Contribution of transcriptional regulation to natural variations in Arabidopsis

BACKGROUND: Genetic control of gene transcription is a key component in genome evolution. To understand the transcriptional basis of natural variation, we have studied genome-wide variations in transcription and characterized the genetic variations in regulatory elements among Arabidopsis accessions. RESULTS: Among five accessions (Col-0, C24, Ler, WS-2, and NO-0) 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis. Two-way ANOVA analysis has identified 60 genes whose mRNA levels differed in different accession backgrounds in an organ-dependent manner. Most of these genes were involved in stress responses and late stages of plant development, such as seed development. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession. CONCLUSION: Genes that show substantial genetic variation in mRNA level are those with functions in signal transduction, transcription and stress response, suggesting the existence of variations in the regulatory mechanisms for these genes among different accessions. This is in contrast to those genes with significant polymorphisms in the coding regions identified by genomic hybridization, which include genes encoding transposon-related proteins, kinases and disease-resistance proteins. While relatively fewer sequence variations were detected on average in the coding regions of these genes, a number of differences were identified from the upstream regions, several of which alter potential cis-regulatory elements. Our results suggest that nucleotide polymorphisms in regulatory elements of genes encoding controlling factors could be primary targets of natural selection and a driving force behind the evolution of Arabidopsis accessions

A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans

Sequencing of the complete genome of Ignicoccus hospitalis gives insight into its association with another species of Archaea, Nanoarchaeum equitans

Impact of elevated nitrate on sulfate-reducing bacteria: A comparative study of Desulfovibrio vulgaris

Sulfate-reducing bacteria have been extensively studied for their potential in heavy-metal bioremediation. However, the occurrence of elevated nitrate in contaminated environments has been shown to inhibit sulfate reduction activity. Although the inhibition has been suggested to result from the competition with nitrate-reducing bacteria, the possibility of direct inhibition of sulfate reducers by elevated nitrate needs to be explored. Using Desulfovibrio vulgaris as a model sulfate-reducing bacterium, functional genomics analysis reveals that osmotic stress contributed to growth inhibition by nitrate as shown by the upregulation of the glycine/betaine transporter genes and the relief of nitrate inhibition by osmoprotectants. The observation that significant growth inhibition was effected by 70 mM NaNO{sub 3} but not by 70 mM NaCl suggests the presence of inhibitory mechanisms in addition to osmotic stress. The differential expression of genes characteristic of nitrite stress responses, such as the hybrid cluster protein gene, under nitrate stress condition further indicates that nitrate stress response by D. vulgaris was linked to components of both osmotic and nitrite stress responses. The involvement of the oxidative stress response pathway, however, might be the result of a more general stress response. Given the low similarities between the response profiles to nitrate and other stresses, less-defined stress response pathways could also be important in nitrate stress, which might involve the shift in energy metabolism. The involvement of nitrite stress response upon exposure to nitrate may provide detoxification mechanisms for nitrite, which is inhibitory to sulfate-reducing bacteria, produced by microbial nitrate reduction as a metabolic intermediate and may enhance the survival of sulfate-reducing bacteria in environments with elevated nitrate level

Regulation of microRNA expression in the heart by the ATF6 branch of the ER stress response

A nodal regulator of endoplasmic reticulum stress is the transcription factor, ATF6, which is activated by ischemia and protects the heart from ischemic damage, in vivo. To explore mechanisms of ATF6-mediated protection in the heart, a whole-genome microRNA (miRNA) array analysis of RNA from the hearts of ATF6 transgenic (TG) mice was performed. The array identified 13 ATF6-regulated miRNAs, eight of which were downregulated, suggesting that they could contribute to increasing levels of their mRNAs. The downregulated miRNAs, including miR-455, were predicted to target 45 mRNAs that we had previously shown by microarray analysis to be up-regulated by ATF6 in the heart. One of the miR-455 targets was calreticulin (Calr), which is up-regulated in the pathologic heart, where it modulates hypertrophic growth, potentially reducing the impact of the pathology. To validate the effects of miR-455, we showed that Calr protein was increased by ATF6 in mouse hearts, in vivo. In cultured cardiac myocytes, treatment with the ER stressor, tunicamycin, or with adenovirus encoding activated ATF6 decreased miR-455 and increased Calr levels, consistent with the effects of ATF6 on miR-455 and Calr, in vivo. Moreover, transfection of cultured cardiac myocytes with a synthetic precursor, premiR-455, decreased Calr levels, while transfection with an antisense, antimiR-455, increased Calr levels. The results of this study suggest that ER stress can regulate gene expression via ATF6-mediated changes in micro-RNA levels. Moreover, these findings support the hypothesis that ATF6-mediated down-regulation of miR-455 augments Calr expression, which may contribute to the protective effects of ATF6 in the heart

Gene Expression Phenotypes of Arabidopsis Associated with Sensitivity to Low Temperatures

Chilling is a common abiotic stress that leads to economic losses in agriculture. By comparing the transcriptome of Arabidopsis under normal (22°C) and chilling (13°C) conditions, we have surveyed the molecular responses of a chilling-resistant plant to acclimate to a moderate reduction in temperature. The mRNA accumulation of approximately 20% of the approximately 8,000 genes analyzed was affected by chilling. In particular, a highly significant number of genes involved in protein biosynthesis displayed an increase in transcript abundance. We have analyzed the molecular phenotypes of 12 chilling-sensitive mutants exposed to 13°C before any visible phenotype could be detected. The number and pattern of expression of chilling-responsive genes in the mutants were consistent with their final degree of chilling injury. The mRNA accumulation profiles for the chilling-lethal mutants chs1, chs2, and chs3 were highly similar and included extensive chilling-induced and mutant-specific alterations in gene expression. The expression pattern of the mutants upon chilling suggests that the normal function of the mutated loci prevents a damaging widespread effect of chilling on transcriptional regulation. In addition, we have identified 634 chilling-responsive genes with aberrant expression in all of the chilling-lethal mutants. This reference gene list, including genes related to lipid metabolism, chloroplast function, carbohydrate metabolism and free radical detoxification, represents a potential source for genes with a critical role in plant acclimation to suboptimal temperatures. The comparison of transcriptome profiles after transfer of Arabidopsis plants from 22°C to 13°C versus transfer to 4°C suggests that quantitative and temporal differences exist between these molecular responses

Nitrate stress response in Desulfovibrio vulgaris Hildenborough: Whole-Genome Transcriptomics and proteomics analyses

Sulfate reducing bacteria (SRB) are of interest for bioremediation with their ability to reduce and immobilize heavy metals. Nitrate, a common co-contaminant in DOE sites, is suggested to inhibit SRB via nitrite. Previous results indicate that nittite is indeed inhibitory to the growth of Desulfovibrio vulgaris. However, growth inhibition by nitrate alone was also observed. In this study, growth and expression responses to various concentrations of nitrate were investigated using the Omnilog phenotype arrays and whole-genome DNA microarrays. Changes in the proteome were examined with 3D-LC followed by MS-MS analysis.Microarray analysis found 5, 50, 115, and 149 genes significantly up-regulated and 36, 113, 205, and 149 down-regulated at 30, 60, 120, and 240 min, respectively. Both transcriptomic and proteomic profiles shared little similarities with those of salt stress, indicating a specific inhibitory mechanism beyond osmotic stress. Many of the genes (-50% at certain time points) with altered expression level were of unknown functions; however, the increasing number of ribosomal protein genes down-regulated with tinle could provide a direct explanation to the growth inhibition effect of nitrate. Further, several lines of evidence suggested that the downregulationof genes coding the ribosomal proteins could be the result of the changes in the energy flow upon nitrate exposure: 1) The down-regulation of genes for the ATPase subunits indicated reduced level of energy generation; 2) the up-regulation of phage shock protein genes (pspA and pspC) might indicate a reduced proton motive force; although damages to the cell envelope could also contribute to this outcome; 3) the gene for the hybrid cluster protein, a redox protein with roles in nitrogen metabolism, was highly up-regulated 120 and 240 min following nitrate stress at both transcriptomic and proteomic level, suggesting that nitrate was being actively reduced, shifting reducing equivalents away from normal energy production; 4) genes in the methionine biosynthesis pathway were among the most highly up-regulated genes throughout the experiment, potentially providing a convenient rnechanism for the simultaneous disposal of excess sulfur (from sulfate reduction) and nitrogen (from nitrate reduction); 5) One gene cluster consistently among the most up-regulated genes consisted of genes encoding two TRAP dicarboxylate family transpollers, a folmate acetyltransferase, and a pyruvate formate-lyase activating enzyme, which might be regulated to provide an increased carbon flow to keep pace with demand from amino acids biosynthesis. These observations indicated that the growth inhibition effect of nitrate might be due to energy limitation. Similar to the observations made during salt stress, the glycine/betaine transporter gene was among genes highly up-regulated, suggesting that NaN03 also constituted osmotic stress which was relieved by the mechanism of osmoprotectant accumulation. Osmoprotectant accumulation as the major resistance mechanism was further validated by the partial relief of growth inhibition by glycine betaine. It is also noted that, similar to nitrite stress, the ferric iron transporter genes were up-regulated during nitrate stress, suggesting an increased demand for iron. Unlike nitrite stress, however, no other genes in the Fur regulon were co-regulated during nitrate stress, pointing to a yet-to-known regulatory signal.In conclusion, excess NaN03 resulted in both osmotic stress and nitrate stress. D. vulgaris shifted nitrogen metabolism and energy production in response to nitrate stress. Resistance to osmotic stress was achieved primarily by the transport of osmoprotectant