Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium Xanthomonas campestris pv. campestris

Sidhu, Vishaldeep; Vorhölter, Frank-Jörg; Niehaus, Karsten; Watt, Stephen A.

doi:10.1186/1471-2180-8-87

Cited by 119 publications

(117 citation statements)

References 40 publications

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“…Importantly, OM vesicles are not a product of cell death since they contain newly synthesized proteins and are produced without concomitant bacterial lysis (96,99,144). Several OM vesicle proteomes have been evaluated recently, and all were determined to be enriched in envelope components, although some cytosolic and inner membrane proteins were also present in these preparations (10,40,84,86,87,124,141).…”

Section: What Are Om Vesicles?mentioning

confidence: 99%

Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles

Ellis

Kuehn

2010

Microbiol Mol Biol Rev

792

736

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SUMMARY Outer membrane (OM) vesicles are ubiquitously produced by Gram-negative bacteria during all stages of bacterial growth. OM vesicles are naturally secreted by both pathogenic and nonpathogenic bacteria. Strong experimental evidence exists to categorize OM vesicle production as a type of Gram-negative bacterial virulence factor. A growing body of data demonstrates an association of active virulence factors and toxins with vesicles, suggesting that they play a role in pathogenesis. One of the most popular and best-studied pathogenic functions for membrane vesicles is to serve as natural vehicles for the intercellular transport of virulence factors and other materials directly into host cells. The production of OM vesicles has been identified as an independent bacterial stress response pathway that is activated when bacteria encounter environmental stress, such as what might be experienced during the colonization of host tissues. Their detection in infected human tissues reinforces this theory. Various other virulence factors are also associated with OM vesicles, including adhesins and degradative enzymes. As a result, OM vesicles are heavily laden with pathogen-associated molecular patterns (PAMPs), virulence factors, and other OM components that can impact the course of infection by having toxigenic effects or by the activation of the innate immune response. However, infected hosts can also benefit from OM vesicle production by stimulating their ability to mount an effective defense. Vesicles display antigens and can elicit potent inflammatory and immune responses. In sum, OM vesicles are likely to play a significant role in the virulence of Gram-negative bacterial pathogens.

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Section: What Are Om Vesicles?mentioning

confidence: 99%

Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles

Ellis

Kuehn

2010

Microbiol Mol Biol Rev

792

736

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“…Recently, proteomics was employed to in-vestigate the outer membrane vesicles of X. campestris pv. campestris B100, while the 30 most abundant cytoplasmic proteins were already identified in 2003 (Sidhu et al, 2008). For this use case, 215 proteins of X. campestris pv.…”

Section: Curation and Application Of Metabolic Networkmentioning

confidence: 95%

“…Protein isolation, two-dimensional (2-D) gel electrophoresis, spot excision, tryptic ingel digestion, and protein identification by mass spectrometric analysis of peptide mass fingerprints were performed as described earlier (Sidhu et al, 2008 (Vorhölter et al, 2008). X. campestris pv.…”

Section: Proteomics Techniquesmentioning

confidence: 99%

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks

Schneider¹,

Vorhölter²,

Trost³

et al. 2010

Genet. Mol. Res.

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ABSTRACT. New sequencing technologies provide ultra-fast access to novel microbial genome data. For their interpretation, an efficient bioinformatics pipeline that facilitates in silico reconstruction of metabolic networks is highly desirable. The software tool CARMEN performs in silico reconstruction of metabolic networks to interpret genome data in a functional context. CARMEN supports the visualization of automatically derived metabolic networks based on pathway information from the KEGG database or from user-defined SBML templates; this software also enables comparative genomics. The reconstructed networks are stored in standardized SBML format. We demonstrated the functionality of CARMEN with a major application 1661 ©FUNPEC-RP www.funpecrp.com.br Genetics and Molecular Research 9 (1): 1660-1672 (2010) In silico metabolic network reconstruction example focusing on the reconstruction of glycolysis and related metabolic reactions of Xanthomonas campestris pv. campestris B100. The curation of such pathways facilitates enhanced visualization of experimental results, simulations and comparative genomics. A second application of this software was performed on a set of corynebacteria to compare and to visualize their carbohydrate metabolism. In conclusion, using CARMEN, we developed highly automated data analysis software that rapidly converts sequence data into new knowledge, replacing the time-consuming manual reconstruction of metabolic networks. This tool is particularly useful for obtaining an overview of newly sequenced genomes and their metabolic blueprints and for comparative genome analysis. The generated pathways provide automated access to modeling and simulation tools that are compliant with the SBML standard. A user-friendly web interface of CARMEN is available at http://carmen.cebitec.uni-bielefeld.de.

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“…For Xcc, proteomics techniques have been initially applied to obtain an insight into the cytoplasmic proteome [157]. Subsequent studies analysed the secretome [158], characterized outer-membrane vesicles [159], and explored the cytoplasmic proteome more comprehensively [160]. Specific applications facilitated the characterization of the MAMPs involved in plant interactions [161].…”

Section: Proteomicsmentioning

confidence: 99%

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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Analysis of outer membrane vesicle associated proteins isolated from the plant pathogenic bacterium Xanthomonas campestris pv. campestris

Cited by 119 publications

References 40 publications

Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles

Virulence and Immunomodulatory Roles of Bacterial Outer Membrane Vesicles

CARMEN - Comparative Analysis and in silico Reconstruction of organism-specific MEtabolic Networks

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

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