Comparative genomic analysis of two-component regulatory proteins in Pseudomonas syringae

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas syringae </it>is a widespread bacterial plant pathogen, and strains of <it>P. syringae </it>may be assigned to different pathovars based on host specificity among different plant species. The genomes of <it>P. syringae </it>pv. <it>syringae </it>(<it>Psy</it>) B728a, pv. <it>tomato </it>(<it>Pto</it>) DC3000 and pv. <it>phaseolicola </it>(<it>Pph</it>) 1448A have been recently sequenced providing a major resource for comparative genomic analysis. A mechanism commonly found in bacteria for signal transduction is the two-component system (TCS), which typically consists of a sensor histidine kinase (HK) and a response regulator (RR). <it>P. syringae </it>requires a complex array of TCS proteins to cope with diverse plant hosts, host responses, and environmental conditions.</p> <p>Results</p> <p>Based on the genomic data, pattern searches with Hidden Markov Model (HMM) profiles have been used to identify putative HKs and RRs. The genomes of <it>Psy </it>B728a, <it>Pto </it>DC3000 and <it>Pph </it>1448A were found to contain a large number of genes encoding TCS proteins, and a core of complete TCS proteins were shared between these genomes: 30 putative TCS clusters, 11 orphan HKs, 33 orphan RRs, and 16 hybrid HKs. A close analysis of the distribution of genes encoding TCS proteins revealed important differences in TCS proteins among the three <it>P. syringae </it>pathovars.</p> <p>Conclusion</p> <p>In this article we present a thorough analysis of the identification and distribution of TCS proteins among the sequenced genomes of <it>P. syringae</it>. We have identified differences in TCS proteins among the three <it>P. syringae </it>pathovars that may contribute to their diverse host ranges and association with plant hosts. The identification and analysis of the repertoire of TCS proteins in the genomes of <it>P. syringae </it>pathovars constitute a basis for future functional genomic studies of the signal transduction pathways in this important bacterial phytopathogen.</p

A Gene Encoding Arginyl-tRNA Synthetase Is Located in the Upstream Region of the lysA Gene in Brevibacterium lactofermentum: Regulation of argS-lysA Cluster Expression by Arginine

International audienceThe Brevibacterium lactofermentum argS gene, which encodes an arginyl-tRNA synthetase, was identified in the upstream region of the lysA gene. The cloned gene was sequenced; it encodes a 550-amino-acid protein with an Mr of 59,797. The deduced amino acid sequence showed 28% identical and 49% similar residues when compared with the sequence of the Escherichia coli arginyl-tRNA synthetase. The B. lactofermentum enzyme showed the highly conserved motifs of class I aminoacyl-tRNA synthetases. Expression of the argS gene in B. lactofermentum and E. coli resulted in an increase in aminoacyl-tRNA synthetase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamide gels of a clear protein band that corresponds to this enzyme. One single transcript of about 3,000 nucleotides and corresponding to the B. lactofermentum argS-lysA operon was identified. The transcription of these genes is repressed by lysine and induced by arginine, showing an interesting pattern of biosynthetic interlock between the pathways of both amino acids in corynebacteria

Genomics and transcriptomics characterization of genes expressed during postharvest at 4°C by the edible basidiomycete Pleurotus ostreatus

Pleurotus ostreatus is an industrially cultivated basidiomycete with nutritional and environmental applications.&nbsp;Its genome, which was sequenced by the Joint Genome Institute, has become a model for lignin degradation and for fungal&nbsp;genomics and transcriptomics studies. The complete P. ostreatus genome contains 35 Mbp organized in 11 chromosomes, and&nbsp;two different haploid genomes have been individually sequenced. In this work, genomics and transcriptomics approaches&nbsp;were employed in the study of P. ostreatus under different physiological conditions. Specifically, we analyzed a collection ofexpressed sequence tags (EST) obtained from cut fruit bodies that had been stored at 4&deg;C for 7 days (postharvest conditions).&nbsp;Studies of the 253 expressed clones that had been automatically and manually annotated provided a detailed picture of the life&nbsp;characteristics of the self-sustained fruit bodies. The results suggested a complex metabolism in which autophagy, RNA&nbsp;metabolism, and protein and carbohydrate turnover are increased. Genes involved in environment sensing and morphogenesis were expressed under these conditions. The data improve our understanding of the decay process in postharvest mushrooms and highlight the use of high-throughput techniques to construct models of living organisms subjected to different environmental conditions

Mecanismos moleculares de control transcripcional en "Brevibacterium lactofermentum"

[ES] El género Corynebacterium fue creado por Lehmann y Neumann en 1896, para clasificar taxonómicamente a los bacilos de la difteria, incluyendo posteriormente unas pocas especies similares parásitas de animales. El género fue definido en base a características morfológicas, corynebacteria proviene del griego korunh (corunë): bastón nudoso y, bakterion (bacterion): bastoncillo. En general, las corinebacterias son bacilos Gram-positivos, pleomorfos, no ramificados, no esporulantes y anaerobios obligados o facultativos. El pleomorfismo en su ciclo de vida se observa en formas bacilares de longitud diversa y frecuentes engrosamientos en los extremos (Figura 1.1), estando marcadamente influido por las condiciones de cultivo (Cure y Keddie, 1973)