Integrative genome‐scale metabolic analysis of
            <i>Vibrio vulnificus</i>
            for drug targeting and discovery

Kim, Hyun Uk; Kim, Soo Young; Jeong, Haeyoung; Kim, Tae Yong; Kim, Jae Jong; Choy, Hyon E.; Yi, Kyu Yang; Rhee, Joon Haeng; Lee, Sang Yup

doi:10.1038/msb.2010.115

Cited by 149 publications

(117 citation statements)

References 74 publications

(93 reference statements)

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“…V. vulnificus strains, E. coli strains, and the plasmids used in this study are listed in Tables 1 and 2. The wild-type V. vulnificus strain used in this study was CMCP6, a highly virulent clinical isolate whose genome sequence was recently reannotated and is regarded as the most complete and accurate of the published V. (26,27). E. coli and V. vulnificus were grown in LuriaBertani (LB) medium and 2.5% NaCl heart infusion (HI) medium, respectively.…”

Section: Methodsmentioning

confidence: 99%

Contribution of Six Flagellin Genes to the Flagellum Biogenesis of Vibrio vulnificus and In Vivo Invasion

et al. 2014

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dVibrio vulnificus is a halophilic pathogenic bacterium that is motile due to the presence of a single polar flagellum. V. vulnificus possesses a total of six flagellin genes organized into two loci (flaFBA and flaCDE). We proved that all six of the flagellin genes were transcribed, whereas only five (FlaA, -B, -C, -D, and -F) of the six flagellin proteins were detected. To understand roles of the six V. vulnificus flagellins in motility and virulence, mutants with single and multiple flagellin deletions were constructed. Mutations in flaB or flaC or the flaCDE locus resulted in a significant decrease in motility, adhesion, and cytotoxicity, whereas single mutations in the other flagellin genes or the flaFBA locus showed little or no effect. The motility was completely abolished only in the mutant lacking all six flagellin genes (flaFBA flaCDE). Surprisingly, a double mutation of flaB and flaD, a gene sharing 99% identity with the flaB at the amino acid level, resulted in the largest decrease in motility, adhesion, and cytotoxicity except for the mutant in which all six genes were deleted (the hexa mutant). Additionally, the 50% lethal doses (LD 50 s) of the flaB flaD and the flaFBA flaCDE mutants increased 23-and 91-fold in a mouse model, respectively, and the in vitro and in vivo invasiveness of the mutants was significantly decreased compared to that of the wild type. Taken together, the multiple flagellin subunits differentially contribute to the flagellum biogenesis and the pathogenesis of V. vulnificus, and among the six flagellin genes, flaB, flaD, and flaC were the most influential components.

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Section: Methodsmentioning

confidence: 99%

Contribution of Six Flagellin Genes to the Flagellum Biogenesis of Vibrio vulnificus and In Vivo Invasion

et al. 2014

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“…The V. vulnificus strains, E. coli strains, and plasmids that were used in this study are listed in Table 1. The wild-type V. vulnificus strain was CMCP6, a highly virulent clinical isolate whose genome sequence was recently reannotated for higher accuracy (23,24). E. coli and V. vulnificus were grown in Luria-Bertani and 2.5% NaCl heart infusion (HI) media, respectively.…”

Section: Methodsmentioning

confidence: 99%

All Three TonB Systems Are Required for Vibrio vulnificus CMCP6 Tissue Invasiveness by Controlling Flagellum Expression

et al. 2016

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e TonB systems actively transport iron-bound substrates across the outer membranes of Gram-negative bacteria. Vibrio vulnificus CMCP6, which causes fatal septicemia and necrotizing wound infections, possesses three active TonB systems. It is not known why V. vulnificus CMCP6 has maintained three TonB systems throughout its evolution. The TonB1 and TonB2 systems are relatively well characterized, while the pathophysiological function of the TonB3 system is still elusive. A reverse transcription-PCR (RT-PCR) study showed that the tonB1 and tonB2 genes are preferentially induced in vivo, whereas tonB3 is persistently transcribed, albeit at low expression levels, under both in vitro and in vivo conditions. The goal of the present study was to elucidate the raison d'être of these three TonB systems. In contrast to previous studies, we constructed in-frame single-, double-, and triple-deletion mutants of the entire structural genes in TonB loci, and the changes in various virulence-related phenotypes were evaluated. Surprisingly, only the tonB123 mutant exhibited a significant delay in killing eukaryotic cells, which was complemented in trans with any TonB operon. Very interestingly, we discovered that flagellum biogenesis was defective in the tonB123 mutant. The loss of flagellation contributed to severe defects in motility and adhesion of the mutant. Because of the difficulty of making contact with host cells, the mutant manifested defective RtxA1 toxin production, which resulted in impaired invasiveness, delayed cytotoxicity, and decreased lethality for mice. Taken together, these results indicate that a series of virulence defects in all three TonB systems of V. vulnificus CMCP6 coordinately complement each other for iron assimilation and full virulence expression by ensuring flagellar biogenesis. Vibrio vulnificus is a halophilic estuarine pathogen that causes fatal septicemia and necrotizing wound infections in patients suffering from hepatic diseases with high levels of circulating iron or who are immunocompromised (1-5). Infection with V. vulnificus typically shows rapid progression and mortality rates greater than 50% (6, 7). In Gram-negative bacteria, the inner membrane protein complex TonB plays a crucial role in the uptake of iron (8, 9), which is an important micronutrient for numerous biological processes (10-12). TonB complexes transduce the proton motive force (PMF) of the cytoplasmic membrane to energize iron-siderophore complex transport through a specific TonB-dependent transporter (TBDT) across the outer membrane (OM) (9,13,14). This system's known biological roles had been restricted to iron complexes (15, 16) and vitamin B 12 (14), but recent experimental evidence of the TonB-energized transport of nickel and various carbohydrates suggests that the number and variety of TonB-dependent substrates have been underestimated (17)(18)(19). Unlike the single TonB system in Escherichia coli (8), the genomes of Vibrio species carry multiple TonB systems. Interestingly, three TonB systems were first report...

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“…A genome-scale model of E. coli was used to provide the organism with direct biocatalytic routes to 1,4-butanediol [212] and to identify better drug targets or biosynthetic pathways for antibiotics [213][214][215][216].…”

Section: Modellingmentioning

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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Integrative genome‐scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery

Cited by 149 publications

References 74 publications

Contribution of Six Flagellin Genes to the Flagellum Biogenesis of Vibrio vulnificus and In Vivo Invasion

Contribution of Six Flagellin Genes to the Flagellum Biogenesis of Vibrio vulnificus and In Vivo Invasion

All Three TonB Systems Are Required for Vibrio vulnificus CMCP6 Tissue Invasiveness by Controlling Flagellum Expression

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

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