1
|
Carter MQ, Quiñones B, Laniohan N, Carychao D, Pham A, He X, Cooley M. Pathogenicity assessment of Shiga toxin-producing Escherichia coli strains isolated from wild birds in a major agricultural region in California. Front Microbiol 2023; 14:1214081. [PMID: 37822735 PMCID: PMC10562709 DOI: 10.3389/fmicb.2023.1214081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) consists of diverse strains differing in genetic make-up and virulence potential. To better understand the pathogenicity potential of STEC carried by the wildlife, three STEC and one E. coli strains isolated from wild birds near a major agricultural region in California were selected for comparative pathogenomic analyses. Three American crow (Corvus brachyrhynchos) strains, RM9088, RM9513, and RM10410, belonging to phylogroup A with serotypes O109:H48, O9:H30, and O113:H4, respectively, and a red-winged blackbird (Agelaius phoeniceus) strain RM14516 in phylogroup D with serotype O17:H18, were examined. Shiga toxin genes were identified in RM9088 (stx1a), RM10410 (stx1a + stx2d), and RM14516 (stx2a). Unlike STEC O157:H7 strain EDL933, none of the avian STEC strains harbored the pathogenicity islands OI-122, OI-57, and the locus of enterocyte effacement, therefore the type III secretion system biogenesis genes and related effector genes were absent in the three avian STEC genomes. Interestingly, all avian STEC strains exhibited greater (RM9088 and RM14516) or comparable (RM10410) cytotoxicity levels compared with EDL933. Comparative pathogenomic analyses revealed that RM9088 harbored numerous genes encoding toxins, toxins delivery systems, and adherence factors, including heat-labile enterotoxin, serine protease autotransporter toxin Pic, type VI secretion systems, protein adhesin Paa, fimbrial adhesin K88, and colonization factor antigen I. RM9088 also harbored a 36-Kb high pathogenicity island, which is related to iron acquisition and pathogenicity in Yersinia spp. Strain RM14516 carried an acid fitness island like the one in EDL933, containing a nine gene cluster involved in iron acquisition. Genes encoding extracellular serine protease EspP, subtilase cytotoxin, F1C fimbriae, and inverse autotransporter adhesin IatC were only detected in RM14516, and genes encoding serine protease autotransporter EspI and P fimbriae were only identified in RM10410. Although all curli genes were present in avian STEC strains, production of curli fimbriae was only detected for RM9088 and RM14516. Consistently, strong, moderate, and little biofilms were observed for RM9088, RM14516, and RM10410, respectively. Our study revealed novel combinations of virulence factors in two avian strains, which exhibited high level of cytotoxicity and strong biofilm formation. Comparative pathogenomics is powerful in assessing pathogenicity and health risk of STEC strains.
Collapse
Affiliation(s)
- Michelle Qiu Carter
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Nicole Laniohan
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Diana Carychao
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Antares Pham
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Xiaohua He
- Foodborne Toxin Detection and Prevention Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| | - Michael Cooley
- Produce Safety and Microbiology Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Western Regional Research Center, Albany, CA, United States
| |
Collapse
|
2
|
Jensen SJ, Ruhe ZC, Williams AF, Nhan DQ, Garza-Sánchez F, Low DA, Hayes CS. Paradoxical Activation of a Type VI Secretion System Phospholipase Effector by Its Cognate Immunity Protein. J Bacteriol 2023; 205:e0011323. [PMID: 37212679 PMCID: PMC10294671 DOI: 10.1128/jb.00113-23] [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: 03/27/2023] [Accepted: 05/03/2023] [Indexed: 05/23/2023] Open
Abstract
Type VI secretion systems (T6SSs) deliver cytotoxic effector proteins into target bacteria and eukaryotic host cells. Antibacterial effectors are invariably encoded with cognate immunity proteins that protect the producing cell from self-intoxication. Here, we identify transposon insertions that disrupt the tli immunity gene of Enterobacter cloacae and induce autopermeabilization through unopposed activity of the Tle phospholipase effector. This hyperpermeability phenotype is T6SS dependent, indicating that the mutants are intoxicated by Tle delivered from neighboring sibling cells rather than by internally produced phospholipase. Unexpectedly, an in-frame deletion of tli does not induce hyperpermeability because Δtli null mutants fail to deploy active Tle. Instead, the most striking phenotypes are associated with disruption of the tli lipoprotein signal sequence, which prevents immunity protein localization to the periplasm. Immunoblotting reveals that most hyperpermeable mutants still produce Tli, presumably from alternative translation initiation codons downstream of the signal sequence. These observations suggest that cytosolic Tli is required for the activation and/or export of Tle. We show that Tle growth inhibition activity remains Tli dependent when phospholipase delivery into target bacteria is ensured through fusion to the VgrG β-spike protein. Together, these findings indicate that Tli has distinct functions, depending on its subcellular localization. Periplasmic Tli acts as a canonical immunity factor to neutralize incoming effector proteins, while a cytosolic pool of Tli is required to activate the phospholipase domain of Tle prior to T6SS-dependent export. IMPORTANCE Gram-negative bacteria use type VI secretion systems deliver toxic effector proteins directly into neighboring competitors. Secreting cells also produce specific immunity proteins that neutralize effector activities to prevent autointoxication. Here, we show the Tli immunity protein of Enterobacter cloacae has two distinct functions, depending on its subcellular localization. Periplasmic Tli acts as a canonical immunity factor to block Tle lipase effector activity, while cytoplasmic Tli is required to activate the lipase prior to export. These results indicate Tle interacts transiently with its cognate immunity protein to promote effector protein folding and/or packaging into the secretion apparatus.
Collapse
Affiliation(s)
- Steven J. Jensen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Zachary C. Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - August F. Williams
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Dinh Q. Nhan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
| | - David A. Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, USA
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, California, USA
| |
Collapse
|
3
|
Jensen SJ, Ruhe ZC, Williams AF, Nhan DQ, Garza-Sánchez F, Low DA, Hayes CS. Paradoxical activation of a type VI secretion system (T6SS) phospholipase effector by its cognate immunity protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.534661. [PMID: 37034769 PMCID: PMC10081291 DOI: 10.1101/2023.03.28.534661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Type VI secretion systems (T6SS) deliver cytotoxic effector proteins into target bacteria and eukaryotic host cells. Antibacterial effectors are invariably encoded with cognate immunity proteins that protect the producing cell from self-intoxication. Here, we identify transposon insertions that disrupt the tli immunity gene of Enterobacter cloacae and induce auto-permeabilization through unopposed activity of the Tle phospholipase effector. This hyper-permeability phenotype is T6SS-dependent, indicating that the mutants are intoxicated by Tle delivered from neighboring sibling cells rather than by internally produced phospholipase. Unexpectedly, an in-frame deletion of tli does not induce hyper-permeability because Δ tli null mutants fail to deploy active Tle. Instead, the most striking phenotypes are associated with disruption of the tli lipoprotein signal sequence, which prevents immunity protein localization to the periplasm. Immunoblotting reveals that most hyper-permeable mutants still produce Tli, presumably from alternative translation initiation codons downstream of the signal sequence. These observations suggest that cytosolic Tli is required for the activation and/or export of Tle. We show that Tle growth inhibition activity remains Tli-dependent when phospholipase delivery into target bacteria is ensured through fusion to the VgrG β-spike protein. Together, these findings indicate that Tli has distinct functions depending on its subcellular localization. Periplasmic Tli acts as a canonical immunity factor to neutralize incoming effector proteins, while a cytosolic pool of Tli is required to activate the phospholipase domain of Tle prior to T6SS-dependent export.
Collapse
|
4
|
Cuthbert BJ, Hayes CS, Goulding CW. Functional and Structural Diversity of Bacterial Contact-Dependent Growth Inhibition Effectors. Front Mol Biosci 2022; 9:866854. [PMID: 35558562 PMCID: PMC9086364 DOI: 10.3389/fmolb.2022.866854] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/07/2022] [Indexed: 12/25/2022] Open
Abstract
Bacteria live in complex communities and environments, competing for space and nutrients. Within their niche habitats, bacteria have developed various inter-bacterial mechanisms to compete and communicate. One such mechanism is contact-dependent growth inhibition (CDI). CDI is found in many Gram-negative bacteria, including several pathogens. These CDI+ bacteria encode a CdiB/CdiA two-partner secretion system that delivers inhibitory toxins into neighboring cells upon contact. Toxin translocation results in the growth inhibition of closely related strains and provides a competitive advantage to the CDI+ bacteria. CdiB, an outer-membrane protein, secretes CdiA onto the surface of the CDI+ bacteria. When CdiA interacts with specific target-cell receptors, CdiA delivers its C-terminal toxin region (CdiA-CT) into the target-cell. CdiA-CT toxin proteins display a diverse range of toxic functions, such as DNase, RNase, or pore-forming toxin activity. CDI+ bacteria also encode an immunity protein, CdiI, that specifically binds and neutralizes its cognate CdiA-CT, protecting the CDI+ bacteria from auto-inhibition. In Gram-negative bacteria, toxin/immunity (CdiA-CT/CdiI) pairs have highly variable sequences and functions, with over 130 predicted divergent toxin/immunity complex families. In this review, we will discuss biochemical and structural advances made in the characterization of CDI. This review will focus on the diverse array of CDI toxin/immunity complex structures together with their distinct toxin functions. Additionally, we will discuss the most recent studies on target-cell recognition and toxin entry, along with the discovery of a new member of the CDI loci. Finally, we will offer insights into how these diverse toxin/immunity complexes could be harnessed to fight human diseases.
Collapse
Affiliation(s)
- Bonnie J. Cuthbert
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
| | - Christopher S. Hayes
- Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Celia W. Goulding
- Molecular Biology and Biochemistry, University of California, Irvine, Irvine, CA, United States
- Pharmaceutical Sciences, University of California, Irvine, Irvine, CA, United States
| |
Collapse
|
5
|
Wang J, Yashiro Y, Sakaguchi Y, Suzuki T, Tomita K. Mechanistic insights into tRNA cleavage by a contact-dependent growth inhibitor protein and translation factors. Nucleic Acids Res 2022; 50:4713-4731. [PMID: 35411396 PMCID: PMC9071432 DOI: 10.1093/nar/gkac228] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/21/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
Contact-dependent growth inhibition is a mechanism of interbacterial competition mediated by delivery of the C-terminal toxin domain of CdiA protein (CdiA–CT) into neighboring bacteria. The CdiA–CT of enterohemorrhagic Escherichia coli EC869 (CdiA–CTEC869) cleaves the 3′-acceptor regions of specific tRNAs in a reaction that requires the translation factors Tu/Ts and GTP. Here, we show that CdiA–CTEC869 has an intrinsic ability to recognize a specific sequence in substrate tRNAs, and Tu:Ts complex promotes tRNA cleavage by CdiA–CTEC869. Uncharged and aminoacylated tRNAs (aa-tRNAs) were cleaved by CdiA–CTEC869 to the same extent in the presence of Tu/Ts, and the CdiA–CTEC869:Tu:Ts:tRNA(aa-tRNA) complex formed in the presence of GTP. CdiA–CTEC869 interacts with domain II of Tu, thereby preventing the 3′-moiety of tRNA to bind to Tu as in canonical Tu:GTP:aa-tRNA complexes. Superimposition of the Tu:GTP:aa-tRNA structure onto the CdiA–CTEC869:Tu structure suggests that the 3′-portion of tRNA relocates into the CdiA–CTEC869 active site, located on the opposite side to the CdiA–CTEC869 :Tu interface, for tRNA cleavage. Thus, CdiA–CTEC869 is recruited to Tu:GTP:Ts, and CdiA–CT:Tu:GTP:Ts recognizes substrate tRNAs and cleaves them. Tu:GTP:Ts serves as a reaction scaffold that increases the affinity of CdiA–CTEC869 for substrate tRNAs and induces a structural change of tRNAs for efficient cleavage by CdiA–CTEC869.
Collapse
Affiliation(s)
- Jing Wang
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa,Chiba277-8562, Japan
| | - Yuka Yashiro
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa,Chiba277-8562, Japan
| | - Yuriko Sakaguchi
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kozo Tomita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa,Chiba277-8562, Japan
| |
Collapse
|
6
|
Abd El-Aleam RH, George RF, Georgey HH, Abdel-Rahman HM. Bacterial virulence factors: a target for heterocyclic compounds to combat bacterial resistance. RSC Adv 2021; 11:36459-36482. [PMID: 35494393 PMCID: PMC9043591 DOI: 10.1039/d1ra06238g] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/01/2021] [Indexed: 12/17/2022] Open
Abstract
Antibiotic resistance is one of the most important challenges of the 21st century. However, the growing understanding of bacterial pathogenesis and cell-to-cell communication has revealed many potential strategies for the discovery of drugs that can be used for the treatment of bacterial infections. Interfering with bacterial virulence and/or quorum sensing could be a particularly interesting approach, because it is believed to exert less selective pressure on the bacterial resistance than with traditional strategies, geared toward killing bacteria or preventing their growth. Here, we discuss the mechanism of bacterial virulence, presenting promising strategies and recently synthesized heterocyclic compounds to combat future bacterial infections.
Collapse
Affiliation(s)
- Rehab H Abd El-Aleam
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Modern University for Technology and Information MTI Cairo 11571 Egypt
| | - Riham F George
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
| | - Hanan H Georgey
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Cairo University Cairo 11562 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy and Drug Technology, Egyptian Chinese University Cairo 11786 Egypt
| | - Hamdy M Abdel-Rahman
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University Assiut 71526 Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Nahda University Beni Suef Egypt
| |
Collapse
|
7
|
Singh RP, Saini N, Sharma G, Rahisuddin R, Patel M, Kaushik A, Kumaran S. Moonlighting Biochemistry of Cysteine Synthase: A Species-specific Global Regulator. J Mol Biol 2021; 433:167255. [PMID: 34547327 DOI: 10.1016/j.jmb.2021.167255] [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: 04/11/2021] [Revised: 09/10/2021] [Accepted: 09/12/2021] [Indexed: 11/18/2022]
Abstract
Cysteine Synthase (CS), the enzyme that synthesizes cysteine, performs non-canonical regulatory roles by binding and modulating functions of disparate proteins. Beyond its role in catalysis and regulation in the cysteine biosynthesis pathway, it exerts its moonlighting effect by binding to few other proteins which possess a C-terminal "CS-binding motif", ending with a terminal ILE. Therefore, we hypothesized that CS might regulate many other disparate proteins with the "CS-binding motif". In this study, we developed an iterative sequence matching method for mapping moonlighting biochemistry of CS and validated our prediction by analytical and structural approaches. Using a minimal protein-peptide interaction system, we show that five previously unknown CS-binder proteins that participate in diverse metabolic processes interact with CS in a species-specific manner. Furthermore, results show that signatures of protein-protein interactions, including thermodynamic, competitive-inhibition, and structural features, highly match the known CS-Binder, serine acetyltransferase (SAT). Together, the results presented in this study allow us to map the extreme multifunctional space (EMS) of CS and reveal the biochemistry of moonlighting space, a subset of EMS. We believe that the integrated computational and experimental workflow developed here could be further modified and extended to study protein-specific moonlighting properties of multifunctional proteins.
Collapse
Affiliation(s)
- Ravi Pratap Singh
- G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India
| | - Neha Saini
- G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Electronic city, Bengaluru, Karnataka 560100, India
| | - R Rahisuddin
- G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India. https://twitter.com/RahisuddinAlig
| | - Madhuri Patel
- G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India
| | - Abhishek Kaushik
- G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India
| | - S Kumaran
- G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research (CSIR), Institute of Microbial Technology (IMTECH), Sector 39-A, Chandigarh 160036, India.
| |
Collapse
|
8
|
Myers-Morales T, Sim MMS, DuCote TJ, Garcia EC. Burkholderia multivorans requires species-specific GltJK for entry of a contact-dependent growth inhibition system protein. Mol Microbiol 2021; 116:957-973. [PMID: 34236112 PMCID: PMC9291907 DOI: 10.1111/mmi.14783] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 07/02/2021] [Accepted: 07/05/2021] [Indexed: 12/04/2022]
Abstract
Interbacterial antagonism and communication are driving forces behind microbial community development. In many Gram‐negative bacteria, contact‐dependent growth inhibition (CDI) systems contribute to these microbial interactions. CDI systems deliver the toxic C‐terminus of a large surface exposed protein to the cytoplasm of neighboring bacteria upon cell−contact. Termed the BcpA‐CT, import of this toxic effector domain is mediated by specific, yet largely unknown receptors on the recipient cell outer and inner membranes. In this study, we demonstrated that cytoplasmic membrane proteins GltJK, components of a predicted ABC‐type transporter, are required for entry of CDI system protein BcpA‐2 into Burkholderia multivorans recipient cells. Consistent with current CDI models, gltJK were also required for recipient cell susceptibility to a distinct BcpA‐CT that shared sequences within the predicted “translocation domain” of BcpA‐2. Strikingly, this translocation domain showed low sequence identity to the analogous region of an Escherichia coli GltJK‐utilizing CDI system protein. Our results demonstrated that recipient bacteria expressing E. coli gltJK were resistant to BcpA‐2‐mediated interbacterial antagonism, suggesting that BcpA‐2 specifically recognizes Burkholderia GltJK. Using a series of chimeric proteins, the specificity determinant was mapped to Burkholderia‐specific sequences at the GltK C‐terminus, providing insight into BcpA transport across the recipient cell cytoplasmic membrane.
Collapse
Affiliation(s)
- Tanya Myers-Morales
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, USA
| | - Martha M S Sim
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, USA
| | - Tanner J DuCote
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, USA
| | - Erin C Garcia
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY, USA
| |
Collapse
|
9
|
Abstract
Studying the interactions of bacterial viruses (phages) with their bacterial hosts may lead to better understanding of bacterial mechanisms and consequently enable better manipulation of bacterial pathogens. In this study, we characterized the activity of a protein from phage T5, called T5.015. This protein binds to another protein, Ung, and uses its activity to selectively cleave dUMP-containing DNA. Such cleavage of the bacterial DNA stops bacterial DNA replication and also prevents bacterial division. Presumably, the phage DNA is protected from this activity as Ung does not act on the phage DNA, probably due to lower incorporation of the Ung substrate, dUMP. We believe that the findings are general to many phages and reveal a mechanism of self-versus-foreign DNA discrimination. Bacteriophages (phages) have evolved efficient means to take over the machinery of the bacterial host. The molecular tools at their disposal may be applied to manipulate bacteria and to divert molecular pathways at will. Here, we describe a bacterial growth inhibitor, gene product T5.015, encoded by the T5 phage. High-throughput sequencing of genomic DNA of bacterial mutants, resistant to this inhibitor, revealed disruptive mutations in the Escherichia coli ung gene, suggesting that growth inhibition mediated by T5.015 depends on the uracil-excision activity of Ung. We validated that growth inhibition is abrogated in the absence of ung and confirmed physical binding of Ung by T5.015. In addition, biochemical assays with T5.015 and Ung indicated that T5.015 mediates endonucleolytic activity at abasic sites generated by the base-excision activity of Ung. Importantly, the growth inhibition resulting from the endonucleolytic activity is manifested by DNA replication and cell division arrest. We speculate that the phage uses this protein to selectively cause cleavage of the host DNA, which possesses more misincorporated uracils than that of the phage. This protein may also enhance phage utilization of the available resources in the infected cell, since halting replication saves nucleotides, and stopping cell division maintains both daughters of a dividing cell.
Collapse
|
10
|
Rosa B, Dickinson ER, Marchetti M, Campanini B, Pioselli B, Bettati S, Rand KD. Revealing the Dynamic Allosteric Changes Required for Formation of the Cysteine Synthase Complex by Hydrogen-Deuterium Exchange MS. Mol Cell Proteomics 2021; 20:100098. [PMID: 34022432 PMCID: PMC8253905 DOI: 10.1016/j.mcpro.2021.100098] [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: 04/10/2021] [Accepted: 05/14/2021] [Indexed: 11/30/2022] Open
Abstract
CysE and CysK, the last two enzymes of the cysteine biosynthetic pathway, engage in a bienzyme complex, cysteine synthase, with yet incompletely characterized three-dimensional structure and regulatory function. Being absent in mammals, the two enzymes and their complex are attractive targets for antibacterial drugs. We have used hydrogen/deuterium exchange MS to unveil how complex formation affects the conformational dynamics of CysK and CysE. Our results support a model where CysE is present in solution as a dimer of trimers, and each trimer can bind one CysK homodimer. When CysK binds to one CysE monomer, intratrimer allosteric communication ensures conformational and dynamic symmetry within the trimer. Furthermore, a long-range allosteric signal propagates through CysE to induce stabilization of the interface between the two CysE trimers, preparing the second trimer for binding the second CysK with a nonrandom orientation. These results provide new molecular insights into the allosteric formation of the cysteine synthase complex and could help guide antibacterial drug design. HDX-MS reveals complex formation impact on conformational dynamics of CysK and CysE. CysK binding ensures conformational symmetry within the CysE trimer. Long-range allostery propagates through CysE stabilizing the inter-trimer interface. Insights into the allostery of CS complex could help guide antibacterial drug design.
Collapse
Affiliation(s)
- Brenda Rosa
- Biopharmanet-TEC Interdepartmental Center, University di Parma, Parma, Italy
| | - Eleanor R Dickinson
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen O, Denmark
| | | | | | | | - Stefano Bettati
- Biopharmanet-TEC Interdepartmental Center, University di Parma, Parma, Italy; Department of Medicine and Surgery, University of Parma, Parma, Italy; Institute of Biophysics, CNR, Pisa, Italy.
| | - Kasper Dyrberg Rand
- Protein Analysis Group, Department of Pharmacy, University of Copenhagen, Copenhagen O, Denmark.
| |
Collapse
|
11
|
Genetic Evidence for SecY Translocon-Mediated Import of Two Contact-Dependent Growth Inhibition (CDI) Toxins. mBio 2021; 12:mBio.03367-20. [PMID: 33531386 PMCID: PMC7858069 DOI: 10.1128/mbio.03367-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Many bacterial species interact via direct cell-to-cell contact using CDI systems, which provide a mechanism to inject toxins that inhibit bacterial growth into one another. Here, we find that two CDI toxins, one that depolarizes membranes and another that degrades RNA, exploit the universally conserved SecY translocon machinery used to export proteins for target cell entry. The C-terminal (CT) toxin domains of contact-dependent growth inhibition (CDI) CdiA proteins target Gram-negative bacteria and must breach both the outer and inner membranes of target cells to exert growth inhibitory activity. Here, we examine two CdiA-CT toxins that exploit the bacterial general protein secretion machinery after delivery into the periplasm. A Ser281Phe amino acid substitution in transmembrane segment 7 of SecY, the universally conserved channel-forming subunit of the Sec translocon, decreases the cytotoxicity of the membrane depolarizing orphan10 toxin from enterohemorrhagic Escherichia coli EC869. Target cells expressing secYS281F and lacking either PpiD or YfgM, two SecY auxiliary factors, are fully protected from CDI-mediated inhibition either by CdiA-CTo10EC869 or by CdiA-CTGN05224, the latter being an EndoU RNase CdiA toxin from Klebsiella aerogenes GN05224 that has a related cytoplasm entry domain. RNase activity of CdiA-CTGN05224 was reduced in secYS281F target cells and absent in secYS281F ΔppiD or secYS281F ΔyfgM target cells during competition co-cultures. Importantly, an allele-specific mutation in secY (secYG313W) renders ΔppiD or ΔyfgM target cells specifically resistant to CdiA-CTGN05224 but not to CdiA-CTo10EC869, further suggesting a direct interaction between SecY and the CDI toxins. Our results provide genetic evidence of a unique confluence between the primary cellular export route for unfolded polypeptides and the import pathways of two CDI toxins.
Collapse
|
12
|
Ogawa T, Takahashi K, Ishida W, Aono T, Hidaka M, Terada T, Masaki H. Substrate recognition mechanism of tRNA-targeting ribonuclease, colicin D, and an insight into tRNA cleavage-mediated translation impairment. RNA Biol 2020; 18:1193-1205. [PMID: 33211605 DOI: 10.1080/15476286.2020.1838782] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Colicin D is a plasmid-encoded bacteriocin that specifically cleaves tRNAArg of sensitive Escherichia coli cells. E. coli has four isoaccepting tRNAArgs; the cleavage occurs at the 3' end of anticodon-loop, leading to translation impairment in the sensitive cells. tRNAs form a common L-shaped structure and have many conserved nucleotides that limit tRNA identity elements. How colicin D selects tRNAArgs from the tRNA pool of sensitive E. coli cells is therefore intriguing. Here, we reveal the recognition mechanism of colicin D via biochemical analyses as well as structural modelling. Colicin D recognizes tRNAArgICG, the most abundant species of E. coli tRNAArgs, at its anticodon-loop and D-arm, and selects it as the most preferred substrate by distinguishing its anticodon-loop sequence from that of others. It has been assumed that translation impairment is caused by a decrease in intact tRNA molecules due to cleavage. However, we found that intracellular levels of intact tRNAArgICG do not determine the viability of sensitive cells after such cleavage; rather, an accumulation of cleaved ones does. Cleaved tRNAArgICG dominant-negatively impairs translation in vitro. Moreover, we revealed that EF-Tu, which is required for the delivery of tRNAs, does not compete with colicin D for binding tRNAArgICG, which is consistent with our structural model. Finally, elevation of cleaved tRNAArgICG level decreases the viability of sensitive cells. These results suggest that cleaved tRNAArgICG transiently occupies ribosomal A-site in an EF-Tu-dependent manner, leading to translation impairment. The strategy should also be applicable to other tRNA-targeting RNases, as they, too, recognize anticodon-loops.Abbreviations: mnm5U: 5-methylaminomethyluridine; mcm5s2U: 5-methoxycarbonylmethyl-2-thiouridine.
Collapse
Affiliation(s)
- Tetsuhiro Ogawa
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Kazutoshi Takahashi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Wataru Ishida
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Toshihiro Aono
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan.,Biotechnology Research Center, The University of Tokyo, Tokyo, Japan
| | - Makoto Hidaka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.,Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo, Japan
| | - Haruhiko Masaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| |
Collapse
|
13
|
Lin HH, Filloux A, Lai EM. Role of Recipient Susceptibility Factors During Contact-Dependent Interbacterial Competition. Front Microbiol 2020; 11:603652. [PMID: 33281802 PMCID: PMC7690452 DOI: 10.3389/fmicb.2020.603652] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/13/2020] [Indexed: 11/13/2022] Open
Abstract
Bacteria evolved multiple strategies to survive and develop optimal fitness in their ecological niche. They deployed protein secretion systems for robust and efficient delivery of antibacterial toxins into their target cells, therefore inhibiting their growth or killing them. To maximize antagonism, recipient factors on target cells can be recognized or hijacked to enhance the entry or toxicity of these toxins. To date, knowledge regarding recipient susceptibility (RS) factors and their mode of action is mostly originating from studies on the type Vb secretion system that is also known as the contact-dependent inhibition (CDI) system. Yet, recent studies on the type VI secretion system (T6SS), and the CDI by glycine-zipper protein (Cdz) system, also reported the emerging roles of RS factors in interbacterial competition. Here, we review these RS factors and their mechanistic impact in increasing susceptibility of recipient cells in response to CDI, T6SS, and Cdz. Past and future strategies for identifying novel RS factors are also discussed, which will help in understanding the interplay between attacker and prey upon secretion system-dependent competition. Understanding these mechanisms would also provide insights for developing novel antibacterial strategies to antagonize aggressive bacteria-killing pathogens.
Collapse
Affiliation(s)
- Hsiao-Han Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
14
|
Contact-Dependent Growth Inhibition in Bacteria: Do Not Get Too Close! Int J Mol Sci 2020; 21:ijms21217990. [PMID: 33121148 PMCID: PMC7662968 DOI: 10.3390/ijms21217990] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/24/2020] [Accepted: 10/26/2020] [Indexed: 12/20/2022] Open
Abstract
Over millions of years of evolution, bacteria have developed complex strategies for intra-and interspecies interactions and competition for ecological niches and resources. Contact-dependent growth inhibition systems (CDI) are designed to realize a direct physical contact of one bacterial cell with other cells in proximity via receptor-mediated toxin delivery. These systems are found in many microorganisms including clinically important human pathogens. The main purpose of these systems is to provide competitive advantages for the growth of the population. In addition, non-competitive roles for CDI toxin delivery systems including interbacterial signal transduction and mediators of bacterial collaboration have been suggested. In this review, our goal was to systematize the recent findings on the structure, mechanisms, and purpose of CDI systems in bacterial populations and discuss the potential biological and evolutionary impact of CDI-mediated interbacterial competition and/or cooperation.
Collapse
|
15
|
Han NC, Kelly P, Ibba M. Translational quality control and reprogramming during stress adaptation. Exp Cell Res 2020; 394:112161. [PMID: 32619498 DOI: 10.1016/j.yexcr.2020.112161] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/26/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022]
Abstract
Organisms encounter stress throughout their lives, and therefore require the ability to respond rapidly to environmental changes. Although transcriptional responses are crucial for controlling changes in gene expression, regulation at the translational level often allows for a faster response at the protein levels which permits immediate adaptation. The fidelity and robustness of protein synthesis are actively regulated under stress. For example, mistranslation can be beneficial to cells upon environmental changes and also alters cellular stress responses. Additionally, stress modulates both global and selective translational regulation through mechanisms including the change of aminoacyl-tRNA activity, tRNA pool reprogramming and ribosome heterogeneity. In this review, we draw on studies from both the prokaryotic and eukaryotic systems to discuss current findings of cellular adaptation at the level of translation, specifically translational fidelity and activity changes in response to a wide array of environmental stressors including oxidative stress, nutrient depletion, temperature variation, antibiotics and host colonization.
Collapse
Affiliation(s)
- Nien-Ching Han
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA
| | - Paul Kelly
- The Ohio State University Molecular, Cellular and Developmental Biology Program, The Ohio State University, Columbus, OH, 43220, USA
| | - Michael Ibba
- Department of Microbiology, The Ohio State University, Columbus, OH, 43220, USA.
| |
Collapse
|
16
|
Guo L, Wang J, Gou Y, Tan L, Liu H, Pan Y, Zhao Y. Comparative proteomics reveals stress responses of Vibrio parahaemolyticus biofilm on different surfaces: Internal adaptation and external adjustment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:138386. [PMID: 32417469 DOI: 10.1016/j.scitotenv.2020.138386] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 06/11/2023]
Abstract
Vibrio parahaemolyticus is a kind of gram-negative marine pathogen, which usually adheres to stainless steel (SS), glass (GS) and other abiotic surfaces in aquaculture and food processing in the form of biofilm and causes the spread of gastrointestinal illness. However, the deeply survival adaptation mechanism of V. parahaemolyticus biofilm cells on these contact surface remained unclear. Here, proteomics was used to investigated the physiological response of the V. parahaemolyticus biofilms cells to different abiotic surfaces (SS, GS and polystyrene (PS)). In addition, the effect of contact materials on the physical-chemical properties of biofilms are also characterized. Results showed that the expression of proteins of biofilm cells established on the SS surface were mainly related to the alleviation of metal ion stress and toxicity. The up-regulated proteins in the biofilm cells formed on the GS surface were mainly involved in the biological processes of sugar uptake, protein synthesis and bacterial chemotaxis. Meanwhile, the significantly expressed proteins in the biofilm cells formed on the PS surface were mainly involved in the cellular physiological activity of aromatic compound metabolism, osmotic stress and nutrient transport. All functional proteins mentioned above were closely related to the interaction characteristics of the contact surface and biofilm. This study provided an in-depth comparison of V. parahaemolyticus biofilm formation on these three abiotic surfaces, and presented a model in first time for the adaptation behavior of biofilm cells on different surfaces as affected by metal ion stress, nutrition, osmotic stress, and sugar utilization, which could facilitate an efficient control strategy for biofilm formation in industrial field.
Collapse
Affiliation(s)
- Linxia Guo
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Jingjing Wang
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China; Department of Food Science, Foshan University, Foshan, 528000, China
| | - Yi Gou
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Ling Tan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China
| | - Haiquan Liu
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China; Engineering Research Center of Food Thermal-processing Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yingjie Pan
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China
| | - Yong Zhao
- College of Food Science & Technology, Shanghai Ocean University, Shanghai, China; Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture, Shanghai, China; Shanghai Engineering Research Center of Aquatic-Product Processing & Preservation, Shanghai, China.
| |
Collapse
|
17
|
Ruhe ZC, Low DA, Hayes CS. Polymorphic Toxins and Their Immunity Proteins: Diversity, Evolution, and Mechanisms of Delivery. Annu Rev Microbiol 2020; 74:497-520. [PMID: 32680451 DOI: 10.1146/annurev-micro-020518-115638] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
All bacteria must compete for growth niches and other limited environmental resources. These existential battles are waged at several levels, but one common strategy entails the transfer of growth-inhibitory protein toxins between competing cells. These antibacterial effectors are invariably encoded with immunity proteins that protect cells from intoxication by neighboring siblings. Several effector classes have been described, each designed to breach the cell envelope of target bacteria. Although effector architectures and export pathways tend to be clade specific, phylogenetically distant species often deploy closely related toxin domains. Thus, diverse competition systems are linked through a common reservoir of toxin-immunity pairs that is shared via horizontal gene transfer. These toxin-immunity protein pairs are extraordinarily diverse in sequence, and this polymorphism underpins an important mechanism of self/nonself discrimination in bacteria. This review focuses on the structures, functions, and delivery mechanisms of polymorphic toxin effectors that mediate bacterial competition.
Collapse
Affiliation(s)
- Zachary C Ruhe
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA;
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, USA; .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, California 93106, USA
| |
Collapse
|
18
|
Kaundal S, Deep A, Kaur G, Thakur KG. Molecular and Biochemical Characterization of YeeF/YezG, a Polymorphic Toxin-Immunity Protein Pair From Bacillus subtilis. Front Microbiol 2020; 11:95. [PMID: 32117125 PMCID: PMC7033585 DOI: 10.3389/fmicb.2020.00095] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/16/2020] [Indexed: 12/25/2022] Open
Abstract
Polymorphic toxins are important and widespread elements of bacterial warfare that help in restricting the growth of competitors, aiding kin selection, and shaping the bacterial communities. Although widespread, polymorphic toxin systems (PTS) have been extensively studied in Gram-negative bacteria, there are limited studies describing PTS in Gram-positive bacteria. The present study characterizes YeeF/YezG, a predicted member of a PF04740 family of the polymorphic toxin-immunity system from a Gram-positive bacteria Bacillus subtilis. The expression of the C-terminal toxic domain of YeeF (YeeF-CT) causes growth inhibition and gross morphological changes in Escherichia coli. The observed toxic effects are neutralized by the co-expression of yezG, a gene present downstream of yeeF, confirming YeeF-CT/YezG as a toxin/immunity protein pair. Biochemical and in vivo studies reveal that YeeF-CT causes toxicity due to its non-specific metal-dependent DNase activity. This is different from the previously reported RNase activity from the three B. subtilis toxins belonging to PF04740 family. Isothermal titration calorimetry (ITC) data analysis suggests that YeeF-CT binds YezG with a dissociation constant in the nanomolar range. Analytical ultracentrifugation studies revealed that YeeF-CT forms a homodimer and binds with two molecules of monomeric YezG immunity protein to form a 2:2 stochiometric heterotetrameric complex. Biolayer interferometry and electrophoretic mobility shift assays show that YeeF-CT/YezG/DNA forms a stable ternary complex implicating that YezG is an exosite inhibitor of YeeF-CT. This study extends the molecular targets of the toxins in the PF04740 family and thus, this family of toxins can be broadly classified as nucleases harboring either DNases or RNases activities.
Collapse
Affiliation(s)
- Soni Kaundal
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific & Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Amar Deep
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific & Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Gundeep Kaur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific & Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific & Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh, India
| |
Collapse
|
19
|
Lin HH, Yu M, Sriramoju MK, Hsu STD, Liu CT, Lai EM. A High-Throughput Interbacterial Competition Screen Identifies ClpAP in Enhancing Recipient Susceptibility to Type VI Secretion System-Mediated Attack by Agrobacterium tumefaciens. Front Microbiol 2020; 10:3077. [PMID: 32117077 PMCID: PMC7012810 DOI: 10.3389/fmicb.2019.03077] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/19/2019] [Indexed: 12/30/2022] Open
Abstract
The type VI secretion system (T6SS) is an effector delivery system used by Gram-negative bacteria to kill other bacteria or eukaryotic hosts to gain fitness. The plant pathogen Agrobacterium tumefaciens utilizes its T6SS to kill other bacteria, such as Escherichia coli. We observed that the A. tumefaciens T6SS-dependent killing outcome differs when using different T6SS-lacking, K-12 E. coli strains as a recipient cell. Thus, we hypothesized that the A. tumefaciens T6SS killing outcome not only relies on the T6SS activity of the attacker cells but also depends on the recipient cells. Here, we developed a high-throughput interbacterial competition platform to test the hypothesis by screening for mutants with reduced killing outcomes caused by A. tumefaciens strain C58. Among the 3,909 strains in the E. coli Keio library screened, 16 mutants with less susceptibility to A. tumefaciens C58 T6SS-dependent killing were identified, and four of them were validated by complementation test. Among the four, the clpP encoding ClpP protease, which is universal and highly conserved in both prokaryotes and eukaryotic organelles, was selected for further characterizations. We demonstrated that ClpP is responsible for enhancing susceptibility to the T6SS killing. Because ClpP protease depends on other adapter proteins such as ClpA and ClpX for substrate recognition, further mutant studies followed by complementation tests were carried out to reveal that ClpP-associated AAA+ ATPase ClpA, but not ClpX, is involved in enhancing susceptibility to A. tumefaciens T6SS killing. Moreover, functional and biochemical studies of various ClpP amino acid substitution variants provided evidence that ClpA–ClpP interaction is critical in enhancing susceptibility to the T6SS killing. This study highlights the importance of recipient factors in determining the outcome of the T6SS killing and shows the universal ClpP protease as a novel recipient factor hijacked by the T6SS of A. tumefaciens.
Collapse
Affiliation(s)
- Hsiao-Han Lin
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.,Institute of Biotechnology, National Taiwan University, Taipei, Taiwan
| | - Manda Yu
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | | | | | - Chi-Te Liu
- Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.,Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| |
Collapse
|
20
|
Annunziato G. Strategies to Overcome Antimicrobial Resistance (AMR) Making Use of Non-Essential Target Inhibitors: A Review. Int J Mol Sci 2019; 20:E5844. [PMID: 31766441 PMCID: PMC6928725 DOI: 10.3390/ijms20235844] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/23/2022] Open
Abstract
Antibiotics have always been considered as one of the most relevant discoveries of the twentieth century. Unfortunately, the dawn of the antibiotic era has sadly corresponded to the rise of the phenomenon of antimicrobial resistance (AMR), which is a natural process whereby microbes evolve in such a way to withstand the action of drugs. In this context, the identification of new potential antimicrobial targets and/or the identification of new chemical entities as antimicrobial drugs are in great demand. To date, among the many possible approaches used to deal with antibiotic resistance is the use of antibiotic adjuvants that hit bacterial non-essential targets. In this review, the author focuses on the discovery of antibiotic adjuvants and on new tools to study and reduce the prevalence of resistant bacterial infections.
Collapse
Affiliation(s)
- Giannamaria Annunziato
- Probes for Targets Group (P4T group), Department of food and Drug, University of Parma, 43124 Parma, Italy
| |
Collapse
|
21
|
Combination of SAXS and Protein Painting Discloses the Three-Dimensional Organization of the Bacterial Cysteine Synthase Complex, a Potential Target for Enhancers of Antibiotic Action. Int J Mol Sci 2019; 20:ijms20205219. [PMID: 31640223 PMCID: PMC6829319 DOI: 10.3390/ijms20205219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 09/10/2019] [Accepted: 09/17/2019] [Indexed: 01/03/2023] Open
Abstract
The formation of multienzymatic complexes allows for the fine tuning of many aspects of enzymatic functions, such as efficiency, localization, stability, and moonlighting. Here, we investigated, in solution, the structure of bacterial cysteine synthase (CS) complex. CS is formed by serine acetyltransferase (CysE) and O-acetylserine sulfhydrylase isozyme A (CysK), the enzymes that catalyze the last two steps of cysteine biosynthesis in bacteria. CysK and CysE have been proposed as potential targets for antibiotics, since cysteine and related metabolites are intimately linked to protection of bacterial cells against redox damage and to antibiotic resistance. We applied a combined approach of small-angle X-ray scattering (SAXS) spectroscopy and protein painting to obtain a model for the solution structure of CS. Protein painting allowed the identification of protein–protein interaction hotspots that were then used as constrains to model the CS quaternary assembly inside the SAXS envelope. We demonstrate that the active site entrance of CysK is involved in complex formation, as suggested by site-directed mutagenesis and functional studies. Furthermore, complex formation involves a conformational change in one CysK subunit that is likely transmitted through the dimer interface to the other subunit, with a regulatory effect. Finally, SAXS data indicate that only one active site of CysK is involved in direct interaction with CysE and unambiguously unveil the quaternary arrangement of CS.
Collapse
|
22
|
Convergent Evolution of the Barnase/EndoU/Colicin/RelE (BECR) Fold in Antibacterial tRNase Toxins. Structure 2019; 27:1660-1674.e5. [PMID: 31515004 DOI: 10.1016/j.str.2019.08.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 08/03/2019] [Accepted: 08/20/2019] [Indexed: 11/20/2022]
Abstract
Contact-dependent growth inhibition (CDI) is a form of interbacterial competition mediated by CdiB-CdiA two-partner secretion systems. CdiA effector proteins carry polymorphic C-terminal toxin domains (CdiA-CT), which are neutralized by specific CdiI immunity proteins to prevent self-inhibition. Here, we present the crystal structures of CdiA-CT⋅CdiI complexes from Klebsiella pneumoniae 342 and Escherichia coli 3006. The toxins adopt related folds that resemble the ribonuclease domain of colicin D, and both are isoacceptor-specific tRNases that cleave the acceptor stem of deacylated tRNAGAUIle. Although the toxins are similar in structure and substrate specificity, CdiA-CTKp342 activity requires translation factors EF-Tu and EF-Ts, whereas CdiA-CTEC3006 is intrinsically active. Furthermore, the corresponding immunity proteins are unrelated in sequence and structure. CdiIKp342 forms a dimeric β sandwich, whereas CdiIEC3006 is an α-solenoid monomer. Given that toxin-immunity genes co-evolve as linked pairs, these observations suggest that the similarities in toxin structure and activity reflect functional convergence.
Collapse
|
23
|
Bartelli NL, Sun S, Gucinski GC, Zhou H, Song K, Hayes CS, Dahlquist FW. The Cytoplasm-Entry Domain of Antibacterial CdiA Is a Dynamic α-Helical Bundle with Disulfide-Dependent Structural Features. J Mol Biol 2019; 431:3203-3216. [PMID: 31181288 PMCID: PMC6727969 DOI: 10.1016/j.jmb.2019.05.049] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 05/01/2019] [Accepted: 05/30/2019] [Indexed: 01/04/2023]
Abstract
Many Gram-negative bacterial species use contact-dependent growth inhibition (CDI) systems to compete with neighboring cells. CDI+ strains express cell-surface CdiA effector proteins, which carry a toxic C-terminal region (CdiA-CT) that is cleaved from the effector upon transfer into the periplasm of target bacteria. The released CdiA-CT consists of two domains. The C-terminal domain is typically a nuclease that inhibits cell growth, and the N-terminal "cytoplasm-entry" domain mediates toxin translocation into the target-cell cytosol. Here, we use NMR and circular dichroism spectroscopic approaches to probe the structure, stability, and dynamics of the cytoplasm-entry domain from Escherichia coli STEC_MHI813. Chemical shift analysis reveals that the CdiA-CTMHI813 entry domain is composed of a C-terminal helical bundle and a dynamic N-terminal region containing two disulfide linkages. Disruption of the disulfides by mutagenesis or chemical reduction destabilizes secondary structure over the N-terminus, but has no effect on the C-terminal helices. Although critical for N-terminal structure, the disulfides have only modest effects on global thermodynamic stability, and the entry domain exhibits characteristics of a molten globule. We find that the disulfides form in vivo as the entry domain dwells in the periplasm of inhibitor cells prior to target-cell recognition. CdiA-CTMHI813 variants lacking either disulfide still kill target bacteria, but disruption of both bonds abrogates growth inhibition activity. We propose that the entry domain's dynamic structural features are critical for function. In its molten globule-like state, the domain resists degradation after delivery, yet remains pliable enough to unfold for membrane translocation.
Collapse
Affiliation(s)
- Nicholas L Bartelli
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Sheng Sun
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Grant C Gucinski
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States
| | - Hongjun Zhou
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States
| | - Kiho Song
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States; Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States.
| | - Frederick W Dahlquist
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, CA 93106, United States; Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106, United States; Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106, United States.
| |
Collapse
|
24
|
Meuskens I, Saragliadis A, Leo JC, Linke D. Type V Secretion Systems: An Overview of Passenger Domain Functions. Front Microbiol 2019; 10:1163. [PMID: 31214135 PMCID: PMC6555100 DOI: 10.3389/fmicb.2019.01163] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022] Open
Abstract
Bacteria secrete proteins for different purposes such as communication, virulence functions, adhesion to surfaces, nutrient acquisition, or growth inhibition of competing bacteria. For secretion of proteins, Gram-negative bacteria have evolved different secretion systems, classified as secretion systems I through IX to date. While some of these systems consist of multiple proteins building a complex spanning the cell envelope, the type V secretion system, the subject of this review, is rather minimal. Proteins of the Type V secretion system are often called autotransporters (ATs). In the simplest case, a type V secretion system consists of only one polypeptide chain with a β-barrel translocator domain in the membrane, and an extracellular passenger or effector region. Depending on the exact domain architecture of the protein, type V secretion systems can be further separated into sub-groups termed type Va through e, and possibly another recently identified subtype termed Vf. While this classification works well when it comes to the architecture of the proteins, this is not the case for the function(s) of the secreted passenger. In this review, we will give an overview of the functions of the passengers of the different AT classes, shedding more light on the variety of functions carried out by type V secretion systems.
Collapse
Affiliation(s)
| | | | | | - Dirk Linke
- Department of Biosciences, Section for Genetics and Evolutionary Biology, University of Oslo, Oslo, Norway
| |
Collapse
|
25
|
Assessment of the Antimicrobial Potentiality and Functionality of Lactobacillus plantarum Strains Isolated from the Conventional Inner Mongolian Fermented Cheese Against Foodborne Pathogens. Pathogens 2019; 8:pathogens8020071. [PMID: 31117307 PMCID: PMC6631976 DOI: 10.3390/pathogens8020071] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/07/2019] [Accepted: 05/13/2019] [Indexed: 12/23/2022] Open
Abstract
Lactobacillus plantarum are amongst the diversified lactic acid bacteria (LAB) species which are being utilized abundantly in the food industry. Numerous L. plantarum strains have been reported to produce several antimicrobial compounds. Diacetyl, hydrogen peroxide, organic acids, as well as bacteriocins can also be exemplified by a variable spectrum of actions. The current study was intended to conduct the screening and characterization of antimicrobial prospective of L. plantarum from traditional Inner Mongolian fermented hard cheese. Foodborne pathogens, Salmonella typhimurium, Escherichia coli O157:H7, Listeria monocytogenes, and Staphylococcus aureus, were examined by using the Oxford cup technique and the mixed culture inhibition assays. The resulting analyses disclosed that L. plantarum KLDS1.0344 indicated broad antimicrobial spectrum against all selected pathogens as compared to other LAB used in this study. Additionally, the decrement of the pathogen population was observed up to 3.47 logs in mixed culture inhibition assays. L. plantarum KLDS 1.0344 acid production was recorded up to 71.8 ± 3.59 °D in mixed culture while antimicrobial particles released in cell free supernatants demonstrated bacteriocin-like characteristics showing substantial pH stability (2.0–6.0), proteolytic enzyme reduced the antibacterial activity (15.2 ± 0.6 mm–20.4 ± 0.8 mm), heat stability (20 min at 120 °C) against selected pathogens. Moreover, the spectrum range of antimicrobial peptides after the partial purification was decreased as compared to the crude bacteriocin-like compound. The SDS-PAGE analysis showed the molecular weight range of partially purified bacteriocin from 12 to 45 kDa. After analyzing the obtained data from the current experimentation showed that the capability of L. plantarum KLDS 1.0344 to oppose the pathogen growth in vitro relies on the occurrence of organic acids along with bacteriocin-like compounds proving L. plantarum KLDS 1.0344 as a potentially appropriate candidate as an alternative bio-control agent against foodborne pathogens.
Collapse
|
26
|
Insights into multifaceted activities of CysK for therapeutic interventions. 3 Biotech 2019; 9:44. [PMID: 30675454 DOI: 10.1007/s13205-019-1572-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 01/10/2019] [Indexed: 01/24/2023] Open
Abstract
CysK (O-acetylserine sulfhydrylase) is a pyridoxal-5' phosphate-dependent enzyme which catalyzes the second step of the de novo cysteine biosynthesis pathway by converting O-acetyl serine (OAS) into l-cysteine in the presence of sulfide. The first step of the cysteine biosynthesis involves formation of OAS from serine and acetyl CoA by CysE (serine acetyltransferase). Apart from role of CysK in cysteine biosynthesis, recent studies have revealed various additional roles of this enzyme in bacterial physiology. Other than the suggested regulatory role in cysteine production, other activities of CysK include involvement of CysK-in contact-dependent toxin activation in Gram-negative pathogens, as a transcriptional regulator of CymR by stabilizing the CymR-DNA interactions, in biofilm formation by providing cysteine and via another mechanism not yet understood, in ofloxacin and tellurite resistance as well as in cysteine desulfurization. Some of these activities involve binding of CysK to another cellular partner, where the complex is regulated by the availability of OAS and/or sulfide (H2S). The aim of this study is to present an overview of current knowledge of multiple functions performed by CysK and identifying structural features involved in alternate functions. Due to possible role in disease, promoting or inhibiting a "moonlighting" function of CysK could be a target for developing novel therapeutic interventions.
Collapse
|
27
|
CDI/CDS system-encoding genes of Burkholderia thailandensis are located in a mobile genetic element that defines a new class of transposon. PLoS Genet 2019; 15:e1007883. [PMID: 30615607 PMCID: PMC6350997 DOI: 10.1371/journal.pgen.1007883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 01/29/2019] [Accepted: 12/07/2018] [Indexed: 01/08/2023] Open
Abstract
Intercellular communication and self-recognition are critical for coordinating cooperative and competitive behaviors during sociomicrobiological community development. Contact-dependent growth inhibition (CDI) proteins are polymorphic toxin delivery systems that inhibit the growth of non-self neighboring bacteria that lack the appropriate immunity protein. In Burkholderia thailandensis, CDI system proteins (encoded by bcpAIOB genes) also induce cooperative behaviors among sibling (self) cells, a phenomenon called contact-dependent signaling (CDS). Here we describe a mobile genetic element (MGE) that carries the bcpAIOB genes in B. thailandensis E264. It is a ~210 kb composite transposon with insertion sequence (IS) elements at each end. Although the ISs are most similar to IS2 of Escherichia coli, the transposase-dependent intermediate molecule displays characteristics more similar to those of the IS26 translocatable unit (TU). A reaction requiring only the “left” IS-encoded transposase results in formation of an extrachromosomal circular dsDNA intermediate (“the megacircle”) composed of the left IS and the sequences intervening between the ISs. Insertion of the megacircle into the chromosome occurs next to a pre-existing copy of an IS2-like element, recreating a functional composite transposon. We found that BcpA activity is required for megacircle formation, and in turn, megacircle formation is required for CDS phenotypes. Our data support a model in which the bcpAIOB genes function as both helping and harming greenbeard genes, simultaneously enhancing the fitness of self bacteria that possess the same allele plus tightly linked genes that mediate cooperative behaviors, and killing non-self bacteria that do not possess the same bcpAIOB allele. Mobility of the megacircle between cells could allow bacteria invading a community to be converted to self, and would facilitate propagation of the bcpAIOB genes in the event that the invading strain is capable of overtaking the resident community. As social organisms, bacteria have evolved multiple ways to communicate and interact with their neighbors. Some of these interactions can be beneficial or harmful to certain members of the community, and others involve sharing of genetic material capable of transforming the recipient cell. In this study, we provide evidence for a mobile genetic element that carries the genes encoding proteins involved in bacterial killing (contact-dependent inhibition, CDI) or cooperation (contact-dependent signaling, CDS) within microbial communities. Our findings suggest the element mobilizes with a copy-out-paste-in mechanism that requires formation of a large circular DNA molecule we call “the megacircle”. We also show that production of the megacircle requires a functional CDI/CDS system and that synthesis of the megacircle is necessary for cooperation-associated phenotypes. We hypothesize that acquisition of the megacircle provides a means to transform a target cell that does not produce the same CDI/CDS system into one that is immune to inhibition via CDI, and that can participate in the cooperative behaviors of the community.
Collapse
|
28
|
Perault AI, Cotter PA. Three Distinct Contact-Dependent Growth Inhibition Systems Mediate Interbacterial Competition by the Cystic Fibrosis Pathogen Burkholderia dolosa. J Bacteriol 2018; 200:e00428-18. [PMID: 30150233 PMCID: PMC6199481 DOI: 10.1128/jb.00428-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/23/2018] [Indexed: 02/08/2023] Open
Abstract
The respiratory tracts of individuals afflicted with cystic fibrosis (CF) harbor complex polymicrobial communities. By an unknown mechanism, species of the Gram-negative Burkholderia cepacia complex, such as Burkholderia dolosa, can displace other bacteria in the CF lung, causing cepacia syndrome, which has a poor prognosis. The genome of Bdolosa strain AU0158 (BdAU0158) contains three loci that are predicted to encode contact-dependent growth inhibition (CDI) systems. CDI systems function by translocating the toxic C terminus of a large exoprotein directly into target cells, resulting in growth inhibition or death unless the target cells produce a cognate immunity protein. We demonstrate here that each of the three bcpAIOB loci in BdAU0158 encodes a distinct CDI system that mediates interbacterial competition in an allele-specific manner. While only two of the three bcpAIOB loci were expressed under the in vitro conditions tested, the third conferred immunity under these conditions due to the presence of an internal promoter driving expression of the bcpI gene. One BdAU0158 bcpAIOB allele is highly similar to bcpAIOB in Burkholderia thailandensis strain E264 (BtE264), and we showed that their BcpI proteins are functionally interchangeable, but contact-dependent signaling (CDS) phenotypes were not observed in BdAU0158. Our findings suggest that the CDI systems of BdAU0158 may provide this pathogen an ecological advantage during polymicrobial infections of the CF respiratory tract.IMPORTANCE Human-associated polymicrobial communities can promote health and disease, and interbacterial interactions influence the microbial ecology of such communities. Polymicrobial infections of the cystic fibrosis respiratory tract impair lung function and lead to the death of individuals suffering from this disorder; therefore, a greater understanding of these microbial communities is necessary for improving treatment strategies. Bacteria utilize contact-dependent growth inhibition systems to kill neighboring competitors and maintain their niche within multicellular communities. Several cystic fibrosis pathogens have the potential to gain an ecological advantage during infection via contact-dependent growth inhibition systems, including Burkholderia dolosa Our research is significant, as it has identified three functional contact-dependent growth inhibition systems in Bdolosa that may provide this pathogen a competitive advantage during polymicrobial infections.
Collapse
Affiliation(s)
- Andrew I Perault
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Peggy A Cotter
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| |
Collapse
|
29
|
Ma W, Wang J, Li Y, Wang X. Cysteine synthase A overexpression in Corynebacterium glutamicum enhances l-isoleucine production. Biotechnol Appl Biochem 2018; 66:74-81. [PMID: 30311712 DOI: 10.1002/bab.1698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/01/2018] [Indexed: 01/12/2023]
Abstract
Cysteine synthase A (CysK) catalyzes the last reaction of l-cysteine synthesis in bacteria, but its moonlighting functions have been revealed recently. In this study, CysK was overexpressed in Corynebacterium glutamicum IWJ001, an l-isoleucine producer. Compared with the control IWJ001/pDXW-8, IWJ001/pDXW-8-cysK cells grew fast during log phase, and produced 26.5% more l-isoleucine in flask fermentation and 23.5% more l-isoleucine in fed-batch fermentation. The key genes aspC, lysC, hom, thrB, ilvA, and ilvBN involved in l-isoleucine biosynthesis were all upregulated in IWJ001/pDXW-8-cysK, compared with IWJ001/pDXW-8. In addition, IWJ001/pDXW-8-cysK cells were longer and thicker than IWJ001/pDXW-8 cells. Compared with IWJ001/pDXW-8, the membrane permeability increased 15.8% and biofilm formation ability decreased 71.3% for IWJ001/pDXW-8-cysK cells. The results demonstrate that CysK overexpression in C. glutamicum is a good approach to enhance l-isoleucine production.
Collapse
Affiliation(s)
- Wenjian Ma
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Jianli Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China
| | - Ye Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, People's Republic of China
| | - Xiaoyuan Wang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, People's Republic of China.,Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, People's Republic of China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, People's Republic of China
| |
Collapse
|
30
|
Michalska K, Quan Nhan D, Willett JLE, Stols LM, Eschenfeldt WH, Jones AM, Nguyen JY, Koskiniemi S, Low DA, Goulding CW, Joachimiak A, Hayes CS. Functional plasticity of antibacterial EndoU toxins. Mol Microbiol 2018; 109:509-527. [PMID: 29923643 PMCID: PMC6173971 DOI: 10.1111/mmi.14007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2018] [Indexed: 01/05/2023]
Abstract
Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact-dependent growth inhibition toxin CdiA-CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His-His-Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate-specific ribonuclease activity that characterizes the superfamily. Comparative sequence analysis indicates that bacterial EndoU domains segregate into at least three major clades based on structural variations in the N-terminal subdomain. Representative EndoU nucleases from clades I and II degrade tRNA molecules with little specificity. In contrast, CdiA-CTSTECO31 and other clade III toxins are specific anticodon nucleases that cleave tRNAGlu between nucleotides C37 and m2 A38. These findings suggest that the EndoU fold is a versatile scaffold for the evolution of novel substrate specificities. Such functional plasticity may account for the widespread use of EndoU effectors by diverse inter-bacterial toxin delivery systems.
Collapse
Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Dinh Quan Nhan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Julia L E Willett
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Lucy M Stols
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA
| | - William H Eschenfeldt
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA
| | - Allison M Jones
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Josephine Y Nguyen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Celia W Goulding
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA.,Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| |
Collapse
|
31
|
Xiaoli L, Figler HM, Goswami Banerjee K, Hayes CS, Dudley EG. Non-pathogenic Escherichia coli Enhance Stx2a Production of E. coli O157:H7 Through Both bamA-Dependent and Independent Mechanisms. Front Microbiol 2018; 9:1325. [PMID: 29973923 PMCID: PMC6020778 DOI: 10.3389/fmicb.2018.01325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/30/2018] [Indexed: 01/14/2023] Open
Abstract
Intestinal colonization by the foodborne pathogen Escherichia coli O157:H7 leads to serious disease symptoms, including hemolytic uremic syndrome (HUS) and hemorrhagic colitis (HC). Synthesis of one or more Shiga toxins (Stx) is essential for HUS and HC development. The genes encoding Stx, including Stx2a, are found within a lambdoid prophage integrated in the E. coli O157:H7 chromosome. Enhanced Stx2a expression was reported when specific non-pathogenic E. coli strains were co-cultured with E. coli O157:H7, and it was hypothesized that this phenotype required the non-pathogenic E. coli to be sensitive to stx-converting phage infection. We tested this hypothesis by generating phage resistant non-pathogenic E. coli strains where bamA (an essential gene and Stx phage receptor) was replaced with an ortholog from other species. Such heterologous gene replacement abolished the ability of the laboratory strain E. coli C600 to enhance toxin production when co-cultured with E. coli O157:H7 strain PA2, which belongs to the hypervirulent clade 8. The extracellular loops of BamA (loop 4, 6, 7) were further shown to be important for infection by stx2a-converting phages. However, similar gene replacement in another commensal E. coli, designated 1.1954, revealed a bamA-independent mechanism for toxin amplification. Toxin enhancement by 1.1954 was not the result of phage infection through an alternative receptor (LamB or FadL), lysogen formation by stx2a-converting phages, or the production of a secreted molecule. Collectively, these data suggest that non-pathogenic E. coli can enhance toxin production through at least two mechanisms.
Collapse
Affiliation(s)
- Lingzi Xiaoli
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Hillary M Figler
- Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, United States
| | - Kakolie Goswami Banerjee
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States
| | - Christopher S Hayes
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, United States
| | - Edward G Dudley
- Department of Food Science, The Pennsylvania State University, University Park, PA, United States.,Center for Immunology and Infectious Disease, The Pennsylvania State University, University Park, PA, United States
| |
Collapse
|
32
|
Chignell JF, De Long SK, Reardon KF. Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells. BIOTECHNOLOGY FOR BIOFUELS 2018; 11:121. [PMID: 29713380 PMCID: PMC5913794 DOI: 10.1186/s13068-018-1111-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Bioelectrochemical systems (BESs) harness electrons from microbial respiration to generate power or chemical products from a variety of organic feedstocks, including lignocellulosic biomass, fermentation byproducts, and wastewater sludge. In some BESs, such as microbial fuel cells (MFCs), bacteria living in a biofilm use the anode as an electron acceptor for electrons harvested from organic materials such as lignocellulosic biomass or waste byproducts, generating energy that may be used by humans. Many BES applications use bacterial biofilm communities, but no studies have investigated protein expression by the anode biofilm community as a whole. RESULTS To discover functional protein expression during current generation that may be useful for MFC optimization, a label-free meta-proteomics approach was used to compare protein expression in acetate-fed anode biofilms before and after the onset of robust electricity generation. Meta-proteomic comparisons were integrated with 16S rRNA gene-based community analysis at four developmental stages. The community composition shifted from dominance by aerobic Gammaproteobacteria (90.9 ± 3.3%) during initial biofilm formation to dominance by Deltaproteobacteria, particularly Geobacter (68.7 ± 3.6%) in mature, electricity-generating anodes. Community diversity in the intermediate stage, just after robust current generation began, was double that at the early stage and nearly double that of mature anode communities. Maximum current densities at the intermediate stage, however, were relatively similar (~ 83%) to those achieved by mature-stage biofilms. Meta-proteomic analysis, correlated with population changes, revealed significant enrichment of categories specific to membrane and transport functions among proteins from electricity-producing biofilms. Proteins detected only in electricity-producing biofilms were associated with gluconeogenesis, the glyoxylate cycle, and fatty acid β-oxidation, as well as with denitrification and competitive inhibition. CONCLUSIONS The results demonstrate that it is possible for an MFC microbial community to generate robust current densities while exhibiting high taxonomic diversity. Moreover, these data provide evidence to suggest that startup growth of air-cathode MFCs under conditions that promote the establishment of aerobic-anaerobic syntrophy may decrease startup times. This study represents the first investigation into protein expression of a complex BES anode biofilm community as a whole. The findings contribute to understanding of the molecular mechanisms at work during BES startup and suggest options for improvement of BES generation of bioelectricity from renewable biomass.
Collapse
Affiliation(s)
- Jeremy F. Chignell
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, USA
| | - Susan K. De Long
- Department of Civil and Environmental Engineering, Colorado State University, Fort Collins, USA
| | - Kenneth F. Reardon
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins, USA
| |
Collapse
|
33
|
Zilelidou EA, Skandamis PN. Growth, detection and virulence of Listeria monocytogenes in the presence of other microorganisms: microbial interactions from species to strain level. Int J Food Microbiol 2018; 277:10-25. [PMID: 29677551 DOI: 10.1016/j.ijfoodmicro.2018.04.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 04/04/2018] [Accepted: 04/06/2018] [Indexed: 01/28/2023]
Abstract
Like with all food microorganisms, many basic aspects of L. monocytogenes life are likely to be influenced by its interactions with bacteria living in close proximity. This pathogenic bacterium is a major concern both for the food industry and health organizations since it is ubiquitous and able to withstand harsh environmental conditions. Due to the ubiquity of Listeria monocytogenes, various strains may contaminate foods at different stages of the supply chain. Consequently, simultaneous exposure of consumers to multiple strains is also possible. In this context even strain-to-strain interactions of L. monocytogenes play a significant role in fundamental processes for the life of the pathogen, such as growth or virulence, and subsequently compromise food safety, affect the evolution of a potential infection, or even introduce bias in the detection by classical enrichment techniques. This article summarizes the impact of microbial interactions on the growth and detection of L. monocytogenes primarily in foods and food-associated environments. Furthermore it provides an overview of L. monocytogenes virulence in the presence of other microorganisms.
Collapse
Affiliation(s)
- Evangelia A Zilelidou
- Agricultural University of Athens, Department of Food Science and Human Nutrition, Laboratory of Food Quality Control and Hygiene, Iera odos 75, 11855 Athens, Greece
| | - Panagiotis N Skandamis
- Agricultural University of Athens, Department of Food Science and Human Nutrition, Laboratory of Food Quality Control and Hygiene, Iera odos 75, 11855 Athens, Greece.
| |
Collapse
|
34
|
Ghosh A, Baltekin Ö, Wäneskog M, Elkhalifa D, Hammarlöf DL, Elf J, Koskiniemi S. Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations. EMBO J 2018; 37:embj.201798026. [PMID: 29572241 DOI: 10.15252/embj.201798026] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 02/08/2018] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
Bacterial populations can use bet-hedging strategies to cope with rapidly changing environments. One example is non-growing cells in clonal bacterial populations that are able to persist antibiotic treatment. Previous studies suggest that persisters arise in bacterial populations either stochastically through variation in levels of global signalling molecules between individual cells, or in response to various stresses. Here, we show that toxins used in contact-dependent growth inhibition (CDI) create persisters upon direct contact with cells lacking sufficient levels of CdiI immunity protein, which would otherwise bind to and neutralize toxin activity. CDI-mediated persisters form through a feedforward cycle where the toxic activity of the CdiA toxin increases cellular (p)ppGpp levels, which results in Lon-mediated degradation of the immunity protein and more free toxin. Thus, CDI systems mediate a population density-dependent bet-hedging strategy, where the fraction of non-growing cells is increased only when there are many cells of the same genotype. This may be one of the mechanisms of how CDI systems increase the fitness of their hosts.
Collapse
Affiliation(s)
- Anirban Ghosh
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Özden Baltekin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Marcus Wäneskog
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Dina Elkhalifa
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Disa L Hammarlöf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| |
Collapse
|
35
|
Abstract
Bacteria host an arsenal of antagonism-mediating molecules to combat for ecologic space. Bacteriocins represent a pivotal group of secreted antibacterial peptides and proteins assisting in this fight, mainly eliminating relatives. Colicin M, a model for peptidoglycan-interfering bacteriocins in Gram-negative bacteria, appears to be part of a set of polymorphic toxins equipped with such a catalytic domain (ColM) targeting lipid II. Diversifying recombination has enabled parasitism of different receptors and has also given rise to hybrid bacteriocins in which ColM is associated with another toxin module. Remarkably, ColM toxins have recruited a diverse array of immunity partners, comprising cytoplasmic membrane-associated proteins with different topologies. Together, these findings suggest that different immunity mechanisms have evolved for ColM, in contrast to bacteriocins with nuclease activities.
Collapse
|
36
|
Michalska K, Gucinski GC, Garza-Sánchez F, Johnson PM, Stols LM, Eschenfeldt WH, Babnigg G, Low DA, Goulding CW, Joachimiak A, Hayes CS. Structure of a novel antibacterial toxin that exploits elongation factor Tu to cleave specific transfer RNAs. Nucleic Acids Res 2017; 45:10306-10320. [PMID: 28973472 PMCID: PMC5737660 DOI: 10.1093/nar/gkx700] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 07/29/2017] [Indexed: 12/23/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a mechanism of inter-cellular competition in which Gram-negative bacteria exchange polymorphic toxins using type V secretion systems. Here, we present structures of the CDI toxin from Escherichia coli NC101 in ternary complex with its cognate immunity protein and elongation factor Tu (EF-Tu). The toxin binds exclusively to domain 2 of EF-Tu, partially overlapping the site that interacts with the 3'-end of aminoacyl-tRNA (aa-tRNA). The toxin exerts a unique ribonuclease activity that cleaves the single-stranded 3'-end from tRNAs that contain guanine discriminator nucleotides. EF-Tu is required to support this tRNase activity in vitro, suggesting the toxin specifically cleaves substrate in the context of GTP·EF-Tu·aa-tRNA complexes. However, superimposition of the toxin domain onto previously solved GTP·EF-Tu·aa-tRNA structures reveals potential steric clashes with both aa-tRNA and the switch I region of EF-Tu. Further, the toxin induces conformational changes in EF-Tu, displacing a β-hairpin loop that forms a critical salt-bridge contact with the 3'-terminal adenylate of aa-tRNA. Together, these observations suggest that the toxin remodels GTP·EF-Tu·aa-tRNA complexes to free the 3'-end of aa-tRNA for entry into the nuclease active site.
Collapse
Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Grant C Gucinski
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9625, USA
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106-9625, USA
| | - Parker M Johnson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
| | - Lucy M Stols
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - William H Eschenfeldt
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
| | - David A Low
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9625, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106-9625, USA
| | - Celia W Goulding
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA.,Department of Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Christopher S Hayes
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA 93106-9625, USA.,Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA 93106-9625, USA
| |
Collapse
|
37
|
Cuthbert BJ, Burley KH, Goulding CW. Introducing the new bacterial branch of the RNase A superfamily. RNA Biol 2017; 15:9-12. [PMID: 29099294 DOI: 10.1080/15476286.2017.1387710] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Bovine pancreatic ribonuclease (RNase A) is the founding member of the RNase A superfamily. Members of this superfamily of ribonucleases have high sequence diversity, but possess a similar structural fold, together with a conserved His-Lys-His catalytic triad and structural disulfide bonds. Until recently, RNase A proteins had exclusively been identified in eukaryotes within vertebrae. Here, we discuss the discovery by Batot et al. of a bacterial RNase A superfamily member, CdiA-CTYkris: a toxin that belongs to an inter-bacterial competition system from Yersinia kristensenii. CdiA-CTYkris exhibits the same structural fold as conventional RNase A family members and displays in vitro and in vivo ribonuclease activity. However, CdiA-CTYkris shares little to no sequence similarity with RNase A, and lacks the conserved disulfide bonds and catalytic triad of RNase A. Interestingly, the CdiA-CTYkris active site more closely resembles the active site composition of various eukaryotic endonucleases. Despite lacking sequence similarity to eukaryotic RNase A family members, CdiA-CTYkris does share high sequence similarity with numerous Gram-negative and Gram-positive bacterial proteins/domains. Nearly all of these bacterial homologs are toxins associated with virulence and bacterial competition, suggesting that the RNase A superfamily has a distinct bacterial subfamily branch, which likely arose by way of convergent evolution. Finally, RNase A interacts directly with the immunity protein of CdiA-CTYkris, thus the cognate immunity protein for the bacterial RNase A member could be engineered as a new eukaryotic RNase A inhibitor.
Collapse
Affiliation(s)
- Bonnie J Cuthbert
- a Department of Molecular Biology and Biochemistry , University of California Irvine , Irvine , CA , USA
| | - Kalistyn H Burley
- b Department of Pharmaceutical Sciences , University of California Irvine , Irvine , CA , USA
| | - Celia W Goulding
- a Department of Molecular Biology and Biochemistry , University of California Irvine , Irvine , CA , USA.,b Department of Pharmaceutical Sciences , University of California Irvine , Irvine , CA , USA
| |
Collapse
|
38
|
Garcia EC. Contact-dependent interbacterial toxins deliver a message. Curr Opin Microbiol 2017; 42:40-46. [PMID: 29078204 DOI: 10.1016/j.mib.2017.09.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 09/06/2017] [Accepted: 09/14/2017] [Indexed: 02/04/2023]
Abstract
Both Gram-negative and Gram-positive organisms harbor systems for delivering toxins to neighboring bacteria upon direct cell contact. These systems, typified by type VI secretion (T6S) and contact-dependent growth inhibition (CDI) systems, are defined by their ability to mediate interbacterial competition in vitro, while their biological roles have remained uncertain. Recent research into the mechanisms of toxin delivery and activity, as well as investigation of contact-dependent toxin function during relevant biological processes, has offered insight into how interbacterial competition might work outside of the laboratory. Furthermore, non-competitive roles for contact-dependent toxin delivery systems, including interbacterial signal transduction, have been described. This review suggests that contact-dependent toxin delivery systems that exhibit functions beyond interbacterial competition are probably more common than currently appreciated.
Collapse
Affiliation(s)
- Erin C Garcia
- Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, KY 40536, United States.
| |
Collapse
|
39
|
Batot G, Michalska K, Ekberg G, Irimpan EM, Joachimiak G, Jedrzejczak R, Babnigg G, Hayes CS, Joachimiak A, Goulding CW. The CDI toxin of Yersinia kristensenii is a novel bacterial member of the RNase A superfamily. Nucleic Acids Res 2017; 45:5013-5025. [PMID: 28398546 PMCID: PMC5435912 DOI: 10.1093/nar/gkx230] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/31/2017] [Indexed: 01/01/2023] Open
Abstract
Contact-dependent growth inhibition (CDI) is an important mechanism of inter-bacterial competition found in many Gram-negative pathogens. CDI+ cells express cell-surface CdiA proteins that bind neighboring bacteria and deliver C-terminal toxin domains (CdiA-CT) to inhibit target-cell growth. CDI+ bacteria also produce CdiI immunity proteins, which specifically neutralize cognate CdiA-CT toxins to prevent self-inhibition. Here, we present the crystal structure of the CdiA-CT/CdiIYkris complex from Yersinia kristensenii ATCC 33638. CdiA-CTYkris adopts the same fold as angiogenin and other RNase A paralogs, but the toxin does not share sequence similarity with these nucleases and lacks the characteristic disulfide bonds of the superfamily. Consistent with the structural homology, CdiA-CTYkris has potent RNase activity in vitro and in vivo. Structure-guided mutagenesis reveals that His175, Arg186, Thr276 and Tyr278 contribute to CdiA-CTYkris activity, suggesting that these residues participate in substrate binding and/or catalysis. CdiIYkris binds directly over the putative active site and likely neutralizes toxicity by blocking access to RNA substrates. Significantly, CdiA-CTYkris is the first non-vertebrate protein found to possess the RNase A superfamily fold, and homologs of this toxin are associated with secretion systems in many Gram-negative and Gram-positive bacteria. These observations suggest that RNase A-like toxins are commonly deployed in inter-bacterial competition.
Collapse
Affiliation(s)
- Gaëlle Batot
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- These authors contributed equally to this work as first authors
| | - Karolina Michalska
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- These authors contributed equally to this work as first authors
| | - Greg Ekberg
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
- These authors contributed equally to this work as first authors
| | - Ervin M. Irimpan
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Grazyna Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Robert Jedrzejczak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Gyorgy Babnigg
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
- Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106-9625, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA
- Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Celia W. Goulding
- Department of Molecular Biology & Biochemistry, University of California Irvine, Irvine, CA 92697, USA
- Department of Pharmaceutical Sciences, University of California Irvine, Irvine, CA 92697, USA
- To whom correspondence should be addressed. Tel: +1 949 824 0337; Fax: +1 949 824 8551
| |
Collapse
|
40
|
Benoni R, Beck CM, Garza-Sánchez F, Bettati S, Mozzarelli A, Hayes CS, Campanini B. Activation of an anti-bacterial toxin by the biosynthetic enzyme CysK: mechanism of binding, interaction specificity and competition with cysteine synthase. Sci Rep 2017; 7:8817. [PMID: 28821763 PMCID: PMC5562914 DOI: 10.1038/s41598-017-09022-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a wide-spread mechanism of inter-bacterial competition. CDI+ bacteria deliver CdiA-CT toxins into neighboring bacteria and produce specific immunity proteins that protect against self-intoxication. The CdiA-CT toxin from uropathogenic Escherichia coli 536 is a latent tRNase that is only active when bound to the cysteine biosynthetic enzyme CysK. Remarkably, the CysK:CdiA-CT binding interaction mimics the ‘cysteine synthase’ complex of CysK:CysE. The C-terminal tails of CysE and CdiA-CT each insert into the CysK active-site cleft to anchor the respective complexes. The dissociation constant for CysK:CdiA-CT (Kd ~ 11 nM) is comparable to that of the E. coli cysteine synthase complex (Kd ~ 6 nM), and both complexes bind through a two-step mechanism with a slow isomerization phase after the initial encounter. However, the second-order rate constant for CysK:CdiA-CT binding is two orders of magnitude slower than that of the cysteine synthase complex, suggesting that CysE should outcompete the toxin for CysK occupancy. However, we find that CdiA-CT can effectively displace CysE from pre-formed cysteine synthase complexes, enabling toxin activation even in the presence of excess competing CysE. This adventitious binding, coupled with the very slow rate of CysK:CdiA-CT dissociation, ensures robust nuclease activity in target bacteria.
Collapse
Affiliation(s)
- Roberto Benoni
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Praha, Czech Republic
| | - Christina M Beck
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA.,Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia, Università di Parma, Parma, Italy.,Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy
| | - Andrea Mozzarelli
- Istituto Nazionale Biostrutture e Biosistemi, Rome, Italy.,Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA, USA. .,Biomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA, USA.
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Parma, Italy.
| |
Collapse
|
41
|
Guérin J, Bigot S, Schneider R, Buchanan SK, Jacob-Dubuisson F. Two-Partner Secretion: Combining Efficiency and Simplicity in the Secretion of Large Proteins for Bacteria-Host and Bacteria-Bacteria Interactions. Front Cell Infect Microbiol 2017; 7:148. [PMID: 28536673 PMCID: PMC5422565 DOI: 10.3389/fcimb.2017.00148] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/10/2017] [Indexed: 12/31/2022] Open
Abstract
Initially identified in pathogenic Gram-negative bacteria, the two-partner secretion (TPS) pathway, also known as Type Vb secretion, mediates the translocation across the outer membrane of large effector proteins involved in interactions between these pathogens and their hosts. More recently, distinct TPS systems have been shown to secrete toxic effector domains that participate in inter-bacterial competition or cooperation. The effects of these systems are based on kin vs. non-kin molecular recognition mediated by specific immunity proteins. With these new toxin-antitoxin systems, the range of TPS effector functions has thus been extended from cytolysis, adhesion, and iron acquisition, to genome maintenance, inter-bacterial killing and inter-bacterial signaling. Basically, a TPS system is made up of two proteins, the secreted TpsA effector protein and its TpsB partner transporter, with possible additional factors such as immunity proteins for protection against cognate toxic effectors. Structural studies have indicated that TpsA proteins mainly form elongated β helices that may be followed by specific functional domains. TpsB proteins belong to the Omp85 superfamily. Open questions remain on the mechanism of protein secretion in the absence of ATP or an electrochemical gradient across the outer membrane. The remarkable dynamics of the TpsB transporters and the progressive folding of their TpsA partners at the bacterial surface in the course of translocation are thought to be key elements driving the secretion process.
Collapse
Affiliation(s)
- Jeremy Guérin
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Sarah Bigot
- Molecular Microbiology and Structural Biochemistry, Centre National de La Recherche Scientifique UMR 5086-Université Lyon 1, Institute of Biology and Chemistry of ProteinsLyon, France
| | - Robert Schneider
- NMR and Molecular Interactions, Université de Lille, Centre National de La Recherche Scientifique, UMR 8576-Unité de Glycobiologie Structurale et FonctionnelleLille, France
| | - Susan K Buchanan
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesda, MD, USA
| | - Françoise Jacob-Dubuisson
- Université de Lille, Centre National de La Recherche Scientifique, Institut National de La Santé et de La Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-Centre d'Infection et d'Immunité de LilleLille, France
| |
Collapse
|
42
|
Can't you hear me knocking: contact-dependent competition and cooperation in bacteria. Emerg Top Life Sci 2017; 1:75-83. [PMID: 29085916 DOI: 10.1042/etls20160019] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Microorganisms are in constant competition for growth niches and environmental resources. In Gram-negative bacteria, contact-dependent growth inhibition (CDI) systems link the fate of one cell with its immediate neighbor through touch-dependent, receptor-mediated toxin delivery. Though discovered for their ability to confer a competitive growth advantage, CDI systems also play significant roles in inter-sibling cooperation, promoting both auto-aggregation and biofilm formation. In this review, we detail the mechanisms of CDI toxin delivery and consider how toxin exchange between isogenic sibling cells could regulate gene expression.
Collapse
|
43
|
Benoni R, De Bei O, Paredi G, Hayes CS, Franko N, Mozzarelli A, Bettati S, Campanini B. Modulation of Escherichia coli serine acetyltransferase catalytic activity in the cysteine synthase complex. FEBS Lett 2017; 591:1212-1224. [PMID: 28337759 DOI: 10.1002/1873-3468.12630] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/20/2017] [Accepted: 03/16/2017] [Indexed: 11/09/2022]
Abstract
In bacteria and plants, serine acetyltransferase (CysE) and O-acetylserine sulfhydrylase-A sulfhydrylase (CysK) collaborate to synthesize l-Cys from l-Ser. CysE and CysK bind one another with high affinity to form the cysteine synthase complex (CSC). We demonstrate that bacterial CysE is activated when bound to CysK. CysE activation results from the release of substrate inhibition, with the Ki for l-Ser increasing from 4 mm for free CysE to 16 mm for the CSC. Feedback inhibition of CysE by l-Cys is also relieved in the bacterial CSC. These findings suggest that the CysE active site is allosterically altered by CysK to alleviate substrate and feedback inhibition in the context of the CSC.
Collapse
Affiliation(s)
- Roberto Benoni
- Dipartimento di Medicina e Chirurgia, Università di Parma, Italy
| | - Omar De Bei
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Italy
| | - Gianluca Paredi
- Centro Interdipartimentale SITEIA.PARMA, Università di Parma, Italy
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Nina Franko
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Italy
| | - Andrea Mozzarelli
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Italy.,INBB (Istituto Nazionale Biostrutture e Biosistemi), Roma, Italy.,Istituto di Biofisica, CNR, Pisa, Italy
| | - Stefano Bettati
- Dipartimento di Medicina e Chirurgia, Università di Parma, Italy.,INBB (Istituto Nazionale Biostrutture e Biosistemi), Roma, Italy
| | - Barbara Campanini
- Dipartimento di Scienze degli Alimenti e del Farmaco, Università di Parma, Italy
| |
Collapse
|
44
|
Abstract
Contact-dependent growth inhibition (CDI) systems encode CdiA effectors, which bind to specific receptors on neighboring bacteria and deliver C-terminal toxin domains to suppress target cell growth. Two classes of CdiA effectors that bind distinct cell surface receptors have been identified, but the molecular basis of receptor specificity is not understood. Alignment of BamA-specific CdiAEC93 from Escherichia coli EC93 and OmpC-specific CdiAEC536 from E. coli 536 suggests that the receptor-binding domain resides within a central region that varies between the two effectors. In support of this hypothesis, we find that CdiAEC93 fragments containing residues Arg1358 to Phe1646 bind specifically to purified BamA. Moreover, chimeric CdiAEC93 that carries the corresponding sequence from CdiAEC536 is endowed with OmpC-binding activity, demonstrating that this region dictates receptor specificity. A survey of E. coli CdiA proteins reveals two additional effector classes, which presumably recognize distinct receptors. Using a genetic approach, we identify the outer membrane nucleoside transporter Tsx as the receptor for a third class of CdiA effectors. Thus, CDI systems exploit multiple outer membrane proteins to identify and engage target cells. These results underscore the modularity of CdiA proteins and suggest that novel effectors can be constructed through genetic recombination to interchange different receptor-binding domains and toxic payloads.IMPORTANCE CdiB/CdiA two-partner secretion proteins mediate interbacterial competition through the delivery of polymorphic toxin domains. This process, known as contact-dependent growth inhibition (CDI), requires stable interactions between the CdiA effector protein and specific receptors on the surface of target bacteria. Here, we localize the receptor-binding domain to the central region of E. coli CdiA. Receptor-binding domains vary between CdiA proteins, and E. coli strains collectively encode at least four distinct effector classes. Further, we show that receptor specificity can be altered by exchanging receptor-binding regions, demonstrating the modularity of this domain. We propose that novel CdiA effectors are naturally generated through genetic recombination to interchange different receptor-binding domains and toxin payloads.
Collapse
|
45
|
Danka ES, Garcia EC, Cotter PA. Are CDI Systems Multicolored, Facultative, Helping Greenbeards? Trends Microbiol 2017; 25:391-401. [PMID: 28285908 DOI: 10.1016/j.tim.2017.02.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 02/15/2017] [Accepted: 02/16/2017] [Indexed: 12/17/2022]
Abstract
Competitive and cooperative interactions between organisms, including bacteria, can significantly impact the composition of a community and the fitness of its members, as well as the fitness of their hosts when communities are living on or within other organisms. Understanding the underlying mechanisms is critical to the development of strategies to control microbiological communities that impact animal and plant health and also for understanding the evolution of social behaviors, which has been challenging for evolutionary biologists. Contact-dependent growth inhibition (CDI) is a phenomenon defined by the delivery of a protein toxin to the cytoplasm of neighboring bacteria upon cell-cell contact, resulting in growth inhibition or death unless a specific immunity protein is present. CDI was first described based on observations of interbacterial killing and has been assumed to function primarily as a means of eliminating competitor cells. However, recent molecular evidence indicates that multiple levels of specificity restrict CDI toxin delivery and activity to the same bacterial strain, and that CDI system proteins can mediate cooperative behaviors among 'self' cells, a phenomenon called contact-dependent signaling (CDS). Here we review these recent findings and discuss potential biological and evolutionary implications of CDI system-mediated interbacterial competition and cooperation.
Collapse
Affiliation(s)
- Elizabeth S Danka
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, NC, USA
| | - Erin C Garcia
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky, KY, USA
| | - Peggy A Cotter
- Department of Microbiology and Immunology, University of North Carolina-Chapel Hill, NC, USA.
| |
Collapse
|
46
|
Activation of contact-dependent antibacterial tRNase toxins by translation elongation factors. Proc Natl Acad Sci U S A 2017; 114:E1951-E1957. [PMID: 28223500 DOI: 10.1073/pnas.1619273114] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a mechanism by which bacteria exchange toxins via direct cell-to-cell contact. CDI systems are distributed widely among Gram-negative pathogens and are thought to mediate interstrain competition. Here, we describe tsf mutations that alter the coiled-coil domain of elongation factor Ts (EF-Ts) and confer resistance to the CdiA-CTEC869 tRNase toxin from enterohemorrhagic Escherichia coli EC869. Although EF-Ts is required for toxicity in vivo, our results indicate that it is dispensable for tRNase activity in vitro. We find that CdiA-CTEC869 binds to elongation factor Tu (EF-Tu) with high affinity and this interaction is critical for nuclease activity. Moreover, in vitro tRNase activity is GTP-dependent, suggesting that CdiA-CTEC869 only cleaves tRNA in the context of translationally active GTP·EF-Tu·tRNA ternary complexes. We propose that EF-Ts promotes the formation of GTP·EF-Tu·tRNA ternary complexes, thereby accelerating substrate turnover for rapid depletion of target-cell tRNA.
Collapse
|
47
|
Ma J, Pan Z, Huang J, Sun M, Lu C, Yao H. The Hcp proteins fused with diverse extended-toxin domains represent a novel pattern of antibacterial effectors in type VI secretion systems. Virulence 2017; 8:1189-1202. [PMID: 28060574 DOI: 10.1080/21505594.2017.1279374] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
The type VI secretion system (T6SS) is a widespread molecular weapon deployed by many bacterial species to target eukaryotic host cells or rival bacteria. Using a dynamic injection mechanism, diverse effectors can be delivered by T6SS directly into recipient cells. Here, we report a new family of T6SS effectors encoded by extended Hcps carrying diverse toxin domains. Bioinformatic analyses revealed that these Hcps with C-terminal extension toxins, designated as Hcp-ET, exist widely in the Enterobacteriaceae. To verify our findings, Hcp-ET1 was tested for its antibacterial effect, and showed effective inhibition of target cell growth via the predicted HNH-DNase activity by T6SS-dependent delivery. Further studies showed that Hcp-ET2 mediated interbacterial antagonism via a Tle1 phospholipase (encoded by DUF2235 domain) activity. Notably, comprehensive analyses of protein homology and genomic neighborhoods revealed that Hcp-ET3-4 is fused with 2 toxin domains (Pyocin S3 and Colicin-DNase) C-terminally, and its encoding gene is followed 3 duplications of the cognate immunity genes. However, some bacteria encode a separated hcp-et3 and an orphan et4 (et4O1) genes caused by a termination-codon mutation in the fusion region between Pyocin S3 and Colicin-DNase encoding fragments. Our results demonstrated that both of these toxins had antibacterial effects. Further, all duplications of the cognate immunity protein contributed to neutralize the DNase toxicity of Pyocin S3 and Colicin, which has not been reported previously. In conclusion, we propose that Hcp-ET proteins are polymorphic T6SS effectors, and thus present a novel encoding pattern of T6SS effectors.
Collapse
Affiliation(s)
- Jiale Ma
- a Department of Veterinary Microbiology and Immunology, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China.,b Key Lab of Animal Bacteriology, Ministry of Agriculture , Nanjing , China
| | - Zihao Pan
- a Department of Veterinary Microbiology and Immunology, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China.,b Key Lab of Animal Bacteriology, Ministry of Agriculture , Nanjing , China
| | - Jinhu Huang
- a Department of Veterinary Microbiology and Immunology, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China.,b Key Lab of Animal Bacteriology, Ministry of Agriculture , Nanjing , China
| | - Min Sun
- a Department of Veterinary Microbiology and Immunology, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China.,b Key Lab of Animal Bacteriology, Ministry of Agriculture , Nanjing , China
| | - Chengping Lu
- a Department of Veterinary Microbiology and Immunology, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China.,b Key Lab of Animal Bacteriology, Ministry of Agriculture , Nanjing , China
| | - Huochun Yao
- a Department of Veterinary Microbiology and Immunology, College of Veterinary Medicine, Nanjing Agricultural University , Nanjing , China.,b Key Lab of Animal Bacteriology, Ministry of Agriculture , Nanjing , China
| |
Collapse
|
48
|
Saak CC, Gibbs KA. The Self-Identity Protein IdsD Is Communicated between Cells in Swarming Proteus mirabilis Colonies. J Bacteriol 2016; 198:3278-3286. [PMID: 27672195 PMCID: PMC5116931 DOI: 10.1128/jb.00402-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/20/2016] [Indexed: 11/20/2022] Open
Abstract
Proteus mirabilis is a social bacterium that is capable of self (kin) versus nonself recognition. Swarming colonies of this bacterium expand outward on surfaces to centimeter-scale distances due to the collective motility of individual cells. Colonies of genetically distinct populations remain separate, while those of identical populations merge. Ids proteins are essential for this recognition behavior. Two of these proteins, IdsD and IdsE, encode identity information for each strain. These two proteins bind in vitro in an allele-restrictive manner. IdsD-IdsE binding is correlated with the merging of populations, whereas a lack of binding is correlated with the separation of populations. Key questions remained about the in vivo interactions of IdsD and IdsE, specifically, whether IdsD and IdsE bind within single cells or whether IdsD-IdsE interactions occur across neighboring cells and, if so, which of the two proteins is exchanged. Here we demonstrate that IdsD must originate from another cell to communicate identity and that this nonresident IdsD interacts with IdsE resident in the recipient cell. Furthermore, we show that unbound IdsD in recipient cells does not cause cell death and instead appears to contribute to a restriction in the expansion radius of the swarming colony. We conclude that P. mirabilis communicates IdsD between neighboring cells for nonlethal kin recognition, which suggests that the Ids proteins constitute a type of cell-cell communication. IMPORTANCE We demonstrate that self (kin) versus nonself recognition in P. mirabilis entails the cell-cell communication of an identity-encoding protein that is exported from one cell and received by another. We further show that this intercellular exchange affects swarm colony expansion in a nonlethal manner, which adds social communication to the list of potential swarm-related regulatory factors.
Collapse
Affiliation(s)
- Christina C Saak
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Karine A Gibbs
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA
| |
Collapse
|
49
|
CdiA Effectors from Uropathogenic Escherichia coli Use Heterotrimeric Osmoporins as Receptors to Recognize Target Bacteria. PLoS Pathog 2016; 12:e1005925. [PMID: 27723824 PMCID: PMC5056734 DOI: 10.1371/journal.ppat.1005925] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 09/10/2016] [Indexed: 12/28/2022] Open
Abstract
Many Gram-negative bacterial pathogens express contact-dependent growth inhibition (CDI) systems that promote cell-cell interaction. CDI+ bacteria express surface CdiA effector proteins, which transfer their C-terminal toxin domains into susceptible target cells upon binding to specific receptors. CDI+ cells also produce immunity proteins that neutralize the toxin domains delivered from neighboring siblings. Here, we show that CdiAEC536 from uropathogenic Escherichia coli 536 (EC536) uses OmpC and OmpF as receptors to recognize target bacteria. E. coli mutants lacking either ompF or ompC are resistant to CDIEC536-mediated growth inhibition, and both porins are required for target-cell adhesion to inhibitors that express CdiAEC536. Experiments with single-chain OmpF fusions indicate that the CdiAEC536 receptor is heterotrimeric OmpC-OmpF. Because the OmpC and OmpF porins are under selective pressure from bacteriophages and host immune systems, their surface-exposed loops vary between E. coli isolates. OmpC polymorphism has a significant impact on CDIEC536 mediated competition, with many E. coli isolates expressing alleles that are not recognized by CdiAEC536. Analyses of recombinant OmpC chimeras suggest that extracellular loops L4 and L5 are important recognition epitopes for CdiAEC536. Loops L4 and L5 also account for much of the sequence variability between E. coli OmpC proteins, raising the possibility that CDI contributes to the selective pressure driving OmpC diversification. We find that the most efficient CdiAEC536 receptors are encoded by isolates that carry the same cdi gene cluster as E. coli 536. Thus, it appears that CdiA effectors often bind preferentially to "self" receptors, thereby promoting interactions between sibling cells. As a consequence, these effector proteins cannot recognize nor suppress the growth of many potential competitors. These findings suggest that self-recognition and kin selection are important functions of CDI. Bacterial pathogens often live in crowded communities where cells reside in close contact with one another. Many of these bacteria possess contact-dependent growth inhibition (CDI) systems, which allow cells to touch and inhibit each other using toxic CdiA proteins. CDI+ bacteria also produce immunity proteins that specifically protect the cell from the CdiA toxins of neighboring sibling cells. The CDI system from Escherichia coli EC93 was the first to be characterized and its CdiA toxin recognizes a receptor (BamA) that is identical in virtually all E. coli isolates. Here, we describe a different CDI system from uropathogenic E. coli 536, which causes urinary tract infections. In contrast to E. coli EC93, CdiA from E. coli 536 binds to receptor proteins (OmpC/OmpF) that vary widely between different E. coli isolates. Thus, uropathogenic E. coli preferentially bind and deliver toxins into sibling cells and other closely related E. coli strains. These results suggest that CDI systems distinguish between "self" and "non-self" cells. Moreover, because sibling cells are immune to CdiA-mediated growth inhibition, these findings raise the possibility that toxin exchange may be used for communication and cooperative behavior between genetically identical bacteria.
Collapse
|
50
|
Annunziato G, Pieroni M, Benoni R, Campanini B, Pertinhez TA, Pecchini C, Bruno A, Magalhães J, Bettati S, Franko N, Mozzarelli A, Costantino G. Cyclopropane-1,2-dicarboxylic acids as new tools for the biophysical investigation of O-acetylserine sulfhydrylases by fluorimetric methods and saturation transfer difference (STD) NMR. J Enzyme Inhib Med Chem 2016; 31:78-87. [DOI: 10.1080/14756366.2016.1218486] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
| | | | - Roberto Benoni
- Department of Neurosciences, University of Parma, Parma, Italy,
| | | | - Thelma A. Pertinhez
- Department of Biochemical, Biotechnological and Translational Sciences, University of Parma, Parma, Italy,
- Transfusion Medicine Unit, ASMN-IRCCS, Reggio, Emilia, Italy,
| | | | | | | | - Stefano Bettati
- National Institute of Biostructures and Biosystems, Rome, Italy, and
| | | | - Andrea Mozzarelli
- Department of Pharmacy, and
- National Institute of Biostructures and Biosystems, Rome, Italy, and
- Institute of Biophysics, CNR, Pisa, Italy
| | | |
Collapse
|