1
|
Phukan H, Sarma A, Rex DAB, Christie SAD, Sabu SK, Hariharan S, Prasad TSK, Madanan MG. Physiological Temperature and Osmotic Changes Drive Dynamic Proteome Alterations in the Leptospiral Outer Membrane and Enhance Protein Export Systems. J Proteome Res 2023; 22:3447-3463. [PMID: 37877620 DOI: 10.1021/acs.jproteome.3c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Leptospirosis, a remerging zoonosis, has no effective vaccine or an unambiguous early diagnostic reagent. Proteins differentially expressed (DE) under pathogenic conditions will be useful candidates for antileptospiral measures. We employed a multipronged approach comprising high-resolution TMT-labeled LC-MS/MS-based proteome analysis coupled with bioinformatics on leptospiral proteins following Triton X-114 subcellular fractionation of leptospires treated under physiological temperature and osmolarity that mimic infection. Although there were significant changes in the DE proteins at the level of the entire cell, there were notable changes in proteins at the subcellular level, particularly on the outer membrane (OM), that show the significance of subcellular proteome analysis. The detergent-enriched proteins, representing outer membrane proteins (OMPs), exhibited a dynamic nature and upregulation under various physiological conditions. It was found that pathogenic proteins showed a higher proportion of upregulation compared to the nonpathogenic proteins in the OM. Further analysis identified 17 virulent proteins exclusively upregulated in the outer membrane during infection that could be useful for vaccine and diagnostic targets. The DE proteins may aid in metabolic adaptation and are enriched in pathways related to signal transduction and antibiotic biosynthesis. Many upregulated proteins belong to protein export systems such as SEC translocase, T2SSs, and T1SSs, indicating their sequential participation in protein transport to the outer leaflet of the OM. Further studies on OM-localized proteins may shed light on the pathogenesis of leptospirosis and serve as the basis for effective countermeasures.
Collapse
Affiliation(s)
- Homen Phukan
- Department of Biochemistry, ICMR - Regional Medical Research Centre, Port Blair 744103, Andaman and Nicobar Islands, India
| | - Abhijit Sarma
- Department of Biochemistry, ICMR - Regional Medical Research Centre, Port Blair 744103, Andaman and Nicobar Islands, India
| | - Devasahayam Arokia Balaya Rex
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | | | - Sarath Kizhakkemuriyil Sabu
- Department of Biochemistry, ICMR - Regional Medical Research Centre, Port Blair 744103, Andaman and Nicobar Islands, India
| | - Suneetha Hariharan
- Department of Biochemistry, ICMR - Regional Medical Research Centre, Port Blair 744103, Andaman and Nicobar Islands, India
| | | | | |
Collapse
|
2
|
Kavela S, Vyas P, CP J, Kushwaha SK, Majumdar SS, Faisal SM. Use of an Integrated Multi-Omics Approach To Identify Molecular Mechanisms and Critical Factors Involved in the Pathogenesis of Leptospira. Microbiol Spectr 2023; 11:e0313522. [PMID: 36853003 PMCID: PMC10100824 DOI: 10.1128/spectrum.03135-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Leptospirosis, a bacterial zoonosis caused by pathogenic Leptospira spp., is prevalent worldwide and has become a serious threat in recent years. Limited understanding of Leptospira pathogenesis and host response has hampered the development of effective vaccine and diagnostics. Although Leptospira is phagocytosed by innate immune cells, it resists its destruction, and the evading mechanism involved is unclear. In the present study, we used an integrative multi-omics approach to identify the critical molecular factors of Leptospira involved in pathogenesis during interaction with human macrophages. Transcriptomic and proteomic analyses were performed at 24 h postinfection of human macrophages (phorbol-12-myristate-13-acetate differentiated THP-1 cells) with the pathogenic Leptospira interrogans serovar Icterohaemorrhagiae strain RGA (LEPIRGA). Our results identified a total of 1,528 transcripts and 871 proteins that were significantly expressed with an adjusted P value of <0.05. The correlations between the transcriptomic and proteomic data were above average (r = 0.844), suggesting the role of the posttranscriptional processes during host interaction. The conjoint analysis revealed the expression of several virulence-associated proteins such as adhesins, invasins, and secretory and chemotaxis proteins that might be involved in various processes of attachment and invasion and as effectors during pathogenesis in the host. Further, the interaction of bacteria with the host cell (macrophages) was a major factor in the differential expression of these proteins. Finally, eight common differentially expressed RNA-protein pairs, predicted as virulent, outer membrane/extracellular proteins were validated by quantitative PCR. This is the first report using integrated multi-omics approach to identify critical factors involved in Leptospira pathogenesis. Validation of these critical factors may lead to the identification of target antigens for the development of improved diagnostics and vaccines against leptospirosis. IMPORTANCE Leptospirosis is a zoonotic disease of global importance. It is caused by a Gram-negative bacterial spirochete of the genus Leptospira. The current challenge is to detect the infection at early stage for treatment or to develop potent vaccines that can induce cross-protection against various pathogenic serovars. Understanding host-pathogen interactions is important to identify the critical factors involved in pathogenesis and host defense for developing improved vaccines and diagnostics. Utilizing an integrated multi-omics approach, our study provides important insight into the interaction of Leptospira with human macrophages and identifies a few critical factors (such as virulence-associated proteins) involved in pathogenesis. These factors can be exploited for the development of novel tools for the detection, treatment, or prevention of leptospirosis.
Collapse
Affiliation(s)
- Sridhar Kavela
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
| | - Pallavi Vyas
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Jusail CP
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Sandeep K. Kushwaha
- Bioinformatics Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Subeer S. Majumdar
- Gene and Protein Engineering Lab, National Institute of Animal Biotechnology, Hyderabad, India
| | - Syed M. Faisal
- Laboratory of Vaccine Immunology, National Institute of Animal Biotechnology, Hyderabad, India
- Regional Centre for Biotechnology, Faridabad, India
| |
Collapse
|
3
|
Abstract
The two-component system PhoP/PhoQ is essential for Salmonella enterica serovar Typhimurium virulence. Here, we report that PhoP is methylated extensively. Two consecutive glutamate (E) and aspartate (D)/E residues, i.e., E8/D9 and E107/E108, and arginine (R) 112 can be methylated. Individual mutation of these above-mentioned residues caused impaired phosphorylation and dimerization or DNA-binding ability of PhoP to a different extent and led to attenuated bacterial virulence. With the help of specific antibodies recognizing methylated E8 and monomethylated R112, we found that the methylation levels of E8 or R112 decreased dramatically when bacteria encountered low magnesium, acidic pH, or phagocytosis by macrophages, under which PhoP can be activated. Furthermore, CheR, a bacterial chemotaxis methyltransferase, was identified to methylate R112. Overexpression of cheR decreased PhoP activity but increased PhoP stability. Together, the current study reveals that methylation plays an important role in regulating PhoP activities in response to environmental cues and, consequently, modulates Salmonella virulence.
Collapse
|
4
|
Zhang J, Chen Z, Kankala RK, Wang SB, Chen AZ. Self-propelling micro-/nano-motors: Mechanisms, applications, and challenges in drug delivery. Int J Pharm 2021; 596:120275. [PMID: 33508344 DOI: 10.1016/j.ijpharm.2021.120275] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/17/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022]
Abstract
In recent times, numerous efforts have been put forward to fabricating the self-propelling micro-/nano-motors (MNMs) for various applications, such as drug delivery, environmental remediation, biosensing, and precision surgery at the micro-/nanoscale, among others. Owing to their potential advantages, the application of such innovative architectures has been increasingly recognized towards addressing various challenges in the related fields. Specifically, these MNMs offer enormous potential in nanomedicine in overcoming the significant challenge of low permeation of the biological barriers. Herein, we emphasize the powered mechanism of MNMs, including artificial and natural-based MNMs, and discuss the characteristics, as well as the challenges being faced by MNMs in drug delivery. Further, the research progress of MNMs as drug carriers in different environments (gastrointestinal tract, saliva, urinary bladder, blood, and extracellular matrix, ECM) of the body in recent years is summarized, highlighting the representative works on MNMs towards in vivo applications. Together, we firmly believe that these innovative MNMs-based designs may play a crucial role in the clinical practice in the future.
Collapse
Affiliation(s)
- Jianting Zhang
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, PR China; Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, PR China
| | - Zhoujiang Chen
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, PR China; Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, PR China.
| | - Ranjith Kumar Kankala
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, PR China; Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, PR China
| | - Shi-Bin Wang
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, PR China; Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, PR China
| | - Ai-Zheng Chen
- Institute of Biomaterials and Tissue Engineering, Huaqiao University, Xiamen 361021, PR China; Fujian Provincial Key Laboratory of Biochemical Technology (Huaqiao University), Xiamen 361021, PR China.
| |
Collapse
|
5
|
Cui G, Zhou Y, Li W, Gao Z, Huang J, Wang Y. A novel bacterial phylum that participates in carbon and osmolyte cycling in the Challenger Deep sediments. Environ Microbiol 2020; 23:3758-3772. [PMID: 33331063 DOI: 10.1111/1462-2920.15363] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 08/18/2020] [Accepted: 09/23/2020] [Indexed: 11/24/2022]
Abstract
Large amounts of detrital organic matter and osmolytes accumulate in the sediments of hadal trenches (>6000 m depth) due to the funnelling effect. It is still unknown whether there are novel active microbes that depend on specific carbon sources in extreme and isolated environments. In this study, we present a novel active bacterial phylum, Candidatus Tianyabacteria in the FCB superphylum, which was enriched in sediments collected from the Challenger Deep. Genome binning resulted in high-quality Ca. Tianyabacteria genomes representing two Ca. Tianyabacteria lineages (L1 and L2) in sediments 0-21 cm below the surface (cmbsf); L1 tends to be abundant in the upper layers (0-9 cmbsf), and L2 seems to be more prevalent in the deeper layers (12-21 cmbsf). Gene annotation and transcriptomics results indicate that the two lineages might import and catalyse amino acids and myo-inositol into central carbon metabolism for a heterotrophic lifestyle. Probably due to differences in environmental oxygen levels, the L2 genomes harbour gene clusters responsible for denitrification and fermentation, while the L1 genomes encode octahaem cytochrome c and multicopper oxidase using unknown substrates. The Ca. Tianyabacteria are thus novel heterotrophic organisms that participate in processes of carbon, nitrogen and organic osmolyte cycling in hadal sediments.
Collapse
Affiliation(s)
- Guojie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yingli Zhou
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Wenli Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhaoming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| | - Jiaomei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China.,Faculty of Marine Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, China
| |
Collapse
|
6
|
Cheng Y, Felix B, Othmer HG. The Roles of Signaling in Cytoskeletal Changes, Random Movement, Direction-Sensing and Polarization of Eukaryotic Cells. Cells 2020; 9:E1437. [PMID: 32531876 PMCID: PMC7348768 DOI: 10.3390/cells9061437] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/28/2020] [Accepted: 05/29/2020] [Indexed: 12/21/2022] Open
Abstract
Movement of cells and tissues is essential at various stages during the lifetime of an organism, including morphogenesis in early development, in the immune response to pathogens, and during wound-healing and tissue regeneration. Individual cells are able to move in a variety of microenvironments (MEs) (A glossary of the acronyms used herein is given at the end) by suitably adapting both their shape and how they transmit force to the ME, but how cells translate environmental signals into the forces that shape them and enable them to move is poorly understood. While many of the networks involved in signal detection, transduction and movement have been characterized, how intracellular signals control re-building of the cyctoskeleton to enable movement is not understood. In this review we discuss recent advances in our understanding of signal transduction networks related to direction-sensing and movement, and some of the problems that remain to be solved.
Collapse
Affiliation(s)
- Yougan Cheng
- Bristol Myers Squibb, Route 206 & Province Line Road, Princeton, NJ 08543, USA;
| | - Bryan Felix
- School of Mathematics, University of Minnesota, Minneapolis, MN 55445, USA;
| | - Hans G. Othmer
- School of Mathematics, University of Minnesota, Minneapolis, MN 55445, USA;
| |
Collapse
|
7
|
Wang Y, Huang JM, Cui GJ, Nunoura T, Takaki Y, Li WL, Li J, Gao ZM, Takai K, Zhang AQ, Stepanauskas R. Genomics insights into ecotype formation of ammonia-oxidizing archaea in the deep ocean. Environ Microbiol 2019; 21:716-729. [PMID: 30592124 DOI: 10.1111/1462-2920.14518] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 12/18/2018] [Accepted: 12/26/2018] [Indexed: 02/05/2023]
Abstract
Various lineages of ammonia-oxidizing archaea (AOA) are present in deep waters, but the mechanisms that determine ecotype formation are obscure. We studied 18 high-quality genomes of the marine group I AOA lineages (alpha, gamma and delta) from the Mariana and Ogasawara trenches. The genomes of alpha AOA resembled each other, while those of gamma and delta lineages were more divergent and had even undergone insertion of some phage genes. The instability of the gamma and delta AOA genomes could be partially due to the loss of DNA polymerase B (polB) and methyladenine DNA glycosylase (tag) genes responsible for the repair of point mutations. The alpha AOA genomes harbour genes encoding a thrombospondin-like outer membrane structure that probably serves as a barrier to gene flow. Moreover, the gamma and alpha AOA lineages rely on vitamin B12 -independent MetE and B12 -dependent MetH, respectively, for methionine synthesis. The delta AOA genome contains genes involved in uptake of sugar and peptide perhaps for heterotrophic lifestyle. Our study provides insights into co-occurrence of cladogenesis and anagenesis in the formation of AOA ecotypes that perform differently in nitrogen and carbon cycling in dark oceans.
Collapse
Affiliation(s)
- Yong Wang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Jiao-Mei Huang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Guo-Jie Cui
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Takuro Nunoura
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Yoshihiro Takaki
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan.,Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Wen-Li Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China.,University of the Chinese Academy of Sciences, Beijing, China
| | - Jun Li
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Zhao-Ming Gao
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ken Takai
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima-cho, Yokosuka, 237-0061, Japan
| | - Ai-Qun Zhang
- Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Ramunas Stepanauskas
- Bigelow Laboratory for Ocean Sciences, 60 Bigelow Drive, East Boothbay, ME, 04544, USA
| |
Collapse
|
8
|
In silico characterization of a novel putative aerotaxis chemosensory system in the myxobacterium, Corallococcus coralloides. BMC Genomics 2018; 19:757. [PMID: 30340510 PMCID: PMC6194562 DOI: 10.1186/s12864-018-5151-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 10/08/2018] [Indexed: 11/23/2022] Open
Abstract
Background An efficient signal transduction system allows a bacterium to sense environmental cues and then to respond positively or negatively to those signals; this process is referred to as taxis. In addition to external cues, the internal metabolic state of any bacterium plays a major role in determining its ability to reside and thrive in its current environment. Similar to external signaling molecules, cytoplasmic signals are also sensed by methyl-accepting chemotaxis proteins (MCPs) via diverse ligand binding domains. Myxobacteria are complex soil-dwelling social microbes that can perform a variety of physiologic and metabolic activities ranging from gliding motility, sporulation, biofilm formation, carotenoid and secondary metabolite biosynthesis, predation, and slime secretion. To live such complex lifestyles, they have evolved efficient signal transduction systems with numerous one- and two-component regulatory system along with a large array of chemosensory systems to perceive and integrate both external and internal cues. Results Here we report the in silico characterization of a putative energy taxis cluster, Cc-5, which is present in only one amongst 34 known and sequenced myxobacterial genomes, Corallococcus coralloides. In addition, we propose that this energy taxis cluster is involved in oxygen sensing, suggesting that C. coralloides can sense (either directly or indirectly) and then respond to changing concentrations of molecular oxygen. Conclusions This hypothesis is based on the presence of a unique MCP encoded in this gene cluster that contains two different oxygen-binding sensor domains, PAS and globin. In addition, the two monooxygenases encoded in this cluster may contribute to aerobic respiration via ubiquinone biosynthesis, which is part of the cytochrome bc1 complex. Finally, we suggest that this cluster was acquired from Actinobacteria, Gammaproteobacteria or Cyanobacteria. Overall, this in silico study has identified a potentially innovative and evolved mechanism of energy taxis in only one of the myxobacteria, C. coralloides. Electronic supplementary material The online version of this article (10.1186/s12864-018-5151-6) contains supplementary material, which is available to authorized users.
Collapse
|
9
|
Cellular Stoichiometry of Methyl-Accepting Chemotaxis Proteins in Sinorhizobium meliloti. J Bacteriol 2018; 200:JB.00614-17. [PMID: 29263102 DOI: 10.1128/jb.00614-17] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 12/15/2017] [Indexed: 12/29/2022] Open
Abstract
The chemosensory system in Sinorhizobium meliloti has several important deviations from the widely studied enterobacterial paradigm. To better understand the differences between the two systems and how they are optimally tuned, we determined the cellular stoichiometry of the methyl-accepting chemotaxis proteins (MCPs) and the histidine kinase CheA in S. meliloti Quantitative immunoblotting was used to determine the total amount of MCPs and CheA per cell in S. meliloti The MCPs are present in the cell in high abundance (McpV), low abundance (IcpA, McpU, McpX, and McpW), and very low abundance (McpY and McpZ), whereas McpT was below the detection limit. The approximate cellular ratio of these three receptor groups is 300:30:1. The chemoreceptor-to-CheA ratio is 23.5:1, highly similar to that seen in Bacillus subtilis (23:1) and about 10 times higher than that in Escherichia coli (3.4:1). Different from E. coli, the high-abundance receptors in S. meliloti are lacking the carboxy-terminal NWETF pentapeptide that binds the CheR methyltransferase and CheB methylesterase. Using transcriptional lacZ fusions, we showed that chemoreceptors are positively controlled by the master regulators of motility, VisNR and Rem. In addition, FlbT, a class IIA transcriptional regulator of flagellins, also positively regulates the expression of most chemoreceptors except for McpT and McpY, identifying chemoreceptors as class III genes. Taken together, these results demonstrate that the chemosensory complex and the adaptation system in S. meliloti deviates significantly from the established enterobacterial paradigm but shares some similarities with B. subtilisIMPORTANCE The symbiotic soil bacterium Sinorhizobium meliloti is of great agricultural importance because of its nitrogen-fixing properties, which enhances growth of its plant symbiont, alfalfa. Chemotaxis provides a competitive advantage for bacteria to sense their environment and interact with their eukaryotic hosts. For a better understanding of the role of chemotaxis in these processes, detailed knowledge on the regulation and composition of the chemosensory machinery is essential. Here, we show that chemoreceptor gene expression in S. meliloti is controlled through the main transcriptional regulators of motility. Chemoreceptor abundance is much lower in S. meliloti than in Escherichia coli and Bacillus subtilis Moreover, the chemoreceptor-to-kinase CheA ratio is different from that of E. coli but similar to that of B. subtilis.
Collapse
|
10
|
Fis is a global regulator critical for modulation of virulence factor production and pathogenicity of Dickeya zeae. Sci Rep 2018; 8:341. [PMID: 29321600 PMCID: PMC5762655 DOI: 10.1038/s41598-017-18578-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 12/11/2017] [Indexed: 12/25/2022] Open
Abstract
Dickeya zeae is the causal agent of rice foot rot disease, which has recently become a great threat to rice planting countries and regions. The pathogen produces a family of phytotoxins named zeamines that is critical for bacterial virulence, but little is known about the signaling pathways and regulatory mechanisms that govern zeamine production. In this study, we showed that a conserved transcriptional regulator Fis is involved in the regulation of zeamine production in D. zeae strain EC1. Deletion mutants were markedly attenuated in the virulence against rice seed germination. Transcriptome and phenotype analyses showed that Fis is a potent global transcriptional regulator modulating various virulence traits, including production of extracellular enzymes and exopolysaccharides, swimming and swarming motility, biofilm formation and cell aggregation. DNA gel retardation analysis showed that Fis directly regulates the transcription of key virulence genes and the genes encoding Vfm quorum sensing system through DNA/protein interaction. Our findings unveil a key regulator associated with the virulence of D. zeae EC1, and present useful clues for further elucidation of the regulatory complex and signaling pathways which govern the virulence of this important pathogen.
Collapse
|
11
|
Samanta S, Layek R, Kar S, Raj MK, Mukhopadhyay S, Chakraborty S. Predicting Escherichia coli's chemotactic drift under exponential gradient. Phys Rev E 2017; 96:032409. [PMID: 29346905 DOI: 10.1103/physreve.96.032409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Bacterial species are known to show chemotaxis, i.e., the directed motions in the presence of certain chemicals, whereas the motion is random in the absence of those chemicals. The bacteria modulate their run time to induce chemotactic drift towards the attractant chemicals and away from the repellent chemicals. However, the existing theoretical knowledge does not exhibit a proper match with experimental validation, and hence there is a need for developing alternate models and validating experimentally. In this paper a more robust theoretical model is proposed to investigate chemotactic drift of peritrichous Escherichia coli under an exponential nutrient gradient. An exponential gradient is used to understand the steady state behavior of drift because of the logarithmic functionality of the chemosensory receptors. Our theoretical estimations are validated through the experimentation and simulation results. Thus, the developed model successfully delineates the run time, run trajectory, and drift velocity as measured from the experiments.
Collapse
Affiliation(s)
- Sibendu Samanta
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology, Kharagpur WB-721302, India
| | - Ritwik Layek
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology, Kharagpur WB-721302, India
| | - Shantimoy Kar
- Advanced Technology Development Centre, Indian Institute of Technology, Kharagpur WB-721302, India
| | - M Kiran Raj
- Advanced Technology Development Centre, Indian Institute of Technology, Kharagpur WB-721302, India
| | - Sudipta Mukhopadhyay
- Department of Electronics and Electrical Communication Engineering, Indian Institute of Technology, Kharagpur WB-721302, India
| | - Suman Chakraborty
- Advanced Technology Development Centre, Indian Institute of Technology, Kharagpur WB-721302, India
- Department of Mechanical Engineering, Microfluidic Laboratory, Indian Institute of Technology, Kharagpur WB-721302, India
- School of Medical Science and Technology, Indian Institute of Technology, Kharagpur WB-721302, India
| |
Collapse
|
12
|
Matsuzaki Y, Ohue M, Uchikoga N, Akiyama Y. Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis. Protein Pept Lett 2015; 21:790-8. [PMID: 23855669 PMCID: PMC4440392 DOI: 10.2174/09298665113209990066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 02/27/2013] [Accepted: 03/03/2013] [Indexed: 11/22/2022]
Abstract
Core elements of cell regulation are made up of protein-protein interaction (PPI) networks. However, many
parts of the cell regulatory systems include unknown PPIs. To approach this problem, we have developed a computational
method of high-throughput PPI network prediction based on all-to-all rigid-body docking of protein tertiary structures.
The prediction system accepts a set of data comprising protein tertiary structures as input and generates a list of possible
interacting pairs from all the combinations as output. A crucial advantage of this docking based method is in providing
predictions of protein pairs that increases our understanding of biological pathways by analyzing the structures of candidate
complex structures, which gives insight into novel interaction mechanisms. Although such exhaustive docking calculation
requires massive computational resources, recent advancements in the computational sciences have made such
large-scale calculations feasible. different rigid-body docking tools with different scoring models. We found that the predicted interactions were different
between the results from the two tools. When the positive predictions from both of the docking tools were combined, all
the core signaling interactions were correctly predicted with the exception of interactions activated by protein phosphorylation.
Large-scale PPI prediction using tertiary structures is an effective approach that has a wide range of potential applications.
This method is especially useful for identifying novel PPIs of new pathways that control cellular behavior.
Collapse
Affiliation(s)
| | | | | | - Yutaka Akiyama
- Graduate School of Information Science and Engineering, Tokyo Institute of Technology, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.
| |
Collapse
|
13
|
Plasmid-encoded MCP is involved in virulence, motility, and biofilm formation of Cronobacter sakazakii ATCC 29544. Infect Immun 2014; 83:197-204. [PMID: 25332122 DOI: 10.1128/iai.02633-14] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The aim of this study was to elucidate the function of the plasmid-borne mcp (methyl-accepting chemotaxis protein) gene, which plays pleiotropic roles in Cronobacter sakazakii ATCC 29544. By searching for virulence factors using a random transposon insertion mutant library, we identified and sequenced a new plasmid, pCSA2, in C. sakazakii ATCC 29544. An in silico analysis of pCSA2 revealed that it included six putative open reading frames, and one of them was mcp. The mcp mutant was defective for invasion into and adhesion to epithelial cells, and the virulence of the mcp mutant was attenuated in rat pups. In addition, we demonstrated that putative MCP regulates the motility of C. sakazakii, and the expression of the flagellar genes was enhanced in the absence of a functional mcp gene. Furthermore, a lack of the mcp gene also impaired the ability of C. sakazakii to form a biofilm. Our results demonstrate a regulatory role for MCP in diverse biological processes, including the virulence of C. sakazakii ATCC 29544. To the best of our knowledge, this study is the first to elucidate a potential function of a plasmid-encoded MCP homolog in the C. sakazakii sequence type 8 (ST8) lineage.
Collapse
|
14
|
Zhang Y, Dong K, Zeng L, Li Q, Liu C, Wang J, Guo X, Zhao GP. Genetic and molecular biological characterization of two homologous cheR genes from Leptospira interrogans. Acta Biochim Biophys Sin (Shanghai) 2013; 45:806-16. [PMID: 23934012 DOI: 10.1093/abbs/gmt081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Leptospira interrogans genome encodes two copies of cheR genes and each of them is able to complement for the swarming defective phenotype of Escherichia coli cheR null mutant RP1254 to certain extent, while over-expression of either of them inhibits the swarming of the chemotactic wild-type E. coli strain, RP437. Therefore, both CheR1 and CheR2 ought to bear the methyltransferase activities, although CheR1 has only one instead of two conserved basic amino acid residues located on the positively charged face of α2-helix. When this residue as well as the Lys48 and Arg55 of CheR2 was mutated, none of the CheRs was able to maintain aforementioned complementation functions, suggesting their critical roles in recognition of methyl-accepting chemotaxis proteins similar to that of E. coli. Demonstrated by microarray assay, the expression of cheR1 in L. interrogans cultured at 28°C in Ellinghausen-McCullough-Johnson-Harris medium was significantly lower than the average transcription level of all other genes, while the transcription of cheR2 was significantly higher than that of cheR1 in accordance with real-time reverse transcriptase-polymerase chain reaction assay. Tandem MS-MS data mining for the proteome of the same culture detected 16 peptides derived from CheR2 but none from CheR1. Therefore, although both genes were shown to be functional in E. coli, the structurally more conserved CheR2 rather than CheR1 might be the major functional component of L. interrogans chemotaxis adaptation system under our laboratory culture conditions.
Collapse
Affiliation(s)
- Yunyi Zhang
- CAS Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Euglena-based neurocomputing with two-dimensional optical feedback on swimming cells in micro-aquariums. Appl Soft Comput 2013. [DOI: 10.1016/j.asoc.2012.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
16
|
Abstract
Microbial rhodopsins, a diverse group of photoactive proteins found in Archaea, Bacteria, and Eukarya, function in photosensing and photoenergy harvesting and may have been present in the resource-limited early global environment. Four different physiological functions have been identified and characterized for nearly 5,000 retinal-binding photoreceptors, these being ion transporters that transport proton or chloride and sensory rhodopsins that mediate light-attractant and/or -repellent responses. The greatest number of rhodopsins previously observed in a single archaeon had been four. Here, we report a newly discovered six-rhodopsin system in a single archaeon, Haloarcula marismortui, which shows a more diverse absorbance spectral distribution than any previously known rhodopsin system, and, for the first time, two light-driven proton transporters that respond to the same wavelength. All six rhodopsins, the greatest number ever identified in a single archaeon, were first shown to be expressed in H. marismortui, and these were then overexpressed in Escherichia coli. The proteins were purified for absorption spectra and photocycle determination, followed by measurement of ion transportation and phototaxis. The results clearly indicate the existence of a proton transporter system with two isochromatic rhodopsins and a new type of sensory rhodopsin-like transducer in H. marismortui.
Collapse
|
17
|
Dong K, Li Q, Liu C, Zhang Y, Zhao G, Guo X. Cloning and characterization of three cheB genes in Leptospira interrogans. Acta Biochim Biophys Sin (Shanghai) 2010; 42:216-23. [PMID: 20213047 DOI: 10.1093/abbs/gmq007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Motility and chemotaxis systems are critical for the virulence of leptospires. There were multiple copies of putative chemotaxis homologs located at leptospires large chromosome. CheB1 and CheB3 from Leptospira interrogans strain Lai are predicted to have a global CheB-like domain, but CheB2 is predicted to have a C-terminal effector domain only. In order to verify the function of three putative cheB genes, they were cloned into pQE31 vector and then expressed, respectively, in wild-type Escherichia coli strain RP437 and cheB defective strain RP4972. The results of swarming assays and the predicted ternary structures of CheB1 and CheB3 of L. interrogans strain Lai suggested that the absence of an N-terminal regulatory domain may be one of the reasons for the failure of CheB2 to complement an E. coli cheB mutant. Furthermore, CheB2 links solely to CheR1 and CheR3 in the interaction network of leptospires. Taken together, these results indicated that CheB2 may not function alone, and under certain physiological conditions, it may require CheB3 and CheR1 to function. The existence of multiple copies of chemotaxis gene homologs suggested that L. interrogans strain Lai might have a more complex chemosensory pathway.
Collapse
Affiliation(s)
- Ke Dong
- Department of Microbiology and Parasitology, Institutes of Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | | | | | | | | | | |
Collapse
|
18
|
Sasaki J, Spudich JL. Signal Transfer in Haloarchaeal Sensory Rhodopsin Transducer Complexes. Photochem Photobiol 2008; 84:863-8. [DOI: 10.1111/j.1751-1097.2008.00314.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
19
|
Igoshin OA, Alves R, Savageau MA. Hysteretic and graded responses in bacterial two-component signal transduction. Mol Microbiol 2008; 68:1196-215. [PMID: 18363790 DOI: 10.1111/j.1365-2958.2008.06221.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacterial two-component systems (TCS) are key signal transduction networks regulating global responses to environmental change. Environmental signals may modulate the phosphorylation state of sensor kinases (SK). The phosphorylated SK transfers the phosphate to its cognate response regulator (RR), which causes physiological response to the signal. Frequently, the SK is bifunctional and, when unphosphorylated, it is also capable of dephosphorylating the RR. The phosphatase activity may also be modulated by environmental signals. Using the EnvZ/OmpR system as an example, we constructed mathematical models to examine the steady-state and kinetic properties of the network. Mathematical modelling reveals that the TCS can show bistable behaviour for a given range of parameter values if unphosphorylated SK and RR form a dead-end complex that prevents SK autophosphorylation. Additionally, for bistability to exist the major dephosphorylation flux of the RR must not depend on the unphosphorylated SK. Structural modelling and published affinity studies suggest that the unphosphorylated SK EnvZ and the RR OmpR form a dead-end complex. However, bistability is not possible because the dephosphorylation of OmpR approximately P is mainly done by unphosphorylated EnvZ. The implications of this potential bistability in the design of the EnvZ/OmpR network and other TCS are discussed.
Collapse
Affiliation(s)
- Oleg A Igoshin
- Department of Bioengineering, Rice University, Houston, TX 77251-1892, USA.
| | | | | |
Collapse
|
20
|
Yan J, Barak R, Liarzi O, Shainskaya A, Eisenbach M. In vivo acetylation of CheY, a response regulator in chemotaxis of Escherichia coli. J Mol Biol 2008; 376:1260-71. [PMID: 18234227 DOI: 10.1016/j.jmb.2007.12.070] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2007] [Revised: 12/26/2007] [Accepted: 12/27/2007] [Indexed: 10/22/2022]
Abstract
CheY, the excitatory response regulator in the chemotaxis system of Escherichia coli, can be modulated by two covalent modifications: phosphorylation and acetylation. Both modifications have been detected in vitro only. The role of CheY acetylation is still obscure, although it is known to be involved in chemotaxis and to occur in vitro by two mechanisms--acetyl-CoA synthetase-catalyzed transfer of acetyl groups from acetate to CheY and autocatalyzed transfer from AcCoA. Here, we succeeded in detecting CheY acetylation in vivo by three means--Western blotting with a specific anti-acetyl-lysine antibody, mass spectrometry, and radiolabeling with [(14)C]acetate in the presence of protein-synthesis inhibitor. Unexpectedly, the level and rate of CheY acetylation in vivo were much higher than that in vitro. Thus, before any treatment, 9-13% of the lysine residues were found acetylated, depending on the growth phase, meaning that, on average, essentially every CheY molecule was acetylated in vivo. This high level was mainly the outcome of autoacetylation. Addition of acetate caused an incremental increase in the acetylation level, in which acetyl-CoA synthetase was involved too. These findings may have far-reaching implications for the structure-function relationship of CheY.
Collapse
Affiliation(s)
- Jianshe Yan
- Department of Biological Chemistry, The Weizmann Institute of Science, 76100 Rehovot, Israel
| | | | | | | | | |
Collapse
|
21
|
Terashima H, Kojima S, Homma M. Flagellar motility in bacteria structure and function of flagellar motor. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 270:39-85. [PMID: 19081534 DOI: 10.1016/s1937-6448(08)01402-0] [Citation(s) in RCA: 174] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bacterial flagella are filamentous organelles that drive cell locomotion. They thrust cells in liquids (swimming) or on surfaces (swarming) so that cells can move toward favorable environments. At the base of each flagellum, a reversible rotary motor, which is powered by the proton- or the sodium-motive force, is embedded in the cell envelope. The motor consists of two parts: the rotating part, or rotor, that is connected to the hook and the filament, and the nonrotating part, or stator, that conducts coupling ion and is responsible for energy conversion. Intensive genetic and biochemical studies of the flagellum have been conducted in Salmonella typhimurium and Escherichia coli, and more than 50 gene products are known to be involved in flagellar assembly and function. The energy-coupling mechanism, however, is still not known. In this chapter, we survey our current knowledge of the flagellar system, based mostly on studies from Salmonella, E. coli, and marine species Vibrio alginolyticus, supplemented with distinct aspects of other bacterial species revealed by recent studies.
Collapse
Affiliation(s)
- Hiroyuki Terashima
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
| | | | | |
Collapse
|
22
|
Lee WK, Ogura K, Loh JT, Cover TL, Berg DE. Quantitative effect of luxS gene inactivation on the fitness of Helicobacter pylori. Appl Environ Microbiol 2006; 72:6615-22. [PMID: 16936059 PMCID: PMC1610275 DOI: 10.1128/aem.01291-06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Furanone metabolites called AI-2 (autoinducer 2), used by some bacterial species for signaling and cell density-regulated changes in gene expression, are made while regenerating S-adenosyl methionine (SAM) after its use as a methyl donor. The luxS-encoded enzyme, in particular, participates in this activated methyl cycle by generating both a pentanedione, which is transformed chemically into these AI-2 compounds, and homocysteine, a precursor of methionine and SAM. Helicobacter pylori seems to contain the genes for this activated methyl cycle, including luxS, but not genes for AI-2 uptake and transcriptional regulation. Here we report that deletion of luxS in H. pylori reference strain SS1 diminished its competitive ability in mice and motility in soft agar, whereas no such effect was seen with an equivalent Delta luxS derivative of the unrelated strain X47. These different outcomes are consistent with H. pylori's considerable genetic diversity and are reminiscent of phenotypes seen after deletion of another nonessential metabolic gene, that encoding polyphosphate kinase 1. We suggest that synthesis of AI-2 by H. pylori may be an inadvertent consequence of metabolite flux in its activated methyl cycle and that impairment of this cycle and/or pathways affected by it, rather than loss of quorum sensing, is deleterious for some H. pylori strains. Also tenable is a model in which AI-2 affects other microbes in H. pylori's gastric ecosystem and thereby modulates the gastric environment in ways to which certain H. pylori strains are particularly sensitive.
Collapse
Affiliation(s)
- Woo-Kon Lee
- Department of Molecular Microbiology, Campus Box 8230, 4940 Parkview Place, Washington University Medical School, St. Louis, MO 63110, USA
| | | | | | | | | |
Collapse
|
23
|
Félix R, Rodrigues R, Machado P, Oliveira S, Rodrigues-Pousada C. A chemotaxis operon in the bacterium Desulfovibrio gigas is induced under several growth conditions. ACTA ACUST UNITED AC 2006; 17:56-64. [PMID: 16753818 DOI: 10.1080/10425170500412488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The chemosensory system of bacteria controls their motility and behaviour in different environments. In the present study, we report the identification of the first chemotaxis operon in Desulfovibrio gigas. Amino acid sequence analysis revealed seven coding regions for polypeptides with a high similarity to chemotaxis proteins from other organisms. D. gigas chemotaxis operon has a similar genetic organisation to chemotaxis operons found in the sequenced genomes of Desulfovibrio desulfuricans and Desulfovibrio vulgaris. Control of gene expression was assessed by real-time reverse transcription-PCR in cells grown under different conditions. mRNA levels were enhanced in the presence of thiosulfate and sulfite and decreased upon exposure to NO. No effect was observed in the presence of O2, NaNO2, pyruvate or fumarate. These results show that the expression of the chemotaxis operon is enhanced in the presence of thiosulfate and sulfite indicating that under these compounds a chemotactic response seems to be triggered in D. gigas.
Collapse
Affiliation(s)
- Rute Félix
- Instituto de Tecnologia Química e Biológica, Apartado 127, Oeiras, 2780-901, Portugal
| | | | | | | | | |
Collapse
|
24
|
Li ZH, Dong K, Yuan JP, Hu BY, Liu JX, Zhao GP, Guo XK. Characterization of the cheY genes from Leptospira interrogans and their effects on the behavior of Escherichia coli. Biochem Biophys Res Commun 2006; 345:858-66. [PMID: 16701553 DOI: 10.1016/j.bbrc.2006.04.159] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2006] [Accepted: 04/11/2006] [Indexed: 11/25/2022]
Abstract
The motility and chemotaxis system are critical for the virulence of pathogenic leptospire, which enable them to penetrate host tissue barriers during infection. The completed genome sequence of a representative virulent serovar type strain (Lai) of Leptospira interrogans serogroups Icterohaemorrhagiae (L. interrogans strain Lai) suggested that there were multiple copies of putative chemotaxis homologues located at its large chromosome. In order to verify the function of these proteins, the putative cheY genes were cloned into pQE31 vector and then expressed, respectively, in wild-type Escherichia coli strain RP437 and cheY defective strain RP5232. The results showed that all the five cheYs could restore the swarming of RP5232 strain to some extend. Overexpression of CheYs in RP437 showed inhibited swarming of RP437. To investigate the mechanism of chemotaxis signaling in L. interrogans strain Lai, certain aspartates (Asp-53, Asp-61, Asp-70, Asp-62, and Asp-66 for L. interrogans strain Lai CheY1, CheY2, CheY3, CheY4, and CheY5, respectively) were mutated. Expression of these mutated cheYs manifested neither restoration of the swarming ability of RP5232 nor inhibition on swarming ability of RP437. Multiple amino acid sequence alignment predicted ternary structures and the result of mutation experiment suggested that these conserved aspartate residues of L. interrogans were analogous to that in E. coli CheY in function and structure. So, L. interrogans and E. coli may have similar mechanisms of activation of the chemotaxis phosphorelay pathway, but there are differences in their control by signal terminator.
Collapse
Affiliation(s)
- Zhen-Hong Li
- Department of Microbiology and Parasitology, 280 South Chongqing Road, Medical school, Shanghai Jiaotong University, Shanghai 200025, PR China
| | | | | | | | | | | | | |
Collapse
|
25
|
Li ZH, Dong K, Sun JC, Yuan JP, Hu BY, Liu JX, Zhao GP, Guo XK. Characterization of cheW genes of Leptospira interrogans and their effects in Escherichia coli. Acta Biochim Biophys Sin (Shanghai) 2006; 38:79-88. [PMID: 16474898 DOI: 10.1111/j.1745-7270.2006.00137.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The motility and chemotaxis systems are critical for the virulence of leptospires. In this study, the phylogenetic profiles method was used to predict the interaction of chemotaxis proteins. It was shown that CheW1 links to CheA1, CheY, CheB and CheW2; CheW3 links to CheA2, MCP (LA2426), CheB3 and CheD1; and CheW2 links only to CheW1. The similarity analysis demonstrated that CheW2 of Leptospira interrogans strain Lai had poor homology with CheW of Escherichia coli in the region of residues 30-50. In order to verify the function of these proteins, the putative cheW genes were cloned into pQE31 vector and expressed in wild-type E. coli strain RP437 or cheW defective strain RP4606. The swarming results indicated that CheW1 and CheW3 could restore swarming of RP4606 while CheW2 could not. Overexpression of CheW1 and CheW3 in RP437 inhibited the swarming of RP437, whereas the inhibitory effect of CheW2 was much lower. Therefore, we presumed that CheW1 and CheW3 might have the function of CheW while CheW2 does not. The existence of multiple copies of chemotaxis homologue genes suggested that L. interrogans strain Lai might have a more complex chemosensory pathway.
Collapse
Affiliation(s)
- Zhen-Hong Li
- Department of Microbiology and Parasitology, Medicine School of Shanghai Jiaotong University, Shanghai 200025, China
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Hughes KT. Keeping your lawn wet. EMBO Rep 2005; 6:518-9. [PMID: 15940284 PMCID: PMC1369100 DOI: 10.1038/sj.embor.7400442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2005] [Accepted: 05/02/2005] [Indexed: 11/09/2022] Open
Affiliation(s)
- Kelly T Hughes
- Department of Biology at the University of Utah, Salt Lake City, Utah 84112, USA.
| |
Collapse
|
27
|
Inoue K, Sasaki J, Morisaki M, Tokunaga F, Terazima M. Time-resolved detection of sensory rhodopsin II-transducer interaction. Biophys J 2005; 87:2587-97. [PMID: 15454453 PMCID: PMC1304677 DOI: 10.1529/biophysj.104.043521] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamics of protein conformational change of Natronobacterium pharaonis sensory rhodopsin II (NpSRII) and of NpSRII fused to cognate transducer (NpHtrII) truncated at 159 amino acid sequence from the N-terminus (NpSRII-DeltaNpHtrII) are investigated in solution phase at room temperature by the laser flash photolysis and the transient grating methods in real time. The diffusion coefficients of both species indicate that the NpSRII-DeltaNpHtrII exists in the dimeric form in 0.6% dodecyl-beta-maltopyranoside (DM) solution. Rate constants of the reaction processes in the photocycles determined by the transient absorption and grating methods agree quite well. Significant differences were found in the volume change and the molecular energy between NpSRII and NpSRII-DeltaNpHtrII samples. The enthalpy of the second intermediate (L) of NpSRII-DeltaNpHtrII is more stabilized compared with that of NpSRII. This stabilization indicates the influence of the transducer to the NpSRII structure in the early intermediate species by the complex formation. Relatively large molecular volume expansion and contraction were observed in the last two steps for NpSRII. Additional volume expansion and contraction were induced by the presence of DeltaNpHtrII. This volume change, which should reflect the conformational change induced by the transducer protein, suggested that this is the signal transduction process of the NpSRII-DeltaNpHtrII.
Collapse
Affiliation(s)
- Keiichi Inoue
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | | | | | | | | |
Collapse
|
28
|
Spengler G, Molnár A, Klausz G, Mándi Y, Kawase M, Motohashi N, Molnár J. The antimotility action of a trifluoromethyl ketone on some gram-negative bacteria. Acta Microbiol Immunol Hung 2004; 51:351-8. [PMID: 15571074 DOI: 10.1556/amicr.51.2004.3.12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The inhibition of bacterial motility was studied by a trifluoro methyl ketone derivative on two Escherichia coli strains (wild strain having a proton pump system and the proton pump-deficient mutant strain) and two Helicobacter pylori strains (clarithromycin susceptible and clarithromycin resistant). Evidence is presented of the inhibitory action of 1-(2-benzoxazolyl)-3,3,3-trifluoro-2-propanone (TF18) on the proton motive forces of the two bacterial strains by affecting the action of biological motor and proton efflux in the membranes. The swimming, the forward motion was more sensitive than the vibration or tumbling to the inhibition. We suppose that the inhibiton of bacterial motility is related to the virulence of bacteria: consequently the pathogenicity can be reduced in the presence of TF18.
Collapse
Affiliation(s)
- Gabriella Spengler
- Departament of Medical Microbiology and Immunobiology, Albert Szent-Györgyi Medical Centre, Faculty of Medicine, University of Szeged, Dóm tér 10, H-6720 Szeged, Hungary
| | | | | | | | | | | | | |
Collapse
|
29
|
Tokarz R, Anderton JM, Katona LI, Benach JL. Combined effects of blood and temperature shift on Borrelia burgdorferi gene expression as determined by whole genome DNA array. Infect Immun 2004; 72:5419-32. [PMID: 15322040 PMCID: PMC517457 DOI: 10.1128/iai.72.9.5419-5432.2004] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Borrelia burgdorferi undergoes differential gene expression during transmission from its tick vector to a vertebrate host. The addition of blood to a spirochete culture at 35 degrees C for 48 h had a dramatic effect on gene expression of this organism. Utilizing B. burgdorferi whole genome DNA arrays, we compared the transcriptomes of the spirochetes following a 2-day temperature shift with blood and without blood. Using combined data from three independent RNA isolations we demonstrated that the addition of blood led to a differential expression of 154 genes. Of these, 75 genes were upregulated, with 49 (65%) of them encoded on plasmids. Blood supplementation of cultures also resulted in the downregulation of 79 genes, where 56 (70%) were plasmid encoded. We verified our results by reverse transcriptase PCR of several genes in both flat and feeding ticks. In the 2-day experiment we observed the effect that exposure to increased temperature and blood combined had on B. burgdorferi gene expression at this crucial time when the spirochetes begin to move from the vector to a new vertebrate host. These changes, among others, coincide with the upregulation of the chemotaxis and sensing regulons, of the lp38-encoded ABC transporter, of proteases capable of remodeling the outer surface of the spirochetes, and of the recombination genes of cp32 as a transient or initial part of the stress response of the phage. These are all functions that could cause or facilitate the changes that spirochetes undergo following a blood meal in the tick.
Collapse
Affiliation(s)
- Rafal Tokarz
- Department of Molecular Genetics and Microbiology, Center for Infectious Diseases, Stony Brook University, 248 Centers for Molecular Medicine, Stony Brook, NY 11794-5120, USA
| | | | | | | |
Collapse
|
30
|
Hutchings MI, Hoskisson PA, Chandra G, Buttner MJ. Sensing and responding to diverse extracellular signals? Analysis of the sensor kinases and response regulators of Streptomyces coelicolor A3(2). Microbiology (Reading) 2004; 150:2795-2806. [PMID: 15347739 DOI: 10.1099/mic.0.27181-0] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Streptomyces coelicolor is a Gram-positive soil bacterium that undergoes a complex developmental life cycle. The genome sequence of this organism was recently completed and has revealed the presence of over 60 sigma factors and a multitude of other transcriptional regulators, with a significant number of these being putative two-component signal transduction proteins. The authors have used the criteria established by Hoch and co-workers (Fabret et al., 1999, J Bacteriol 181, 1975-1983) to identify sensor kinase and response regulator genes encoded within the S. coelicolor genome. This analysis has revealed the presence of 84 sensor kinase genes, 67 of which lie adjacent to genes encoding response regulators. This strongly suggests that these paired genes encode two-component systems. In addition there are 13 orphan response regulators encoded in the genome, several of which have already been characterized and are implicated in development and antibiotic production, and 17 unpaired and as yet uncharacterized sensor kinases. This article attempts to infer useful information from sequence analysis and reviews what is currently known about the two-component systems, unpaired sensor kinases and orphan response regulators of S. coelicolor from both published reports and the authors' own unpublished data.
Collapse
Affiliation(s)
- Matthew I Hutchings
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Paul A Hoskisson
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| | - Mark J Buttner
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
| |
Collapse
|
31
|
Bibikov SI, Miller AC, Gosink KK, Parkinson JS. Methylation-independent aerotaxis mediated by the Escherichia coli Aer protein. J Bacteriol 2004; 186:3730-7. [PMID: 15175286 PMCID: PMC419962 DOI: 10.1128/jb.186.12.3730-3737.2004] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aer is a membrane-associated protein that mediates aerotactic responses in Escherichia coli. Its C-terminal half closely resembles the signaling domains of methyl-accepting chemotaxis proteins (MCPs), which undergo reversible methylation at specific glutamic acid residues to adapt their signaling outputs to homogeneous chemical environments. MCP-mediated behaviors are dependent on two specific enzymes, CheR (methyltransferase) and CheB (methylesterase). The Aer signaling domain contains unorthodox methylation sites that do not conform to the consensus motif for CheR or CheB substrates, suggesting that Aer, unlike conventional MCPs, might be a methylation-independent transducer. Several lines of evidence supported this possibility. (i) The Aer protein was not detectably modified by either CheR or CheB. (ii) Amino acid replacements at the putative Aer methylation sites generally had no deleterious effect on Aer function. (iii) Aer promoted aerotactic migrations on semisolid media in strains that lacked all four of the E. coli MCPs. CheR and CheB function had no influence on the rate of aerotactic movements in those strains. Thus, Aer senses and signals efficiently in the absence of deamidation or methylation, methylation changes, methylation enzymes, and methyl-accepting chemotaxis proteins. We also found that chimeric transducers containing the PAS-HAMP sensing domain of Aer joined to the signaling domain and methylation sites of Tar, an orthodox MCP, exhibited both methylation-dependent and methylation-independent aerotactic behavior. The hybrid Aear transducers demonstrate that methylation independence does not emanate from the Aer signaling domain but rather may be due to transience of the cellular redox changes that are thought to trigger Aer-mediated behavioral responses.
Collapse
Affiliation(s)
- Sergei I Bibikov
- Biology Department, University of Utah, 257 South 1400 East, Salt Lake City, UT 84112, USA
| | | | | | | |
Collapse
|