Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

<p>Abstract</p> <p>Background</p> <p><it>Candida </it>species are the most common cause of opportunistic fungal infection worldwide. Recent sequencing efforts have provided a wealth of <it>Candida </it>genomic data. We have developed the <it>Candida </it>Gene Order Browser (CGOB), an online tool that aids comparative syntenic analyses of <it>Candida </it>species. CGOB incorporates all available <it>Candida </it>clade genome sequences including two <it>Candida albicans </it>isolates (SC5314 and WO-1) and 8 closely related species (<it>Candida dubliniensis</it>, <it>Candida tropicalis</it>, <it>Candida parapsilosis</it>, <it>Lodderomyces elongisporus</it>, <it>Debaryomyces hansenii</it>, <it>Pichia stipitis</it>, <it>Candida guilliermondii </it>and <it>Candida lusitaniae</it>). <it>Saccharomyces cerevisiae </it>is also included as a reference genome.</p> <p>Results</p> <p>CGOB assignments of homology were manually curated based on sequence similarity and synteny. In total CGOB includes 65617 genes arranged into 13625 homology columns. We have also generated improved <it>Candida </it>gene sets by merging/removing partial genes in each genome. Interrogation of CGOB revealed that the majority of tandemly duplicated genes are under strong purifying selection in all <it>Candida </it>species. We identified clusters of adjacent genes involved in the same metabolic pathways (such as catabolism of biotin, galactose and N-acetyl glucosamine) and we showed that some clusters are species or lineage-specific. We also identified one example of intron gain in <it>C. albicans</it>.</p> <p>Conclusions</p> <p>Our analysis provides an important resource that is now available for the <it>Candida </it>community. CGOB is available at <url>http://cgob.ucd.ie</url>.</p

Comparative genome analysis and gene finding in Candida species using CGOB.

The Candida Gene Order Browser (CGOB) was developed as a tool to visualize and analyze synteny relationships in multiple Candida species, and to provide an accurate, manually curated set of orthologous Candida genes for evolutionary analyses. Here, we describe major improvements to CGOB. The underlying structure of the database has been changed significantly. Genomic features are now based directly on genome annotations rather than on protein sequences, which allows non-protein features such as centromere locations in Candida albicans and tRNA genes in all species to be included. The data set has been expanded to 13 species, including genomes of pathogens (C. albicans, C. parapsilosis, C. tropicalis, and C. orthopsilosis), and those of xylose-degrading species with important biotechnological applications (C. tenuis, Scheffersomyces stipitis, and Spathaspora passalidarum). Updated annotations of C. parapsilosis, C. dubliniensis, and Debaryomyces hansenii have been incorporated. We discovered more than 1,500 previously unannotated genes among the 13 genomes, ranging in size from 29 to 3,850 amino acids. Poorly conserved and rapidly evolving genes were also identified. Re-analysis of the mating type loci of the xylose degraders suggests that C. tenuis is heterothallic, whereas both Spa. passalidarum and S. stipitis are homothallic. As well as hosting the browser, the CGOB website (http://cgob.ucd.ie) gives direct access to all the underlying genome annotations, sequences, and curated orthology data

Sexually dimorphic gene expression in bovine conceptuses at the initiation of implantation

In cattle, maternal recognition of pregnancy occurs on Day 16 via secretion of interferon tau (IFNT) by the conceptus. The endometrium can distinguish between embryos with different developmental competencies. In eutherian mammals, X-chromosome inactivation (XCI) is required to ensure an equal transcriptional level of most X-linked genes for both male and female embryos in adult tissues, but this process is markedly different in cattle than mice. We examined how sexual dimorphism affected conceptus transcript abundance and amino acid composition as well as the endometrial transcriptome during the peri-implantation period of pregnancy. Of the 5132 genes that were differentially expressed on Day 19 in male compared to female conceptuses, 2.7% were located on the X-chromosome. Concentrations of specific amino acids were higher in the uterine luminal fluid of male compared to female conceptuses, while female conceptuses had higher transcript abundance of specific amino acid transporters (SLC6A19 and SLC1A35). Of note, the endometrial transcriptome was not different in cattle gestating a male or a female conceptus. These data support the hypothesis that, far from being a blastocyst specific phenomenon, XCI is incomplete before and during implantation in cattle. Despite differences in transcript abundance and amino acid utilization in male versus female conceptuses, the sex of the conceptus itself does not elicit a different transcriptomic response in the endometrium

An Oligopeptide Transporter of Mycobacterium tuberculosis Regulates Cytokine Release and Apoptosis of Infected Macrophages

Background: The Mycobacterium tuberculosis genome encodes two peptide transporters encoded by Rv3665c-Rv3662c and Rv1280c-Rv1283c. Both belong to the family of ABC transporters containing two nucleotide-binding subunits, two integral membrane proteins and one substrate-binding polypeptide. However, little is known about their functions in M. tuberculosis. Here we report functional characterization of the Rv1280c-Rv1283c-encoded transporter and its substrate-binding polypeptide OppA(MTB). Methodology/Principal Findings: OppA(MTB) was capable of binding the tripeptide glutathione and the nonapeptide bradykinin, indicative of a somewhat broad substrate specificity. Amino acid residues G109, N110, N230, D494 and F496, situated at the interface between domains I and III of OppA, were required for optimal peptide binding. Complementaton of an oppA knockout mutant of M. smegmatis with OppA(MTB) confirmed the role of this transporter in importing glutathione and the importance of the aforesaid amino acid residues in peptide transport. Interestingly, this transporter regulated the ability of M. tuberculosis to lower glutathione levels in infected compared to uninfected macrophages. This ability was partly offset by inactivation of oppD. Concomitantly, inactivation of oppD was associated with lowered levels of methyl glyoxal in infected macrophages and reduced apoptosis-inducing ability of the mutant. The ability to induce the production of the cytokines IL-1 beta, IL-6 and TNF-alpha was also compromised after inactivation of oppD. Conclusions: Taken together, these studies uncover the novel observations that this peptide transporter modulates the innate immune response of macrophages infected with M. tuberculosis

Molecular Analysis of the Enterobacter sakazakii O-Antigen Gene Locus▿

Nucleotide polymorphism associated with the O-antigen-encoding locus, rfb, in Enterobacter sakazakii was determined by PCR-restriction fragment length polymorphism analysis. Based on the analysis of these DNA profiles, 12 unique banding patterns were detected among a collection of 62 strains from diverse origins. Two common profiles were identified and were designated serotypes O:1 and O:2. DNA sequencing of the 12,500-bp region flanked by galF and gnd identified 11 open reading frames, all with the same transcriptional direction. Analysis of the proximal region of both sequences demonstrated remarkable heterogeneity. A PCR assay targeting genes specific for the two prominent serotypes was developed and applied for the identification of these strains recovered from food, environmental, and clinical samples