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Raustad N, Dai Y, Iinishi A, Mohapatra A, Soo MW, Hay E, Hernandez GM, Geisinger E. A phosphorylation signal activates genome-wide transcriptional control by BfmR, the global regulator of Acinetobacter resistance and virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.16.599214. [PMID: 38948834 PMCID: PMC11212878 DOI: 10.1101/2024.06.16.599214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
The nosocomial pathogen Acinetobacter baumannii is a major threat to human health. The sensor kinase-response regulator system, BfmS-BfmR, is essential to multidrug resistance and virulence in the bacterium and represents a potential antimicrobial target. Important questions remain about how the system controls resistance and pathogenesis. Although BfmR knockout alters expression of >1000 genes, its direct regulon is undefined. Moreover, how phosphorylation controls the regulator is unclear. Here, we address these problems by combining mutagenesis, ChIP-seq, and in vitro phosphorylation to study the functions of phospho-BfmR. We show that phosphorylation is required for BfmR-mediated gene regulation, antibiotic resistance, and sepsis development in vivo. Consistent with activating the protein, phosphorylation induces dimerization and target DNA affinity. Integrated analysis of genome-wide binding and transcriptional profiles of BfmR led to additional key findings: (1) Phosphorylation dramatically expands the number of genomic sites BfmR binds; (2) DNA recognition involves a direct repeat motif widespread across promoters; (3) BfmR directly regulates 303 genes as activator (eg, capsule, peptidoglycan, and outer membrane biogenesis) or repressor (pilus biogenesis); (4) BfmR controls several non-coding sRNAs. These studies reveal the centrality of a phosphorylation signal in driving A. baumannii disease and disentangle the extensive pathogenic gene-regulatory network under its control.
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Affiliation(s)
- Nicole Raustad
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Yunfei Dai
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Akira Iinishi
- Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Arpita Mohapatra
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Mark W. Soo
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | - Everett Hay
- Department of Biology, Northeastern University, Boston, MA 02115, USA
| | | | - Edward Geisinger
- Department of Biology, Northeastern University, Boston, MA 02115, USA
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2
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Pérez Jorge G, Gontijo M, Silva MFE, Goes ICRDS, Jaimes-Florez YP, Coser LDO, Rocha FJS, Giorgio S, Brocchi M. Attenuated mutants of Salmonella enterica Typhimurium mediate melanoma regression via an immune response. Exp Biol Med (Maywood) 2024; 249:10081. [PMID: 38974834 PMCID: PMC11224151 DOI: 10.3389/ebm.2024.10081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 05/07/2024] [Indexed: 07/09/2024] Open
Abstract
The lack of effective treatment options for an increasing number of cancer cases highlights the need for new anticancer therapeutic strategies. Immunotherapy mediated by Salmonella enterica Typhimurium is a promising anticancer treatment. Candidate strains for anticancer therapy must be attenuated while retaining their antitumor activity. Here, we investigated the attenuation and antitumor efficacy of two S. enterica Typhimurium mutants, ΔtolRA and ΔihfABpmi, in a murine melanoma model. Results showed high attenuation of ΔtolRA in the Galleria mellonella model, and invasion and survival in tumor cells. However, it showed weak antitumor effects in vitro and in vivo. Contrastingly, lower attenuation of the attenuated ΔihfABpmi strain resulted in regression of tumor mass in all mice, approximately 6 days after the first treatment. The therapeutic response induced by ΔihfABpmi was accompanied with macrophage accumulation of antitumor phenotype (M1) and significant increase in the mRNAs of proinflammatory mediators (TNF-α, IL-6, and iNOS) and an apoptosis inducer (Bax). Our findings indicate that the attenuated ΔihfABpmi exerts its antitumor activity by inducing macrophage infiltration or reprogramming the immunosuppressed tumor microenvironment to an activated state, suggesting that attenuated S. enterica Typhimurium strains based on nucleoid-associated protein genes deletion could be immunotherapeutic against cancer.
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Affiliation(s)
- Genesy Pérez Jorge
- Departamento de Genética, Evolução, Microbiologia e Immunologia, Instituto de Biologia, Universidade Estadual de Campinas—UNICAMP, Campinas, SP, Brazil
- Research Group: Statistics and Mathematical Modeling Applied to Educational Quality, University of Sucre, Sincelejo, Sucre, Colombia
| | - Marco Gontijo
- Departamento de Genética, Evolução, Microbiologia e Immunologia, Instituto de Biologia, Universidade Estadual de Campinas—UNICAMP, Campinas, SP, Brazil
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Duke Medicine Cir, Durham, NC, United States
| | - Marina Flóro e Silva
- Departamento de Genética, Evolução, Microbiologia e Immunologia, Instituto de Biologia, Universidade Estadual de Campinas—UNICAMP, Campinas, SP, Brazil
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas—UNICAMP, Campinas, SP, Brazil
| | | | - Yessica Paola Jaimes-Florez
- Departamento de Genética, Evolução, Microbiologia e Immunologia, Instituto de Biologia, Universidade Estadual de Campinas—UNICAMP, Campinas, SP, Brazil
- GIMBIO Group, Department of Microbiology, Faculty of Basic Sciences, Universidad de Pamplona, Pamplona, Colombia
| | - Lilian de Oliveira Coser
- Departamento de Biologia Estrutural e Funcional, Laboratório de Regeneração Nervosa, Instituto de Biologia, Universidade Estadual de Campinas—UNICAMP, Campinas, SP, Brazil
| | - Francisca Janaína Soares Rocha
- Área Acadêmica de Medicina Tropical, Centro de Ciências Médicas, Universidade Federal de Pernambuco, Recife, Pernambuco, Brazil
| | - Selma Giorgio
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas—UNICAMP, Campinas, SP, Brazil
| | - Marcelo Brocchi
- Departamento de Genética, Evolução, Microbiologia e Immunologia, Instituto de Biologia, Universidade Estadual de Campinas—UNICAMP, Campinas, SP, Brazil
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3
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Islam F, Mishra PP. Molecular Insight into the Structural Dynamics of Holliday Junctions Modulated by Integration Host Factor. J Phys Chem B 2024; 128:5642-5657. [PMID: 38812070 DOI: 10.1021/acs.jpcb.4c02997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The integration host factor (IHF) in Escherichia coli is a nucleoid-associated protein with multifaceted roles that encompass DNA packaging, viral DNA integration, and recombination. IHF binds to double-stranded DNA featuring a 13-base pair (bp) consensus sequence with high affinity, causing a substantial bend of approximately 160° upon binding. Although wild-type IHF (WtIHF) is principally involved in DNA bending to facilitate foreign DNA integration into the host genome, its engineered counterpart, single-chain IHF (ScIHF), was specifically designed for genetic engineering and biotechnological applications. Our study delves into the interactions of both IHF variants with Holliday junctions (HJs), pivotal intermediates in DNA repair, and homologous recombination. HJs are dynamic structures capable of adopting open or stacked conformations, with the open conformation facilitating processes such as branch migration and strand exchange. Using microscale thermophoresis, we quantitatively assessed the binding of IHF to four-way DNA junctions that harbor specific binding sequences H' and H1. Our findings demonstrate that both IHF variants exhibit a strong affinity for HJs, signifying a structure-based recognition mechanism. Circular dichroism (CD) experiments unveiled the impact of the protein on the junction's conformation. Furthermore, single-molecule Förster resonance energy transfer (smFRET) confirmed the influence of IHF on the junction's dynamicity. Intriguingly, our results revealed that WtIHF and ScIHF binding shifts the population toward the open conformation of the junction and stabilizes it in that state. In summary, our findings underscore the robust affinity of the IHF for HJs and its capacity to stabilize the open conformation of these junctions.
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Affiliation(s)
- Farhana Islam
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
| | - Padmaja Prasad Mishra
- Single Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India
- Homi Bhabha National Institute, Mumbai 400094, India
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Norris V, Kayser C, Muskhelishvili G, Konto-Ghiorghi Y. The roles of nucleoid-associated proteins and topoisomerases in chromosome structure, strand segregation, and the generation of phenotypic heterogeneity in bacteria. FEMS Microbiol Rev 2023; 47:fuac049. [PMID: 36549664 DOI: 10.1093/femsre/fuac049] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
How to adapt to a changing environment is a fundamental, recurrent problem confronting cells. One solution is for cells to organize their constituents into a limited number of spatially extended, functionally relevant, macromolecular assemblies or hyperstructures, and then to segregate these hyperstructures asymmetrically into daughter cells. This asymmetric segregation becomes a particularly powerful way of generating a coherent phenotypic diversity when the segregation of certain hyperstructures is with only one of the parental DNA strands and when this pattern of segregation continues over successive generations. Candidate hyperstructures for such asymmetric segregation in prokaryotes include those containing the nucleoid-associated proteins (NAPs) and the topoisomerases. Another solution to the problem of creating a coherent phenotypic diversity is by creating a growth-environment-dependent gradient of supercoiling generated along the replication origin-to-terminus axis of the bacterial chromosome. This gradient is modulated by transcription, NAPs, and topoisomerases. Here, we focus primarily on two topoisomerases, TopoIV and DNA gyrase in Escherichia coli, on three of its NAPs (H-NS, HU, and IHF), and on the single-stranded binding protein, SSB. We propose that the combination of supercoiling-gradient-dependent and strand-segregation-dependent topoisomerase activities result in significant differences in the supercoiling of daughter chromosomes, and hence in the phenotypes of daughter cells.
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Affiliation(s)
- Vic Norris
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Clara Kayser
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
| | - Georgi Muskhelishvili
- Agricultural University of Georgia, School of Natural Sciences, 0159 Tbilisi, Georgia
| | - Yoan Konto-Ghiorghi
- University of Rouen, Laboratory of Bacterial Communication and Anti-infection Strategies, EA 4312, 76821 Mont Saint Aignan, France
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Fan Z, Fu T, Li Z, Du B, Cui X, Zhang R, Feng Y, Zhao H, Xue G, Cui J, Yan C, Gan L, Feng J, Xu Z, Yu Z, Tian Z, Ding Z, Chen J, Chen Y, Yuan J. The role of integration host factor in biofilm and virulence of high-alcohol-producing Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0117023. [PMID: 37732783 PMCID: PMC10581059 DOI: 10.1128/spectrum.01170-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 07/28/2023] [Indexed: 09/22/2023] Open
Abstract
Klebsiella pneumoniae is a well-known human nosocomial pathogen with an arsenal of virulence factors, including capsular polysaccharides (CPS), fimbriae, flagella, and lipopolysaccharides (LPS). Our previous study found that alcohol acted as an essential virulence factor for high-alcohol-producing K. pneumoniae (HiAlc Kpn). Integration host factor (IHF) is a nucleoid-associated protein that functions as a global virulence regulator in Escherichia coli. However, the regulatory role of IHF in K. pneumoniae remains unknown. In the present study, we found that deletion of ihfA or ihfB resulted in a slight defect in bacterial growth, a severe absence of biofilm formation and cytotoxicity, and a significant reduction in alcohol production. RNA sequencing differential gene expression analysis showed that compared with the wild-type control, the expression of many virulence factor genes was downregulated in ΔihfA and ΔihfB strains, such as those related to CPS (rcsA, galF, wzi, and iscR), LPS (rfbABCD), type I and type III fimbriae (fim and mrk operon), cellulose (bcs operon), iron transporter (feoABC, fhuA, fhuF, tonB, exbB, and exbD), quorum sensing (lsr operon and sdiA), type II secretion system (T2SS) and type VI secretion system (T6SS) (tssG, hcp, and gspE). Of these virulence factors, CPS, LPS, fimbriae, and cellulose are involved in biofilm formation. In addition, IHF could affect the alcohol production by regulating genes related to glucose intake (ptsG), pyruvate formate-lyase, alcohol dehydrogenase, and the tricarboxylic acid (TCA) cycle. Our data provided new insights into the importance of IHF in regulating the virulence of HiAlc Kpn. IMPORTANCE Klebsiella pneumoniae is a well-known human nosocomial pathogen that causes various infectious diseases, including urinary tract infections, hospital-acquired pneumonia, bacteremia, and liver abscesses. Our previous studies demonstrated that HiAlc Kpn mediated the development of nonalcoholic fatty liver disease by producing excess endogenous alcohol in vivo. However, the regulators regulating the expression of genes related to metabolism, biofilm formation, and virulence of HiAlc Kpn remain unclear. In this study, the regulator IHF was found to positively regulate biofilm formation and many virulence factors including CPS, LPS, type I and type III fimbriae, cellulose, iron transporter, AI-2 quorum sensing, T2SS, and T6SS in HiAlc Kpn. Furthermore, IHF positively regulated alcohol production in HiAlc Kpn. Our results suggested that IHF could be a potential drug target for treating various infectious diseases caused by K. pneumoniae. Hence, the regulation of different virulence factors by IHF in K. pneumoniae requires further investigation.
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Affiliation(s)
- Zheng Fan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Tongtong Fu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zhoufei Li
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Bing Du
- University of Edinburgh, Edinburgh, United Kingdom
| | - Xiaohu Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Rui Zhang
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
- Graduate School of Peking Union Medical College, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinghua Cui
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Lin Gan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Junxia Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziying Xu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zihui Yu
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Ziyan Tian
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Zanbo Ding
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jinfeng Chen
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Yujie Chen
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Yuan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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6
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Chen S, Hu M, Hu A, Xue Y, Wang S, Liu F, Li C, Zhou X, Zhou J. The integration host factor regulates multiple virulence pathways in bacterial pathogen Dickeya zeae MS2. MOLECULAR PLANT PATHOLOGY 2022; 23:1487-1507. [PMID: 35819797 PMCID: PMC9452768 DOI: 10.1111/mpp.13244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Dickeya zeae is an aggressive bacterial phytopathogen that infects a wide range of host plants. It has been reported that integration host factor (IHF), a nucleoid-associated protein consisting of IHFα and IHFβ subunits, regulates gene expression by influencing nucleoid structure and DNA bending. To define the role of IHF in the pathogenesis of D. zeae MS2, we deleted either and both of the IHF subunit encoding genes ihfA and ihfB, which significantly reduced the production of cell wall-degrading enzymes (CWDEs), an unknown novel phytotoxin and the virulence factor-modulating (VFM) quorum-sensing (QS) signal, cell motility, biofilm formation, and thereafter the infection ability towards both potato slices and banana seedlings. To characterize the regulatory pathways of IHF protein associated with virulence, IHF binding sites (consensus sequence 5'-WATCAANNNNTTR-3') were predicted and 272 binding sites were found throughout the genome. The expression of 110 tested genes was affected by IHF. Electrophoretic mobility shift assay (EMSA) showed direct interaction of IhfA protein with the promoters of vfmE, speA, pipR, fis, slyA, prtD, hrpL, hecB, hcp, indA, hdaA, flhD, pilT, gcpJ, arcA, arcB, and lysR. This study clarified the contribution of IHF in the pathogenic process of D. zeae by controlling the production of VFM and putrescine QS signals, phytotoxin, and indigoidine, the luxR-solo system, Fis, SlyA, and FlhD transcriptional regulators, and secretion systems from type I to type VI. Characterization of the regulatory networks of IHF in D. zeae provides a target for prevention and control of plant soft rot disease.
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Affiliation(s)
- Shanshan Chen
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Ming Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Anqun Hu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Yang Xue
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Si Wang
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Fan Liu
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Chuhao Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Xiaofan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease ControlIntegrative Microbiology Research Center, South China Agricultural UniversityGuangzhouChina
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7
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Giacomucci S, Mathieu-Denoncourt A, Vincent AT, Jannadi H, Duperthuy M. Experimental evolution of Vibrio cholerae identifies hypervesiculation as a way to increase motility in the presence of polymyxin B. Front Microbiol 2022; 13:932165. [PMID: 36090081 PMCID: PMC9454949 DOI: 10.3389/fmicb.2022.932165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/27/2022] [Indexed: 11/28/2022] Open
Abstract
Vibrio cholerae includes strains responsible for the cholera disease and is a natural inhabitant of aquatic environments. V. cholerae possesses a unique polar flagellum essential for motility, adhesion, and biofilm formation. In a previous study, we showed that motility and biofilm formation are altered in the presence of subinhibitory concentrations of polymyxin B in V. cholerae O1 and O139. In this study, we performed an experimental evolution to identify the genes restoring the motility in the presence of a subinhibitory concentration of polymyxin B. Mutations in five genes have been identified in three variants derived from two different parental strains A1552 and MO10: ihfA that encodes a subunit of the integration host factor (IHF), vacJ (mlaA) and mlaF, two genes belonging to the maintenance of the lipid asymmetry (Mla) pathway, dacB that encodes a penicillin-binding protein (PBP4) and involved in cell wall synthesis, and ccmH that encodes a c-type cytochrome maturation protein. We further demonstrated that the variants derived from MO10 containing mutations in vacJ, mlaF, and dacB secrete more and larger membrane vesicles that titer the polymyxin B, which increases the bacterial survival and is expected to limit its impact on the bacterial envelope and participate in the flagellum’s retention and motility.
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Affiliation(s)
- Sean Giacomucci
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | | | - Antony T. Vincent
- Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec, QC, Canada
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec, QC, Canada
| | - Hanen Jannadi
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
| | - Marylise Duperthuy
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC, Canada
- *Correspondence: Marylise Duperthuy,
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Pineau M, Martis B. S, Forquet R, Baude J, Villard C, Grand L, Popowycz F, Soulère L, Hommais F, Nasser W, Reverchon S, Meyer S. What is a supercoiling-sensitive gene? Insights from topoisomerase I inhibition in the Gram-negative bacterium Dickeya dadantii. Nucleic Acids Res 2022; 50:9149-9161. [PMID: 35950487 PMCID: PMC9458453 DOI: 10.1093/nar/gkac679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/04/2022] [Accepted: 07/27/2022] [Indexed: 12/24/2022] Open
Abstract
DNA supercoiling is an essential mechanism of bacterial chromosome compaction, whose level is mainly regulated by topoisomerase I and DNA gyrase. Inhibiting either of these enzymes with antibiotics leads to global supercoiling modifications and subsequent changes in global gene expression. In previous studies, genes responding to DNA relaxation induced by DNA gyrase inhibition were categorised as 'supercoiling-sensitive'. Here, we studied the opposite variation of DNA supercoiling in the phytopathogen Dickeya dadantii using the non-marketed antibiotic seconeolitsine. We showed that the drug is active against topoisomerase I from this species, and analysed the first transcriptomic response of a Gram-negative bacterium to topoisomerase I inhibition. We find that the responding genes essentially differ from those observed after DNA relaxation, and further depend on the growth phase. We characterised these genes at the functional level, and also detected distinct patterns in terms of expression level, spatial and orientational organisation along the chromosome. Altogether, these results highlight that the supercoiling-sensitivity is a complex feature, which depends on the action of specific topoisomerases, on the physiological conditions, and on their genomic context. Based on previous in vitro expression data of several promoters, we propose a qualitative model of SC-dependent regulation that accounts for many of the contrasting transcriptomic features observed after DNA gyrase or topoisomerase I inhibition.
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Affiliation(s)
- Maïwenn Pineau
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Shiny Martis B.
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Raphaël Forquet
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Jessica Baude
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Camille Villard
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Lucie Grand
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS UMR 5246, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 69622 Villeurbanne, France
| | - Florence Popowycz
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS UMR 5246, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 69622 Villeurbanne, France
| | - Laurent Soulère
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CPE Lyon, CNRS UMR 5246, Institut de Chimie et Biochimie Moléculaires et Supramoléculaires, 69622 Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS UMR5240, Laboratoire de Microbiologie, Adaptation et Pathogénie, 69621 Villeurbanne, France
| | - Sam Meyer
- To whom correspondence should be addressed. Tel: +33 4 72 43 85 16;
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9
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Muskhelishvili G, Sobetzko P, Travers A. Spatiotemporal Coupling of DNA Supercoiling and Genomic Sequence Organization-A Timing Chain for the Bacterial Growth Cycle? Biomolecules 2022; 12:biom12060831. [PMID: 35740956 PMCID: PMC9221221 DOI: 10.3390/biom12060831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 01/25/2023] Open
Abstract
In this article we describe the bacterial growth cycle as a closed, self-reproducing, or autopoietic circuit, reestablishing the physiological state of stationary cells initially inoculated in the growth medium. In batch culture, this process of self-reproduction is associated with the gradual decline in available metabolic energy and corresponding change in the physiological state of the population as a function of "travelled distance" along the autopoietic path. We argue that this directional alteration of cell physiology is both reflected in and supported by sequential gene expression along the chromosomal OriC-Ter axis. We propose that during the E. coli growth cycle, the spatiotemporal order of gene expression is established by coupling the temporal gradient of supercoiling energy to the spatial gradient of DNA thermodynamic stability along the chromosomal OriC-Ter axis.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Natural Sciences, Biology Program, Agricultural University of Georgia, 0159 Tbilisi, Georgia
- Correspondence:
| | - Patrick Sobetzko
- Synmikro, Loewe Center for Synthetic Microbiology, Philipps-Universität Marburg, 35043 Marburg, Germany;
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
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10
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Relationship between the Chromosome Structural Dynamics and Gene Expression—A Chicken and Egg Dilemma? Microorganisms 2022; 10:microorganisms10050846. [PMID: 35630292 PMCID: PMC9144111 DOI: 10.3390/microorganisms10050846] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 04/14/2022] [Indexed: 02/06/2023] Open
Abstract
Prokaryotic transcription was extensively studied over the last half-century. A great deal of data has been accumulated regarding the control of gene expression by transcription factors regulating their target genes by binding at specific DNA sites. However, there is a significant gap between the mechanistic description of transcriptional control obtained from in vitro biochemical studies and the complexity of transcriptional regulation in the context of the living cell. Indeed, recent studies provide ample evidence for additional levels of complexity pertaining to the regulation of transcription in vivo, such as, for example, the role of the subcellular localization and spatial organization of different molecular components involved in the transcriptional control and, especially, the role of chromosome configurational dynamics. The question as to how the chromosome is dynamically reorganized under the changing environmental conditions and how this reorganization is related to gene expression is still far from being clear. In this article, we focus on the relationships between the chromosome structural dynamics and modulation of gene expression during bacterial adaptation. We argue that spatial organization of the bacterial chromosome is of central importance in the adaptation of gene expression to changing environmental conditions and vice versa, that gene expression affects chromosome dynamics.
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11
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Pozdeev G, Beckett MC, Mogre A, Thomson NR, Dorman CJ. Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence. Microb Genom 2022; 8. [PMID: 35166652 PMCID: PMC8942017 DOI: 10.1099/mgen.0.000768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The Integration Host Factor (IHF) is a heterodimeric nucleoid-associated protein that plays roles in bacterial nucleoid architecture and genome-wide gene regulation. The ihfA and ihfB genes encode the subunits and are located 350 kbp apart, in the Right replichore of the Salmonella chromosome. IHF is composed of one IhfA and one IhfB subunit. Despite this 1 : 1 stoichiometry, MS revealed that IhfB is produced in 2-fold excess over IhfA. We re-engineered Salmonella to exchange reciprocally the protein-coding regions of ihfA and ihfB, such that each relocated protein-encoding region was driven by the expression signals of the other's gene. MS showed that in this 'rewired' strain, IhfA is produced in excess over IhfB, correlating with enhanced stability of the hybrid ihfB-ihfA mRNA that was expressed from the ihfB promoter. Nevertheless, the rewired strain grew at a similar rate to the wild-type and was similar in competitive fitness. However, compared to the wild-type, it was less motile, had growth-phase-specific reductions in SPI-1 and SPI-2 gene expression, and was engulfed at a higher rate by RAW macrophage. Our data show that while exchanging the physical locations of its ihf genes and the rewiring of their regulatory circuitry are well tolerated in Salmonella, genes involved in the production of type 3 secretion systems exhibit dysregulation accompanied by altered phenotypes.
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Affiliation(s)
- German Pozdeev
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Michael C Beckett
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | - Aalap Mogre
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
| | | | - Charles J Dorman
- Department of Microbiology, Moyne Institute of Preventive Medicine, Trinity College Dublin, Dublin 2, Ireland
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12
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Watson GD, Chan EW, Leake MC, Noy A. Structural interplay between DNA-shape protein recognition and supercoiling: The case of IHF. Comput Struct Biotechnol J 2022; 20:5264-5274. [PMID: 36212531 PMCID: PMC9519438 DOI: 10.1016/j.csbj.2022.09.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 09/12/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022] Open
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13
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Sarkar S, Dey U, Khohliwe TB, Yella VR, Kumar A. Analysis of nucleoid-associated protein-binding regions reveals DNA structural features influencing genome organization in Mycobacterium tuberculosis. FEBS Lett 2021; 595:2504-2521. [PMID: 34387867 DOI: 10.1002/1873-3468.14178] [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: 06/11/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022]
Abstract
Nucleoid-associated proteins (NAPs) maintain bacterial nucleoid configuration through their architectural properties of DNA bending, wrapping, and bridging. However, the contribution of DNA structural alterations to DNA-NAP recognition at the genomic scale remains unresolved. Present work dissects the DNA sequence, shape and altered structural preferences at a genomic scale for six NAPs in Mycobacterium tuberculosis. Results suggest narrower minor groove width (MGW) and higher DNA rigidity are marked for the binding sites of EspR and Lsr2, while mIHF, MtHU and NapM have heterogeneous DNA structural predilections. In contrast, WhiB4-DNA-binding sites were characterized by wider MGW, highly deformable and less curved DNA. This work provides systematic insight into NAP-mediated genome organization as a function of DNA structural features.
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Affiliation(s)
- Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | | | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
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14
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Bergkessel M. Bacterial transcription during growth arrest. Transcription 2021; 12:232-249. [PMID: 34486930 PMCID: PMC8632087 DOI: 10.1080/21541264.2021.1968761] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/12/2022] Open
Abstract
Bacteria in most natural environments spend substantial periods of time limited for essential nutrients and not actively dividing. While transcriptional activity under these conditions is substantially reduced compared to that occurring during active growth, observations from diverse organisms and experimental approaches have shown that new transcription still occurs and is important for survival. Much of our understanding of transcription regulation has come from measuring transcripts in exponentially growing cells, or from in vitro experiments focused on transcription from highly active promoters by the housekeeping RNA polymerase holoenzyme. The fact that transcription during growth arrest occurs at low levels and is highly heterogeneous has posed challenges for its study. However, new methods of measuring low levels of gene expression activity, even in single cells, offer exciting opportunities for directly investigating transcriptional activity and its regulation during growth arrest. Furthermore, much of the rich structural and biochemical data from decades of work on the bacterial transcriptional machinery is also relevant to growth arrest. In this review, the physiological changes likely affecting transcription during growth arrest are first considered. Next, possible adaptations to help facilitate ongoing transcription during growth arrest are discussed. Finally, new insights from several recently published datasets investigating mRNA transcripts in single bacterial cells at various growth phases will be explored. Keywords: Growth arrest, stationary phase, RNA polymerase, nucleoid condensation, population heterogeneity.
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15
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Leonard S, Villard C, Nasser W, Reverchon S, Hommais F. RNA Chaperones Hfq and ProQ Play a Key Role in the Virulence of the Plant Pathogenic Bacterium Dickeya dadantii. Front Microbiol 2021; 12:687484. [PMID: 34248909 PMCID: PMC8264596 DOI: 10.3389/fmicb.2021.687484] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/31/2021] [Indexed: 12/01/2022] Open
Abstract
Dickeya dadantii is an important pathogenic bacterium that infects a number of crops including potato and chicory. While extensive works have been carried out on the control of the transcription of its genes encoding the main virulence functions, little information is available on the post-transcriptional regulation of these functions. We investigated the involvement of the RNA chaperones Hfq and ProQ in the production of the main D. dadantii virulence functions. Phenotypic assays on the hfq and proQ mutants showed that inactivation of hfq resulted in a growth defect, a modified capacity for biofilm formation and strongly reduced motility, and in the production of degradative extracellular enzymes (proteases, cellulase, and pectate lyases). Accordingly, the hfq mutant failed to cause soft rot on chicory leaves. The proQ mutant had reduced resistance to osmotic stress, reduced extracellular pectate lyase activity compared to the wild-type strain, and reduced virulence on chicory leaves. Most of the phenotypes of the hfq and proQ mutants were related to the low amounts of mRNA of the corresponding virulence factors. Complementation of the double mutant hfq-proQ by each individual protein and cross-complementation of each chaperone suggested that they might exert their effects via partially overlapping but different sets of targets. Overall, it clearly appeared that the two Hfq and ProQ RNA chaperones are important regulators of pathogenicity in D. dadantii. This underscores that virulence genes are regulated post-transcriptionally by non-coding RNAs.
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Affiliation(s)
- Simon Leonard
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5240 MAP, Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Camille Villard
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5240 MAP, Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - William Nasser
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5240 MAP, Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Sylvie Reverchon
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5240 MAP, Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
| | - Florence Hommais
- Université de Lyon, INSA Lyon, Université Claude Bernard Lyon 1, CNRS, UMR 5240 MAP, Microbiologie, Adaptation, Pathogénie, Villeurbanne, France
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Muskhelishvili G, Sobetzko P, Mehandziska S, Travers A. Composition of Transcription Machinery and Its Crosstalk with Nucleoid-Associated Proteins and Global Transcription Factors. Biomolecules 2021; 11:biom11070924. [PMID: 34206477 PMCID: PMC8301835 DOI: 10.3390/biom11070924] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 11/24/2022] Open
Abstract
The coordination of bacterial genomic transcription involves an intricate network of interdependent genes encoding nucleoid-associated proteins (NAPs), DNA topoisomerases, RNA polymerase subunits and modulators of transcription machinery. The central element of this homeostatic regulatory system, integrating the information on cellular physiological state and producing a corresponding transcriptional response, is the multi-subunit RNA polymerase (RNAP) holoenzyme. In this review article, we argue that recent observations revealing DNA topoisomerases and metabolic enzymes associated with RNAP supramolecular complex support the notion of structural coupling between transcription machinery, DNA topology and cellular metabolism as a fundamental device coordinating the spatiotemporal genomic transcription. We analyse the impacts of various combinations of RNAP holoenzymes and global transcriptional regulators such as abundant NAPs, on genomic transcription from this viewpoint, monitoring the spatiotemporal patterns of couplons—overlapping subsets of the regulons of NAPs and RNAP sigma factors. We show that the temporal expression of regulons is by and large, correlated with that of cognate regulatory genes, whereas both the spatial organization and temporal expression of couplons is distinctly impacted by the regulons of NAPs and sigma factors. We propose that the coordination of the growth phase-dependent concentration gradients of global regulators with chromosome configurational dynamics determines the spatiotemporal patterns of genomic expression.
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Affiliation(s)
- Georgi Muskhelishvili
- School of Natural Sciences, Agricultural University of Georgia, David Aghmashenebeli Alley 24, Tbilisi 0159, Georgia
- Correspondence:
| | - Patrick Sobetzko
- Department of Chromosome Biology, Philipps-Universität Marburg, LOEWE-Zentrum für Synthetische Mikrobiologie, Hans-Meerwein-Straße, 35043 Marburg, Germany;
| | - Sanja Mehandziska
- School of Engineering and Science, Campus Ring 1, Jacobs University Bremen, 28759 Bremen, Germany;
| | - Andrew Travers
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK;
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1GA, UK
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