Biomedical subjects

Sam Cartinhour

Publications and source records attributed to Sam Cartinhour.

3 recordsLinked to original sources

PubMed2005

Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition.

Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.

Bacterial Proteins↗

PubMed2005

Identification of a twin-arginine translocation system in Pseudomonas syringae pv. tomato DC3000 and its contribution to pathogenicity and fitness.

The bacterial plant pathogen Pseudomonas syringae pv. tomato DC3000 (DC3000) causes disease in Arabidopsis thaliana and tomato plants, and it elicits the hypersensitive response in nonhost plants such as Nicotiana tabacum and Nicotiana benthamiana. While these events chiefly depend upon the type III protein secretion system and the effector proteins that this system translocates into plant cells, additional factors have been shown to contribute to DC3000 virulence and still many others are likely to exist. Therefore, we explored the contribution of the twin-arginine translocation (Tat) system to the physiology of DC3000. We found that a tatC mutant strain of DC3000 displayed a number of phenotypes, including loss of motility on soft agar plates, deficiency in siderophore synthesis and iron acquisition, sensitivity to copper, loss of extracellular phospholipase activity, and attenuated virulence in host plant leaves. In the latter case, we provide evidence that decreased virulence of tatC mutants likely arises from a synergistic combination of (i) compromised fitness of bacteria in planta; (ii) decreased efficiency of type III translocation; and (iii) cytoplasmically retained virulence factors. Finally, we demonstrate a novel broad-host-range genetic reporter based on the green fluorescent protein for the identification of Tat-targeted secreted virulence factors that should be generally applicable to any gram-negative bacterium. Collectively, our evidence supports the notion that virulence of DC3000 is a multifactorial process and that the Tat system is an important virulence determinant of this phytopathogenic bacterium.

Anti-Bacterial Agents↗

PubMed2002

Gramene, a tool for grass genomics.

Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice (Oryza sativa). It combines a semi-automatically generated database of cereal genomic and expressed sequence tag sequences, genetic maps, map relations, and publications, with a curated database of rice mutants (genes and alleles), molecular markers, and proteins. Gramene curators read and extract detailed information from published sources, summarize that information in a structured format, and establish links to related objects both inside and outside the database, providing seamless connections between independent sources of information. Genetic, physical, and sequence-based maps of rice serve as the fundamental organizing units and provide a common denominator for moving across species and genera within the grass family. Comparative maps of rice, maize (Zea mays), sorghum (Sorghum bicolor), barley (Hordeum vulgare), wheat (Triticum aestivum), and oat (Avena sativa) are anchored by a set of curated correspondences. In addition to sequence-based mappings found in comparative maps and rice genome displays, Gramene makes extensive use of controlled vocabularies to describe specific biological attributes in ways that permit users to query those domains and make comparisons across taxonomic groups. Proteins are annotated for functional significance using gene ontology terms that have been adopted by numerous model species databases. Genetic variants including phenotypes are annotated using plant ontology terms common to all plants and trait ontology terms that are specific to rice. In this paper, we present a brief overview of the search tools available to the plant research community in Gramene.

Avena↗