Novel member of Ras family proteins from Disk Abalone (Haliotis discus discus): Structural profiling and its transcriptional modulation under host pathologic conditions

Among small GTPases, the Ras family proteins capture a remarkable place in dictating cellular proliferation, differentiation and survival in development of an organism. Major members of the Ras family include Ras (H-Ras, K-Ras, N-Ras), Rap1, and Rap2, all of which can act as oncogenes upon mutation. In the present study, a novel Ras family protein (AbRFP) was characterized from Disk Abalone (Haliotis discus discus), an economically important, edible marine gastropod; further analyzing its transcriptional profile in healthy and immune-challenged animals. The full-length cDNA of AbRFP is 2704 bp and it consists of an open reading frame of 552 bp, encoding a 184 amino acid peptide with a calculated molecular mass of ~21 kDa and isoelectric point of 8.63. The amino acid sequence resembles the characteristic features of typical Ras family proteins, including GTP/Mg2+ binding sites and guanine nucleotide exchange factor (GEF) interaction sites, as predicted by the NCBI-conserved domain database server. Phylogenetic study of AbRFP showed the generally accepted relationships, with AbRFP exhibiting highest proximity to a Ras protein from Portuguese oyster. Quantitative real-time PCR detected ubiquitous AbRFP mRNA expression, with strongest levels in muscle along with mantle and the lowest level in hepatopancreas. The AbRFP transcriptional profile in gills of Abalone challenged with Vibrio parahaemolyticus or viral hemorrhagic septicemia virus (VHSV) demonstrated significant up-regulations (p < 0.05) at 12 h and 24 h post-injection (p.i.), respectively. Moreover, significant elevation (p < 0.05) of mRNA expression was detected in hemocytes at 72 h p.i. with V. parahaemolyticus. These findings suggest that AbRFP may play a role under pathological conditions in Disk Abalon

Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium

<p>Abstract</p> <p>Background</p> <p>Cyanobacteria are the only known prokaryotes capable of oxygenic photosynthesis. They play significant roles in global biogeochemical cycles and carbon sequestration, and have recently been recognized as potential vehicles for production of renewable biofuels. <it>Synechocystis </it>sp. PCC 6803 has been extensively used as a model organism for cyanobacterial studies. DNA microarray studies in <it>Synechocystis </it>have shown varying degrees of transcriptome reprogramming under altered environmental conditions. However, it is not clear from published work how transcriptome reprogramming affects pre-existing networks of fine-tuned cellular processes.</p> <p>Results</p> <p>We have integrated 163 transcriptome data sets generated in response to numerous environmental and genetic perturbations in <it>Synechocystis</it>. Our analyses show that a large number of genes, defined as the core transcriptional response (CTR), are commonly regulated under most perturbations. The CTR contains nearly 12% of <it>Synechocystis </it>genes found on its chromosome. The majority of genes in the CTR are involved in photosynthesis, translation, energy metabolism and stress protection. Our results indicate that a large number of differentially regulated genes identified in most reported studies in <it>Synechocystis </it>under different perturbations are associated with the general stress response. We also find that a majority of genes in the CTR are coregulated with 25 regulatory genes. Some of these regulatory genes have been implicated in cellular responses to oxidative stress, suggesting that reactive oxygen species are involved in the regulation of the CTR. A Bayesian network, based on the regulation of various KEGG pathways determined from the expression patterns of their associated genes, has revealed new insights into the coordination between different cellular processes.</p> <p>Conclusion</p> <p>We provide here the first integrative analysis of transcriptome data sets generated in a cyanobacterium. This compilation of data sets is a valuable resource to researchers for all cyanobacterial gene expression related queries. Importantly, our analysis provides a global description of transcriptional reprogramming under different perturbations and a basic framework to understand the strategies of cellular adaptations in <it>Synechocystis</it>.</p

The genome of Cyanothece 51142, a unicellular diazotrophic cyanobacterium important in the marine nitrogen cycle

Unicellular cyanobacteria have recently been recognized for their contributions to nitrogen fixation in marine environments, a function previously thought to be filled mainly by filamentous cyanobacteria such as Trichodesmium. To begin a systems level analysis of the physiology of the unicellular N2-fixing microbes, we have sequenced to completion the genome of Cyanothece sp. ATCC 51142, the first such organism. Cyanothece 51142 performs oxygenic photosynthesis and nitrogen fixation, separating these two incompatible processes temporally within the same cell, while concomitantly accumulating metabolic products in inclusion bodies that are later mobilized as part of a robust diurnal cycle. The 5,460,377-bp Cyanothece 51142 genome has a unique arrangement of one large circular chromosome, four small plasmids, and one linear chromosome, the first report of a linear element in the genome of a photosynthetic bacterium. On the 429,701-bp linear chromosome is a cluster of genes for enzymes involved in pyruvate metabolism, suggesting an important role for the linear chromosome in fermentative processes. The annotation of the genome was significantly aided by simultaneous global proteomic studies of this organism. Compared with other nitrogen-fixing cyanobacteria, Cyanothece 51142 contains the largest intact contiguous cluster of nitrogen fixation-related genes. We discuss the implications of such an organization on the regulation of nitrogen fixation. The genome sequence provides important information regarding the ability of Cyanothece 51142 to accomplish metabolic compartmentalization and energy storage, as well as how a unicellular bacterium balances multiple, often incompatible, processes in a single cell