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Gutierrez MDLP, Damron FH, Sisti F, Fernández J. BvgR is important for virulence-related phenotypes in Bordetella bronchiseptica. Microbiol Spectr 2024:e0079424. [PMID: 39365045 DOI: 10.1128/spectrum.00794-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 08/05/2024] [Indexed: 10/05/2024] Open
Abstract
Bordetella bronchiseptica is a pathogenic bacterium that causes respiratory infections in mammals. Adhesins, toxins, and secretion systems necessary for infection are regulated by the two-component system BvgAS. When the BvgAS system is inactive, there is no transcription of virulence-activated genes, and virulence-repressed genes (vrg) are expressed. The regulation of some vrgs in B. bronchiseptica is dependent upon the virulence-activated gene bvgR. Although having a regulatory role, no DNA-binding domain is described for BvgR. Instead, it contains an EAL domain, usually found in cyclic-di-GMP (c-di-GMP)-specific phosphodiesterases. c-di-GMP is a bacterial second messenger that regulates multiple phenotypes in bacteria, including B. bronchiseptica. The current study aimed to deepen our knowledge about BvgR. We employed RNA-seq analysis to define the BvgR regulon, and then we investigated the phenotypes in which BvgR regulation might be involved such as biofilm formation, cytotoxicity, and virulence. Our result revealed that BvgR inhibits biofilm formation and flagellin expression in virulent phase. Although BvgR has long been considered a repressor protein, our results show that it also upregulates almost 100 genes. This regulation is likely indirect, as BvgR lacks a DNA-binding domain. Notably, among the upregulated genes, we identified 15 associated with the type three secretion system. Consistent with these findings, a B. bronchiseptica strain deficient in bvgR was less cytotoxic than the wild-type strain, elicited a milder immune response, and was less able to persist in the lower respiratory tract of mice.IMPORTANCEBordetella bronchiseptica is a harmful bacterium responsible for respiratory infections in mammals. Its ability to cause disease is tightly regulated by a system called BvgAS. In this study, we focused on understanding the role of a specific gene called bvgR in regulating B. bronchiseptica's virulence factors. Our findings revealed that BvgR, previously thought to primarily repress gene expression, actually plays a complex role in both activating and inhibiting various genes involved in bacterial virulence. This newfound understanding sheds light on the intricate mechanisms underlying B. bronchiseptica's ability to cause infections, providing valuable insights for developing strategies to combat these infections in humans and animals.
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Affiliation(s)
- Maria de la Paz Gutierrez
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM)-CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, West Virginia, USA
| | - Federico Sisti
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM)-CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
| | - Julieta Fernández
- Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular (IBBM)-CCT-CONICET-La Plata, Universidad Nacional de La Plata, La Plata, Argentina
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Elongation factor P modulates Acinetobacter baumannii physiology and virulence as a cyclic dimeric guanosine monophosphate effector. Proc Natl Acad Sci U S A 2022; 119:e2209838119. [PMID: 36191190 PMCID: PMC9564936 DOI: 10.1073/pnas.2209838119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cyclic diguanosine monophosphate (c-di-GMP) is widely used by bacteria to control biological functions in response to diverse signals or cues. A previous study showed that potential c-di-GMP metabolic enzymes play a role in the regulation of biofilm formation and motility in Acinetobacter baumannii. However, it was unclear whether and how A. baumannii cells use c-di-GMP signaling to modulate biological functions. Here, we report that c-di-GMP is an important intracellular signal in the modulation of biofilm formation, motility, and virulence in A. baumannii. The intracellular level of c-di-GMP is principally controlled by the diguanylate cyclases (DGCs) A1S_1695, A1S_2506, and A1S_3296 and the phosphodiesterase (PDE) A1S_1254. Intriguingly, we revealed that A1S_2419 (an elongation factor P [EF-P]), is a novel c-di-GMP effector in A. baumannii. Response to a c-di-GMP signal boosted A1S_2419 activity to rescue ribosomes from stalling during synthesis of proteins containing consecutive prolines and thus regulate A. baumannii physiology and pathogenesis. Our study presents a unique and widely conserved effector that controls bacterial physiology and virulence by sensing the second messenger c-di-GMP.
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Awasthi A, Sharma P, Jangir L, Kamakshi, Awasthi G, Awasthi KK, Awasthi K. Dose dependent enhanced antibacterial effects and reduced biofilm activity against Bacillus subtilis in presence of ZnO nanoparticles. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 113:111021. [DOI: 10.1016/j.msec.2020.111021] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Revised: 04/15/2020] [Accepted: 04/25/2020] [Indexed: 11/26/2022]
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A Cyclic-di-GMP signalling network regulates biofilm formation and surface associated motility of Acinetobacter baumannii 17978. Sci Rep 2020; 10:1991. [PMID: 32029764 PMCID: PMC7005169 DOI: 10.1038/s41598-020-58522-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/16/2020] [Indexed: 11/30/2022] Open
Abstract
Acinetobacter baumannii has emerged as an increasing multidrug-resistant threat in hospitals and a common opportunistic nosocomial pathogen worldwide. However, molecular details of the pathogenesis and physiology of this bacterium largely remain to be elucidated. Here we identify and characterize the c-di-GMP signalling network and assess its role in biofilm formation and surface associated motility. Bioinformatic analysis revealed eleven candidate genes for c-di-GMP metabolizing proteins (GGDEF/EAL domain proteins) in the genome of A. baumannii strain 17978. Enzymatic activity of the encoded proteins was assessed by molecular cloning and expression in the model organisms Salmonella typhimurium and Vibrio cholerae. Ten of the eleven GGDEF/EAL proteins altered the rdar morphotype of S. typhimurium and the rugose morphotype of V. cholerae. The over expression of three GGDEF proteins exerted a pronounced effect on colony formation of A. baumannii on Congo Red agar plates. Distinct panels of GGDEF/EAL proteins were found to alter biofilm formation and surface associated motility of A. baumannii upon over expression. The GGDEF protein A1S_3296 appeared as a major diguanylate cyclase regulating macro-colony formation, biofilm formation and the surface associated motility. AIS_3296 promotes Csu pili mediated biofilm formation. We conclude that a functional c-di-GMP signalling network in A. baumannii regulates biofilm formation and surface associated motility of this increasingly important opportunistic bacterial pathogen.
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He J, Ruan W, Sun J, Wang F, Yan W. Functional Characterization of c-di-GMP Signaling-Related Genes in the Probiotic Lactobacillus acidophilus. Front Microbiol 2018; 9:1935. [PMID: 30210464 PMCID: PMC6123363 DOI: 10.3389/fmicb.2018.01935] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Accepted: 07/30/2018] [Indexed: 01/03/2023] Open
Abstract
The bacterial second messenger cyclic diguanylate monophosphate (c-di-GMP) regulates a series of cellular functions, including biofilm formation, motility, virulence, and other processes. In this study, we confirmed the presence of several c-di-GMP related genes and evaluated their activities and functions in Lactobacillus species. Bioinformatic and biochemical analyses revealed that Lactobacillus acidophilus La-14 have an active c-di-GMP phosphodiesterase (PdeA) that may act in the metabolic cycle of c-di-GMP. A GGDEF protein (DgcA) induced two c-di-GMP-dependent phenotypes (low motility and high production of curli fimbriae) in Escherichia coli by heterologously expressed in vivo but showed no diguanylate cyclases activity in vitro while in the expression without the N-terminal transmembrane domain. The degenerated EAL-domain protein (PdeB), encoded by the last gene in the gts operon, serve as a c-di-GMP receptor which may be associated with exopolysaccharide (EPS) synthesis in L. acidophilus. Heterologously expressed GtsA and GtsB, encoded by the gts operon, stimulated EPS and biofilm formation in E. coli BL21. Constitutive expression in L. acidophilus revealed that a high concentration of intracellular DgcA levels increased EPS production in L. acidophilus and enhanced the co-aggregation ability with E. coli MG1655, which may be beneficial to the probiotic properties of Lactobacillus species. Our study imply that the c-di-GMP metabolism-related genes, in L. acidophilus, work jointly to regulate its functions in EPS formation and co-aggregation.
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Affiliation(s)
- Jiahui He
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Neurobiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China.,Department of Stomatology, The Affiliated Shenzhen Maternity and Child Healthcare Hospital of the South Medical University, Shenzhen, China
| | - Wenhao Ruan
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jieli Sun
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Fang Wang
- Department of Neurobiology, School of Basic Medical Science, Southern Medical University, Guangzhou, China
| | - Wenjuan Yan
- Department of Stomatology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Stand-Alone EAL Domain Proteins Form a Distinct Subclass of EAL Proteins Involved in Regulation of Cell Motility and Biofilm Formation in Enterobacteria. J Bacteriol 2017; 199:JB.00179-17. [PMID: 28652301 DOI: 10.1128/jb.00179-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/16/2017] [Indexed: 12/20/2022] Open
Abstract
The second messenger cyclic dimeric GMP (c-di-GMP) is almost ubiquitous among bacteria as are the c-di-GMP turnover proteins, which mediate the transition between motility and sessility. EAL domain proteins have been characterized as c-di-GMP-specific phosphodiesterases. While most EAL domain proteins contain additional, usually N-terminal, domains, there is a distinct family of proteins with stand-alone EAL domains, exemplified by Salmonella enterica serovar Typhimurium proteins STM3611 (YhjH/PdeH), a c-di-GMP-specific phosphodiesterase, and the enzymatically inactive STM1344 (YdiV/CdgR) and STM1697, which regulate bacterial motility through interaction with the flagellar master regulator, FlhDC. We have analyzed the phylogenetic distribution of EAL-only proteins and their potential functions. Genes encoding EAL-only proteins were found in various bacterial phyla, although most of them were seen in proteobacteria, particularly enterobacteria. Based on the conservation of the active site residues, nearly all stand-alone EAL domains encoded by genomes from phyla other than proteobacteria appear to represent functional phosphodiesterases. Within enterobacteria, EAL-only proteins were found to cluster either with YhjH or with one of the subfamilies of YdiV-related proteins. EAL-only proteins from Shigella flexneri, Klebsiella pneumoniae, and Yersinia enterocolitica were tested for their ability to regulate swimming and swarming motility and formation of the red, dry, and rough (rdar) biofilm morphotype. In these tests, YhjH-related proteins S4210, KPN_01159, KPN_03274, and YE4063 displayed properties typical of enzymatically active phosphodiesterases, whereas S1641 and YE1324 behaved like members of the YdiV/STM1697 subfamily, with Yersinia enterocolitica protein YE1324 shown to downregulate motility in its native host. Of two closely related EAL-only proteins, YE2225 is an active phosphodiesterase, while YE1324 appears to interact with FlhD. These results suggest that in FlhDC-harboring beta- and gammaproteobacteria, some EAL-only proteins evolved to become catalytically inactive and regulate motility and biofilm formation by interacting with FlhDC.IMPORTANCE The EAL domain superfamily consists mainly of proteins with cyclic dimeric GMP-specific phosphodiesterase activity, but individual domains have been classified in three classes according to their functions and conserved amino acid signatures. Proteins that consist solely of stand-alone EAL domains cannot rely on other domains to form catalytically active dimers, and most of them fall into one of two distinct classes: catalytically active phosphodiesterases with well-conserved residues of the active site and the dimerization loop, and catalytically inactive YdiV/CdgR-like proteins that regulate bacterial motility by binding to the flagellar master regulator, FlhDC, and are found primarily in enterobacteria. The presence of apparently inactive EAL-only proteins in the bacteria that do not express FlhD suggests the existence of additional EAL interaction partners.
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Le Guyon S, Simm R, Rehn M, Römling U. Dissecting the cyclic di-guanylate monophosphate signalling network regulating motility in Salmonella enterica serovar Typhimurium. Environ Microbiol 2015; 17:1310-20. [PMID: 25059628 DOI: 10.1111/1462-2920.12580] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 07/22/2014] [Indexed: 11/26/2022]
Abstract
Flagella-mediated swimming and swarming motility in Salmonella enterica serovar Typhimurium is intercalated with the cyclic di-guanylate monophosphate (c-di-GMP) signalling network. In this study, we identified the GGDEF domain proteins STM2672, STM4551 and STM1987 as key di-guanylate cyclases involved in regulation of motility in a ΔyhjH phosphodiesterase gene deletion mutant with elevated c-di-GMP levels inhibiting motility. Surprisingly, these di-guanylate cyclases distinctively inhibited motility through the c-di-GMP receptors YcgR and the cellulose synthase BcsA, whereby STM2672 corresponded to YcgR, STM1987 to BcsA and STM4551 to both receptors. Although downregulation of motility is believed to prepare the bacterial cells for surface adhesion and biofilm formation, the major biofilm regulator CsgD of S. sv. Typhimurium was not involved in the regulation of swimming or swarming motility. Together with previously identified c-di-GMP networks regulating flagella-related phenotypes, flagella biosynthesis is a major target of c-di-GMP signalling in S. sv. Typhimurium.
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Affiliation(s)
- Soazig Le Guyon
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
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Cyclic di-GMP: the first 25 years of a universal bacterial second messenger. Microbiol Mol Biol Rev 2013; 77:1-52. [PMID: 23471616 DOI: 10.1128/mmbr.00043-12] [Citation(s) in RCA: 1224] [Impact Index Per Article: 111.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Twenty-five years have passed since the discovery of cyclic dimeric (3'→5') GMP (cyclic di-GMP or c-di-GMP). From the relative obscurity of an allosteric activator of a bacterial cellulose synthase, c-di-GMP has emerged as one of the most common and important bacterial second messengers. Cyclic di-GMP has been shown to regulate biofilm formation, motility, virulence, the cell cycle, differentiation, and other processes. Most c-di-GMP-dependent signaling pathways control the ability of bacteria to interact with abiotic surfaces or with other bacterial and eukaryotic cells. Cyclic di-GMP plays key roles in lifestyle changes of many bacteria, including transition from the motile to the sessile state, which aids in the establishment of multicellular biofilm communities, and from the virulent state in acute infections to the less virulent but more resilient state characteristic of chronic infectious diseases. From a practical standpoint, modulating c-di-GMP signaling pathways in bacteria could represent a new way of controlling formation and dispersal of biofilms in medical and industrial settings. Cyclic di-GMP participates in interkingdom signaling. It is recognized by mammalian immune systems as a uniquely bacterial molecule and therefore is considered a promising vaccine adjuvant. The purpose of this review is not to overview the whole body of data in the burgeoning field of c-di-GMP-dependent signaling. Instead, we provide a historic perspective on the development of the field, emphasize common trends, and illustrate them with the best available examples. We also identify unresolved questions and highlight new directions in c-di-GMP research that will give us a deeper understanding of this truly universal bacterial second messenger.
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Ahmad I, Wigren E, Le Guyon S, Vekkeli S, Blanka A, El Mouali Y, Anwar N, Chuah ML, Lünsdorf H, Frank R, Rhen M, Liang ZX, Lindqvist Y, Römling U. The EAL-like protein STM1697 regulates virulence phenotypes, motility and biofilm formation in Salmonella typhimurium. Mol Microbiol 2013; 90:1216-32. [PMID: 24127899 DOI: 10.1111/mmi.12428] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 11/30/2022]
Abstract
The ubiquitous second messenger c-di-GMP regulates the switching of bacterial lifestyles from motility to sessility and acute to chronic virulence to adjust bacterial fitness to altered environmental conditions. Conventionally, EAL proteins being c-di-GMP phosphodiesterases promote motility and acute virulence phenotypes such as invasion into epithelial cells and inhibit biofilm formation. We report here that in contradiction, the EAL-like protein STM1697 of Salmonella typhimurium suppresses motility, invasion into HT-29 epithelial cell line and secretion of the type three secretion system 1 effector protein SipA, whereas it promotes rdar biofilm formation and CsgD expression. STM1697 can, however, functionally replace the EAL-like protein STM1344 and vice versa, whereby both proteins neither degrade nor bind c-di-GMP. Like STM1344, STM1697 suppresses the transcription of class 2 and class 3 flagella regulon genes by binding to FlhD, a component of the master regulator of the flagella regulon FlhD4 C2 and act additively under numerous conditions. Interestingly, the interaction interface of STM1697 with FlhD2 is distinct from its paralogue STM1344. We predict that the stand alone EAL domain proteins STM1697 and STM1344 belong to a subclass of EAL domain proteins in S. typhimurium, which are all involved in motility, biofilm and virulence regulation through interaction with proteins that regulate flagella function.
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Affiliation(s)
- Irfan Ahmad
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177, Stockholm, Sweden
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Zheng Y, Sambou T, Bogomolnaya LM, Cirillo JD, McClelland M, Andrews-Polymenis H. The EAL domain containing protein STM2215 (rtn) is needed during Salmonella infection and has cyclic di-GMP phosphodiesterase activity. Mol Microbiol 2013; 89:403-19. [PMID: 23734719 DOI: 10.1111/mmi.12284] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2013] [Indexed: 12/22/2022]
Abstract
Salmonella Typhimurium gene STM2215 (rtn) is conserved among many enterobacteriaceae. Mutants lacking STM2215 poorly colonized the liver and spleen in intraperitoneal infection of mice and poorly colonized the intestine and deeper tissues in oral infection. These phenotypes were complemented by a wild-type copy of STM2215 provided in trans. STM2215 deletion mutants grew normally in J774A.1 murine macrophages but were unable to invade Caco-2 colonic epithelial cells. Consistent with this finding, mutants in STM2215 produced lower levels of effectors of the TTSS-1. STM2215 is a predicted c-di-GMP phosphodiesterase, but lacks identifiable sensor domains. Biochemical analysis of STM2215 determined that it is located in the inner membrane and has c-di-GMP phosphodiesterase activity in vitro dependent on an intact EAL motif. Unlike some previously identified members of this family, STM2215 did not affect motility, was expressed on plates, and in liquid media at late exponential and early stationary phase during growth. Defined mutations in STM2215 revealed that neither the predicted periplasmic domain nor the anchoring of the protein to the inner membrane is necessary for the activity of this protein during infection. However, the EAL domain of STM2215 is required during infection, suggesting that its phosphodiesterase activity is necessary during infection.
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Affiliation(s)
- Yi Zheng
- Department of Microbial and Molecular Pathogenesis, College of Medicine, Texas A&M University System Health Science Center, 8447 Hwy 47, Bryan, TX 77807, USA
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Wang ZC, Huang CJ, Huang YJ, Wu CC, Peng HL. FimK regulation on the expression of type 1 fimbriae in Klebsiella pneumoniae CG43S3. MICROBIOLOGY-SGM 2013; 159:1402-1415. [PMID: 23704787 DOI: 10.1099/mic.0.067793-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Klebsiella pneumoniae CG43, a heavy encapsulated liver abscess isolate, mainly expresses type 3 fimbriae. Type 1 fimbriae expression was only apparent in CG43S3ΔmrkA (the type 3 fimbriae-deficient strain). The expression of type 1 fimbriae in CG43S3ΔmrkA was reduced by deleting the fimK gene, but was unaffected by removing the 3' end of fimK encoding the C-terminal EIL domain (EILfimK). Quantitative RT-PCR and promoter activity analysis showed that the putative DNA-binding region at the N terminus, but not the C-terminal EIL domain, of FimK positively affects transcription of the type 1 fimbrial major subunit, fimA. An electrophoretic mobility shift assay demonstrated that the recombinant FimK could specifically bind to fimS, which is located upstream of fimA and contains a vegetative promoter for the fim operon, also reflecting possible transcriptional regulation. EILfimK was shown to encode a functional phosphodiesterase (PDE) via enhancing motility in Escherichia coli JM109 and in vitro using PDE activity assays. Moreover, EILfimK exhibited higher PDE activity than FimK, implying that the N-terminal DNA-binding domain may negatively affect the PDE activity of FimK. FimA expression was detected in CG43S3 expressing EILfimK or AILfimK, suggesting that FimA expression is not directly influenced by the c-di-GMP level. In summary, FimK influences type 1 fimbriation by binding to fimS at the N-terminal domain, and thereafter, the altered protein structure may activate C-terminal PDE activity to reduce the intracellular c-di-GMP level.
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Affiliation(s)
- Zhe-Chong Wang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China
| | - Ching-Jou Huang
- Institute of Molecular Medicine and Bioengineering, School of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China
| | - Ying-Jung Huang
- Department of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China
| | - Chien-Chen Wu
- Department of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China
| | - Hwei-Ling Peng
- Institute of Molecular Medicine and Bioengineering, School of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China.,Department of Biological Science and Technology, National Chiao Tung University, Hsin Chu, Taiwan, Republic of China
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Li B, Li N, Wang F, Guo L, Huang Y, Liu X, Wei T, Zhu D, Liu C, Pan H, Xu S, Wang HW, Gu L. Structural insight of a concentration-dependent mechanism by which YdiV inhibits Escherichia coli flagellum biogenesis and motility. Nucleic Acids Res 2012; 40:11073-85. [PMID: 23002140 PMCID: PMC3510510 DOI: 10.1093/nar/gks869] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
YdiV is a negative regulator of cell motility. It interacts with FlhD4C2 complex, a product of flagellar master operon, which works as the transcription activator of all other flagellar operons. Here, we report the crystal structures of YdiV and YdiV2–FlhD2 complex at 1.9 Å and 2.9 Å resolutions, respectively. Interestingly, YdiV formed multiple types of complexes with FlhD4C2. YdiV1–FlhD4C2 and YdiV2–FlhD4C2 still bound to DNA, while YdiV3–FlhD4C2 and YdiV4–FlhD4C2 did not. DNA bound FlhD4C2 through wrapping around the FlhC subunit rather than the FlhD subunit. Structural analysis showed that only two peripheral FlhD subunits were accessible for YdiV binding, forming the YdiV2–FlhD4C2 complex without affecting the integrity of ring-like structure. YdiV2–FlhD2 structure and the negative staining electron microscopy reconstruction of YdiV4–FlhD4C2 suggested that the third and fourth YdiV molecule bound to the FlhD4C2 complex through squeezing into the ring-like structure of FlhD4C2 between the two internal D subunits. Consequently, the ring-like structure opened up, and the complex lost DNA-binding ability. Thus, YdiV inhibits FlhD4C2 only at relatively high concentrations.
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Affiliation(s)
- Bingqing Li
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China
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Math RK, Jin HM, Kim JM, Hahn Y, Park W, Madsen EL, Jeon CO. Comparative genomics reveals adaptation by Alteromonas sp. SN2 to marine tidal-flat conditions: cold tolerance and aromatic hydrocarbon metabolism. PLoS One 2012; 7:e35784. [PMID: 22563400 PMCID: PMC3338528 DOI: 10.1371/journal.pone.0035784] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 03/21/2012] [Indexed: 11/19/2022] Open
Abstract
Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat.
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Affiliation(s)
- Renukaradhya K. Math
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Hyun Mi Jin
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Jeong Myeong Kim
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Yoonsoo Hahn
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
| | - Woojun Park
- Division of Environmental Science and Ecological Engineering, Korea University, Seoul, Republic of Korea
| | - Eugene L. Madsen
- Department of Microbiology, Cornell University, Ithaca, New York, United States of America
| | - Che Ok Jeon
- School of Biological Sciences, Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, Republic of Korea
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Ahmad I, Lamprokostopoulou A, Le Guyon S, Streck E, Barthel M, Peters V, Hardt WD, Römling U. Complex c-di-GMP signaling networks mediate transition between virulence properties and biofilm formation in Salmonella enterica serovar Typhimurium. PLoS One 2011; 6:e28351. [PMID: 22164276 PMCID: PMC3229569 DOI: 10.1371/journal.pone.0028351] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Accepted: 11/07/2011] [Indexed: 11/21/2022] Open
Abstract
Upon Salmonella enterica serovar Typhimurium infection of the gut, an early line of defense is the gastrointestinal epithelium which senses the pathogen and intrusion along the epithelial barrier is one of the first events towards disease. Recently, we showed that high intracellular amounts of the secondary messenger c-di-GMP in S. typhimurium inhibited invasion and abolished induction of a pro-inflammatory immune response in the colonic epithelial cell line HT-29 suggesting regulation of transition between biofilm formation and virulence by c-di-GMP in the intestine. Here we show that highly complex c-di-GMP signaling networks consisting of distinct groups of c-di-GMP synthesizing and degrading proteins modulate the virulence phenotypes invasion, IL-8 production and in vivo colonization in the streptomycin-treated mouse model implying a spatial and timely modulation of virulence properties in S. typhimurium by c-di-GMP signaling. Inhibition of the invasion and IL-8 induction phenotype by c-di-GMP (partially) requires the major biofilm activator CsgD and/or BcsA, the synthase for the extracellular matrix component cellulose. Inhibition of the invasion phenotype is associated with inhibition of secretion of the type three secretion system effector protein SipA, which requires c-di-GMP metabolizing proteins, but not their catalytic activity. Our findings show that c-di-GMP signaling is at least equally important in the regulation of Salmonella-host interaction as in the regulation of biofilm formation at ambient temperature.
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Affiliation(s)
- Irfan Ahmad
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
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Brown R, Marchesi JR, Morby AP. Functional characterisation of Lp_2714, an EAL-domain protein from Lactobacillus plantarum. Biochem Biophys Res Commun 2011; 411:132-6. [PMID: 21723265 DOI: 10.1016/j.bbrc.2011.06.112] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 06/16/2011] [Indexed: 10/18/2022]
Abstract
Bioinformatic analysis of lp_2714 from Lactobacillus plantarum WCFS1 demonstrates that it encodes an EAL-domain protein associated with a membrane targeting signal-sequence. Comparison of the predicted primary amino-acid sequence of Lp_2714 shows that it lacks critical catalytic residues and heterologous expression has determined that it does not encode a functional phosphodiesterase. We designate Lp_2714 as a class-3 EAL domain protein probably involved in regulating polysaccharide synthesis on the cell surface the cell.
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Affiliation(s)
- Richard Brown
- School of Biosciences, Cardiff University, Cardiff CF10 3US, United Kingdom
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Matilla MA, Travieso ML, Ramos JL, Ramos-González MI. Cyclic diguanylate turnover mediated by the sole GGDEF/EAL response regulator in Pseudomonas putida: its role in the rhizosphere and an analysis of its target processes. Environ Microbiol 2011; 13:1745-66. [PMID: 21554519 DOI: 10.1111/j.1462-2920.2011.02499.x] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
GGDEF and EAL/HD-GYP protein domains are responsible for the synthesis and hydrolysis of the bacterial secondary messenger cyclic diguanylate (c-di-GMP) through their diguanylate cyclase and phosphodiesterase activities, respectively. Forty-three genes in Pseudomonas putida KT2440 are putatively involved in the turnover of c-di-GMP. Of them only rup4959 (locus PP4959) encodes a GGDEF/EAL response regulator, which was identified in a genome wide analysis as preferentially induced while this bacterium colonizes roots and adjacent soil areas (the rhizosphere). By using fusions to reporter genes it was confirmed that the rup4959 promoter is active in the rhizosphere and inducible by corn plant root exudates and microaerobiosis. Transcription of rup4959 was strictly dependent on the alternative transcriptional factor σ(S) . The inactivation of the rup4959-4957 operon altered the expression of 22 genes in the rhizosphere and had a negative effect upon oligopeptide utilization and biofilm formation. In multicopy or when overexpressed, rup4959 enhanced adhesin LapA-dependent biofilm formation, the development of wrinkly colony morphology, and increased Calcofluor stainable exopolysaccharides (EPS). Under these conditions the inhibition of swarming motility was total and plant root tip colonization considerably less efficient, whereas swimming was partially diminished. This pleiotropic phenotype, which correlated with an increase in the global level of c-di-GMP, was not acquired with increased levels of Rup4959 catalytic mutant at GGDEF as a proof of this response regulator exhibiting diguanylate cyclase activity. A screen for mutants in putative targets of c-di-GMP led to the identification of a surface polysaccharide specific to KT2440, which is encoded by the genes cluster PP3133-PP3141, as essential for phenotypes associated with increased c-di-GMP. Cellulose and alginate were discarded as the overproduced EPS, and lipopolysaccharide (LPS) core and O-antigen were found to be essential for the development of wrinkly colony morphology.
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Affiliation(s)
- Miguel A Matilla
- Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Profesor Albareda 1, Granada 18008, Spain
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17
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Qin QL, Li Y, Zhang YJ, Zhou ZM, Zhang WX, Chen XL, Zhang XY, Zhou BC, Wang L, Zhang YZ. Comparative genomics reveals a deep-sea sediment-adapted life style of Pseudoalteromonas sp. SM9913. THE ISME JOURNAL 2011; 5:274-84. [PMID: 20703316 PMCID: PMC3105692 DOI: 10.1038/ismej.2010.103] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2010] [Revised: 05/21/2010] [Accepted: 06/13/2010] [Indexed: 11/09/2022]
Abstract
Deep-sea sediment is one of the most important microbial-driven ecosystems, yet it is not well characterized. Genome sequence analyses of deep-sea sedimentary bacteria would shed light on the understanding of this ecosystem. In this study, the complete genome of deep-sea sedimentary bacterium Pseudoalteromonas sp. SM9913 (SM9913) is described and compared with that of the closely related Antarctic surface sea-water ecotype Pseudoalteromonas haloplanktis TAC125 (TAC125). SM9913 has fewer dioxygenase genes than TAC125, indicating a possible sensitivity to reactive oxygen species. Accordingly, experimental results showed that SM9913 was less tolerant of H(2)O(2) than TAC125. SM9913 has gene clusters related to both polar and lateral flagella biosynthesis. Lateral flagella, which are usually present in deep-sea bacteria and absent in the related surface bacteria, are important for the survival of SM9913 in deep-sea environments. With these two flagellar systems, SM9913 can swim in sea water and swarm on the sediment particle surface, favoring the acquisition of nutrients from particulate organic matter and reflecting the particle-associated alternative lifestyle of SM9913 in the deep sea. A total of 12 genomic islands were identified in the genome of SM9913 that may confer specific features unique to SM9913 and absent from TAC125, such as drug and heavy metal resistance. Many signal transduction genes and a glycogen production operon were also present in the SM9913 genome, which may help SM9913 respond to food pulses and store carbon and energy in a deep-sea environment.
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Affiliation(s)
- Qi-Long Qin
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Yang Li
- State Key Lab of Microbial Technology, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yan-Jiao Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Zhe-Min Zhou
- State Key Lab of Microbial Technology, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Wei-Xin Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Xiu-Lan Chen
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Xi-Ying Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Bai-Cheng Zhou
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
| | - Lei Wang
- State Key Lab of Microbial Technology, TEDA School of Biological Sciences and Biotechnology, Nankai University, Tianjin, People's Republic of China
| | - Yu-Zhong Zhang
- State Key Lab of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Jinan, People's Republic of China
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18
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Yi X, Yamazaki A, Biddle E, Zeng Q, Yang CH. Genetic analysis of two phosphodiesterases reveals cyclic diguanylate regulation of virulence factors in Dickeya dadantii. Mol Microbiol 2010; 77:787-800. [PMID: 20584146 DOI: 10.1111/j.1365-2958.2010.07246.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Cyclic diguanylate (c-di-GMP) is a second messenger implicated in the regulation of various cellular properties in several bacterial species. However, its function in phytopathogenic bacteria is not yet understood. In this study we investigated a panel of GGDEF/EAL domain proteins which have the potential to regulate c-di-GMP levels in the phytopathogen Dickeya dadantii 3937. Two proteins, EcpB (contains GGDEF and EAL domains) and EcpC (contains an EAL domain) were shown to regulate multiple cellular behaviours and virulence gene expression. Deletion of ecpB and/or ecpC enhanced biofilm formation but repressed swimming/swarming motility. In addition, the ecpB and ecpC mutants displayed a significant reduction in pectate lyase production, a virulence factor of this bacterium. Gene expression analysis showed that deletion of ecpB and ecpC significantly reduced expression of the type III secretion system (T3SS) and its virulence effector proteins. Expression of the T3SS genes is regulated by HrpL and possibly RpoN, two alternative sigma factors. In vitro biochemical assays showed that EcpC has phosphodiesterase activity to hydrolyse c-di-GMP into linear pGpG. Most of the enterobacterial pathogens encode at least one T3SS, a major virulence factor which functions to subvert host defences. The current study broadens our understanding of the interplay between c-di-GMP, RpoN and T3SS and the potential role of c-di-GMP in T3SS regulation among a wide range of bacterial pathogens.
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Affiliation(s)
- Xuan Yi
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
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