraza‐Reyes, M. (2007) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409230701597717 · Cited by 55
The stringent response and Mycobacterium tuberculosis pathogenesis
Prusa, J., Zhu, D. X., & Stallings, C. L. (2018) · Pathogens and Disease · doi:10.1093/femspd/fty054 · Cited by 54
Transcriptome and proteome analyses in response to 2‐methylhydroquinone and 6‐brom‐2‐vinyl‐chroman‐4‐on reveal different degradation systems involved in the catabolism of aromatic compounds in Bacillus subtilis
Nguyễn, V. D., Wolf, C., Mäder, U., Lalk, M., Langer, P., Lindequist, U., Hecker, M., & Antelmann, H. (2007) · PROTEOMICS · doi:10.1002/pmic.200700008 · Cited by 53
Self-citation
Roles and regulation of the glutamate racemase isogenes, racE and yrpC, in Bacillus subtilis
Kimura, K., Tran, L. P., & Itoh, Y. (2004) · Microbiology · doi:10.1099/mic.0.27045-0 · Cited by 53
The multidrug ABC transporter BmrC / BmrD of Bacillus subtilis is regulated via a ribosome-mediated transcriptional attenuation mechanism
Reilman, E., Mars, R. A. T., van Dijl, J. M., & Denham, E. L. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku832 · Cited by 51
Characterization of the global impact of low temperature gas plasma on vegetative microorganisms
Winter, T., Winter, J., Polák, M., Kusch, K., Mäder, U., Sietmann, R., Ehlbeck, J., van Hijum, S. A. F. T., Weltmann, K., Hecker, M., et al. (2011) · PROTEOMICS · doi:10.1002/pmic.201000637 · Cited by 52
Self-citation
Comparative transcriptome analysis of Lactococcus lactis subsp. cremoris strains under conditions simulating Cheddar cheese manufacture
Taïbi, A., Dabour, N., Lamoureux, M., Roy, D., & LaPointe, G. (2011) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2011.02.034 · Cited by 52
Rapid changes in gene expression: DNA determinants of promoter regulation by the concentration of the transcription initiating NTP in Bacillus subtilis
Sojka, L., Kouba, T., Barvı́k, I., Šanderová, H., Maderová, Z., Jonák, J., & Krásný, L. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr032 · Cited by 52
SpoT-Triggered Stringent Response Controls usp Gene Expression in Pseudomonas aeruginosa
Boes, N., Schreiber, K., & Schobert, M. (2008) · Journal of Bacteriology · doi:10.1128/jb.00600-08 · Cited by 52
Proteomic signatures uncover thiol-specific electrophile resistance mechanisms inBacillus subtilis
Antelmann, H., Hecker, M., & Zuber, P. (2008) · Expert Review of Proteomics · doi:10.1586/14789450.5.1.77 · Cited by 51
Self-citation
Role of (p)ppGpp in antibiotic resistance, tolerance, persistence and survival in Firmicutes
Salzer, A., & Wolz, C. (2023) · microLife · doi:10.1093/femsml/uqad009 · Cited by 48
The YheI/YheH heterodimer from Bacillus subtilis is a multidrug ABC transporter
Torres, C., Galián, C., Freiberg, C., Fantino, J., & Jault, J. (2009) · Biochimica et Biophysica Acta (BBA) - Biomembranes · doi:10.1016/j.bbamem.2008.12.012 · Cited by 50
In vitro Phosphorylation of Key Metabolic Enzymes from Bacillus subtilis: PrkC Phosphorylates Enzymes from Different Branches of Basic Metabolism
Pietack, N., Becher, D., Schmidl, S. R., Saier, M. H., Hecker, M., Commichau, F. M., & Stülke, J. (2010) · Microbial Physiology · doi:10.1159/000308512 · Cited by 50
Self-citation
Growth rate regulated genes and their wide involvement in the Lactococcus lactis stress responses
Dressaire, C., Redon, E., Milhem, H., Besse, P. C., Loubière, P., & Cocaign‐Bousquet, M. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-343 · Cited by 50
Highly Precise Quantification of Protein Molecules per Cell During Stress and Starvation Responses in Bacillus subtilis
Maaß, S., Wachlin, G., Bernhardt, J., Eymann, C., Fromion, V., Riedel, K., Becher, D., & Hecker, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.035741 · Cited by 49
Self-citation
Physiological and Transcriptional Responses of Different Industrial Microbes at Near-Zero Specific Growth Rates
Ercan, O., Bisschops, M. M. M., Overkamp, W., Jørgensen, T. R., Ram, A. F. J., Smid, E. J., Pronk, J. T., Kuipers, O. P., Daran-Lapujade, P. A. S., & Kleerebezem, M. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.00944-15 · Cited by 49
The role of peptide deformylase in protein biosynthesis: A proteomic study
Bandow, J. E., Becher, D., Büttner, K., Hochgräfe, F., Freiberg, C., Brötz, H., & Hecker, M. (2003) · PROTEOMICS · doi:10.1002/pmic.200390043 · Cited by 49
Self-citation
CtsR inactivation during thiol-specific stress in low GC, Gram+ bacteria
Elsholz, A. K. W., Hempel, K., Pöther, D., Becher, D., Hecker, M., & Gerth, U. (2010) · Molecular Microbiology · doi:10.1111/j.1365-2958.2010.07489.x · Cited by 48
Self-citation
From genomics via proteomics to cellular physiology of the Gram-positive model organism Bacillus subtilis
Völker, U., & Hecker, M. (2005) · Cellular Microbiology · doi:10.1111/j.1462-5822.2005.00555.x · Cited by 48
Self-citation
Comparison of Proteomic Responses as Global Approach to Antibiotic Mechanism of Action Elucidation
Senges, C. H. R., Stepanek, J. J., Wenzel, M., Raatschen, N., Ay, Ü., Märtens, Y., Prochnow, P., Vázquez‐Hernández, M., Yayci, A., Schubert, B., et al. (2020) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.01373-20 · Cited by 47
Functional genomics in antibacterial drug discovery
Freiberg, C., & Brötz‐Oesterhelt, H. (2005) · Drug Discovery Today · doi:10.1016/s1359-6446(05)03474-4 · Cited by 47
Post-transcriptional regulation of the Bacillus subtilis pst operon encoding a phosphate-specific ABC transporter
Allenby, N., O'Connor, N., Prágai, Z., Carter, N. M., Miethke, M., Engelmann, S., Hecker, M., Wipat, A., Ward, A. C., & Harwood, C. R. (2004) · Microbiology · doi:10.1099/mic.0.27126-0 · Cited by 47
Self-citation
The Response of Lactococcus lactis to Membrane Protein Production
Marreddy, R. K. R., Pinto, J. P. C., Wolters, J. C., Geertsma, E. R., Fusetti, F., Permentier, H. P., Kuipers, O. P., Kok, J., & Poolman, B. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024060 · Cited by 47
Inducible expression of (pp)pGpp synthetases in Staphylococcus aureus is associated with activation of stress response genes
Horvatek, P., Salzer, A., Hanna, A. M. F., Gratani, F. L., Keinhörster, D., Korn, N., Borisova, M., Mayer, C., Rejman, D., Mäder, U., et al. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1009282 · Cited by 44
Iron Starvation Triggers the Stringent Response and Induces Amino Acid Biosynthesis for Bacillibactin Production in Bacillus subtilis
Miethke, M., Westers, H., Blom, E.-J., Kuipers, O. P., & Marahiel, M. A. (2006) · Journal of Bacteriology · doi:10.1128/jb.01049-06 · Cited by 44
Essentiality of c-di-AMP in Bacillus subtilis: Bypassing mutations converge in potassium and glutamate homeostasis
Krüger, L., Herzberg, C., Rath, H., Pedreira, T., Ischebeck, T., Poehlein, A., Gundlach, J., Daniel, R., Völker, U., Mäder, U., et al. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009092 · Cited by 44
Comparative proteomics using 2-D gel electrophoresis and mass spectrometry as tools to dissect stimulons and regulons in bacteria with sequenced or partially sequenced genomes
Encarnación‐Guevara, S., Hernández, M., Martínez-Batallar, G., Contreras, S., Vargas, M. D. C., & Mora, J. (2005) · Biological Procedures Online · doi:10.1251/bpo110 · Cited by 46
Tricksy Business: Transcriptome Analysis Reveals the Involvement of Thioredoxin A in Redox Homeostasis, Oxidative Stress, Sulfur Metabolism, and Cellular Differentiation inBacillus subtilis
Smits, W. K., Dubois, J. F., Bron, S., van Dijl, J. M., & Kuipers, O. P. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.12.3921-3930.2005 · Cited by 45
Molecular Mechanisms Underlying the Positive Stringent Response of the Bacillus subtilis ilv-leu Operon, Involved in the Biosynthesis of Branched-Chain Amino Acids
Tojo, S., Satomura, T., Kumamoto, K., Hirooka, K., & Fujita, Y. (2008) · Journal of Bacteriology · doi:10.1128/jb.00606-08 · Cited by 44
Definition of the σW Regulon of Bacillus subtilis in the Absence of Stress
Zweers, J. C., Nicolas, P., Wiegert, T., van Dijl, J. M., & Denham, E. L. (2012) · PLoS ONE · doi:10.1371/journal.pone.0048471 · Cited by 45
Global Rsh-dependent transcription profile of Brucella suisduring stringent response unravels adaptation to nutrient starvation and cross-talk with other stress responses
Hanna, N., Ouahrani‐Bettache, S., Drake, K. L., Adams, L. G., Köhler, S., & Occhialini, A. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-459 · Cited by 42
Gene expression regulation in the plant growth promoting Bacillus atrophaeus UCMB-5137 stimulated by maize root exudates
Mwita, L. A., Chan, W. Y., Pretorius, T., Lyantagaye, S., Lapa, S. V., Avdeeva, L., & Reva, O. N. (2016) · Gene · doi:10.1016/j.gene.2016.05.045 · Cited by 44
Staphylococcus aureus ClpC ATPase is a late growth phase effector of metabolism and persistence
Chatterjee, I., Schmitt, S., Batzilla, C. F., Engelmann, S., Keller, A., Ring, M. W., Kautenburger, R., Ziebuhr, W., Hecker, M., Preissner, K. T., et al. (2009) · PROTEOMICS · doi:10.1002/pmic.200800586 · Cited by 43
Self-citation
Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics
Hess, B., Xue, J., Markillie, L. M., Taylor, R. C., Wiley, H. S., Ahring, B. K., & Linggi, B. E. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066104 · Cited by 42
(p)ppGpp and drug resistance
Wu, J., Long, Q., & Xie, J. (2010) · Journal of Cellular Physiology · doi:10.1002/jcp.22158 · Cited by 41
Localization and Expression of MreB in Vibrio parahaemolyticus under Different Stresses
Chiu, S.-W., Chen, S.-Y., & Wong, H. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.01020-08 · Cited by 40
Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging
Parker, D. J., Lalanne, J., 木村聡, Johnson, G. E., Waldor, M. K., & Li, G. (2020) · Cell Systems · doi:10.1016/j.cels.2020.07.005 · Cited by 39
Proteomic analysis of the probiotic Lactobacillus reuteri CRL1098 reveals novel tolerance biomarkers to bile acid-induced stress
Bustos, A. Y., de Valdez, G. F., Raya, R. R., de Almeida, A. M., Fadda, S., & Taranto, M. P. (2015) · Food Research International · doi:10.1016/j.foodres.2015.10.001 · Cited by 39
The ζ Toxin Induces a Set of Protective Responses and Dormancy
Lioy, V. S., Machón, C., Tabone, M., González‐Pastor, J. E., Daugelavičius, R., Ayora, S., & Alonso, J. C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0030282 · Cited by 39
Cell envelope gene expression in phosphate-limited Bacillus subtilis cells
Botella, E., Hübner, S., Hokamp, K., Hansen, A., Bisicchia, P., Noone, D., Powell, L. G., Salzberg, L. I., & Devine, K. M. (2011) · Microbiology · doi:10.1099/mic.0.049205-0 · Cited by 39
Absence of ppGpp Leads to Increased Mobilization of Intermediately Accumulated Poly(3-Hydroxybutyrate) in Ralstonia eutropha H16
Juengert, J. R., Borisova, M., Mayer, C., Wolz, C., Brigham, C. J., Sinskey, A. J., & Jendrossek, D. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.00755-17 · Cited by 39
Activity Control of the ClpC Adaptor McsB in Bacillus subtilis
Elsholz, A. K. W., Hempel, K., Michalik, S., Gronau, K., Becher, D., Hecker, M., & Gerth, U. (2011) · Journal of Bacteriology · doi:10.1128/jb.00079-11 · Cited by 39
Self-citation
Phosphate Starvation Induces the Sporulation Killing Factor of Bacillus subtilis
Allenby, N., Watts, C. A., Homuth, G., Prágai, Z., Wipat, A., Ward, A. C., & Harwood, C. R. (2006) · Journal of Bacteriology · doi:10.1128/jb.00084-06 · Cited by 37
Self-citation
Quantification of global transcription patterns in prokaryotes using spotted microarrays
Sidders, B. S., Withers, M., Kendall, S. L., Bacon, J., Waddell, S. J., Hinds, J., Golby, P., Movahedzadeh, F., Cox, R. A., Frita, R., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-12-r265 · Cited by 37
The YvfTU Two-component System is involved in plcR expression in Bacillus cereus
Brillard, J., Susanna, K. A., Michaud, C., Dargaignaratz, C., Gohar, M., Nielsen‐LeRoux, C., Ramarao, N., Kolstø, A., Nguyen‐The, C., Lereclus, D., et al. (2008) · BMC Microbiology · doi:10.1186/1471-2180-8-183 · Cited by 35
Sense and nonsense from a systems biology approach to microbial recombinant protein production
Sevastsyanovich, Y. R., Alfasi, S., & Cole, J. A. (2010) · Biotechnology and Applied Biochemistry · doi:10.1042/ba20090174 · Cited by 35
A Proteomic View of Cell Physiology of Bacillus subtilis — Bringing the Genome Sequence to Life
Hecker, M. (2003) · Advances in biochemical engineering, biotechnology · doi:10.1007/3-540-36459-5_3 · Cited by 35
Self-citation
Mapping of Interactions between Human Macrophages and Staphylococcus aureus Reveals an Involvement of MAP Kinase Signaling in the Host Defense
Miller, M., Dreisbach, A., Otto, A., Becher, D., Bernhardt, J., Hecker, M., Peppelenbosch, M. P., & van Dijl, J. M. (2011) · Journal of Proteome Research · doi:10.1021/pr200224x · Cited by 34
Self-citation
A Novel Two-Component System Involved in the Transition to Secondary Metabolism in Streptomyces coelicolor
Rozas, D., Gullón, S., & Mellado, R. P. (2012) · PLoS ONE · doi:10.1371/journal.pone.0031760 · Cited by 33
Antibiotic Resistance to Mycobacterium tuberculosis and Potential Use of Natural and Biological Products as Alternative Anti-Mycobacterial Agents
Arrigoni, R., Ballini, A., Topi, S., Bottalico, L., Jirillo, E., & Santacroce, L. (2022) · Antibiotics · doi:10.3390/antibiotics11101431 · Cited by 36
Proteomic analysis reveals the strategies of Bacillus thuringiensis YBT‐1520 for survival under long‐term heat stress
Wu, D., He, J., Gong, Y., Chen, D., Zhu, X., Qiu, N., Sun, M., Li, M., & Yu, Z. (2011) · PROTEOMICS · doi:10.1002/pmic.201000392 · Cited by 33
New Insights into the Enterococcus faecalis CroRS Two-Component System Obtained Using a Differential-Display Random Arbitrarily Primed PCR Approach
Breton, Y. S. L., Muller, C., Auffray, Y., & Rincé, A. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00390-07 · Cited by 33
Zinc oxide induces the stringent response and major reorientations in the central metabolism of Bacillus subtilis
Luche, S., Eymard-Vernain, E., Diemer, H., DORSSELAER, A. V., Rabilloud, T., & Lelong, C. (2015) · Journal of Proteomics · doi:10.1016/j.jprot.2015.07.018 · Cited by 30
Rickettsia conorii Transcriptional Response within Inoculation Eschar
Renesto, P., Rovery, C., Schrenzel, J., Leroy, Q., Huyghe, A., Li, W., Lépidi, H., François, P., & Raoult, D. (2008) · PLoS ONE · doi:10.1371/journal.pone.0003681 · Cited by 30
Review of microarray studies for host–intracellular pathogen interactions
Leroy, Q., & Raoult, D. (2010) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2010.02.008 · Cited by 29
Genetic and Transcriptomic Analyses of Ciprofloxacin-Tolerant Staphylococcus aureus Isolated by the Replica Plating Tolerance Isolation System (REPTIS)
Matsuo, M., Hiramatsu, M., Singh, M., Sasaki, T., Hishinuma, T., Yamamoto, N., Morimoto, Y., Kirikae, T., & Hiramatsu, K. (2018) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02019-18 · Cited by 29
The iron‐regulated transcriptome and proteome of Neisseria meningitidis serogroup C
Basler, M., Linhartová, I., Halada, P., Novotná, J., Bezoušková, S., Osička, R., Weiser, J., Vohradský, J., & Šebo, P. (2006) · PROTEOMICS · doi:10.1002/pmic.200600312 · Cited by 29
A Novel Domain in Translational GTPase BipA Mediates Interaction with the 70S Ribosome and Influences GTP Hydrolysis
deLivron, M. A., Makanji, H. S., Lane, M. C., & Robinson, V. L. (2009) · Biochemistry · doi:10.1021/bi901026z · Cited by 29
Modulators of Enterococcus faecalis Cell Envelope Integrity and Antimicrobial Resistance Influence Stable Colonization of the Mammalian Gastrointestinal Tract
Banla, I. L., Kommineni, S., Hayward, M., Rodrigues, M., Palmer, K. L., Salzman, N. H., & Kristich, C. J. (2017) · Infection and Immunity · doi:10.1128/iai.00381-17 · Cited by 28
Proteomic profiling of cellular stresses in Bacillus subtilis reveals cellular networks and assists in elucidating antibiotic mechanisms of action
Bandow, J. E., & Hecker, M. (2007) · Birkhäuser Basel eBooks · doi:10.1007/978-3-7643-7567-6_4 · Cited by 29
Self-citation
Induction of σB-dependent general stress genes by amino acid starvation in a spo0H mutant of Bacillus subtilis
Eymann, C., & Hecker, M. (2001) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2001.tb10678.x · Cited by 29
Self-citation
Physiological and cell morphology adaptation of B acillus subtilis at near‐zero specific growth rates: a transcriptome analysis
Overkamp, W., Ercan, O., Herber, M., van Maris, A. J. A., Kleerebezem, M., & Kuipers, O. P. (2014) · Environmental Microbiology · doi:10.1111/1462-2920.12676 · Cited by 26
Spx, the central regulator of the heat and oxidative stress response in B. subtilis, can repress transcription of translation‐related genes
Schäfer, H., Heinz, A., Sudzinová, P., Voß, M., Hantke, I., Krásný, L., & Turgay, K. (2018) · Molecular Microbiology · doi:10.1111/mmi.14171 · Cited by 29
Progress in functional genomics approaches to antifungal drug target discovery
Backer, M. D. D., & Dijck, P. V. (2003) · Trends in Microbiology · doi:10.1016/j.tim.2003.08.008 · Cited by 29
Role of RelGsuin Stress Response and Fe(III) Reduction inGeobacter sulfurreducens
DiDonato, L. N., Sullivan, S. A., Methé, B. A., Nevin, K. P., England, R. R., & Lovley, D. R. (2006) · Journal of Bacteriology · doi:10.1128/jb.01278-06 · Cited by 26
Proteome profiling and its use in metabolic and cellular engineering
Han, M., & Lee, S. Y. (2003) · PROTEOMICS · doi:10.1002/pmic.200300508 · Cited by 27
Stringent Response in Mycobacteria: From Biology to Therapeutic Potential
Gupta, K. R., Arora, G., Mattoo, A. R., & Sajid, A. (2021) · Pathogens · doi:10.3390/pathogens10111417 · Cited by 27
Common versus noble B acillus subtilis differentially responds to air and argon gas plasma
Winter, T., Bernhardt, J., Winter, J., Mäder, U., Schlüter, R., Weltmann, K., Hecker, M., & Kusch, H. (2013) · PROTEOMICS · doi:10.1002/pmic.201200343 · Cited by 26
Self-citation
The Bacillus subtilis ywjI ( glpX ) Gene Encodes a Class II Fructose-1,6-Bisphosphatase, Functionally Equivalent to the Class III Fbp Enzyme
Jules, M., Chat, L. L., Aymerich, S., & Coq, D. L. (2009) · Journal of Bacteriology · doi:10.1128/jb.01783-08 · Cited by 26
The role of thioredoxin TrxA in Bacillus subtilis: A proteomics and transcriptomics approach
Mostertz, J., Hochgräfe, F., Jürgen, B., Schweder, T., & Hecker, M. (2008) · PROTEOMICS · doi:10.1002/pmic.200701015 · Cited by 26
Self-citation
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
Proteomic Studies of Bacillus Anthracis
Chitlaru, T., & Avigdor Shafferman, C. (2009) · Future Microbiology · doi:10.2217/fmb.09.73 · Cited by 25
Changes of DNA topology affect the global transcription landscape and allow rapid growth of a Bacillus subtilis mutant lacking carbon catabolite repression
Reuß, D. R., Rath, H., Thürmer, A., Benda, M., Daniel, R., Völker, U., Mäder, U., Commichau, F. M., & Stülke, J. (2017) · Metabolic Engineering · doi:10.1016/j.ymben.2017.12.004 · Cited by 21
Overflow of a hyper‐produced secretory protein from the Bacillus Sec pathway into the Tat pathway for protein secretion as revealed by proteogenomics
Kouwen, T. R. H. M., van der Ploeg, R., Antelmann, H., Hecker, M., Homuth, G., Mäder, U., & van Dijl, J. M. (2009) · PROTEOMICS · doi:10.1002/pmic.200800580 · Cited by 24
Self-citation
Comparative analysis of the responses of related pathogenic and environmental bacteria to oxidative stress
Tu, W. Y., Pohl, S., Summpunn, P., Hering, S., Kerstan, S., & Harwood, C. R. (2011) · Microbiology · doi:10.1099/mic.0.057000-0 · Cited by 23
The Bifunctional Enzyme SpoT Is Involved in the Clarithromycin Tolerance of Helicobacter pylori by Upregulating the Transporters HP0939, HP1017, HP0497, and HP0471
Geng, X., Li, W., Chen, Z., Gao, S., Hong, W., Ge, X., Hou, G., Hu, Z., Zhou, Y., Zeng, B., et al. (2017) · Antimicrobial Agents and Chemotherapy · doi:10.1128/aac.02011-16 · Cited by 23
l-Valine biosynthesis during batch and fed-batch cultivations of Corynebacterium glutamicum: Relationship between changes in bacterial growth rate and intracellular metabolism
Ruklisha, M., Paegle, L., & Deniņa, I. (2006) · Process Biochemistry · doi:10.1016/j.procbio.2006.11.008 · Cited by 23
Epithelial cell responses induced upon adherence of pathogenic Neisseria
Plant, L., Asp, V., Lövkvist, L., Sundqvist, J., & Jonsson, A. (2004) · Cellular Microbiology · doi:10.1111/j.1462-5822.2004.00393.x · Cited by 23
Localization of rRNA Synthesis inBacillus subtilis: Characterization of Loci Involved in Transcription Focus Formation
Davies, K. M., & Lewis, P. J. (2003) · Journal of Bacteriology · doi:10.1128/jb.185.7.2346-2353.2003 · Cited by 23
The Iron-Binding Protein Dps2 Confers Peroxide Stress Resistance on Bacillus anthracis
Tu, W. Y., Pohl, S., Gizynski, K., & Harwood, C. R. (2011) · Journal of Bacteriology · doi:10.1128/jb.06005-11 · Cited by 22
High growth rate and substrate exhaustion results in rapid cell death and lysis in the thermophilic bacterium Geobacillus thermoleovorans
Pavlostathis, S. G., Marchant, R., Banat, I. M., Ternan, N. G., & McMullan, G. (2006) · Biotechnology and Bioengineering · doi:10.1002/bit.20962 · Cited by 22
Global Gene Expression Profiling of Bacillus subtilis in Response to Ammonium and Tryptophan Starvation as Revealed by Transcriptome and Proteome Analysis
Tam, L. T., Eymann, C., Antelmann, H., Albrecht, D., & Hecker, M. (2006) · Microbial Physiology · doi:10.1159/000096467 · Cited by 22
Self-citation
Bacterial Chromosome Replication and DNA Repair During the Stringent Response
Sinha, A. K., Løbner‐Olesen, A., & Riber, L. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.582113 · Cited by 21
Omics (Genomics, Proteomics, Metabolomics, Etc.) Tools to Study the Environmental Microbiome and Bioremediation
Singh, D., Geat, N., Mehriya, M., Rajawat, M. V. S., Prasanna, R., Kumar, A., Kumari, G., & Jha, M. N. (2020) · Springer eBooks · doi:10.1007/978-981-33-4347-4_10 · Cited by 21
Mfd protects against oxidative stress in Bacillus subtilis independently of its canonical function in DNA repair
Martin, H. A., Porter, K. E., Vallin, C., Ermi, T., Contreras, N., Pedraza‐Reyes, M., & Robleto, E. A. (2019) · BMC Microbiology · doi:10.1186/s12866-019-1394-x · Cited by 23
Streptomyces coelicolor XdhR is a direct target of (p)ppGpp that controls expression of genes encoding xanthine dehydrogenase to promote purine salvage
Sivapragasam, S., & Grove, A. (2016) · Molecular Microbiology · doi:10.1111/mmi.13342 · Cited by 21

Authors: Eymann, C., Homuth, G., Scharf, C., & Hecker, M.
Affiliations: Universität Greifswald (DE)
Corresponding author: Hecker, Michael
ORCID: Eymann, Christine
Homuth, Georg
Scharf, Christian
Venue: Journal of Bacteriology
Publisher: American Society for Microbiology
Published: 2002-05
Volume: 184
Issue: 9
Pages: 2500-2520
ISSN: 0021-9193 (ISSN-L)
1098-5530
DOI: 10.1128/jb.184.9.2500-2520.2002
PMC: PMC134987
OpenAlex: W2161630640
Cited by: 306
References: 96
Citations by year: 2026: 10 · 2025: 8 · 2024: 3 · 2023: 5 · 2022: 5 · 2021: 6 · 2020: 16 · 2019: 2 · 2018: 9 · 2017: 12 · 2016: 5 · 2015: 9 · 2014: 12 · 2013: 7 · 2012: 12
FWCI: 12.77
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: journals.asm.org/non-commercial-tdm-license (tdm)
Locations: Journal of Bacteriology (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Funders: Fonds der Chemischen Industrie
Deutsche Forschungsgemeinschaft
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biochemical and Molecular Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
Keywords: stringent response, Bacillus subtilis, RelA, (p)ppGpp, protein synthesis regulation, transcriptome, proteome, gene expression profiling, ribosome biogenesis, glycolytic enzymes
MeSH terms: Bacillus subtilis, Bacterial Proteins, Guanosine Tetraphosphate, Ligases, RNA, Messenger, Transcription, Genetic, Protein Biosynthesis, Valine, Electrophoresis, Gel, Two-Dimensional, Gene Expression, Gene Expression Regulation, Bacterial, DNA, Complementary, Regulon, Oligonucleotide Array Sequence Analysis, Proteome

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Bacillus subtilis functional genomics: global characterization of the stringent response by proteome and transcriptome analysis

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks