Lipoproteins of Mycobacterium tuberculosis : an abundant and functionally diverse class of cell envelope components

Mycobacterium tuberculosis remains the predominant bacterial scourge of mankind. Understanding of its biology and pathogenicity has been greatly advanced by the determination of whole genome sequences for this organism. Bacterial lipoproteins are a functionally diverse class of membrane-anchored proteins. The signal peptides of these proteins direct their export and post-translational lipid modification. These signal peptides are amenable to bioinformatic analysis, allowing the lipoproteins encoded in whole genomes to be catalogued. This review applies bioinformatic methods to the identification and functional characterisation of the lipoproteins encoded in the M. tuberculosis genomes. Ninety nine putative lipoproteins were identified and so this family of proteins represents ca. 2.5% of the M. tuberculosis predicted proteome. Thus, lipoproteins represent an important class of cell envelope proteins that may contribute to the virulence of this major pathogen

Prescottia equi gen. nov., comb. nov.: a new home for an old pathogen

The taxonomic status of Rhodococcus equi, originally isolated from foal specimens, has been the subject of discussion for a number of years. The chequered history of the taxon has prompted this polyphasic analysis of R. equi strains, close members of the genus Rhodococcus and representatives of other genera classified in the order Corynebacteriales, to establish the taxonomic position of this taxon. Thirty one R. equi strains, including the type strain, were examined for genotypic and numerical taxonomic properties. The resultant data are consistent with their classification in the order Corynebacteriales but the R. equi strains formed a distinct phyletic clade away from representatives of other members of the genus Rhodococcus in the 16S rRNA gene tree. Representatives of this clade shared their highest pairwise 16S rRNA gene sequence similarities with the type strain of Rhodococcus kunmingensis (95.2–98.1 %). However, the R. equi taxon was readily distinguished from R. kunmingensis and from the other members of the order Corynebacteriales using a combination of genotypic, chemotypic and phenotypic properties. On the basis of these data the R. equi strains are considered to represent a new genus. The name proposed for this taxon is Prescottia gen. nov., with Prescottia equi comb. nov. as the type species containing the type strain, C 7T (= ATCC 25729T = ATCC 6939T = CCUG 892T = CIP 54.72T = DSM 20307T = HAMBI 2061T = NBRC 14956T = JCM 1311T = JCM 3209T = LMG 18452T = NBRC 101255T = NCTC 1621T = NRRL B-16538T = VKM Ac-953T)

Reflections on the introduction of the Digital Protologue Database – a partial success? [Editorial]

Modern science revolves around databases, be they the massive (e.g. NCBI) or the bespoke (e.g. EzBioCloud). There are enormous databases covering the sequence world and the protein world but what of the organisms from which they are derived? With this is mind, we have argued (Sutcliffe et al. 2012; Rosselló-Móra 2012; Rosselló-Móra and Amann 2015; Sutcliffe 2015; Rossello-Mora and Whitman 2019) that microbial systematics needs to become a database driven science. After all, if it has taken more than a century to characterise  10 m prokaryotic species (< 0.2%), then a flexible repository will be needed if we are to complete a timely systematic census of the microbial world. An ideal database would integrate information on the characteristics of a taxon with nomenclatural information and links out to other databases, particularly for sequence data, and back to the original data source (primary publication). Entries would range from the minimal information needed to delineate a novel taxon through to maximal descriptions of well characterised taxa

Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii)

Rhodococcus defluvii strain Ca11T was isolated from a bioreactor involved in extensive phosphorus removal. We have sequenced the whole genome of this strain and our comparative genomic and phylogenetic analyses confirm its close relatedness with Rhodococcus equi (Rhodococcus hoagii) strains, which share >80% of the gene content. The R. equi virulence plasmid is absent though most of the chromosomal R. equi virulence-associated genes are present in R. defluvii Ca11T. These data suggest that although R. defluvii is an environmental organism, it has the potential to colonise animal hosts

Out with the old and in with the new: time to rethink twentieth century chemotaxonomic practices in bacterial taxonomy

Chemotaxonomic methods played an important role in the development of the polyphasic approach to classification of Archaea and Bacteria. However, we here argue that routine application of these methods is unnecessary in an era when genomic data are available and sufficient for species delineation. Thus, authors who choose not to utilize such methods should not be forced to do so during the peer review and editorial handling of manuscripts describing novel species. Instead, we argue that chemotaxonomy will thrive if improved analytical methods are introduced and deployed, primarily by specialist laboratories, in studies at taxonomic levels above the characterisation of novel species

Proteomic investigation of the group B streptococcus

The Group B Streptococcus (GBS) is a Gram-positive opportunistic pathogen which is a leading cause of neonatal disease globally. In 2000-2001, the general incidence of neonatal GBS infection was 0.72 per 1000 live births in U.K. and the mortality rate is about 10%, because of which neonatal GBS disease is a significant burden on society. GBS is part of the commensal flora, colonising the vagina and gastrointestinal tract of women. Vertical transmission is the main cause of early onset GBS disease. During the process of GBS neonatal disease, GBS must be able to survive in several very different host environments, including the vagina, amniotic fluid, the neonate's lung and blood. The vagina is normally acidic, low oxygen and with limited nutrients while the neonate's lung and blood are neutral, high oxygen and with abundant nutrient. Proteomic investigations of GBS protein expression under conditions representing those associated with benign maternal colonisation and foetal exposure may help us understand the molecular basis of GBS virulence. GBS growth characteristics, long term survival, acid adaptation, viable but non-culturable state and biofilm formation were investigated to help us understand how GBS survives in different environments and also help us to develop an in vitro model to reflect in vivo conditions during GBS disease development. An in vitro model of GBS growth under conditions reflecting maternal vaginal carriage (low pH, low oxygen, nutrient stress) and exposure to body fluids during invasive disease (neutral pH, aeration, nutrient sufficient) was established. Proteins expressed under each growth conditions were separated by two dimensional electrophoresis. Individual proteins were subjected to in-gel trypsin digestion and identified using liquid chromatography-mass spectrometry with peptide mass fingerprinting followed with bioinformatic research. A total of 76 proteins were identified and 16 of these were expressed differentially. The putative virulence factor C protein β antigen and proteins involved in responses to oxidative stress were up-regulated under the conditions reflecting neonatal exposure. Another in vitro model of GBS growth on Todd Hewitt agar in the presence or absence of 10% human serum was established and followed by proteomic investigation of proteins differentially expressed under these two conditions, as this model reflects GBS neonatal septicaemia (exposure to serum). A total of 84 proteins were identified and 11 of which were expressed differentially. The putative virulence factor C protein β antigen, arginine deiminase, an ABC transporter substrate-binding protein and glyceraldehyde-3-phosphate dehydrogenase were up-regulated in the presence of human serum.EThOS - Electronic Theses Online ServiceGreat Britain-China Educational Trust : Henry Lester Trust LimitedGBUnited Kingdo