1
|
Jin C, Kang SM, Kim DH, Lee Y, Lee BJ. Discovery of Antimicrobial Agents Based on Structural and Functional Study of the Klebsiella pneumoniae MazEF Toxin-Antitoxin System. Antibiotics (Basel) 2024; 13:398. [PMID: 38786127 PMCID: PMC11117207 DOI: 10.3390/antibiotics13050398] [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: 03/20/2024] [Revised: 04/15/2024] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
Klebsiella pneumoniae causes severe human diseases, but its resistance to current antibiotics is increasing. Therefore, new antibiotics to eradicate K. pneumoniae are urgently needed. Bacterial toxin-antitoxin (TA) systems are strongly correlated with physiological processes in pathogenic bacteria, such as growth arrest, survival, and apoptosis. By using structural information, we could design the peptides and small-molecule compounds that can disrupt the binding between K. pneumoniae MazE and MazF, which release free MazF toxin. Because the MazEF system is closely implicated in programmed cell death, artificial activation of MazF can promote cell death of K. pneumoniae. The effectiveness of a discovered small-molecule compound in bacterial cell killing was confirmed through flow cytometry analysis. Our findings can contribute to understanding the bacterial MazEF TA system and developing antimicrobial agents for treating drug-resistant K. pneumoniae.
Collapse
Affiliation(s)
- Chenglong Jin
- The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul 08826, Republic of Korea;
- Mastermeditech Ltd., Gangseo-gu, Seoul 16499, Republic of Korea
| | - Sung-Min Kang
- College of Pharmacy, Duksung Women’s University, Seoul 01369, Republic of Korea;
| | - Do-Hee Kim
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
| | - Yuno Lee
- Korea Research Institute of Chemical Technology, Korea Chemical Bank Daejeon, Daejeon 34114, Republic of Korea;
| | - Bong-Jin Lee
- Mastermeditech Ltd., Gangseo-gu, Seoul 16499, Republic of Korea
- College of Pharmacy, Ajou University, Yeongtong-gu, Suwon 16499, Republic of Korea
| |
Collapse
|
2
|
Jiang YN, Tamiya-Ishitsuka H, Aoi R, Okabe T, Yokota A, Noda N. MazEF Homologs in Symbiobacterium thermophilum Exhibit Cross-Neutralization with Non-Cognate MazEFs. Toxins (Basel) 2024; 16:81. [PMID: 38393159 PMCID: PMC10893535 DOI: 10.3390/toxins16020081] [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: 12/28/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
Toxin-antitoxin systems are preserved by nearly every prokaryote. The type II toxin MazF acts as a sequence-specific endoribonuclease, cleaving ribonucleotides at specific sequences that vary from three to seven bases, as has been reported in different host organisms to date. The present study characterized the MazEF module (MazEF-sth) conserved in the Symbiobacterium thermophilum IAM14863 strain, a Gram-negative syntrophic bacterium that can be supported by co-culture with multiple bacteria, including Bacillus subtilis. Based on a method combining massive parallel sequencing and the fluorometric assay, MazF-sth was determined to cleave ribonucleotides at the UACAUA motif, which is markedly similar to the motifs recognized by MazF from B. subtilis (MazF-bs), and by several MazFs from Gram-positive bacteria. MazF-sth, with mutations at conserved amino acid residues Arg29 and Thr52, lost most ribonuclease activity, indicating that these residues that are crucial for MazF-bs also play significant roles in MazF-sth catalysis. Further, cross-neutralization between MazF-sth and the non-cognate MazE-bs was discovered, and herein, the neutralization mechanism is discussed based on a protein-structure simulation via AlphaFold2 and multiple sequence alignment. The conflict between the high homology shared by these MazF amino acid sequences and the few genetic correlations among their host organisms may provide evidence of horizontal gene transfer.
Collapse
Affiliation(s)
- Yu-Nong Jiang
- Master’s/Doctoral Program in Life Science Innovation, Graduate School of Comprehensive Human Sciences, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
| | - Hiroko Tamiya-Ishitsuka
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
| | - Rie Aoi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku 162-8480, Tokyo, Japan
| | - Takuma Okabe
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku 162-8480, Tokyo, Japan
| | - Akiko Yokota
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
| | - Naohiro Noda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8566, Ibaraki, Japan
- Department of Life Science and Medical Bioscience, Waseda University, Shinjuku-ku 162-8480, Tokyo, Japan
- Master’s/Doctoral Program in Life Science Innovation, School of Integrative and Global Majors, University of Tsukuba, Tsukuba 305-8572, Ibaraki, Japan
| |
Collapse
|
3
|
Pizzolato-Cezar LR, Spira B, Machini MT. Bacterial toxin-antitoxin systems: Novel insights on toxin activation across populations and experimental shortcomings. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 5:100204. [PMID: 38024808 PMCID: PMC10643148 DOI: 10.1016/j.crmicr.2023.100204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
The alarming rise in hard-to-treat bacterial infections is of great concern to human health. Thus, the identification of molecular mechanisms that enable the survival and growth of pathogens is of utmost urgency for the development of more efficient antimicrobial therapies. In challenging environments, such as presence of antibiotics, or during host infection, metabolic adjustments are essential for microorganism survival and competitiveness. Toxin-antitoxin systems (TASs) consisting of a toxin with metabolic modulating activity and a cognate antitoxin that antagonizes that toxin are important elements in the arsenal of bacterial stress defense. However, the exact physiological function of TA systems is highly debatable and with the exception of stabilization of mobile genetic elements and phage inhibition, other proposed biological functions lack a broad consensus. This review aims at gaining new insights into the physiological effects of TASs in bacteria and exploring the experimental shortcomings that lead to discrepant results in TAS research. Distinct control mechanisms ensure that only subsets of cells within isogenic cultures transiently develop moderate levels of toxin activity. As a result, TASs cause phenotypic growth heterogeneity rather than cell stasis in the entire population. It is this feature that allows bacteria to thrive in diverse environments through the creation of subpopulations with different metabolic rates and stress tolerance programs.
Collapse
Affiliation(s)
- Luis R. Pizzolato-Cezar
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Beny Spira
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - M. Teresa Machini
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
4
|
Allsopp LP, Bernal P. Killing in the name of: T6SS structure and effector diversity. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001367. [PMID: 37490402 PMCID: PMC10433429 DOI: 10.1099/mic.0.001367] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
The life of bacteria is challenging, to endure bacteria employ a range of mechanisms to optimize their environment, including deploying the type VI secretion system (T6SS). Acting as a bacterial crossbow, this system delivers effectors responsible for subverting host cells, killing competitors and facilitating general secretion to access common goods. Due to its importance, this lethal machine has been evolutionarily maintained, disseminated and specialized to fulfil these vital functions. In fact, T6SS structural clusters are present in over 25 % of Gram-negative bacteria, varying in number from one to six different genetic clusters per organism. Since its discovery in 2006, research on the T6SS has rapidly progressed, yielding remarkable breakthroughs. The identification and characterization of novel components of the T6SS, combined with biochemical and structural studies, have revealed fascinating mechanisms governing its assembly, loading, firing and disassembly processes. Recent findings have also demonstrated the efficacy of this system against fungal and Gram-positive cells, expanding its scope. Ongoing research continues to uncover an extensive and expanding repertoire of T6SS effectors, the genuine mediators of T6SS function. These studies are shedding light on new aspects of the biology of prokaryotic and eukaryotic organisms. This review provides a comprehensive overview of the T6SS, highlighting recent discoveries of its structure and the diversity of its effectors. Additionally, it injects a personal perspective on avenues for future research, aiming to deepen our understanding of this combative system.
Collapse
Affiliation(s)
- Luke P. Allsopp
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
| |
Collapse
|
5
|
A secreted effector with a dual role as a toxin and as a transcriptional factor. Nat Commun 2022; 13:7779. [PMID: 36522324 PMCID: PMC9755527 DOI: 10.1038/s41467-022-35522-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022] Open
Abstract
Bacteria have evolved multiple secretion systems for delivering effector proteins into the cytosol of neighboring cells, but the roles of many of these effectors remain unknown. Here, we show that Yersinia pseudotuberculosis secretes an effector, CccR, that can act both as a toxin and as a transcriptional factor. The effector is secreted by a type VI secretion system (T6SS) and can enter nearby cells of the same species and other species (such as Escherichia coli) via cell-cell contact and in a contact-independent manner. CccR contains an N-terminal FIC domain and a C-terminal DNA-binding domain. In Y. pseudotuberculosis cells, CccR inhibits its own expression by binding through its DNA-binding domain to the cccR promoter, and affects the expression of other genes through unclear mechanisms. In E. coli cells, the FIC domain of CccR AMPylates the cell division protein FtsZ, inducing cell filamentation and growth arrest. Thus, our results indicate that CccR has a dual role, modulating gene expression in neighboring cells of the same species, and inhibiting the growth of competitors.
Collapse
|
6
|
Berkvens A, Chauhan P, Bruggeman FJ. Integrative biology of persister cell formation: molecular circuitry, phenotypic diversification and fitness effects. JOURNAL OF THE ROYAL SOCIETY, INTERFACE 2022; 19:20220129. [PMID: 36099930 PMCID: PMC9470271 DOI: 10.1098/rsif.2022.0129] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Microbial populations often contain persister cells, which reduce the extinction risk upon sudden stresses. Persister cell formation is deeply intertwined with physiology. Due to this complexity, it cannot be satisfactorily understood by focusing only on mechanistic, physiological or evolutionary aspects. In this review, we take an integrative biology perspective to identify common principles of persister cell formation, which might be applicable across evolutionary-distinct microbes. Persister cells probably evolved to cope with a fundamental trade-off between cellular stress and growth tasks, as any biosynthetic resource investment in growth-supporting proteins is at the expense of stress tasks and vice versa. Natural selection probably favours persister cell subpopulation formation over a single-phenotype strategy, where each cell is prepared for growth and stress to a suboptimal extent, since persister cells can withstand harsher environments and their coexistence with growing cells leads to a higher fitness. The formation of coexisting phenotypes requires bistable molecular circuitry. Bistability probably emerges from growth-modulated, positive feedback loops in the cell's growth versus stress control network, involving interactions between sigma factors, guanosine pentaphosphate and toxin-antitoxin (TA) systems. We conclude that persister cell formation is most likely a response to a sudden reduction in growth rate, which can be achieved by antibiotic addition, nutrient starvation, sudden stresses, nutrient transitions or activation of a TA system.
Collapse
Affiliation(s)
- Alicia Berkvens
- Systems Biology Lab, AIMMS, VU University, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Priyanka Chauhan
- Systems Biology Lab, AIMMS, VU University, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Biology Lab, AIMMS, VU University, De Boelelaan 1087, 1081 HV Amsterdam, The Netherlands
| |
Collapse
|
7
|
Tomasek K, Leithner A, Glatzova I, Lukesch MS, Guet CC, Sixt M. Type 1 piliated uropathogenic Escherichia coli hijack the host immune response by binding to CD14. eLife 2022; 11:78995. [PMID: 35881547 PMCID: PMC9359703 DOI: 10.7554/elife.78995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 07/19/2022] [Indexed: 11/13/2022] Open
Abstract
A key attribute of persistent or recurring bacterial infections is the ability of the pathogen to evade the host’s immune response. Many Enterobacteriaceae express type 1 pili, a pre-adapted virulence trait, to invade host epithelial cells and establish persistent infections. However, the molecular mechanisms and strategies by which bacteria actively circumvent the immune response of the host remain poorly understood. Here, we identified CD14, the major co-receptor for lipopolysaccharide detection, on mouse dendritic cells (DCs) as a binding partner of FimH, the protein located at the tip of the type 1 pilus of Escherichia coli. The FimH amino acids involved in CD14 binding are highly conserved across pathogenic and non-pathogenic strains. Binding of the pathogenic strain CFT073 to CD14 reduced DC migration by overactivation of integrins and blunted expression of co-stimulatory molecules by overactivating the NFAT (nuclear factor of activated T-cells) pathway, both rate-limiting factors of T cell activation. This response was binary at the single-cell level, but averaged in larger populations exposed to both piliated and non-piliated pathogens, presumably via the exchange of immunomodulatory cytokines. While defining an active molecular mechanism of immune evasion by pathogens, the interaction between FimH and CD14 represents a potential target to interfere with persistent and recurrent infections, such as urinary tract infections or Crohn’s disease.
Collapse
Affiliation(s)
- Kathrin Tomasek
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Ivana Glatzova
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | | | - Calin C Guet
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| | - Michael Sixt
- Institute of Science and Technology Austria, Klosterneuburg, Austria
| |
Collapse
|
8
|
Nikolic N, Sauert M, Albanese TG, Moll I. Quantifying heterologous gene expression during ectopic MazF production in Escherichia coli. BMC Res Notes 2022; 15:173. [PMID: 35562780 PMCID: PMC9102682 DOI: 10.1186/s13104-022-06061-9] [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] [Received: 03/24/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022] Open
Abstract
Objective MazF is a sequence-specific endoribonuclease-toxin of the MazEF toxin–antitoxin system. MazF cleaves single-stranded ribonucleic acid (RNA) regions at adenine–cytosine–adenine (ACA) sequences in the bacterium Escherichia coli. The MazEF system has been used in various biotechnology and synthetic biology applications. In this study, we infer how ectopic mazF overexpression affects production of heterologous proteins. To this end, we quantified the levels of fluorescent proteins expressed in E. coli from reporters translated from the ACA-containing or ACA-less messenger RNAs (mRNAs). Additionally, we addressed the impact of the 5′-untranslated region of these reporter mRNAs under the same conditions by comparing expression from mRNAs that comprise (canonical mRNA) or lack this region (leaderless mRNA). Results Flow cytometry analysis indicates that during mazF overexpression, fluorescent proteins are translated from the canonical as well as leaderless mRNAs. Our analysis further indicates that longer mazF overexpression generally increases the concentration of fluorescent proteins translated from ACA-less mRNAs, however it also substantially increases bacterial population heterogeneity. Finally, our results suggest that the strength and duration of mazF overexpression should be optimized for each experimental setup, to maximize the heterologous protein production and minimize the amount of phenotypic heterogeneity in bacterial populations, which is unfavorable in biotechnological processes. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06061-9.
Collapse
Affiliation(s)
- Nela Nikolic
- Institute of Science and Technology Austria (ISTA), Klosterneuburg, Austria. .,Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria. .,Living Systems Institute, University of Exeter, Exeter, UK.
| | - Martina Sauert
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Tanino G Albanese
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Isabella Moll
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria.
| |
Collapse
|
9
|
Griego A, Douché T, Gianetto QG, Matondo M, Manina G. RNase E and HupB dynamics foster mycobacterial cell homeostasis and fitness. iScience 2022; 25:104233. [PMID: 35521527 PMCID: PMC9062218 DOI: 10.1016/j.isci.2022.104233] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/12/2022] [Accepted: 04/07/2022] [Indexed: 12/26/2022] Open
Abstract
RNA turnover is a primary source of gene expression variation, in turn promoting cellular adaptation. Mycobacteria leverage reversible mRNA stabilization to endure hostile conditions. Although RNase E is essential for RNA turnover in several species, its role in mycobacterial single-cell physiology and functional phenotypic diversification remains unexplored. Here, by integrating live-single-cell and quantitative-mass-spectrometry approaches, we show that RNase E forms dynamic foci, which are associated with cellular homeostasis and fate, and we discover a versatile molecular interactome. We show a likely interaction between RNase E and the nucleoid-associated protein HupB, which is particularly pronounced during drug treatment and infection, where phenotypic diversity increases. Disruption of RNase E expression affects HupB levels, impairing Mycobacterium tuberculosis growth homeostasis during treatment, intracellular replication, and host spread. Our work lays the foundation for targeting the RNase E and its partner HupB, aiming to undermine M. tuberculosis cellular balance, diversification capacity, and persistence. Single mycobacterial cells exhibit phenotypic variation in RNase E expression RNase E is implicated in the maintenance of mycobacterial cell growth homeostasis RNase E and HupB show a functional interplay in single mycobacterial cells RNase E-HupB disruption impairs Mycobacterium tuberculosis fate under drug and in macrophages
Collapse
|
10
|
Abstract
Despite their ubiquitous nature, few antisense RNAs have been functionally characterized, and this class of RNAs is considered by some to be transcriptional noise. Here, we report that an antisense RNA (asRNA), aMEF (antisense mazEF), functions as a dual regulator for the type II toxin-antitoxin (TA) system mazEF. Unlike type I TA systems and many other regulatory asRNAs, aMEF stimulates the synthesis and translation of mazEF rather than inhibition and degradation. Our data indicate that a double-stranded RNA intermediate and RNase III are not necessary for aMEF-dependent regulation of mazEF expression. The lack of conservation of asRNA promoters has been used to support the hypothesis that asRNAs are spurious transcriptional noise and nonfunctional. We demonstrate that the aMEF promoter is active and functional in Escherichia coli despite poor sequence conservation, indicating that the lack of promoter sequence conservation should not be correlated with functionality. IMPORTANCE Next-generation RNA sequencing of numerous organisms has revealed that transcription is widespread across the genome, termed pervasive transcription, and does not adhere to annotated gene boundaries. The function of pervasive transcription is enigmatic and has generated considerable controversy as to whether it is transcriptional noise or biologically relevant. Antisense transcription is one class of pervasive transcription that occurs from the DNA strand opposite an annotated gene. Relatively few pervasively transcribed asRNAs have been functionally characterized, and their regulatory roles or lack thereof remains unknown. It is important to study examples of these asRNAs and determine if they are functional regulators. In this study, we elucidate the function of an asRNA (aMEF) demonstrating that pervasive transcripts can be functional.
Collapse
|
11
|
A minimal model for gene expression dynamics of bacterial type II toxin-antitoxin systems. Sci Rep 2021; 11:19516. [PMID: 34593858 PMCID: PMC8484670 DOI: 10.1038/s41598-021-98570-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/07/2021] [Indexed: 02/08/2023] Open
Abstract
Toxin-antitoxin (TA) modules are part of most bacteria's regulatory machinery for stress responses and general aspects of their physiology. Due to the interplay of a long-lived toxin with a short-lived antitoxin, TA modules have also become systems of interest for mathematical modelling. Here we resort to previous modelling efforts and extract from these a minimal model of type II TA system dynamics on a timescale of hours, which can be used to describe time courses derived from gene expression data of TA pairs. We show that this model provides a good quantitative description of TA dynamics for the 11 TA pairs under investigation here, while simpler models do not. Our study brings together aspects of Biophysics with its focus on mathematical modelling and Computational Systems Biology with its focus on the quantitative interpretation of 'omics' data. This mechanistic model serves as a generic transformation of time course information into kinetic parameters. The resulting parameter vector can, in turn, be mechanistically interpreted. We expect that TA pairs with similar mechanisms are characterized by similar vectors of kinetic parameters, allowing us to hypothesize on the mode of action for TA pairs still under discussion.
Collapse
|
12
|
Gu Q, He P, Wang D, Ma J, Zhong X, Zhu Y, Zhang Y, Bai Q, Pan Z, Yao H. An Auto-Regulating Type II Toxin-Antitoxin System Modulates Drug Resistance and Virulence in Streptococcus suis. Front Microbiol 2021; 12:671706. [PMID: 34475853 PMCID: PMC8406773 DOI: 10.3389/fmicb.2021.671706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/26/2021] [Indexed: 11/13/2022] Open
Abstract
Toxin-antitoxin (TA) systems are ubiquitous genetic elements that play an essential role in multidrug tolerance and virulence of bacteria. So far, little is known about the TA systems in Streptococcus suis. In this study, the Xress-MNTss TA system, composed of the MNTss toxin in the periplasmic space and its interacting Xress antitoxin, was identified in S. suis. β-galactosidase activity and electrophoretic mobility shift assay (EMSA) revealed that Xress and the Xress-MNTss complex could bind directly to the Xress-MNTss promoter as well as downregulate streptomycin adenylyltransferase ZY05719_RS04610. Interestingly, the Xress deletion mutant was less pathogenic in vivo following a challenge in mice. Transmission electron microscopy and adhesion assays pointed to a significantly thinner capsule but greater biofilm-formation capacity in ΔXress than in the wild-type strain. These results indicate that Xress-MNTss, a new type II TA system, plays an important role in antibiotic resistance and pathogenicity in S. suis.
Collapse
Affiliation(s)
- Qibing Gu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
| | - Peijuan He
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
| | - Dan Wang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
| | - Jiale Ma
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
| | - Xiaojun Zhong
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China.,College of Animal Science and Technology, College of Veterinary Medicine, Zhejiang A&F University, Hangzhou, China
| | - Yinchu Zhu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China.,Institute of Animal Husbandry and Veterinary Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yue Zhang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China.,College of Veterinary Medicine, Henan Agricultural University, Zhengzhou, China
| | - Qiankun Bai
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
| | - Zihao Pan
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China.,Key Laboratory of Animal Bacteriology, Ministry of Agriculture, Nanjing, China.,OIE Reference Laboratory for Swine Streptococcosis, Nanjing, China
| |
Collapse
|
13
|
Abstract
Ribonucleases (RNases) are essential for almost every aspect of RNA metabolism. However, despite their important metabolic roles, RNases can also be destructive enzymes. As a consequence, cells must carefully regulate the amount, the activity, and the localization of RNases to avoid the inappropriate degradation of essential RNA molecules. In addition, bacterial cells often must adjust RNase levels as environmental situations demand, also requiring careful regulation of these critical enzymes. As the need for strict control of RNases has become more evident, multiple mechanisms for this regulation have been identified and studied, and these are described in this review. The major conclusion that emerges is that no common regulatory mechanism applies to all RNases, or even to a family of RNases; rather, a wide variety of processes have evolved that act on these enzymes, and in some cases, multiple regulatory mechanisms can even act on a single RNase. Expected final online publication date for the Annual Review of Microbiology, Volume 75 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Murray P Deutscher
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, Florida 33101, USA;
| |
Collapse
|
14
|
Sierra R, Prados J, Panasenko OO, Andrey DO, Fleuchot B, Redder P, Kelley WL, Viollier PH, Renzoni A. Insights into the global effect on Staphylococcus aureus growth arrest by induction of the endoribonuclease MazF toxin. Nucleic Acids Res 2020; 48:8545-8561. [PMID: 32735661 PMCID: PMC7470975 DOI: 10.1093/nar/gkaa617] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 06/18/2020] [Accepted: 07/27/2020] [Indexed: 12/22/2022] Open
Abstract
A crucial bacterial strategy to avoid killing by antibiotics is to enter a growth arrested state, yet the molecular mechanisms behind this process remain elusive. The conditional overexpression of mazF, the endoribonuclease toxin of the MazEF toxin–antitoxin system in Staphylococcus aureus, is one approach to induce bacterial growth arrest, but its targets remain largely unknown. We used overexpression of mazF and high-throughput sequence analysis following the exact mapping of non-phosphorylated transcriptome ends (nEMOTE) technique to reveal in vivo toxin cleavage sites on a global scale. We obtained a catalogue of MazF cleavage sites and unearthed an extended MazF cleavage specificity that goes beyond the previously reported one. We correlated transcript cleavage and abundance in a global transcriptomic profiling during mazF overexpression. We observed that MazF affects RNA molecules involved in ribosome biogenesis, cell wall synthesis, cell division and RNA turnover and thus deliver a plausible explanation for how mazF overexpression induces stasis. We hypothesize that autoregulation of MazF occurs by directly modulating the MazEF operon, such as the rsbUVW genes that regulate the sigma factor SigB, including an observed cleavage site on the MazF mRNA that would ultimately play a role in entry and exit from bacterial stasis.
Collapse
Affiliation(s)
- Roberto Sierra
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Julien Prados
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Olesya O Panasenko
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland
| | - Diego O Andrey
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Betty Fleuchot
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Peter Redder
- Centre de Biologie Intégrative, Université de Toulouse III, Toulouse 31400, France
| | - William L Kelley
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Patrick H Viollier
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Adriana Renzoni
- Service of Infectious Diseases, Department of Medical Specialties, Geneva University Hospitals and Medical School, Geneva 1211, Switzerland.,Department of Microbiology and Molecular Medicine, University of Geneva, Geneva 1211, Switzerland
| |
Collapse
|
15
|
Lopatkin AJ, Collins JJ. Predictive biology: modelling, understanding and harnessing microbial complexity. Nat Rev Microbiol 2020; 18:507-520. [DOI: 10.1038/s41579-020-0372-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
|
16
|
|
17
|
Planson AG, Sauveplane V, Dervyn E, Jules M. Bacterial growth physiology and RNA metabolism. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194502. [PMID: 32044462 DOI: 10.1016/j.bbagrm.2020.194502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/17/2020] [Accepted: 02/06/2020] [Indexed: 12/31/2022]
Abstract
Bacteria are sophisticated systems with high capacity and flexibility to adapt to various environmental conditions. Each prokaryote however possesses a defined metabolic network, which sets its overall metabolic capacity, and therefore the maximal growth rate that can be reached. To achieve optimal growth, bacteria adopt various molecular strategies to optimally adjust gene expression and optimize resource allocation according to the nutrient availability. The resulting physiological changes are often accompanied by changes in the growth rate, and by global regulation of gene expression. The growth-rate-dependent variation of the abundances in the cellular machineries, together with condition-specific regulatory mechanisms, affect RNA metabolism and fate and pose a challenge for rational gene expression reengineering of synthetic circuits. This article is part of a Special Issue entitled: RNA and gene control in bacteria, edited by Dr. M. Guillier and F. Repoila.
Collapse
Affiliation(s)
- Anne-Gaëlle Planson
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Vincent Sauveplane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Etienne Dervyn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| | - Matthieu Jules
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France.
| |
Collapse
|
18
|
Kim J, Darlington A, Salvador M, Utrilla J, Jiménez JI. Trade-offs between gene expression, growth and phenotypic diversity in microbial populations. Curr Opin Biotechnol 2019; 62:29-37. [PMID: 31580950 PMCID: PMC7208540 DOI: 10.1016/j.copbio.2019.08.004] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/15/2019] [Accepted: 08/20/2019] [Indexed: 12/13/2022]
Abstract
Limitations in molecular resources for gene expression influence bacterial physiology. Bacteria optimise trade-offs between resource allocation and growth. Resource allocation plays a role in the emergence of phenotypic heterogeneity. Trade-offs between bet-hedging and growth can be harnessed in biotechnology.
Bacterial cells have a limited number of resources that can be allocated for gene expression. The intracellular competition for these resources has an impact on the cell physiology. Bacteria have evolved mechanisms to optimize resource allocation in a variety of scenarios, showing a trade-off between the resources used to maximise growth (e.g. ribosome synthesis) and the rest of cellular functions. Limitations in gene expression also play a role in generating phenotypic diversity, which is advantageous in fluctuating environments, at the expenses of decreasing growth rates. Our current understanding of these trade-offs can be exploited for biotechnological applications benefiting from the selective manipulation of the allocation of resources.
Collapse
Affiliation(s)
- Juhyun Kim
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | | | - Manuel Salvador
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom
| | - José Utrilla
- Centre for Genomic Sciences, Universidad Nacional Autónoma de México, Campus Morelos, Av. Universidad s/n Col. Chamilpa 62210, Cuernavaca, Mexico
| | - José I Jiménez
- Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, United Kingdom.
| |
Collapse
|
19
|
Vet S, Vandervelde A, Gelens L. Excitable dynamics through toxin-induced mRNA cleavage in bacteria. PLoS One 2019; 14:e0212288. [PMID: 30794601 PMCID: PMC6386449 DOI: 10.1371/journal.pone.0212288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/30/2019] [Indexed: 11/19/2022] Open
Abstract
Toxin-antitoxin (TA) systems in bacteria and archaea are small genetic elements consisting of the genes coding for an intracellular toxin and an antitoxin that can neutralize this toxin. In various cases, the toxins cleave the mRNA. In this theoretical work we use deterministic and stochastic modeling to explain how toxin-induced cleavage of mRNA in TA systems can lead to excitability, allowing large transient spikes in toxin levels to be triggered. By using a simplified network where secondary complex formation and transcriptional regulation are not included, we show that a two-dimensional, deterministic model captures the origin of such toxin excitations. Moreover, it allows to increase our understanding by examining the dynamics in the phase plane. By systematically comparing the deterministic results with Gillespie simulations we demonstrate that even though the real TA system is intrinsically stochastic, toxin excitations can be accurately described deterministically. A bifurcation analysis of the system shows that the excitable behavior is due to a nearby Hopf bifurcation in the parameter space, where the system becomes oscillatory. The influence of stress is modeled by varying the degradation rate of the antitoxin and the translation rate of the toxin. We find that stress increases the frequency of toxin excitations. The inclusion of secondary complex formation and transcriptional regulation does not fundamentally change the mechanism of toxin excitations. Finally, we show that including growth rate suppression and translational inhibition can lead to longer excitations, and even cause excitations in cases when the system would otherwise be non-excitable. To conclude, the deterministic model used in this work provides a simple and intuitive explanation of toxin excitations in TA systems.
Collapse
Affiliation(s)
- Stefan Vet
- Applied Physics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels (IB2), VUB-ULB, Brussels, Belgium
- Unité de Chronobiologie théorique, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Lendert Gelens
- Applied Physics Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Laboratory of Dynamics in Biological Systems, KU Leuven, Leuven, Belgium
- * E-mail:
| |
Collapse
|
20
|
Nikolic N. Autoregulation of bacterial gene expression: lessons from the MazEF toxin-antitoxin system. Curr Genet 2019; 65:133-138. [PMID: 30132188 PMCID: PMC6343021 DOI: 10.1007/s00294-018-0879-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/13/2018] [Accepted: 08/14/2018] [Indexed: 11/30/2022]
Abstract
Autoregulation is the direct modulation of gene expression by the product of the corresponding gene. Autoregulation of bacterial gene expression has been mostly studied at the transcriptional level, when a protein acts as the cognate transcriptional repressor. A recent study investigating dynamics of the bacterial toxin-antitoxin MazEF system has shown how autoregulation at both the transcriptional and post-transcriptional levels affects the heterogeneity of Escherichia coli populations. Toxin-antitoxin systems hold a crucial but still elusive part in bacterial response to stress. This perspective highlights how these modules can also serve as a great model system for investigating basic concepts in gene regulation. However, as the genomic background and environmental conditions substantially influence toxin activation, it is important to study (auto)regulation of toxin-antitoxin systems in well-defined setups as well as in conditions that resemble the environmental niche.
Collapse
Affiliation(s)
- Nela Nikolic
- Institute of Science and Technology (IST) Austria, 3400, Klosterneuburg, Austria.
| |
Collapse
|
21
|
Mets T, Kasvandik S, Saarma M, Maiväli Ü, Tenson T, Kaldalu N. Fragmentation of Escherichia coli mRNA by MazF and MqsR. Biochimie 2019; 156:79-91. [DOI: 10.1016/j.biochi.2018.10.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/06/2018] [Indexed: 01/21/2023]
|