A phylogenomic analysis of the Actinomycetales mce operons

Coppola, Nicola; Riley, Lee W.

doi:10.1186/1471-2164-8-60

Cited by 216 publications

(268 citation statements)

References 95 publications

(115 reference statements)

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“…These two genes are intact in M. ulcerans ecovar Liflandii Lipoproteins. Lipoproteins in mycobacteria have been implicated in signal transduction (34) and evasion of mammalian cells (35), and some have a direct role in virulence as a part of transport systems (36). These proteins can be surface exposed and anchored by hydrophobic interactions, potentially to mycolic acids within the cell wall (37,52).…”

Section: Resultsmentioning

confidence: 99%

Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii

Tobias

Doig

Medema

et al. 2012

Journal of Bacteriology

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f In 2004, a previously undiscovered mycobacterium resembling Mycobacterium ulcerans (the agent of Buruli ulcer) was reported in an outbreak of a lethal mycobacteriosis in a laboratory colony of the African clawed frog Xenopus tropicalis. This mycobacterium makes mycolactone and is one of several strains of M. ulcerans-like mycolactone-producing mycobacteria recovered from ectotherms around the world. Here, we describe the complete 6,399,543-bp genome of this frog pathogen (previously unofficially named "Mycobacterium liflandii"), and we show that it has undergone an intermediate degree of reductive evolution between the M. ulcerans Agy99 strain and the fish pathogen Mycobacterium marinum M strain. Like M. ulcerans Agy99, it has the pMUM mycolactone plasmid, over 200 chromosomal copies of the insertion sequence IS2404, and a high proportion of pseudogenes. However, M. liflandii has a larger genome that is closer in length, sequence, and architecture to M. marinum M than to M. ulcerans Agy99, suggesting that the M. ulcerans Agy99 strain has undergone accelerated evolution. Scrutiny of the genes specifically lost suggests that M. liflandii is a tryptophan, tyrosine, and phenylalanine auxotroph. A once-extensive M. marinum-like secondary metabolome has also been diminished through reductive evolution. Our analysis shows that M. liflandii, like M. ulcerans Agy99, has the characteristics of a niche-adapted mycobacterium but also has several distinctive features in important metabolic pathways that suggest that it is responding to different environmental pressures, supporting earlier proposals that it could be considered an M. ulcerans ecotype, hence the name M. ulcerans ecovar Liflandii.A n interesting member of the Mycobacterium marinum and Mycobacterium ulcerans complex was discovered in the summer of 2001, when an outbreak of generalized cutaneous lesions developed in a colony of Xenopus tropicalis at the University of Berkeley in California (1). Infected frogs developed granulomatous skin lesions along with coelomic distention, generalized edema, and septicemia (1). Cytological examinations confirmed the presence of acid-fast bacilli in smears from the liver, spleen, kidney, and skin. Based on histopathology and some molecular testing, it was concluded that these frogs were suffering from a mycobacteriosis caused by a Mycobacterium ulcerans-like bacterium (1). There have been ongoing reports and high lethality of this disease in captive frogs across the United States and those imported from the United States to Europe (2-4), but this mycobacterium has not been reported to cause illness in humans. Further characterization of the frog pathogen revealed that it harbored the M. ulcerans pMUM megaplasmid and produced mycolactone E, a unique structural variant of the polyketide toxin that is key for pathogenesis in M. ulcerans (5, 6). Limited genotype analysis suggests that a single clone of this pathogen is circulating worldwide in institutions housing and breeding anurans. The species name "Mycobacterium liflandii" w...

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Section: Resultsmentioning

confidence: 99%

Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii

Tobias

Doig

Medema

et al. 2012

Journal of Bacteriology

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“…It was reported previously that the vacJ mutant is less able than wild-type S. flexneri to escape the double membrane formed when the bacterium moves from one cell to another; about 50% of cells of the intracellular vacJ mutant were unable to escape the double membrane (26). Since it has been suggested that vacJ and vpsC are linked functionally (27), it is possible that the defect in cell-to-cell spread of the vpsC mutant can also be attributed to an inability to escape the doublemembrane vacuole.…”

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

“…Suzuki et al (26) observed a similar phenotype for an S. flexneri vacJ mutant. While the S. flexneri vacJ gene is not part of the vps operon, it is predicted to be part of the Vps/VacJ ABC transporter system, since it is found in an operon with vps homologs in other bacteria (27).In addition to the defect in plaque formation, the S. flexneri vpsA and vpsC mutants were more sensitive to sodium dodecyl sulfate (SDS) than was wild-type S. flexneri, suggesting an increase in outer membrane permeability of the mutants (25). The greater sensitivity of the vpsC mutant to SDS did not appear to be due to changes in the lipopolysaccharide (LPS) structure, since the mutant had the same LPS distribution as wild-type bacteria (25).…”

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The Vps/VacJ ABC Transporter Is Required for Intercellular Spread of Shigella flexneri

et al. 2014

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The Vps/VacJ ABC transporter system is proposed to function in maintaining the lipid asymmetry of the outer membrane. Mutations in vps or vacJ in Shigella flexneri resulted in increased sensitivity to lysis by the detergent sodium dodecyl sulfate (SDS), and the vpsC mutant showed minor differences in its phospholipid profile compared to the wild type. vpsC mutants were unable to form plaques in cultured epithelial cells, but this was not due to a failure to invade, to replicate intracellularly, or to polymerize actin via IcsA for movement within epithelial cells. The addition of the outer membrane phospholipase gene pldA on a multicopy plasmid in a vpsC or vacJ mutant restored its resistance to SDS, suggesting a restoration of lipid asymmetry to the outer membrane. However, the pldA plasmid did not restore the mutant's ability to form plaques in tissue culture cells. Increased PldA levels also failed to restore the mutant's phospholipid profile to that of the wild type. We propose a dual function of the Vps/VacJ ABC transporter system in S. flexneri in both the maintenance of lipid asymmetry in the outer membrane and the intercellular spread of the bacteria between adjacent epithelial cells. Shigella flexneri is the causative agent of bacillary dysentery in humans. The bacteria invade the colonic epithelium, replicate intracellularly, and spread cell to cell, provoking the acute inflammatory response that is characteristic of the disease (1). While much is known about the initial invasion of epithelial cells by Shigella, less is understood about the requirements for intracellular replication and intercellular spread.Many of the genes required for pathogenesis of S. flexneri are carried on a large plasmid (2, 3). Plasmid-encoded virulence factors include the invasion plasmid antigen (Ipa) effector proteins required for S. flexneri to enter the host cell and escape from the vacuole (4-6). These effector proteins are secreted by a type III secretion system (TTSS) that is also encoded on the virulence plasmid. When the effectors contact epithelial cells, they induce cytoskeletal changes leading to internalization of the bacteria (7,8). Once engulfed by the epithelial cell, the bacteria lyse the vacuole and replicate inside the cytosol of the host cell (6).Within the host cell cytoplasm, S. flexneri uses another virulence plasmid-encoded protein, IcsA, to polymerize actin at one pole of the cell, resulting in the propulsion of the bacteria throughout the host cell (9, 10). This actin-based motility also promotes movement of the bacteria into adjacent epithelial cells. Intercellular movement results in S. flexneri cells being surrounded by a double membrane, one from the cell which the bacteria are exiting and another from the cell which they are entering (11). The secreted effector proteins are required for the bacteria to escape this double-membrane-bound vacuole, and once free in the cytoplasm, the bacteria repeat the cycle of replication and intercellular spread (12, 13).An understanding of the mechanisms of invas...

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“…Although mce clusters, which have identical structures consisting of two yrbE genes (yrbEA and yrbEB), encoding integral membrane proteins, followed by six mce genes (mceA to mceF), encoding exported or membrane-tethered proteins, were first identified due to their critical role in bacterial invasion and survival in mammalian cells (55), not all bacteria possessing mce clusters are found as pathogens (such as Mycobacterium smegmatis and Streptomyces coelicolor). This indicates that the products of mce clusters have physiological functions other than acting as virulence factors, e.g., acting as novel ABC uptake transporters (56). This speculation was soon proved by showing that the Mce4 system of Rhodococcus jostii RHA1 functions as a steroid uptake transporter (34).…”

Section: Resultsmentioning

confidence: 95%

Insights into the Microbial Degradation of Rubber and Gutta-Percha by Analysis of the Complete Genome of Nocardia nova SH22a

Luo

Hiessl

Poehlein

et al. 2014

Appl Environ Microbiol

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cThe complete genome sequence of Nocardia nova SH22a was determined in light of the remarkable ability of rubber and guttapercha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G؉C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide-and/or nonribosomal peptide-type secondary metabolites, were detected. Based on in silico analyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include, inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid-AMP ligase and arabinofuranosyltransferase), ␤-oxidation (␣-methylacyl-coenzyme A [␣-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genus Nocardia regarding metabolic diversity.

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A phylogenomic analysis of the Actinomycetales mce operons

Cited by 216 publications

References 95 publications

Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii

Complete Genome Sequence of the Frog Pathogen Mycobacterium ulcerans Ecovar Liflandii

The Vps/VacJ ABC Transporter Is Required for Intercellular Spread of Shigella flexneri

Insights into the Microbial Degradation of Rubber and Gutta-Percha by Analysis of the Complete Genome of Nocardia nova SH22a

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