1
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Heiman CM, Antar H, Fournes F, Keel C, Vacheron J. The repressor PrtR1 and the global H-NS-like regulators MvaT and MvaV enable the fine-tuning of R-tailocin expression in Pseudomonas protegens. BMC Microbiol 2025; 25:286. [PMID: 40350448 PMCID: PMC12066065 DOI: 10.1186/s12866-025-03983-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Accepted: 04/21/2025] [Indexed: 05/14/2025] Open
Abstract
BACKGROUND Bacteria rely on an arsenal of weapons to challenge their opponents in highly competitive environments. To specifically counter closely related bacteria, specialized weapons with a narrow activity spectrum are deployed, particularly contractile phage tail-like particles or R-tailocins. Their production leads to the lysis of the producing cells, indicating that their expression must be carefully orchestrated so that only a small percentage of cells produce R-tailocins for the benefit of the entire population. RESULTS In this study, we set out to better understand how the production of these phage tail-like weapons is regulated in environmental pseudomonads using the competitive plant root colonizer and environmental model strain Pseudomonas protegens CHA0. Using an RNA sequencing (RNA-seq) approach, we found that genes involved in DNA repair, particularly the SOS response program, are upregulated following exposure of the pseudomonad to the DNA-damaging agents mitomycin C and hydrogen peroxide, while genes involved in cell division and primary metabolism are downregulated. The R-tailocin and prophage gene clusters were also upregulated in response to these DNA damaging agents. By combining reverse genetics, transcriptional reporters and chromatin immunoprecipitation sequencing (ChIP-seq), we show that the R-tailocin locus-specific LexA-like regulator PrtR1 represses R-tailocin gene expression by binding directly to the promoter region of the cluster, while the histone-like nucleoid structuring (H-NS) proteins MvaT and MvaV act as master regulators that indirectly regulate R-tailocin cluster expression. CONCLUSION Our results suggest that at least these three regulators operate in concert to ensure tight control of R-tailocin expression and cell lytic release in environmental Pseudomonas protegens strains.
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Affiliation(s)
- Clara Margot Heiman
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Hammam Antar
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Florian Fournes
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland.
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Biophore Building, Lausanne, CH-1015, Switzerland.
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2
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Chen H, Zheng F, Feng X, Huang Z, Yang W, Zhang C, Du W, Makarova KS, Koonin EV, Zeng Z. Engineering archaeal membrane-spanning lipid GDGT biosynthesis in bacteria: Implications for early life membrane transformations. MLIFE 2025; 4:193-204. [PMID: 40313982 PMCID: PMC12042123 DOI: 10.1002/mlf2.70001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2024] [Revised: 11/17/2024] [Accepted: 12/25/2024] [Indexed: 05/03/2025]
Abstract
Eukaryotes are hypothesized to be archaeal-bacterial chimeras. Given the different chemical structures of membrane phospholipids in archaea and bacteria, transformations of membranes during eukaryogenesis that led to the bacterial-type membranes of eukaryotic cells remain a major conundrum. One of the possible intermediates of eukaryogenesis could involve an archaeal-bacterial hybrid membrane. So far, organisms with hybrid membranes have not been discovered, and experimentation on such membranes has been limited. To generate mixed membranes, we reconstructed the archaeal membrane lipid biosynthesis pathway in Escherichia coli, creating three strains that individually produced archaeal lipids ranging from simple, such as DGGGOH (digeranylgeranylglycerol) and archaeol, to complex, such as GDGT (glycerol dialkyl glycerol tetraether). The physiological responses became more pronounced as the hybrid membrane incorporated more complex archaeal membrane lipids. In particular, biosynthesis of GDGT induced a pronounced SOS response, accompanied by cellular filamentation, explosive cell lysis, and ATP accumulation. Thus, bacteria seem to be able to incorporate simple archaeal membrane lipids, such as DGGGOH and archaeol, without major fitness costs, compatible with the involvement of hybrid membranes at the early stages of cell evolution and in eukaryogenesis. By contrast, the acquisition of more complex, structurally diverse membrane lipids, such as GDGT, appears to be strongly deleterious to bacteria, suggesting that this type of lipid is an archaeal innovation.
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Affiliation(s)
- Huahui Chen
- Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Fengfeng Zheng
- Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Xi Feng
- Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Zijing Huang
- Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Wei Yang
- Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Chuanlun Zhang
- Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
| | - Wenbin Du
- State Key Laboratory of Microbial Resources, Institute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Kira S. Makarova
- National Center for Biotechnology Information, National Library of MedicineBethesdaMarylandUSA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of MedicineBethesdaMarylandUSA
| | - Zhirui Zeng
- Department of Ocean Science and EngineeringSouthern University of Science and TechnologyShenzhenChina
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3
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He Y, Qin Y, Greenwich J, Balaban S, Darcera MVL, Gozzi K, Chai Y. A novel regulation on the developmental checkpoint protein Sda that controls sporulation and biofilm formation in Bacillus subtilis. J Bacteriol 2025; 207:e0021024. [PMID: 39932315 PMCID: PMC11925247 DOI: 10.1128/jb.00210-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 11/19/2024] [Indexed: 03/21/2025] Open
Abstract
Biofilm formation by Bacillus subtilis is triggered by an unusually simple environmental sensing mechanism. Certain serine codons, the four TCN codons (N for A, T, C, or G), in the gene for the biofilm repressor SinR caused lowered SinR translation and subsequent biofilm induction during transition from exponential to stationary growth. Global ribosome profiling showed that ribosomes pause when translating the four UCN (U for T on the mRNA) serine codons on mRNA, but not the two AGC/AGU serine codons. We proposed a serine codon hierarchy (AGC/AGT vs TCN) in that genes enriched in the TCN serine codons may experience reduced translation efficiency when serine is limited. In this study, we designed an algorithm to score all protein-coding genes in B. subtilis NCIB3610 based on the serine codon hierarchy. We generated a short list of 50 genes that could be subject to regulation by this novel mechanism. We further investigated one such gene from the list, sda, which encodes a developmental checkpoint protein regulating both sporulation and biofilm formation. We showed that synonymously switching the TCN serine codons to AGC in sda led to delayed biofilm formation and sporulation. This engineered strain also outgrew strains with other synonymously substituted sda alleles (TCN) in competition assays for biofilm formation and sporulation. Finally, we showed that the AGC serine codon substitutions in sda elevated the Sda protein levels. This serine codon hierarchy-based novel signaling mechanism could be exploited by bacteria in adapting to stationary phase and regulating important biological processes. IMPORTANCE Genome-wide ribosome profiling in Bacillus subtilis shows that under serine limitation, ribosomes pause on the four TCN (N for A, C, G, and T), but not AGC/AGT serine codons, during translation at a global scale. This serine codon hierarchy (AGC/T vs TCN) differentially influences the translation efficiency of genes enriched in certain serine codons. In this study, we designed an algorithm to score all 4,000+ genes in the B. subtilis genome and generated a list of 50 genes that could be subject to this novel serine codon hierarchy-mediated regulation. We further investigated one such gene, sda, encoding a developmental checkpoint protein. We show that sda and cell developments controlled by Sda are also regulated by this novel mechanism.
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Affiliation(s)
- Yinghao He
- Biology Department, Northeastern University, Boston, Massachusetts, USA
| | - Yuxuan Qin
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | | | - Samantha Balaban
- Biology Department, Northeastern University, Boston, Massachusetts, USA
| | | | - Kevin Gozzi
- The Rowland Institute at Harvard, Cambridge, Massachusetts, USA
| | - Yunrong Chai
- Biology Department, Northeastern University, Boston, Massachusetts, USA
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4
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Cheng K. Structure, function and evolution of the bacterial DinG-like proteins. Comput Struct Biotechnol J 2025; 27:1124-1139. [PMID: 40206346 PMCID: PMC11981726 DOI: 10.1016/j.csbj.2025.03.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2024] [Revised: 03/10/2025] [Accepted: 03/13/2025] [Indexed: 04/11/2025] Open
Abstract
The damage-inducible G (DinG)-like proteins represent a widespread superfamily 2 (SF2) of DNA helicases, exhibiting remarkable diversity in domain architecture, substrate specificity, regulatory mechanisms, biological functions, interaction partners, and taxonomic distribution. Many characterized DinG-like proteins play critical roles in bacterial stress responses and immunity, including the SOS response, DNA repair, and phage interference. This review aims to provide a summary of bacterial DinG-like proteins, categorizing them into subgroups such as DinG, YoaA, CasDinG, CasDinG-HNH, ExoDinG, pExoDinG, EndoDinG, RadC-like DinG, sDinG, and others. This classification provides an analysis of sequence-structure-function relationships within this superfamily. Further sequence clustering revealed inter-cluster relationships and subgroup heterogeneity, suggesting potential functional divergence. Integrating sequence analysis, domain architecture, structural data, and genomic context enabled functional predictions for these DinG-like protein subgroups, shedding light on their evolutionary and biological significance.
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Affiliation(s)
- Kaiying Cheng
- Zhejiang Key Laboratory of Medical Epigenetics, Department of Immunology and Pathogen Biology, School of Basic Medical Sciences, Affiliated Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou 310003, China
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5
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O’Neal LG, Drucker MN, Lai NK, Clemente AF, Campbell AP, Way LE, Hong S, Holmes EE, Rancic SJ, Sawyer N, Wang X, Thrall ES. "The B. subtilis replicative polymerases bind the sliding clamp with different strengths to tune replication processivity and fidelity". BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.10.642433. [PMID: 40161823 PMCID: PMC11952451 DOI: 10.1101/2025.03.10.642433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/02/2025]
Abstract
Ring-shaped sliding clamp proteins are essential components of the replication machinery, the replisome, across all domains of life. In bacteria, DNA polymerases bind the sliding clamp, DnaN, through conserved short peptide sequences called clamp-binding motifs. Clamp binding increases the processivity and rate of DNA synthesis and is generally required for polymerase activity. The current understanding of clamp-polymerase interactions was elucidated in the model bacterium Escherichia coli, which has a single replicative polymerase, Pol III. However, many bacteria have two essential replicative polymerases, such as PolC and DnaE in Bacillus subtilis. PolC performs the bulk of DNA synthesis whereas the error-prone DnaE only synthesizes short stretches of DNA on the lagging strand. How the clamp interacts with the two polymerases and coordinates their activity is unknown. We investigated this question by combining in vivo single-molecule fluorescence microscopy with biochemical and microbiological assays. We found that PolC-DnaN binding is essential for replication, although weakening the interaction is tolerated with only minimal effects. In contrast, the DnaE-DnaN interaction is dispensable for replication. Altering the clamp-binding strength of DnaE produces only subtle effects on DnaE cellular localization and dynamics, but it has a substantial impact on mutagenesis. Our results support a model in which DnaE acts distributively during replication but can be stabilized on the DNA template by clamp binding. This study provides new insights into the coordination of multiple replicative polymerases in bacteria and the role of the clamp in polymerase processivity, fidelity, and exchange.
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Affiliation(s)
- Luke G. O’Neal
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Madeline N. Drucker
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Ngoc Khanh Lai
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Ashley F. Clemente
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Alyssa P. Campbell
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Lindsey E. Way
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Sinwoo Hong
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Emily E. Holmes
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Sarah J. Rancic
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Nicholas Sawyer
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
| | - Xindan Wang
- Department of Biology, Indiana University, Bloomington, IN 47405
| | - Elizabeth S. Thrall
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458
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6
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Marrin ME, Foster MR, Santana CM, Choi Y, Jassal AS, Rancic SJ, Greenwald CR, Drucker MN, Feldman DT, Thrall ES. The translesion polymerase Pol Y1 is a constitutive component of the B. subtilis replication machinery. Nucleic Acids Res 2024; 52:9613-9629. [PMID: 39051562 PMCID: PMC11381352 DOI: 10.1093/nar/gkae637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 07/03/2024] [Accepted: 07/08/2024] [Indexed: 07/27/2024] Open
Abstract
Unrepaired DNA damage encountered by the cellular replication machinery can stall DNA replication, ultimately leading to cell death. In the DNA damage tolerance pathway translesion synthesis (TLS), replication stalling is alleviated by the recruitment of specialized polymerases to synthesize short stretches of DNA near a lesion. Although TLS promotes cell survival, most TLS polymerases are low-fidelity and must be tightly regulated to avoid harmful mutagenesis. The gram-negative bacterium Escherichia coli has served as the model organism for studies of the molecular mechanisms of bacterial TLS. However, it is poorly understood whether these same mechanisms apply to other bacteria. Here, we use in vivo single-molecule fluorescence microscopy to investigate the TLS polymerase Pol Y1 in the model gram-positive bacterium Bacillus subtilis. We find significant differences in the localization and dynamics of Pol Y1 in comparison to its E. coli homolog, Pol IV. Notably, Pol Y1 is constitutively enriched at or near sites of replication in the absence of DNA damage through interactions with the DnaN clamp; in contrast, Pol IV has been shown to be selectively enriched only upon replication stalling. These results suggest key differences in the roles and mechanisms of regulation of TLS polymerases across different bacterial species.
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Affiliation(s)
- McKayla E Marrin
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Michael R Foster
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Chloe M Santana
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Yoonhee Choi
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Avtar S Jassal
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Sarah J Rancic
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Carolyn R Greenwald
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Madeline N Drucker
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Denholm T Feldman
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
| | - Elizabeth S Thrall
- Department of Chemistry and Biochemistry, Fordham University, Bronx, NY 10458, USA
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7
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Sass TH, Lovett ST. The DNA damage response of Escherichia coli, revisited: Differential gene expression after replication inhibition. Proc Natl Acad Sci U S A 2024; 121:e2407832121. [PMID: 38935560 PMCID: PMC11228462 DOI: 10.1073/pnas.2407832121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 05/29/2024] [Indexed: 06/29/2024] Open
Abstract
In 1967, in this journal, Evelyn Witkin proposed the existence of a coordinated DNA damage response in Escherichia coli, which later came to be called the "SOS response." We revisited this response using the replication inhibitor azidothymidine (AZT) and RNA-Seq analysis and identified several features. We confirm the induction of classic Save our ship (SOS) loci and identify several genes, including many of the pyrimidine pathway, that have not been previously demonstrated to be DNA damage-inducible. Despite a strong dependence on LexA, these genes lack LexA boxes and their regulation by LexA is likely to be indirect via unknown factors. We show that the transcription factor "stringent starvation protein" SspA is as important as LexA in the regulation of AZT-induced genes and that the genes activated by SspA change dramatically after AZT exposure. Our experiments identify additional LexA-independent DNA damage inducible genes, including 22 small RNA genes, some of which appear to activated by SspA. Motility and chemotaxis genes are strongly down-regulated by AZT, possibly as a result of one of more of the small RNAs or other transcription factors such as AppY and GadE, whose expression is elevated by AZT. Genes controlling the iron siderophore, enterobactin, and iron homeostasis are also strongly induced, independent of LexA. We confirm that IraD antiadaptor protein is induced independent of LexA and that a second antiadaptor, IraM is likewise strongly AZT-inducible, independent of LexA, suggesting that RpoS stabilization via these antiadaptor proteins is an integral part of replication stress tolerance.
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Affiliation(s)
- Thalia H. Sass
- Department of Biology, Brandeis University, Waltham, MA02454-9110
- Rosenstiel Basic Medical Sciences Research Center MS029, Brandeis University, Waltham, MA02454-9110
| | - Susan T. Lovett
- Department of Biology, Brandeis University, Waltham, MA02454-9110
- Rosenstiel Basic Medical Sciences Research Center MS029, Brandeis University, Waltham, MA02454-9110
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8
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Pedraza-Reyes M, Abundiz-Yañez K, Rangel-Mendoza A, Martínez LE, Barajas-Ornelas RC, Cuéllar-Cruz M, Leyva-Sánchez HC, Ayala-García VM, Valenzuela-García LI, Robleto EA. Bacillus subtilis stress-associated mutagenesis and developmental DNA repair. Microbiol Mol Biol Rev 2024; 88:e0015823. [PMID: 38551349 PMCID: PMC11332352 DOI: 10.1128/mmbr.00158-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
SUMMARYThe metabolic conditions that prevail during bacterial growth have evolved with the faithful operation of repair systems that recognize and eliminate DNA lesions caused by intracellular and exogenous agents. This idea is supported by the low rate of spontaneous mutations (10-9) that occur in replicating cells, maintaining genome integrity. In contrast, when growth and/or replication cease, bacteria frequently process DNA lesions in an error-prone manner. DNA repairs provide cells with the tools needed for maintaining homeostasis during stressful conditions and depend on the developmental context in which repair events occur. Thus, different physiological scenarios can be anticipated. In nutritionally stressed bacteria, different components of the base excision repair pathway may process damaged DNA in an error-prone approach, promoting genetic variability. Interestingly, suppressing the mismatch repair machinery and activating specific DNA glycosylases promote stationary-phase mutations. Current evidence also suggests that in resting cells, coupling repair processes to actively transcribed genes may promote multiple genetic transactions that are advantageous for stressed cells. DNA repair during sporulation is of interest as a model to understand how transcriptional processes influence the formation of mutations in conditions where replication is halted. Current reports indicate that transcriptional coupling repair-dependent and -independent processes operate in differentiating cells to process spontaneous and induced DNA damage and that error-prone synthesis of DNA is involved in these events. These and other noncanonical ways of DNA repair that contribute to mutagenesis, survival, and evolution are reviewed in this manuscript.
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Affiliation(s)
- Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Karen Abundiz-Yañez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Alejandra Rangel-Mendoza
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Lissett E. Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Rocío C. Barajas-Ornelas
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | - Mayra Cuéllar-Cruz
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato, Mexico
| | | | | | - Luz I. Valenzuela-García
- Department of Sustainable Engineering, Advanced Materials Research Center (CIMAV), Arroyo Seco, Durango, Mexico
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9
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Candra B, Cook D, Hare J. Repression of Acinetobacter baumannii DNA damage response requires DdrR-assisted binding of UmuDAb dimers to atypical SOS box. J Bacteriol 2024; 206:e0043223. [PMID: 38727225 PMCID: PMC11332147 DOI: 10.1128/jb.00432-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/14/2024] [Indexed: 06/21/2024] Open
Abstract
The DNA damage response of the multi-drug-resistant nosocomial pathogen Acinetobacter baumannii possesses multiple features that distinguish it from the commonly used LexA repression system. These include the absence of LexA in this genus, the evolution of a UmuD polymerase manager into the UmuDAb repressor of error-prone polymerases, the use of a corepressor unique to Acinetobacter (DdrR), and an unusually large UmuDAb binding site. We defined cis- and trans-acting factors required for UmuDAb DNA binding and gene repression, and tested whether DdrR directly enhances its DNA binding. We used DNA binding assays to characterize UmuDAb's binding to its proposed operator present upstream of the six co-repressed umuDC or umuC genes. UmuDAb bound tightly and cooperatively to this site with ~10-fold less affinity than LexA. DdrR enhanced the binding of both native and dimerization-deficient UmuDAb forms, but only in greater than equimolar ratios relative to UmuDAb. UmuDAb mutants unable to dimerize or effect gene repression showed impaired DNA binding, and a strain expressing the G124D dimerization mutant could not repress transcription of the UmuDAb-DdrR regulon. Competition electrophoretic mobility shift assays conducted with mutated operator probes showed that, unlike typical SOS boxes, the UmuDAb operator possessed a five-base pair central core whose sequence was more crucial for binding than the flanking palindrome. The presence of only one of the two flanking arms of the palindrome was necessary for UmuDAb binding. Overall, the data supported a model of an operator with two UmuDAb binding sites. The distinct characteristics of UmuDAb and its regulated promoters differ from the typical LexA repression model, demonstrating a novel method of repression.IMPORTANCEAcinetobacter baumannii is a gram-negative bacterium responsible for hospital-acquired infections. Its unique DNA damage response can activate multiple error-prone polymerase genes, allowing it to gain mutations that can increase its virulence and antibiotic resistance. The emergence of infectious strains carrying multiple antibiotic resistance genes, including carbapenem resistance, lends urgency to discovering and developing ways to combat infections resistant to treatment with known antibiotics. Deciphering how the regulators UmuDAb and DdrR repress the error-prone polymerases could lead to developing complementary treatments to halt this mechanism of generating resistance.
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Affiliation(s)
- Belinda Candra
- Baylor College of Medicine, Houston, Texas, USA
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, USA
| | - Deborah Cook
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, USA
| | - Janelle Hare
- Department of Biology and Chemistry, Morehead State University, Morehead, Kentucky, USA
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10
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Suyamud B, Lohwacharin J, Ngamratanapaiboon S. Effect of dissolved organic matter on bacterial regrowth and response after ultraviolet disinfection. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171864. [PMID: 38521274 DOI: 10.1016/j.scitotenv.2024.171864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 03/25/2024]
Abstract
The effect of dissolved organic matter (DOM) on bacterial regrowth in water after disinfection using ultraviolet (UV) light emitting diodes (UVLEDs) is still unclear. Herein, the regrowth and responses of Vibrio parahaemolyticus and Bacillus cereus were investigated after being exposed to UVLEDs at combined wavelengths (265 and 280 nm) in a phosphate-buffered saline consisting of Suwannee River natural organic matter (SRNOM) and Suwannee River fulvic acid (SRFA). Low-molecular-weight (MW) organic compounds, which may form into intermediary photoproducts, and indicate bacterial repair metabolism, were characterized through non-target screening using orbitrap mass spectrometry. This study demonstrates the ability of the UVLEDs-inactivated cells to regrow. After UV exposure, a considerable upregulation of RecA was observed in two strains. With increasing the incubation time, the expression levels of RecA in V. parahaemolyticus increased, which may be attributed to the dark repair mechanism. Coexisting anionic DOM affects both the disinfection and bacterial regrowth processes. The time required for bacterial regrowth after UV exposure reflects the time needed for the individual cells to reactivate, and it differs in the presence or absence of DOM. In the presence of DOM, the cells were less damaged and required less time to grow. The UVLEDs exposure results in the occurrence of low-MW organic compounds, including carnitine or acryl-carnitine with N-acetylmuramic acid, which are associated with bacterial repair metabolism. Overall, the results of this study expand the understanding of the effects of water matrices on bacterial health risks. This can aid in the development of more effective strategies for water disinfection.
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Affiliation(s)
- Bongkotrat Suyamud
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Jenyuk Lohwacharin
- Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, 254 Phayathai Road, Pathumwan, Bangkok 10330, Thailand; Professor Aroon Sorathesn Center of Excellence in Environmental Engineering, Department of Environmental Engineering, Faculty of Engineering, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Surachai Ngamratanapaiboon
- Division of Pharmacology, Department of Basic Medical Science, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, Dusit, Bangkok 10300, Thailand
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11
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Muñoz-Gutierrez V, Cornejo FA, Schmidt K, Frese CK, Halte M, Erhardt M, Elsholz AKW, Turgay K, Charpentier E. Bacillus subtilis remains translationally active after CRISPRi-mediated replication initiation arrest. mSystems 2024; 9:e0022124. [PMID: 38546227 PMCID: PMC11019786 DOI: 10.1128/msystems.00221-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/06/2024] [Indexed: 04/17/2024] Open
Abstract
Initiation of bacterial DNA replication takes place at the origin of replication (oriC), a region characterized by the presence of multiple DnaA boxes that serve as the binding sites for the master initiator protein DnaA. This process is tightly controlled by modulation of the availability or activity of DnaA and oriC during development or stress conditions. Here, we aimed to uncover the physiological and molecular consequences of stopping replication in the model bacterium Bacillus subtilis. We successfully arrested replication in B. subtilis by employing a clustered regularly interspaced short palindromic repeats interference (CRISPRi) approach to specifically target the key DnaA boxes 6 and 7, preventing DnaA binding to oriC. In this way, other functions of DnaA, such as a transcriptional regulator, were not significantly affected. When replication initiation was halted by this specific artificial and early blockage, we observed that non-replicating cells continued translation and cell growth, and the initial replication arrest did not induce global stress conditions such as the SOS response.IMPORTANCEAlthough bacteria constantly replicate under laboratory conditions, natural environments expose them to various stresses such as lack of nutrients, high salinity, and pH changes, which can trigger non-replicating states. These states can enable bacteria to (i) become tolerant to antibiotics (persisters), (ii) remain inactive in specific niches for an extended period (dormancy), and (iii) adjust to hostile environments. Non-replicating states have also been studied because of the possibility of repurposing energy for the production of additional metabolites or proteins. Using clustered regularly interspaced short palindromic repeats interference (CRISPRi) targeting bacterial replication initiation sequences, we were able to successfully control replication initiation in Bacillus subtilis. This precise approach makes it possible to study non-replicating phenotypes, contributing to a better understanding of bacterial adaptive strategies.
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Affiliation(s)
- Vanessa Muñoz-Gutierrez
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | | | - Katja Schmidt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
| | | | - Manuel Halte
- Humboldt-Universität zu Berlin, Institute of Biology – Molecular Microbiology, Berlin, Germany
| | - Marc Erhardt
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Humboldt-Universität zu Berlin, Institute of Biology – Molecular Microbiology, Berlin, Germany
| | | | - Kürşad Turgay
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Microbiology, Leibniz Universität Hannover, Hannover, Germany
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany
- Institute of Biology, Humboldt-Universität zu Berlin, Berlin, Germany
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12
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Öktem A, Pranoto DA, van Dijl JM. Post-translational secretion stress regulation in Bacillus subtilis is controlled by intra- and extracellular proteases. N Biotechnol 2024; 79:71-81. [PMID: 38158017 DOI: 10.1016/j.nbt.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/20/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
The Gram-positive bacterium Bacillus subtilis is a prolific producer of industrial enzymes that are effectively harvested from the fermentation broth. However, the high capacity of B. subtilis for protein secretion has so far not been exploited to the full due to particular bottlenecks, including product degradation by extracellular proteases and counterproductive secretion stress responses. To unlock the Bacillus secretion pathway for difficult-to-produce proteins, various cellular interventions have been explored, including genome engineering. Our previous research has shown a superior performance of genome-reduced B. subtilis strains in the production of staphylococcal antigens compared to the parental strain 168. This was attributed, at least in part, to redirected secretion stress responses, including the presentation of elevated levels of the quality control proteases HtrA and HtrB that also catalyse protein folding. Here we show that this relates to the elimination of two homologous serine proteases, namely the cytosolic protease AprX and the extracellular protease AprE. This unprecedented posttranslational regulation of secretion stress effectors, like HtrA and HtrB, by the concerted action of cytosolic and extracellular proteases has important implications for the biotechnological application of microbial cell factories. In B. subtilis, this conclusion is underscored by extracellular degradation of the staphylococcal antigen IsaA by both AprX and AprE. Extracellular activity of the cytosolic protease AprX is remarkable since it shows that not only extracellular, but also intracellular proteases impact extracellular product levels. We therefore conclude that intracellular proteases represent new targets for improved recombinant protein production in microbial cell factories like B. subtilis.
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Affiliation(s)
- Ayşegül Öktem
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Dicky A Pranoto
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands
| | - Jan Maarten van Dijl
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, the Netherlands.
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13
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Martínez LE, Gómez G, Ramírez N, Franco B, Robleto EA, Pedraza-Reyes M. 8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis. Antioxidants (Basel) 2024; 13:332. [PMID: 38539865 PMCID: PMC10968225 DOI: 10.3390/antiox13030332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/27/2024] [Accepted: 03/05/2024] [Indexed: 04/04/2024] Open
Abstract
The guanine oxidized (GO) system of Bacillus subtilis, composed of the YtkD (MutT), MutM and MutY proteins, counteracts the cytotoxic and genotoxic effects of the oxidized nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, the genetic inactivation of GO system potentiated mutagenesis (HPM), and subsequent hyperresistance, contributes to the damaging effects of hydrogen peroxide (H2O2) (HPHR). The mechanism(s) that connect the accumulation of the mutagenic lesion 8-OxoG with the ability of B. subtilis to evolve and survive the noxious effects of oxidative stress were dissected. Genetic and biochemical evidence indicated that the synthesis of KatA was exacerbated, in a PerR-independent manner, and the transcriptional coupling repair factor, Mfd, contributed to HPHR and HPM of the ΔGO strain. Moreover, these phenotypes are associated with wider pleiotropic effects, as revealed by a global proteome analysis. The inactivation of the GO system results in the upregulated production of KatA, and it reprograms the synthesis of the proteins involved in distinct types of cellular stress; this has a direct impact on (i) cysteine catabolism, (ii) the synthesis of iron-sulfur clusters, (iii) the reorganization of cell wall architecture, (iv) the activation of AhpC/AhpF-independent organic peroxide resistance, and (v) increased resistance to transcription-acting antibiotics. Therefore, to contend with the cytotoxic and genotoxic effects derived from the accumulation of 8-OxoG, B. subtilis activates the synthesis of proteins belonging to transcriptional regulons that respond to a wide, diverse range of cell stressors.
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Affiliation(s)
- Lissett E. Martínez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Gerardo Gómez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Norma Ramírez
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Bernardo Franco
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
| | - Eduardo A. Robleto
- School of Life Sciences, University of Nevada, Las Vegas, NV 89557, USA;
| | - Mario Pedraza-Reyes
- Department of Biology, Division of Natural and Exact Sciences, University of Guanajuato, Guanajuato 36050, Mexico; (L.E.M.); (G.G.); (N.R.); (B.F.)
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14
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Carrasco B, Torres R, Moreno-del Álamo M, Ramos C, Ayora S, Alonso JC. Processing of stalled replication forks in Bacillus subtilis. FEMS Microbiol Rev 2024; 48:fuad065. [PMID: 38052445 PMCID: PMC10804225 DOI: 10.1093/femsre/fuad065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 12/07/2023] Open
Abstract
Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent model system for studying the pathways required to cope with replication stress to preserve genomic stability. This review focuses on the genetics, single molecule choreography, and biochemical properties of the proteins that act to circumvent the replicative arrest allowing the resumption of DNA synthesis. The RecA recombinase, its mediators (RecO, RecR, and RadA/Sms) and modulators (RecF, RecX, RarA, RecU, RecD2, and PcrA), repair licensing (DisA), fork remodelers (RuvAB, RecG, RecD2, RadA/Sms, and PriA), Holliday junction resolvase (RecU), nucleases (RnhC and DinG), and translesion synthesis DNA polymerases (PolY1 and PolY2) are key functions required to overcome a replication stress, provided that the fork does not collapse.
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Affiliation(s)
- Begoña Carrasco
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - María Moreno-del Álamo
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Cristina Ramos
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin Str, 28049 Madrid, Spain
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15
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Idris AL, Li W, Huang F, Lin F, Guan X, Huang T. Impacts of UV radiation on Bacillus biocontrol agents and their resistance mechanisms. World J Microbiol Biotechnol 2024; 40:58. [PMID: 38165488 DOI: 10.1007/s11274-023-03856-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Bacillus biocontrol agent(s) BCA(s) such as Bacillus cereus, Bacillus thuringiensis and Bacillus subtilis have been widely applied to control insects' pests of plants and pathogenic microbes, improve plant growth, and facilitate their resistance to environmental stresses. In the last decade, researchers have shown that, the application of Bacillus biocontrol agent(s) BCA(s) optimized agricultural production yield, and reduced disease risks in some crops. However, these bacteria encountered various abiotic stresses, among which ultraviolet (UV) radiation severely decrease their efficiency. Researchers have identified several strategies by which Bacillus biocontrol agents resist the negative effects of UV radiation, including transcriptional response, UV mutagenesis, biochemical and artificial means (addition of protective agents). These strategies are governed by distinct pathways, triggered by UV radiation. Herein, the impact of UV radiation on Bacillus biocontrol agent(s) BCA(s) and their mechanisms of resistance were discussed.
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Affiliation(s)
- Aisha Lawan Idris
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wenting Li
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fugui Huang
- Fujian Polytechnic of Information Technology, Fuzhou, 350003, China
| | - Fuyong Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiong Guan
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Tianpei Huang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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16
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Burton AT, Pospíšilová D, Sudzinova P, Snider EV, Burrage AM, Krásný L, Kearns DB. The alternative sigma factor SigN of Bacillus subtilis is intrinsically toxic. J Bacteriol 2023; 205:e0011223. [PMID: 37728605 PMCID: PMC10601692 DOI: 10.1128/jb.00112-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 07/13/2023] [Indexed: 09/21/2023] Open
Abstract
Sigma factors bind and direct the RNA polymerase core to specific promoter sequences, and alternative sigma factors direct transcription of different regulons of genes. Here, we study the pBS32 plasmid-encoded sigma factor SigN of Bacillus subtilis to determine how it contributes to DNA damage-induced cell death. We find that SigN causes cell death when expressed at high levels and does so in the absence of its regulon suggesting it is intrinsically toxic. One way toxicity was relieved was by curing the pBS32 plasmid, which eliminated a positive feedback loop that led to SigN hyper-accumulation. Another way toxicity was relieved was through mutating the chromosomally encoded transcriptional repressor protein AbrB, thereby derepressing a potent antisense transcript that antagonized SigN expression. SigN efficiently competed with the vegetative sigma factor SigA in vitro, and SigN accumulation in the absence of positive feedback reduced SigA-dependent transcription suggesting that toxicity may be due to competitive inhibition of one or more essential transcripts. Why B. subtilis encodes a toxic sigma factor is unclear but SigN may function in host-inhibition during lytic conversion, as phage lysogen genes are also encoded on pBS32. IMPORTANCE Alternative sigma factors activate entire regulons of genes to improve viability in response to environmental stimuli. The pBS32 plasmid-encoded alternative sigma factor SigN of Bacillus subtilis however, is activated by the DNA damage response and leads to cellular demise. Here we find that SigN impairs viability by hyper-accumulating and outcompeting the vegetative sigma factor for the RNA polymerase core. Why B. subtilis retains a plasmid with a deleterious alternative sigma factor is unknown.
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Affiliation(s)
- Aisha T. Burton
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Debora Pospíšilová
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague, Czechia
| | - Petra Sudzinova
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague, Czechia
| | | | - Andrew M. Burrage
- Department of Biology, Indiana University, Bloomington, Indiana, USA
| | - Libor Krásný
- Institute of Microbiology, Czech Academy of Sciences, Vídeňská, Prague, Czechia
| | - Daniel B. Kearns
- Department of Biology, Indiana University, Bloomington, Indiana, USA
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17
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van Gestel J, Wagner A, Ackermann M. Pleiotropic hubs drive bacterial surface competition through parallel changes in colony composition and expansion. PLoS Biol 2023; 21:e3002338. [PMID: 37844064 PMCID: PMC10578586 DOI: 10.1371/journal.pbio.3002338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/18/2023] [Indexed: 10/18/2023] Open
Abstract
Bacteria commonly adhere to surfaces where they compete for both space and resources. Despite the importance of surface growth, it remains largely elusive how bacteria evolve on surfaces. We previously performed an evolution experiment where we evolved distinct Bacilli populations under a selective regime that favored colony spreading. In just a few weeks, colonies of Bacillus subtilis showed strongly advanced expansion rates, increasing their radius 2.5-fold relative to that of the ancestor. Here, we investigate what drives their rapid evolution by performing a uniquely detailed analysis of the evolutionary changes in colony development. We find mutations in diverse global regulators, RicT, RNAse Y, and LexA, with strikingly similar pleiotropic effects: They lower the rate of sporulation and simultaneously facilitate colony expansion by either reducing extracellular polysaccharide production or by promoting filamentous growth. Combining both high-throughput flow cytometry and gene expression profiling, we show that regulatory mutations lead to highly reproducible and parallel changes in global gene expression, affecting approximately 45% of all genes. This parallelism results from the coordinated manner by which regulators change activity both during colony development-in the transition from vegetative growth to dormancy-and over evolutionary time. This coordinated activity can however also break down, leading to evolutionary divergence. Altogether, we show how global regulators function as major pleiotropic hubs that drive rapid surface adaptation by mediating parallel changes in both colony composition and expansion, thereby massively reshaping gene expression.
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Affiliation(s)
- Jordi van Gestel
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Andreas Wagner
- Department of Evolutionary Biology and Environmental Studies, University of Zürich, Zürich, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
- Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
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18
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Angelini LL, Dos Santos RAC, Fox G, Paruthiyil S, Gozzi K, Shemesh M, Chai Y. Pulcherrimin protects Bacillus subtilis against oxidative stress during biofilm development. NPJ Biofilms Microbiomes 2023; 9:50. [PMID: 37468524 PMCID: PMC10356805 DOI: 10.1038/s41522-023-00418-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 07/04/2023] [Indexed: 07/21/2023] Open
Abstract
Pulcherrimin is an iron-binding reddish pigment produced by various bacterial and yeast species. In the soil bacterium Bacillus subtilis, this pigment is synthesized intracellularly as the colorless pulcherriminic acid by using two molecules of tRNA-charged leucine as the substrate; pulcherriminic acid molecules are then secreted and bind to ferric iron extracellularly to form the red-colored pigment pulcherrimin. The biological importance of pulcherrimin is not well understood. A previous study showed that secretion of pulcherrimin caused iron depletion in the surroundings and growth arrest on cells located at the edge of a B. subtilis colony biofilm. In this study, we identified that pulcherrimin is primarily produced under biofilm conditions and provides protection to cells in the biofilm against oxidative stress. We presented molecular evidence on how pulcherrimin lowers the level of reactive oxygen species (ROS) and alleviates oxidative stress and DNA damage caused by ROS accumulation in a mature biofilm. We also performed global transcriptome profiling to identify differentially expressed genes in the pulcherrimin-deficient mutant compared with the wild type, and further characterized the regulation of genes by pulcherrimin that are related to iron homeostasis, DNA damage response (DDR), and oxidative stress response. Based on our findings, we propose pulcherrimin as an important antioxidant that modulates B. subtilis biofilm development.
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Affiliation(s)
| | | | - Gabriel Fox
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
| | - Srinand Paruthiyil
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
- Medical Scientist Training Program (MSTP), Washington University School of Medicine, 660 S Euclid Ave, St. Louis, MO, 63110, USA
| | - Kevin Gozzi
- Department of Biology, Northeastern University, Boston, MA, 02115, USA
- The Rowland Institute at Harvard, 100 Edwin H. Land Blvd., Cambridge, MA, 02142, USA
| | - Moshe Shemesh
- Department of Food Science, Agricultural Research Organization The Volcani Institute, Derech Hamacabim, POB 15159, Rishon LeZion, 7528809, Israel
| | - Yunrong Chai
- Department of Biology, Northeastern University, Boston, MA, 02115, USA.
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19
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Li J, Xiao X, Zhou M, Zhang Y. Strategy for the Adaptation to Stressful Conditions of the Novel Isolated Conditional Piezophilic Strain Halomonas titanicae ANRCS81. Appl Environ Microbiol 2023; 89:e0130422. [PMID: 36912687 PMCID: PMC10057041 DOI: 10.1128/aem.01304-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 02/10/2023] [Indexed: 03/14/2023] Open
Abstract
Microorganisms have successfully predominated deep-sea ecosystems, while we know little about their adaptation strategy to multiple environmental stresses therein, including high hydrostatic pressure (HHP). Here, we focused on the genus Halomonas, one of the most widely distributed halophilic bacterial genera in marine ecosystems and isolated a piezophilic strain Halomonas titanicae ANRCS81 from Antarctic deep-sea sediment. The strain grew under a broad range of temperatures (2 to 45°C), pressures (0.1 to 55 MPa), salinities (NaCl, 0.5 to 17.5%, wt/vol), and chaotropic agent (Mg2+, 0 to 0.9 M) with either oxygen or nitrate as an electron acceptor. Genome annotation revealed that strain ANRCS81 expressed potential antioxidant genes/proteins and possessed versatile energy generation pathways. Based on the transcriptomic analysis, when the strain was incubated at 40 MPa, genes related to antioxidant defenses, anaerobic respiration, and fermentation were upregulated, indicating that HHP induced intracellular oxidative stress. Under HHP, superoxide dismutase (SOD) activity increased, glucose consumption increased with less CO2 generation, and nitrate/nitrite consumption increased with more ammonium generation. The cellular response to HHP represents the common adaptation developed by Halomonas to inhabit and drive geochemical cycling in deep-sea environments. IMPORTANCE Microbial growth and metabolic responses to environmental changes are core aspects of adaptation strategies developed during evolution. In particular, high hydrostatic pressure (HHP) is the most common but least examined environmental factor driving microbial adaptation in the deep sea. According to recent studies, microorganisms developed a common adaptation strategy to multiple stresses, including HHP, with antioxidant defenses and energy regulation as key components, but experimental data are lacking. Meanwhile, cellular SOD activity is elevated under HHP. The significance of this research lies in identifying the HHP adaptation strategy of a Halomonas strain at the genomic, transcriptomic, and metabolic activity levels, which will allow researchers to bridge environmental factors with the ecological function of marine microorganisms.
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Affiliation(s)
- Jiakang Li
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Xiang Xiao
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, China
| | - Meng Zhou
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Zhang
- Shanghai Key Laboratory of Polar Life and Environment Sciences, School of Oceanography, Shanghai Jiao Tong University, Shanghai, China
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20
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Sazykin IS, Sazykina MA. The role of oxidative stress in genome destabilization and adaptive evolution of bacteria. Gene X 2023; 857:147170. [PMID: 36623672 DOI: 10.1016/j.gene.2023.147170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 12/14/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023] Open
Abstract
The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.
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Affiliation(s)
- I S Sazykin
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation
| | - M A Sazykina
- Southern Federal University, 194/2 Stachki Avenue, Rostov-on-Don 344090, Russian Federation.
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21
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McKeithen-Mead SA, Grossman AD. Timing of integration into the chromosome is critical for the fitness of an integrative and conjugative element and its bacterial host. PLoS Genet 2023; 19:e1010524. [PMID: 36780569 PMCID: PMC9956884 DOI: 10.1371/journal.pgen.1010524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 02/24/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
Integrative and conjugative elements (ICEs) are major contributors to genome plasticity in bacteria. ICEs reside integrated in the chromosome of a host bacterium and are passively propagated during chromosome replication and cell division. When activated, ICEs excise from the chromosome and may be transferred through the ICE-encoded conjugation machinery into a recipient cell. Integration into the chromosome of the new host generates a stable transconjugant. Although integration into the chromosome of a new host is critical for the stable acquisition of ICEs, few studies have directly investigated the molecular events that occur in recipient cells during generation of a stable transconjugant. We found that integration of ICEBs1, an ICE of Bacillus subtilis, occurred several generations after initial transfer to a new host. Premature integration in new hosts led to cell death and hence decreased fitness of the ICE and transconjugants. Host lethality due to premature integration was caused by rolling circle replication that initiated in the integrated ICEBs1 and extended into the host chromosome, resulting in catastrophic genome instability. Our results demonstrate that the timing of integration of an ICE is linked to cessation of autonomous replication of the ICE, and that perturbing this linkage leads to a decrease in ICE and host fitness due to a loss of viability of transconjugants. Linking integration to cessation of autonomous replication appears to be a conserved regulatory scheme for mobile genetic elements that both replicate and integrate into the chromosome of their host.
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Affiliation(s)
- Saria A. McKeithen-Mead
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States of America
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22
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Ferrando J, Filluelo O, Zeigler DR, Picart P. Barriers to simultaneous multilocus integration in Bacillus subtilis tumble down: development of a straightforward screening method for the colorimetric detection of one-step multiple gene insertion using the CRISPR-Cas9 system. Microb Cell Fact 2023; 22:21. [PMID: 36721198 PMCID: PMC9890709 DOI: 10.1186/s12934-023-02032-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Despite recent advances in genetic engineering tools for effectively regulating and manipulating genes, efficient simultaneous multigene insertion methods have not been established in Bacillus subtilis. To date, multilocus integration systems in B. subtilis, which is one of the main industrial enzyme producers and a GRAS (generally regarded as safe) microbial host, rely on iterative rounds of plasmid construction for sequential insertions of genes into the B. subtilis chromosome, which is tedious and time consuming. RESULTS In this study, we present development and proof-of-concept of a novel CRISPR-Cas9-based genome-editing strategy for the colorimetric detection of one-step multiple gene insertion in B. subtilis. First, up to three copies of the crtMN operon from Staphylococcus aureus, encoding a yellow pigment, were incorporated at three ectopic sites within the B. subtilis chromosome, rendering engineered strains able to form yellow colonies. Second, a single CRISPR-Cas9-based plasmid carrying a highly specific single guide RNA (sgRNA) targeting crtMN operon and a changeable editing template was constructed to facilitate simultaneous insertion of multiple gene-copies through homology-directed repair (HDR). Upon transformation of engineered strains with engineered plasmids, strains harboring up to three gene copies integrated into the chromosome formed white colonies because of the removal of the crtMN operon, clearly distinguishable from yellow colonies harboring undesired genetic modifications. As a result, construction of a plasmid-less, marker-free, high-expression stable producer B. subtilis strain can be completed in only seven days, demonstrating the potential that the implementation of this technology may bring for biotechnology purposes. CONCLUSIONS The novel technology expands the genome-editing toolset for B. subtilis and means a substantial improvement over current methodology, offering new application possibilities that we envision should significantly boost the development of B. subtilis as a chassis in the field of synthetic biology.
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Affiliation(s)
- Jordi Ferrando
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | - Oriana Filluelo
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
| | | | - Pere Picart
- grid.5841.80000 0004 1937 0247Microbiology Section, Department of Biology, Healthcare and Environment, Faculty of Pharmacy and Food Sciences, Universitat de Barcelona, Barcelona, Catalonia Spain
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23
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Sass P. Antibiotics: Precious Goods in Changing Times. Methods Mol Biol 2023; 2601:3-26. [PMID: 36445576 DOI: 10.1007/978-1-0716-2855-3_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antibiotics represent a first line of defense of diverse microorganisms, which produce and use antibiotics to counteract natural enemies or competitors for nutritional resources in their nearby environment. For antimicrobial activity, nature has invented a great variety of antibiotic modes of action that involve the perturbation of essential bacterial structures or biosynthesis pathways of macromolecules such as the bacterial cell wall, DNA, RNA, or proteins, thereby threatening the specific microbial lifestyle and eventually even survival. However, along with highly inventive modes of antibiotic action, nature also developed a comparable set of resistance mechanisms that help the bacteria to circumvent antibiotic action. Microorganisms have evolved specific adaptive responses that allow to appropriately react to the presence of antimicrobial agents, thereby ensuring survival during antimicrobial stress. In times of rapid development and spread of antibiotic (multi-)resistance, new resistance-breaking strategies to counteract bacterial infections are desperately needed. This chapter is an update to Chapter 1 of the first edition of this book and intends to give an overview of common antibiotics and their target pathways. It will also present examples for new antibiotics with novel modes of action, illustrating that nature's repertoire of innovative new antimicrobial agents has not been fully exploited yet, and we still might find new drugs that help to evade established antimicrobial resistance strategies.
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Affiliation(s)
- Peter Sass
- Interfaculty Institute for Microbiology and Infection Medicine, Microbial Bioactive Compounds, University of Tübingen, Tübingen, Germany.
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24
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Schons-Fonseca L, Lazova MD, Smith JL, Anderson ME, Grossman AD. Beneficial and detrimental genes in the cellular response to replication arrest. PLoS Genet 2022; 18:e1010564. [PMID: 36574412 PMCID: PMC9836290 DOI: 10.1371/journal.pgen.1010564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/12/2023] [Accepted: 12/09/2022] [Indexed: 12/28/2022] Open
Abstract
DNA replication is essential for all living organisms. Several events can disrupt replication, including DNA damage (e.g., pyrimidine dimers, crosslinking) and so-called "roadblocks" (e.g., DNA-binding proteins or transcription). Bacteria have several well-characterized mechanisms for repairing damaged DNA and then restoring functional replication forks. However, little is known about the repair of stalled or arrested replication forks in the absence of chemical alterations to DNA. Using a library of random transposon insertions in Bacillus subtilis, we identified 35 genes that affect the ability of cells to survive exposure to an inhibitor that arrests replication elongation, but does not cause chemical alteration of the DNA. Genes identified include those involved in iron-sulfur homeostasis, cell envelope biogenesis, and DNA repair and recombination. In B. subtilis, and many bacteria, two nucleases (AddAB and RecJ) are involved in early steps in repairing replication forks arrested by chemical damage to DNA and loss of either nuclease causes increased sensitivity to DNA damaging agents. These nucleases resect DNA ends, leading to assembly of the recombinase RecA onto the single-stranded DNA. Notably, we found that disruption of recJ increased survival of cells following replication arrest, indicating that in the absence of chemical damage to DNA, RecJ is detrimental to survival. In contrast, and as expected, disruption of addA decreased survival of cells following replication arrest, indicating that AddA promotes survival. The different phenotypes of addA and recJ mutants appeared to be due to differences in assembly of RecA onto DNA. RecJ appeared to promote too much assembly of RecA filaments. Our results indicate that in the absence of chemical damage to DNA, RecA is dispensable for cells to survive replication arrest and that the stable RecA nucleofilaments favored by the RecJ pathway may lead to cell death by preventing proper processing of the arrested replication fork.
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Affiliation(s)
- Luciane Schons-Fonseca
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Milena D. Lazova
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Janet L. Smith
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Mary E. Anderson
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
| | - Alan D. Grossman
- Department of Biology Massachusetts Institute of Technology Cambridge, Massachusetts, United States of America
- * E-mail:
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25
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Stress-Associated and Growth-Dependent Mutagenesis Are Divergently Regulated by c-di-AMP Levels in Bacillus subtilis. Int J Mol Sci 2022; 24:ijms24010455. [PMID: 36613897 PMCID: PMC9820435 DOI: 10.3390/ijms24010455] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
A previous proteomic study uncovered a relationship between nutritional stress and fluctuations in levels of diadenylate cyclases (DACs) and other proteins that regulate DAC activity, degrade, or interact with c-di-AMP, suggesting a possible role of this second messenger in B. subtilis stress-associated mutagenesis (SAM). Here, we investigated a possible role of c-di-AMP in SAM and growth-associated mutagenesis (GAM). Our results showed that in growing cells of B. subtilis YB955 (hisC952, metB25 and leuC427), the DACs CdaA and DisA, which play crucial roles in cell wall homeostasis and chromosomal fidelity, respectively, counteracted spontaneous and Mitomycin-C-induced mutagenesis. However, experiments in which hydrogen peroxide was used to induce mutations showed that single deficiencies in DACs caused opposite effects compared to each other. In contrast, in the stationary-phase, DACs promoted mutations in conditions of nutritional stress. These results tracked with intracellular levels of c-di-AMP, which are significantly lower in cdaA- and disA-deficient strains. The restoration of DAC-deficient strains with single functional copies of the cdaA and/or disA returned SAM and GAM levels to those observed in the parental strain. Taken together, these results reveal a role for c-di-AMP in promoting genetic diversity in growth-limiting conditions in B. subtilis. Finally, we postulate that this novel function of c-di-AMP can be exerted through proteins that possess binding domains for this second messenger and play roles in DNA repair, ion transport, transcriptional regulation, as well as oxidative stress protection.
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26
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Wu Y, Kawabata H, Kita K, Ishikawa S, Tanaka K, Yoshida KI. Constitutive glucose dehydrogenase elevates intracellular NADPH levels and luciferase luminescence in Bacillus subtilis. Microb Cell Fact 2022; 21:266. [PMID: 36539761 PMCID: PMC9768902 DOI: 10.1186/s12934-022-01993-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Genetic modifications in Bacillus subtilis have allowed the conversion of myo-inositol into scyllo-inositol, which is proposed as a therapeutic agent for Alzheimer's disease. This conversion comprises two reactions catalyzed by two distinct inositol dehydrogenases, IolG and IolW. The IolW-mediated reaction requires the intracellular regeneration of NADPH, and there appears to be a limit to the endogenous supply of NADPH, which may be one of the rate-determining factors for the conversion of inositol. The primary mechanism of NADPH regeneration in this bacterium remains unclear. RESULTS The gdh gene of B. subtilis encodes a sporulation-specific glucose dehydrogenase that can use NADP+ as a cofactor. When gdh was modified to be constitutively expressed, the intracellular NADPH level was elevated, increasing the conversion of inositol. In addition, the bacterial luciferase derived from Photorhabdus luminescens became more luminescent in cells in liquid culture and colonies on culture plates. CONCLUSION The results indicated that the luminescence of luciferase was representative of intracellular NADPH levels. Luciferase can therefore be employed to screen for mutations in genes involved in NADPH regeneration in B. subtilis, and artificial manipulation to enhance NADPH regeneration can promote the production of substances such as scyllo-inositol.
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Affiliation(s)
- Yuzheng Wu
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Honami Kawabata
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kyosuke Kita
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Shu Ishikawa
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
| | - Kan Tanaka
- grid.32197.3e0000 0001 2179 2105Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan ,grid.419082.60000 0004 1754 9200Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Tokyo, Japan
| | - Ken-ichi Yoshida
- grid.31432.370000 0001 1092 3077Department of Science, Technology and Innovation, Kobe University, 1-1 Rokkodai, Nada, Kobe, 657 8501 Japan
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27
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Fichant A, Felten A, Gallet A, Firmesse O, Bonis M. Identification of Genetic Markers for the Detection of Bacillus thuringiensis Strains of Interest for Food Safety. Foods 2022; 11:foods11233924. [PMID: 36496733 PMCID: PMC9739007 DOI: 10.3390/foods11233924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/09/2022] Open
Abstract
Bacillus thuringiensis (Bt), belonging to the Bacillus cereus (Bc) group, is commonly used as a biopesticide worldwide due to its ability to produce insecticidal crystals during sporulation. The use of Bt, especially subspecies aizawai and kurstaki, to control pests such as Lepidoptera, generally involves spraying mixtures containing spores and crystals on crops intended for human consumption. Recent studies have suggested that the consumption of commercial Bt strains may be responsible for foodborne outbreaks (FBOs). However, its genetic proximity to Bc strains has hindered the development of routine tests to discriminate Bt from other Bc, especially Bacillus cereus sensu stricto (Bc ss), well known for its involvement in FBOs. Here, to develop tools for the detection and the discrimination of Bt in food, we carried out a genome-wide association study (GWAS) on 286 complete genomes of Bc group strains to identify and validate in silico new molecular markers specific to different Bt subtypes. The analyses led to the determination and the in silico validation of 128 molecular markers specific to Bt, its subspecies aizawai, kurstaki and four previously described proximity clusters associated with these subspecies. We developed a command line tool based on a 14-marker workflow, to carry out a computational search for Bt-related markers from a putative Bc genome, thereby facilitating the detection of Bt of interest for food safety, especially in the context of FBOs.
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Affiliation(s)
- Arnaud Fichant
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France
- Université Côte d’Azur, CNRS, INRAE, ISA, France
| | - Arnaud Felten
- Ploufragan-Plouzané-Niort Laboratory, Viral Genetics and Biosafety Unit, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 22440 Ploufragan, France
| | - Armel Gallet
- Université Côte d’Azur, CNRS, INRAE, ISA, France
| | - Olivier Firmesse
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France
| | - Mathilde Bonis
- Laboratory for Food Safety, University Paris-Est, French Agency for Food, Environmental and Occupational Health & Safety (ANSES), 94700 Maisons-Alfort, France
- Correspondence:
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28
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Pavlin A, Lovše A, Bajc G, Otoničar J, Kujović A, Lengar Ž, Gutierrez-Aguirre I, Kostanjšek R, Konc J, Fornelos N, Butala M. A small bacteriophage protein determines the hierarchy over co-residential jumbo phage in Bacillus thuringiensis serovar israelensis. Commun Biol 2022; 5:1286. [PMID: 36434275 PMCID: PMC9700832 DOI: 10.1038/s42003-022-04238-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 11/08/2022] [Indexed: 11/26/2022] Open
Abstract
Bacillus thuringiensis serovar israelensis is the most widely used biopesticide against insects, including vectors of animal and human diseases. Among several extrachromosomal elements, this endospore-forming entomopathogen harbors two bacteriophages: a linear DNA replicon named GIL01 that does not integrate into the chromosome during lysogeny and a circular-jumbo prophage known as pBtic235. Here, we show that GIL01 hinders the induction of cohabiting prophage pBtic235. The GIL01-encoded small protein, gp7, which interacts with the host LexA repressor, is a global transcription regulator and represses the induction of pBtic235 after DNA damage to presumably allow GIL01 to multiply first. In a complex with host LexA in stressed cells, gp7 down-regulates the expression of more than 250 host and pBtic235 genes, many of which are involved in the cellular functions of genome maintenance, cell-wall transport, and membrane and protein stability. We show that gp7 homologs that are found exclusively in bacteriophages act in a similar fashion to enhance LexA's binding to DNA, while likely also affecting host gene expression. Our results provide evidence that GIL01 influences both its host and its co-resident bacteriophage.
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Affiliation(s)
- Anja Pavlin
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Anže Lovše
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia ,Genialis, Inc., Boston, MA USA
| | - Gregor Bajc
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Jan Otoničar
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Amela Kujović
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Živa Lengar
- grid.419523.80000 0004 0637 0790Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Ion Gutierrez-Aguirre
- grid.419523.80000 0004 0637 0790Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Rok Kostanjšek
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Janez Konc
- grid.454324.00000 0001 0661 0844Theory Department, National Institute of Chemistry, Ljubljana, Slovenia
| | - Nadine Fornelos
- grid.66859.340000 0004 0546 1623Broad Institute of MIT and Harvard, Cambridge, MA USA
| | - Matej Butala
- grid.8954.00000 0001 0721 6013Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
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29
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Lima-Noronha MA, Fonseca DLH, Oliveira RS, Freitas RR, Park JH, Galhardo RS. Sending out an SOS - the bacterial DNA damage response. Genet Mol Biol 2022; 45:e20220107. [PMID: 36288458 PMCID: PMC9578287 DOI: 10.1590/1678-4685-gmb-2022-0107] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/15/2022] [Indexed: 11/04/2022] Open
Abstract
The term “SOS response” was first coined by Radman in 1974, in an intellectual effort to put together the data suggestive of a concerted gene expression program in cells undergoing DNA damage. A large amount of information about this cellular response has been collected over the following decades. In this review, we will focus on a few of the relevant aspects about the SOS response: its mechanism of control and the stressors which activate it, the diversity of regulated genes in different species, its role in mutagenesis and evolution including the development of antimicrobial resistance, and its relationship with mobile genetic elements.
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Affiliation(s)
- Marco A. Lima-Noronha
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Douglas L. H. Fonseca
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Renatta S. Oliveira
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rúbia R. Freitas
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Jung H. Park
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Rodrigo S. Galhardo
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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30
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Wozniak KJ, Burby PE, Nandakumar J, Simmons LA. Structure and kinase activity of bacterial cell cycle regulator CcrZ. PLoS Genet 2022; 18:e1010196. [PMID: 35576203 PMCID: PMC9135335 DOI: 10.1371/journal.pgen.1010196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/26/2022] [Accepted: 04/09/2022] [Indexed: 11/24/2022] Open
Abstract
CcrZ is a recently discovered cell cycle regulator that connects DNA replication initiation with cell division in pneumococci and may have a similar function in related bacteria. CcrZ is also annotated as a putative kinase, suggesting that CcrZ homologs could represent a novel family of bacterial kinase-dependent cell cycle regulators. Here, we investigate the CcrZ homolog in Bacillus subtilis and show that cells lacking ccrZ are sensitive to a broad range of DNA damage. We demonstrate that increased expression of ccrZ results in over-initiation of DNA replication. In addition, increased expression of CcrZ activates the DNA damage response. Using sensitivity to DNA damage as a proxy, we show that the negative regulator for replication initiation (yabA) and ccrZ function in the same pathway. We show that CcrZ interacts with replication initiation proteins DnaA and DnaB, further suggesting that CcrZ is important for replication timing. To understand how CcrZ functions, we solved the crystal structure bound to AMP-PNP to 2.6 Å resolution. The CcrZ structure most closely resembles choline kinases, consisting of a bilobal structure with a cleft between the two lobes for binding ATP and substrate. Inspection of the structure reveals a major restructuring of the substrate-binding site of CcrZ relative to the choline-binding pocket of choline kinases, consistent with our inability to detect activity with choline for this protein. Instead, CcrZ shows activity on D-ribose and 2-deoxy-D-ribose, indicating adaptation of the choline kinase fold in CcrZ to phosphorylate a novel substrate. We show that integrity of the kinase active site is required for ATPase activity in vitro and for function in vivo. This work provides structural, biochemical, and functional insight into a newly identified, and conserved group of bacterial kinases that regulate DNA replication initiation.
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Affiliation(s)
- Katherine J. Wozniak
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Peter E. Burby
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jayakrishnan Nandakumar
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Lyle A. Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
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31
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Tian J, Xing B, Li M, Xu C, Huo YX, Guo S. Efficient Large-Scale and Scarless Genome Engineering Enables the Construction and Screening of Bacillus subtilis Biofuel Overproducers. Int J Mol Sci 2022; 23:ijms23094853. [PMID: 35563243 PMCID: PMC9099979 DOI: 10.3390/ijms23094853] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bacillus subtilis is a versatile microbial cell factory that can produce valuable proteins and value-added chemicals. Long fragment editing techniques are of great importance for accelerating bacterial genome engineering to obtain desirable and genetically stable host strains. Herein, we develop an efficient CRISPR-Cas9 method for large-scale and scarless genome engineering in the Bacillus subtilis genome, which can delete up to 134.3 kb DNA fragments, 3.5 times as long as the previous report, with a positivity rate of 100%. The effects of using a heterologous NHEJ system, linear donor DNA, and various donor DNA length on the engineering efficiencies were also investigated. The CRISPR-Cas9 method was then utilized for Bacillus subtilis genome simplification and construction of a series of individual and cumulative deletion mutants, which are further screened for overproducer of isobutanol, a new generation biofuel. These results suggest that the method is a powerful genome engineering tool for constructing and screening engineered host strains with enhanced capabilities, highlighting the potential for synthetic biology and metabolic engineering.
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32
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Alternative Pathways to Ciprofloxacin Resistance in Neisseria gonorrhoeae: An In Vitro Study of the WHO-P and WHO-F Reference Strains. Antibiotics (Basel) 2022; 11:antibiotics11040499. [PMID: 35453249 PMCID: PMC9026730 DOI: 10.3390/antibiotics11040499] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/04/2022] [Accepted: 04/06/2022] [Indexed: 01/21/2023] Open
Abstract
Emerging resistance to ceftriaxone and azithromycin has led to renewed interest in using ciprofloxacin to treat Neisseria gonorrhoeae. This could lead to the rapid emergence and spread of ciprofloxacin resistance. Previous studies investigating the emergence of fluoroquinolone resistance have been limited to a single strain of N. gonorrhoeae. It is unknown if different genetic backgrounds affect the evolution of fluoroquinolone resistance in N. gonorrhoeae, as has been shown in other bacterial species. This study evaluated the molecular pathways leading to ciprofloxacin resistance in two reference strains of N.gonorrhoeae-WHO-F and WHO-P. Three clones of each of the two strains of N.gonorrhoeae were evolved in the presence of ciprofloxacin, and isolates from different time points were whole-genome sequenced. We found evidence of strain-specific differences in the emergence of ciprofloxacin resistance. Two out of three clones from WHO-P followed the canonical pathway to resistance proceeding via substitutions in GyrA-S91F, GyrA-D95N and ParC. None of the three WHO-F clones followed this pathway. In addition, mutations in gyrB, uvrA and rne frequently occurred in WHO-F clones, whereas mutations in yhgF, porB and potA occurred in WHO-P.
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33
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Hu J, Ye H, Wang S, Wang J, Han D. Prophage Activation in the Intestine: Insights Into Functions and Possible Applications. Front Microbiol 2021; 12:785634. [PMID: 34966370 PMCID: PMC8710666 DOI: 10.3389/fmicb.2021.785634] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/25/2021] [Indexed: 01/20/2023] Open
Abstract
Prophage activation in intestinal environments has been frequently reported to affect host adaptability, pathogen virulence, gut bacterial community composition, and intestinal health. Prophage activation is mostly caused by various stimulators, such as diet, antibiotics, some bacterial metabolites, gastrointestinal transit, inflammatory environment, oxidative stress, and quorum sensing. Moreover, with advancements in biotechnology and the deepening cognition of prophages, prophage activation regulation therapy is currently applied to the treatment of some bacterial intestinal diseases such as Shiga toxin-producing Escherichia coli infection. This review aims to make headway on prophage induction in the intestine, in order to make a better understanding of dynamic changes of prophages, effects of prophage activation on physiological characteristics of bacteria and intestinal health, and subsequently provide guidance on prophage activation regulation therapy.
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Affiliation(s)
| | | | | | | | - Dandan Han
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Torres R, Alonso JC. Bacillus subtilis RecA, DisA, and RadA/Sms Interplay Prevents Replication Stress by Regulating Fork Remodeling. Front Microbiol 2021; 12:766897. [PMID: 34880841 PMCID: PMC8645862 DOI: 10.3389/fmicb.2021.766897] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/04/2021] [Indexed: 12/04/2022] Open
Abstract
Reviving Bacillus subtilis spores require the recombinase RecA, the DNA damage checkpoint sensor DisA, and the DNA helicase RadA/Sms to prevent a DNA replication stress. When a replication fork stalls at a template lesion, RecA filaments onto the lesion-containing gap and the fork is remodeled (fork reversal). RecA bound to single-strand DNA (ssDNA) interacts with and recruits DisA and RadA/Sms on the branched DNA intermediates (stalled or reversed forks), but DisA and RadA/Sms limit RecA activities and DisA suppresses its c-di-AMP synthesis. We show that RecA, acting as an accessory protein, activates RadA/Sms to unwind the nascent lagging-strand of the branched intermediates rather than to branch migrate them. DisA limits the ssDNA-dependent ATPase activity of RadA/Sms C13A, and inhibits the helicase activity of RadA/Sms by a protein-protein interaction. Finally, RadA/Sms inhibits DisA-mediated c-di-AMP synthesis and indirectly inhibits cell proliferation, but RecA counters this negative effect. We propose that the interactions among DisA, RecA and RadA/Sms, which are mutually exclusive, contribute to generate the substrate for replication restart, regulate the c-di-AMP pool and limit fork restoration in order to maintain cell survival.
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Affiliation(s)
- Rubén Torres
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
| | - Juan C Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, Madrid, Spain
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Aframian N, Omer Bendori S, Kabel S, Guler P, Stokar-Avihail A, Manor E, Msaeed K, Lipsman V, Grinberg I, Mahagna A, Eldar A. Dormant phages communicate via arbitrium to control exit from lysogeny. Nat Microbiol 2021; 7:145-153. [PMID: 34887546 DOI: 10.1038/s41564-021-01008-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/26/2021] [Indexed: 01/23/2023]
Abstract
Temperate bacterial viruses (phages) can transition between lysis-replicating and killing the host-and lysogeny, that is, existing as dormant prophages while keeping the host viable. Recent research showed that on invading a naïve cell, some phages communicate using a peptide signal, termed arbitrium, to control the decision of entering lysogeny. Whether communication can also serve to regulate exit from lysogeny (known as phage induction) is unclear. Here we show that arbitrium-coding prophages continue to communicate from the lysogenic state by secreting and sensing the arbitrium signal. Signalling represses DNA damage-dependent phage induction, enabling prophages to reduce the induction rate when surrounded by other lysogens. We show that in certain phages, DNA damage and communication converge to regulate the expression of the arbitrium-responsive gene aimX, while in others integration of DNA damage and communication occurs downstream of aimX expression. Additionally, signalling by prophages tilts the decision of nearby infecting phages towards lysogeny. Altogether, we find that phages use small-molecule communication throughout their entire life cycle to sense the abundance of lysogens in the population, thus avoiding lysis when they are likely to encounter established lysogens rather than permissive uninfected hosts.
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Affiliation(s)
- Nitzan Aframian
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Shira Omer Bendori
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Stav Kabel
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Polina Guler
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Erica Manor
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Kholod Msaeed
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Valeria Lipsman
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.,Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Grinberg
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Alaa Mahagna
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Avigdor Eldar
- Shmunis School of Biomedicine and Cancer Research, Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv, Israel.
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R S, Nakkeeran S, Saranya N, Senthilraja C, Renukadevi P, Krishnamoorthy A, El Enshasy HA, El-Adawi H, Malathi V, Salmen SH, Ansari MJ, Khan N, Sayyed RZ. Mining the Genome of Bacillus velezensis VB7 (CP047587) for MAMP Genes and Non-Ribosomal Peptide Synthetase Gene Clusters Conferring Antiviral and Antifungal Activity. Microorganisms 2021; 9:microorganisms9122511. [PMID: 34946111 PMCID: PMC8708206 DOI: 10.3390/microorganisms9122511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/25/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
Chemical pesticides have an immense role in curbing the infection of plant viruses and soil-borne pathogens of high valued crops. However, the usage of chemical pesticides also contributes to the development of resistance among pathogens. Hence, attempts were made in this study to identify a suitable bacterial antagonist for managing viral and fungal pathogens infecting crop plants. Based on our earlier investigations, we identified Bacillus amyloliquefaciens VB7 as a potential antagonist for managing Sclerotinia sclerotiorum infecting carnation, tobacco streak virus infecting cotton and groundnut bud necrosis infecting tomato. Considering the multifaceted action of B. amyloliquefaciens VB7, attempts were made for whole-genome sequencing to assess the antiviral activity against tomato spotted wilt virus infecting chrysanthemum and antifungal action against Fusarium oxysporum f. sp. cubense (Foc). Genome annotation of the isolate B. amyloliquefaciens VB7 was confirmed as B. velezensis VB7 with accession number CP047587. Genome analysis revealed the presence of 9,231,928 reads with an average read length of 149 bp. Assembled genome had 1 contig, with a total length of 3,021,183 bp and an average G+C content of 46.79%. The protein-coding sequences (CDS) in the genome was 3090, transfer RNA (tRNA) genes were 85 with 29 ribosomal RNA (rRNA) genes and 21 repeat regions. The genome of B. velezensis VB7 had 506 hypothetical proteins and 2584 proteins with functional assignments. VB7 genome had the presence of flagellin protein FlaA with 987 nucleotides and translation elongation factor TU (Ef-Tu) with 1191 nucleotides. The identified ORFs were 3911 with 47.22% GC content. Non ribosomal pepide synthetase cluster (NRPS) gene clusters in the genome of VB7, coded for the anti-microbial peptides surfactin, butirosin A/butirosin B, fengycin, difficidin, bacillibactin, bacilysin, and mersacidin the Ripp lanthipeptide. Antiviral action of VB7 was confirmed by suppression of local lesion formation of TSWV in the local lesion host cowpea (Co-7). Moreover, combined application of B. velezensis VB7 with phyto-antiviral principles M. Jalapa and H. cupanioides increased shoot length, shoot diameter, number of flower buds per plant, flower diameter, and fresh weight of chrysanthemum. Further, screening for antifungal action of VB7 expressed antifungal action against Foc in vitro by producing VOC/NVOC compounds, including hexadecanoic acid, linoelaidic acid, octadecanoic acid, clindamycin, formic acid, succinamide, furanone, 4H-pyran, nonanol and oleic acid, contributing to the total suppression of Foc apart from the presence of NRPS gene clusters. Thus, our study confirmed the scope for exploring B. velezensis VB7 on a commercial scale to manage tomato spotted wilt virus, groundnut bud necrosis virus, tobacco streak virus, S. sclerotiorum, and Foc causing panama wilt of banana.
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Affiliation(s)
- Saravanan R
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - S Nakkeeran
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
- Correspondence: (S.N.); (R.Z.S.)
| | - N Saranya
- Department of Plant Biotechnology and Bioinformatics, Tamil Nadu Agricultural University, Coimbatore 641003, India;
| | - C Senthilraja
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - P Renukadevi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - A.S. Krishnamoorthy
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - Hesham Ali El Enshasy
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
- Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru 81310, Malaysia;
- Faculty of Engineering School of Chemical and Energy Engineering, Universiti Teknologi Malaysia (UTM), Skudai, Johor Bahru 81310, Malaysia
- City of Scientific Research and Technology Applications (SRTA), New Burg Al Arab, Alexandria 21934, Egypt;
| | - Hala El-Adawi
- City of Scientific Research and Technology Applications (SRTA), New Burg Al Arab, Alexandria 21934, Egypt;
| | - V.G. Malathi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore 641003, India; (S.R.); (C.S.); (P.R.); (A.S.K.); (V.G.M.)
| | - Saleh H. Salmen
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
| | - M. J. Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University, Bareilly 244001, India;
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA;
| | - R. Z. Sayyed
- Department of Microbiology, PSGVP Mandal’s Arts, Science, and Commerce College, Shahada 425409, India
- Asian PGPR Society for Sustainable Agriculture, Auburn University, Auburn, AL 36830, USA
- Correspondence: (S.N.); (R.Z.S.)
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Gándara C, Torres R, Carrasco B, Ayora S, Alonso JC. DisA Restrains the Processing and Cleavage of Reversed Replication Forks by the RuvAB-RecU Resolvasome. Int J Mol Sci 2021; 22:11323. [PMID: 34768753 PMCID: PMC8583203 DOI: 10.3390/ijms222111323] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/04/2021] [Accepted: 10/16/2021] [Indexed: 11/17/2022] Open
Abstract
DNA lesions that impede fork progression cause replisome stalling and threaten genome stability. Bacillus subtilis RecA, at a lesion-containing gap, interacts with and facilitates DisA pausing at these branched intermediates. Paused DisA suppresses its synthesis of the essential c-di-AMP messenger. The RuvAB-RecU resolvasome branch migrates and resolves formed Holliday junctions (HJ). We show that DisA prevents DNA degradation. DisA, which interacts with RuvB, binds branched structures, and reduces the RuvAB DNA-dependent ATPase activity. DisA pre-bound to HJ DNA limits RuvAB and RecU activities, but such inhibition does not occur if the RuvAB- or RecU-HJ DNA complexes are pre-formed. RuvAB or RecU pre-bound to HJ DNA strongly inhibits DisA-mediated synthesis of c-di-AMP, and indirectly blocks cell proliferation. We propose that DisA limits RuvAB-mediated fork remodeling and RecU-mediated HJ cleavage to provide time for damage removal and replication restart in order to preserve genome integrity.
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Affiliation(s)
| | | | | | - Silvia Ayora
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain; (C.G.); (R.T.); (B.C.)
| | - Juan C. Alonso
- Department of Microbial Biotechnology, Centro Nacional de Biotecnología, CNB-CSIC, 3 Darwin St, 28049 Madrid, Spain; (C.G.); (R.T.); (B.C.)
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Hebdon SD, Gerritsen AT, Chen YP, Marcano JG, Chou KJ. Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum. Front Microbiol 2021; 12:695517. [PMID: 34566906 PMCID: PMC8457756 DOI: 10.3389/fmicb.2021.695517] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 12/02/2022] Open
Abstract
Clostridium thermocellum is a thermophilic bacterium recognized for its natural ability to effectively deconstruct cellulosic biomass. While there is a large body of studies on the genetic engineering of this bacterium and its physiology to-date, there is limited knowledge in the transcriptional regulation in this organism and thermophilic bacteria in general. The study herein is the first report of a large-scale application of DNA-affinity purification sequencing (DAP-seq) to transcription factors (TFs) from a bacterium. We applied DAP-seq to > 90 TFs in C. thermocellum and detected genome-wide binding sites for 11 of them. We then compiled and aligned DNA binding sequences from these TFs to deduce the primary DNA-binding sequence motifs for each TF. These binding motifs are further validated with electrophoretic mobility shift assay (EMSA) and are used to identify individual TFs’ regulatory targets in C. thermocellum. Our results led to the discovery of novel, uncharacterized TFs as well as homologues of previously studied TFs including RexA-, LexA-, and LacI-type TFs. We then used these data to reconstruct gene regulatory networks for the 11 TFs individually, which resulted in a global network encompassing the TFs with some interconnections. As gene regulation governs and constrains how bacteria behave, our findings shed light on the roles of TFs delineated by their regulons, and potentially provides a means to enable rational, advanced genetic engineering of C. thermocellum and other organisms alike toward a desired phenotype.
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Affiliation(s)
- Skyler D Hebdon
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Alida T Gerritsen
- Computational Sciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Yi-Pei Chen
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Joan G Marcano
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
| | - Katherine J Chou
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, United States
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Korry BJ, Lee SYE, Chakrabarti AK, Choi AH, Ganser C, Machan JT, Belenky P. Genotoxic Agents Produce Stressor-Specific Spectra of Spectinomycin Resistance Mutations Based on Mechanism of Action and Selection in Bacillus subtilis. Antimicrob Agents Chemother 2021; 65:e0089121. [PMID: 34339280 PMCID: PMC8448107 DOI: 10.1128/aac.00891-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 07/23/2021] [Indexed: 11/20/2022] Open
Abstract
Mutagenesis is integral for bacterial evolution and the development of antibiotic resistance. Environmental toxins and stressors are known to elevate the rate of mutagenesis through direct DNA toxicity, known as stress-associated mutagenesis, or via a more general stress-induced process that relies on intrinsic bacterial pathways. Here, we characterize the spectra of mutations induced by an array of different stressors using high-throughput sequencing to profile thousands of spectinomycin-resistant colonies of Bacillus subtilis. We found 69 unique mutations in the rpsE and rpsB genes, and that each stressor leads to a unique and specific spectrum of antibiotic-resistance mutations. While some mutations clearly reflected the DNA damage mechanism of the stress, others were likely the result of a more general stress-induced mechanism. To determine the relative fitness of these mutants under a range of antibiotic selection pressures, we used multistrain competitive fitness experiments and found an additional landscape of fitness and resistance. The data presented here support the idea that the environment in which the selection is applied (mutagenic stressors that are present), as well as changes in local drug concentration, can significantly alter the path to spectinomycin resistance in B. subtilis.
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Affiliation(s)
- Benjamin J. Korry
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Stella Ye Eun Lee
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Amit K. Chakrabarti
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Ashley H. Choi
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Collin Ganser
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
| | - Jason T. Machan
- Department of Orthopedics, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
- Department of Surgery, Warren Alpert Medical School of Brown University, Providence, Rhode Island, USA
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, Rhode Island, USA
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Abstract
Staphylococcus aureus is a common cause of both superficial and invasive infections of humans and animals. Despite a potent host response and apparently appropriate antibiotic therapy, staphylococcal infections frequently become chronic or recurrent, demonstrating a remarkable ability of S. aureus to withstand the hostile host environment. There is growing evidence that staphylococcal DNA repair makes important contributions to the survival of the pathogen in host tissues, as well as promoting the emergence of mutants that resist host defenses and antibiotics. While much of what we know about DNA repair in S. aureus is inferred from studies with model organisms, the roles of specific repair mechanisms in infection are becoming clear and differences with Bacillus subtilis and Escherichia coli have been identified. Furthermore, there is growing interest in staphylococcal DNA repair as a target for novel therapeutics that sensitize the pathogen to host defenses and antibiotics. In this review, we discuss what is known about staphylococcal DNA repair and its role in infection, examine how repair in S. aureus is similar to, or differs from, repair in well-characterized model organisms, and assess the potential of staphylococcal DNA repair as a novel therapeutic target.
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Constructing of Bacillus subtilis-Based Lux-Biosensors with the Use of Stress-Inducible Promoters. Int J Mol Sci 2021; 22:ijms22179571. [PMID: 34502476 PMCID: PMC8431380 DOI: 10.3390/ijms22179571] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/17/2022] Open
Abstract
Here, we present a new lux-biosensor based on Bacillus subtilis for detecting of DNA-tropic and oxidative stress-causing agents. Hybrid plasmids pNK-DinC, pNK-AlkA, and pNK-MrgA have been constructed, in which the Photorhabdus luminescens reporter genes luxABCDE are transcribed from the stress-inducible promoters of B. subtilis: the SOS promoter PdinC, the methylation-specific response promoter PalkA, and the oxidative stress promoter PmrgA. The luminescence of B. subtilis-based biosensors specifically increases in response to the appearance in the environment of such common toxicants as mitomycin C, methyl methanesulfonate, and H2O2. Comparison with Escherichia coli-based lux-biosensors, where the promoters PdinI, PalkA, and Pdps were used, showed generally similar characteristics. However, for B. subtilis PdinC, a higher response amplitude was observed, and for B. subtilis PalkA, on the contrary, both the amplitude and the range of detectable toxicant concentrations were decreased. B. subtilis PdinC and B. subtilis PmrgA showed increased sensitivity to the genotoxic effects of the 2,2'-bis(bicyclo [2.2.1] heptane) compound, which is a promising propellant, compared to E. coli-based lux-biosensors. The obtained biosensors are applicable for detection of toxicants introduced into soil. Such bacillary biosensors can be used to study the differences in the mechanisms of toxicity against Gram-positive and Gram-negative bacteria.
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RecA is required for the assembly of RecN into DNA repair complexes on the nucleoid. J Bacteriol 2021; 203:e0024021. [PMID: 34339298 DOI: 10.1128/jb.00240-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Homologous recombination requires the coordinated effort of several proteins to complete break resection, homologous pairing and resolution of DNA crossover structures. RecN is a conserved bacterial protein important of double strand break repair and a member of the Structural Maintenance of Chromosomes (SMC) protein family. Current models in Bacillus subtilis propose that RecN responds to double stranded breaks prior to RecA and end processing suggesting that RecN is among the very first proteins responsible for break detection. Here, we investigate the contribution of RecA and end processing by AddAB to RecN recruitment into repair foci in vivo. Using this approach, we found that recA is required for RecN-GFP focus formation on the nucleoid during normal growth and in response to DNA damage. In the absence of recA function, RecN foci form in a low percentage of cells, RecN localizes away from the nucleoid, and RecN fails to assemble in response to DNA damage. In contrast, we show that the response of RecA-GFP foci to DNA damage is unchanged in the presence or absence of recN. In further support of RecA activity preceding RecN we show that ablation of the double-strand break end processing enzyme addAB results in a failure of RecN to form foci in response to DNA damage. With these results, we conclude that RecA and end processing function prior to RecN establishing a critical step for the recruitment and participation of RecN during DNA break repair in Bacillus subtilis. IMPORTANCE Homologous recombination is important for the repair of DNA double-strand breaks. RecN is a highly conserved protein that has been shown to be important for sister chromatid cohesion and for survival to break-inducing clastogens. Here, we show that the assembly of RecN into repair foci on the bacterial nucleoid requires the end processing enzyme AddAB and the recombinase RecA. In the absence of either recA or end processing RecN-GFP foci are no longer DNA damage inducible and foci form in a subset of cells as large complexes in regions away from the nucleoid. Our results establish the stepwise order of action, where double-strand break end processing and RecA association precede the participation of RecN during break repair in Bacillus subtilis.
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Abstract
Phages are viruses of bacteria and are the smallest and most common biological entities in the environment. They can reproduce immediately after infection or integrate as a prophage into their host genome. SPβ is a prophage of the Gram-positive model organism Bacillus subtilis 168, and it has been known for more than 50 years. It is sensitive to dsDNA damage and is induced through exposure to mitomycin C or UV radiation. When induced from the prophage, SPβ requires 90 min to produce and release about 30 virions. Genomes of sequenced related strains range between 128 and 140 kb, and particle-packed dsDNA exhibits terminal redundancy. Formed particles are of the Siphoviridae morphotype. Related isolates are known to infect other B. subtilis clade members. When infecting a new host, SPβ presumably follows a two-step strategy, adsorbing primarily to teichoic acid and secondarily to a yet unknown factor. Once in the host, SPβ-related phages pass through complex lysis-lysogeny decisions and either enter a lytic cycle or integrate as a dormant prophage. As prophages, SPβ-related phages integrate at the host chromosome's replication terminus, and frequently into the spsM or kamA gene. As a prophage, it imparts additional properties to its host via phage-encoded proteins. The most notable of these functional proteins is sublancin 168, which is used as a molecular weapon by the host and ensures prophage maintenance. In this review, we summarise the existing knowledge about the biology of the phage regarding its life cycle and discuss its potential as a research object.
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Affiliation(s)
- Katharina Kohm
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany
| | - Robert Hertel
- FG Synthetic Microbiology, Institute for Biotechnology, BTU Cottbus-Senftenberg, 01968, Senftenberg, Germany.
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Sheng DH, Wang Y, Wu SG, Duan RQ, Li YZ. The Regulation of LexA on UV-Induced SOS Response in Myxococcus xanthus Based on Transcriptome Analysis. J Microbiol Biotechnol 2021; 31:912-920. [PMID: 34024894 PMCID: PMC9705874 DOI: 10.4014/jmb.2103.03047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 12/15/2022]
Abstract
SOS response is a conserved response to DNA damage in prokaryotes and is negatively regulated by LexA protein, which recognizes specifically an "SOS-box" motif present in the promoter region of SOS genes. Myxococcus xanthus DK1622 possesses a lexA gene, and while the deletion of lexA had no significant effect on either bacterial morphology, UV-C resistance, or sporulation, it did delay growth. UV-C radiation resulted in 651 upregulated genes in M. xanthus, including the typical SOS genes lexA, recA, uvrA, recN and so on, mostly enriched in the pathways of DNA replication and repair, secondary metabolism, and signal transduction. The UV-irradiated lexA mutant also showed the induced expression of SOS genes and these SOS genes enriched into a similar pathway profile to that of wild-type strain. Without irradiation treatment, the absence of LexA enhanced the expression of 122 genes that were not enriched in any pathway. Further analysis of the promoter sequence revealed that in the 122 genes, only the promoters of recA2, lexA and an operon composed of three genes (pafB, pafC and cyaA) had SOS box sequence to which the LexA protein is bound directly. These results update our current understanding of SOS response in M. xanthus and show that UV induces more genes involved in secondary metabolism and signal transduction in addition to DNA replication and repair; and while the canonical LexA-dependent regulation on SOS response has shrunk, only 5 SOS genes are directly repressed by LexA.
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Affiliation(s)
- Duo-hong Sheng
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China,
D-h. Sheng Phone: +86-532-58631538 E-mail:
| | - Ye Wang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Shu-ge Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Rui-qin Duan
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Yue-zhong Li
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China,Corresponding authors Y.Z. Li Phone: +86-532-58631539 E-mail:
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45
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Masser EA, Burby PE, Hawkins WD, Gustafson BR, Lenhart JS, Simmons LA. DNA damage checkpoint activation affects peptidoglycan synthesis and late divisome components in Bacillus subtilis. Mol Microbiol 2021; 116:707-722. [PMID: 34097787 DOI: 10.1111/mmi.14765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 11/28/2022]
Abstract
During normal DNA replication, all cells encounter damage to their genetic material. As a result, organisms have developed response pathways that provide time for the cell to complete DNA repair before cell division occurs. In Bacillus subtilis, it is well established that the SOS-induced cell division inhibitor YneA blocks cell division after genotoxic stress; however, it remains unclear how YneA enforces the checkpoint. Here, we identify mutations that disrupt YneA activity and mutations that are refractory to the YneA-induced checkpoint. We find that YneA C-terminal truncation mutants and point mutants in or near the LysM peptidoglycan binding domain render YneA incapable of checkpoint enforcement. In addition, we develop a genetic method which isolated mutations in the ftsW gene that completely bypassed checkpoint enforcement while also finding that YneA interacts with late divisome components FtsL, Pbp2b, and Pbp1. Characterization of an FtsW variant resulted in considerably shorter cells during the DNA damage response indicative of hyperactive initiation of cell division and bypass of the YneA-enforced DNA damage checkpoint. With our results, we present a model where YneA inhibits septal cell wall synthesis by binding peptidoglycan and interfering with interaction between late arriving divisome components causing DNA damage checkpoint activation.
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Affiliation(s)
- Emily A Masser
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Peter E Burby
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Wayne D Hawkins
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Brooke R Gustafson
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Justin S Lenhart
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Lyle A Simmons
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
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Mérida-Floriano A, Rowe WPM, Casadesús J. Genome-Wide Identification and Expression Analysis of SOS Response Genes in Salmonella enterica Serovar Typhimurium. Cells 2021; 10:cells10040943. [PMID: 33921732 PMCID: PMC8072944 DOI: 10.3390/cells10040943] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/14/2021] [Accepted: 04/16/2021] [Indexed: 01/24/2023] Open
Abstract
A bioinformatic search for LexA boxes, combined with transcriptomic detection of loci responsive to DNA damage, identified 48 members of the SOS regulon in the genome of Salmonella enterica serovar Typhimurium. Single cell analysis using fluorescent fusions revealed that heterogeneous expression is a common trait of SOS response genes, with formation of SOSOFF and SOSON subpopulations. Phenotypic cell variants formed in the absence of external DNA damage show gene expression patterns that are mainly determined by the position and the heterology index of the LexA box. SOS induction upon DNA damage produces SOSOFF and SOSON subpopulations that contain live and dead cells. The nature and concentration of the DNA damaging agent and the time of exposure are major factors that influence the population structure upon SOS induction. An analogy can thus be drawn between the SOS response and other bacterial stress responses that produce phenotypic cell variants.
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Affiliation(s)
- Angela Mérida-Floriano
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, E-41080 Sevilla, Spain;
| | - Will P. M. Rowe
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK;
| | - Josep Casadesús
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Apartado 1095, E-41080 Sevilla, Spain;
- Correspondence: ; Tel.: +34-95-455-7105
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47
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Wex KW, Saur JS, Handel F, Ortlieb N, Mokeev V, Kulik A, Niedermeyer THJ, Mast Y, Grond S, Berscheid A, Brötz-Oesterhelt H. Bioreporters for direct mode of action-informed screening of antibiotic producer strains. Cell Chem Biol 2021; 28:1242-1252.e4. [PMID: 33761329 DOI: 10.1016/j.chembiol.2021.02.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/27/2021] [Accepted: 02/23/2021] [Indexed: 01/17/2023]
Abstract
A big challenge in natural product research of today is rapid dereplication of already known substances, to free capacities for the exploration of new agents. Prompt information on bioactivities and mode of action (MOA) speeds up the lead discovery process and is required for rational compound optimization. Here, we present a bioreporter approach as a versatile strategy for combined bioactivity- and MOA-informed primary screening for antimicrobials. The approach is suitable for directly probing producer strains grown on agar, without need for initial compound enrichment or purification, and works along the entire purification pipeline with culture supernatants, extracts, fractions, and pure substances. The technology allows for MOA-informed purification to selectively prioritize activities of interest. In combination with high-resolution mass spectrometry, the biosensor panel is an efficient and sensitive tool for compound deconvolution. Concomitant information on the affected metabolic pathway enables the selection of appropriate follow-up assays to elucidate the molecular target.
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Affiliation(s)
- Katharina W Wex
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Julian S Saur
- Biomolecular Chemistry, Institute of Organic Chemistry, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Franziska Handel
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Nico Ortlieb
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Vladislav Mokeev
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Andreas Kulik
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Timo H J Niedermeyer
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department of Pharmaceutical Biology/Pharmacognosy Institute of Pharmacy, Martin-Luther-University Halle-Wittenberg, Halle, Sachsen-Anhalt 06120, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Yvonne Mast
- Department of Microbiology and Biotechnology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Department Bioresources for Bioeconomy and Health Research, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Niedersachsen 38124, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Stephanie Grond
- Biomolecular Chemistry, Institute of Organic Chemistry, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany
| | - Anne Berscheid
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany
| | - Heike Brötz-Oesterhelt
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; German Center for Infection Research (DZIF), Partner Site Tuebingen, Tuebingen, Baden-Württemberg 72076, Germany; Cluster of Excellence EXC 2124 - Controlling Microbes to Fight Infections, Tuebingen, Baden-Württemberg 72076, Germany.
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48
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Kılıç S, Sánchez-Osuna M, Collado-Padilla A, Barbé J, Erill I. Flexible comparative genomics of prokaryotic transcriptional regulatory networks. BMC Genomics 2020; 21:466. [PMID: 33327941 PMCID: PMC7739468 DOI: 10.1186/s12864-020-06838-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/16/2020] [Indexed: 11/25/2022] Open
Abstract
Background Comparative genomics methods enable the reconstruction of bacterial regulatory networks using available experimental data. In spite of their potential for accelerating research into the composition and evolution of bacterial regulons, few comparative genomics suites have been developed for the automated analysis of these regulatory systems. Available solutions typically rely on precomputed databases for operon and ortholog predictions, limiting the scope of analyses to processed complete genomes, and several key issues such as the transfer of experimental information or the integration of regulatory information in a probabilistic setting remain largely unaddressed. Results Here we introduce CGB, a flexible platform for comparative genomics of prokaryotic regulons. CGB has few external dependencies and enables fully customized analyses of newly available genome data. The platform automates the merging of experimental information and uses a gene-centered, Bayesian framework to generate and integrate easily interpretable results. We demonstrate its flexibility and power by analyzing the evolution of type III secretion system regulation in pathogenic Proteobacteria and by characterizing the SOS regulon of a new bacterial phylum, the Balneolaeota. Conclusions Our results demonstrate the applicability of the CGB pipeline in multiple settings. CGB’s ability to automatically integrate experimental information from multiple sources and use complete and draft genomic data, coupled with its non-reliance on precomputed databases and its easily interpretable display of gene-centered posterior probabilities of regulation provide users with an unprecedented level of flexibility in launching comparative genomics analyses of prokaryotic transcriptional regulatory networks. The analyses of type III secretion and SOS response regulatory networks illustrate instances of convergent and divergent evolution of these regulatory systems, showcasing the power of formal ancestral state reconstruction at inferring the evolutionary history of regulatory networks.
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Affiliation(s)
- Sefa Kılıç
- University of Maryland Baltimore County, Baltimore, MD, 21250, USA
| | | | | | - Jordi Barbé
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Spain
| | - Ivan Erill
- University of Maryland Baltimore County, Baltimore, MD, 21250, USA.
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49
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Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome. Nat Commun 2020; 11:6338. [PMID: 33311500 PMCID: PMC7732839 DOI: 10.1038/s41467-020-20153-9] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022] Open
Abstract
The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse conditions, creating an unbiased summary of gene expression. We obtain 83 independently modulated gene sets that explain most of the variance in expression and demonstrate that 76% of them represent the effects of known regulators. The TRN structure and its condition-dependent activity uncover putative or recently discovered roles for at least five regulons, such as a relationship between histidine utilization and quorum sensing. The TRN also facilitates quantification of population-level sporulation states. As this TRN covers the majority of the transcriptome and concisely characterizes the global expression state, it could inform research on nearly every aspect of transcriptional regulation in B. subtilis. The systems-level regulatory structure underlying gene expression in bacteria can be inferred using machine learning algorithms. Here we show this structure for Bacillus subtilis, present five hypotheses gleaned from it, and analyse the process of sporulation from its perspective.
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50
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Zhu Z, Surujon D, Ortiz-Marquez JC, Huo W, Isberg RR, Bento J, van Opijnen T. Entropy of a bacterial stress response is a generalizable predictor for fitness and antibiotic sensitivity. Nat Commun 2020; 11:4365. [PMID: 32868761 PMCID: PMC7458919 DOI: 10.1038/s41467-020-18134-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 08/06/2020] [Indexed: 02/07/2023] Open
Abstract
Current approaches explore bacterial genes that change transcriptionally upon stress exposure as diagnostics to predict antibiotic sensitivity. However, transcriptional changes are often specific to a species or antibiotic, limiting implementation to known settings only. While a generalizable approach, predicting bacterial fitness independent of strain, species or type of stress, would eliminate such limitations, it is unclear whether a stress-response can be universally captured. By generating a multi-stress and species RNA-Seq and experimental evolution dataset, we highlight the strengths and limitations of existing gene-panel based methods. Subsequently, we build a generalizable method around the observation that global transcriptional disorder seems to be a common, low-fitness, stress response. We quantify this disorder using entropy, which is a specific measure of randomness, and find that in low fitness cases increasing entropy and transcriptional disorder results from a loss of regulatory gene-dependencies. Using entropy as a single feature, we show that fitness and quantitative antibiotic sensitivity predictions can be made that generalize well beyond training data. Furthermore, we validate entropy-based predictions in 7 species under antibiotic and non-antibiotic conditions. By demonstrating the feasibility of universal predictions of bacterial fitness, this work establishes the fundamentals for potentially new approaches in infectious disease diagnostics.
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Affiliation(s)
- Zeyu Zhu
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Defne Surujon
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA
| | | | - Wenwen Huo
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - Ralph R Isberg
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, 02111, USA
| | - José Bento
- Computer Science Department, Boston College, Chestnut Hill, MA, 02467, USA
| | - Tim van Opijnen
- Biology Department, Boston College, Chestnut Hill, MA, 02467, USA.
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