Molecular characterization, expression pattern and function analysis of the <i>OsHSP90</i> family in rice

<p>The HSP90 is an abundant chaperone protein that is conserved in all eukaryotes. The main function of HSP90 is to assist other proteins to fold properly. In this study, we uncovered and analysed nine OsHSP90 (OsHSP90-1--OsHSP90-9) family members in rice <i>Nipponbare</i>, in which three distinct motifs were identified. All the HSP90 proteins were classified into three major groups (I, II, III) by phylogenetic analysis. The expression of <i>OsHSP90</i> family in 10 tissues was examined by real-time polymerase chain reaction (PCR). <i>OsHSP90-4</i>, <i>OsHSP90-6</i> and <i>OsHSP90-7</i> had high expression, while <i>OsHSP90-5</i> and <i>OsHSP90-8</i> had very low expression across almost all 10 samples. The gene that encodes <i>OsHSP90-1</i> was preferentially expressed in embryo at 14 days after flowering. It has been reported that some heat shock proteins were up-regulated in response to heat or other stresses. However, in our study the expression pattern of <i>OsHSP90</i> genes is heterogeneous under a range of stress conditions. The expression of <i>OsHSP90-2</i> and <i>OsHSP90-4</i> was up-regulated under drought, salt, cold and heat conditions, while the expression of <i>OsHSP90-3</i> and <i>OsHSP90-5</i> was down-regulated under salt and drought conditions. <i>OsHSP90-7</i> and <i>OsHSP90-9</i> were down-regulated only under drought conditions. <i>OsHSP90-6</i> did not change its expression across all conditions compared to control. Overexpression of <i>OsHSP90-2</i> in <i>E. coli</i> could enhance cell viability and significantly improved resistance to heat, high salinity and drought stress conditions. The results presented here may provide new insights into the function of <i>OsHSP90</i> family in rice.</p

Molecular characterization and function analysis of the rice <i>OsDUF946</i> family

<p>The domain of unknown function DUF946 family consists of plant proteins with an average length of around 239 residues that have no characterized function. The gene family needs deeper characterization and functional analysis of its members. In this study, we report five <i>OsDUF</i><i>946</i> (<i>OsDUF946.1</i>–<i>OsDUF946.5</i>) family members in rice <i>Nipponbare</i> with three distinct motifs. All the OsDUF946 proteins were classified into three major groups (I, II, III) by phylogenetic analysis. Real-time polymerase chain reaction showed that the expression patterns of the five <i>OsDUF946</i> family members were different in 15 different rice tissues as well as under various stress conditions and abscisic acid treatment. The expression of <i>OsDUF946.1</i> was significantly downregulated under salt, cold and heat stress, while the expression of <i>OsDUF946.4</i> and <i>OsDUF946.5</i> was significantly upregulated under drought and salt conditions. Overexpression of <i>OsDUF946.4</i> in <i>E</i><i>scherichia</i> <i>coli</i> significantly improved the resistance to salt and drought, while overexpression of <i>OsDUF946.5</i> in <i>E. coli</i> did not have such an effect. The obtained results provide a starting point for further research into the function of the <i>OsDUF946</i> family in rice.</p

Molecular characterization, expression pattern and function analysis of the rice <i>OsDUF866</i> family

<p>Domain-of-unknown function (DUF) proteins represent a number of gene families with no functional annotation in the Pfam database. So far, the <i>DUF866</i> family has not been characterized, and no member has been functionally studied. In this study, we uncovered and analysed four OsDUF866 (OsDUF866.1–OsDUF866.4) family members in rice <i>Nipponbare</i>, in which three distinct motifs were identified. The expression of <i>OsDUF866</i> family in nine tissues was examined by real-time polymerase chain reaction (PCR), and the highest expression of four genes members was found in embryos at 14 days after flowering. We performed real-time PCR to examine the expression of <i>OsDUF866</i> family under abiotic stress and abscisic acid (ABA) treatment conditions. The expression level of <i>OsDUF866.1</i> displayed significant decrease under drought and salt conditions, while significant increase under heat conditions. The expression level of <i>OsDUF866.2</i> displayed significant decrease under drought conditions. The expression level of <i>OsDUF866.3</i> was significantly elevated under drought and cold, while lowered under heat conditions. The expression level of <i>OsDUF866.4</i> was increased under cold and heat conditions, while decreased under drought conditions. Interestingly, the expression level of <i>OsDUF866</i> members was approximately constant under ABA treatment conditions. Overexpression of <i>OsDUF866.1</i> in <i>Escherichia coli</i> could enhance cell viability and significantly improve the resistance to heat stress conditions. The results may provide new insights into the function of <i>OsDUF866</i> family in rice.</p

Genome-wide identification and analyses of the rice <i>OsDUF936</i> family

<p>The domain of unknown function <i>DUF936</i> family consists of proteins with an average length of around 328 residues that have no characterized function in rice. In this study, we report nine <i>OsDUF936</i> (<i>OsDUF936.1</i>–<i>OsDUF936.9</i>) family members in rice Nipponbare with three distinct motifs. All the <i>OsDUF936</i> proteins were classified into four major groups (I, II, III and IV) by phylogenetic analysis. The expression level of <i>OsDUF936.3</i>, <i>OsDUF936.5</i> and <i>OsDUF936.6</i> displayed significant increase under salt stress conditions. Overexpression of <i>OsDUF936.6</i> in <i>Escherichia coli</i> significantly improved the tolerance to salt, while overexpression of <i>OsDUF936.3</i> and <i>OsDUF936.5</i> in <i>E. coli</i> did not have such an effect. The results presented here would be helpful for further study on the function of the <i>OsDUF936</i> family in rice.</p

Identification and characterization of a novel abiotic stress responsive sulphotransferase gene (<i>OsSOT9</i>) from rice

<p>Abiotic stresses may seriously affect plant growth and development. In order to explore new stress tolerance genes in rice (<i>Oryza sativa</i> L.), expression profiles were obtained for leaf and panicle tissues. They were taken at seedling, booting, heading and flowering stages of <i>indica</i> cultivar Pei'ai 64S plants under cold, drought and heat stresses by using the GeneChip Rice Genome Array (Affymetrix), which includes 51,279 transcripts from <i>japonica</i> and <i>indica</i> rice. <i>O. sativa</i> L. cytosolic sulphotransferase-like gene (<i>OsSOT9</i>) was highly induced in leafs and panicles during different developmental stages, in response to all stresses, especially at booting stage under cold stress. The quantitative real-time polymerase chain reaction analysis showed that this result was almost consensus with GeneChip Rice Genome Array. cDNA of <i>OsSOT9</i> was cloned to study its function in stress tolerance through reverse transcription PCR. Sequence analysis showed that the cDNA encoded a protein with molecular weight of about 37.78 kDa and pl of about 6.6, which was composed of 343 amino acid residues. Bioinformatics data showed that the protein contained a conservative domain of the sulphotransferase (SOT) family gene. <i>OsSOT9</i> was found to be closely related to the cytosolic sulphotransferase after comparison of the protein sequences. Analysis of the putative promoter region found 12 kinds of <i>cis</i>-elements related to stress response. On the basis of the above analyses, we suggested that <i>OsSOT9</i> is a novel candidate gene involved in stress tolerance in rice.</p

Molecular characterization and function analysis of the rice <i>OsDUF829</i> family

<p>Although the number of sequenced plant genomes has been rapidly increasing, many plant proteins in public databases are recognized as proteins with domains of unknown function (DUF). The domain of unknown function DUF829 family consists of plant proteins with an average length of around 220 residues. In this study, we attempted to uncover the biological functions of four DUF829 members (OsDUF829.1–OsDUF829.4) in rice Nipponbare. We classified these proteins into three groups (group I, II and III) using phylogenetic analysis. Real time polymerase chain reaction (PCR) showed that the expression patterns of the four <i>OsDUF829</i> family members were different in 15 different rice tissues. Under salt and heat stress conditions, the expression level of <i>OsDUF829.2</i> and <i>OsDUF829.4</i> was significantly elevated. Overexpression of <i>OsDUF829.2</i> and <i>OsDUF829.4</i> in <i>Escherichia coli</i> significantly improved the resistance to salt stress. The obtained results provide important implications for further functional studies of the OsDUF829 family in rice.</p

Additional file 1 of Overexpression of OsHAD3, a Member of HAD Superfamily, Decreases Drought Tolerance of Rice

Additional file 1. Figure S1 Detection of transcript level of OsHAD3 in transgenic plants. Figure S2 Detection of transcript levels of other family members in WT and transgenic plants. Table S1 Primers used in this study

Molecular characterisation and function analysis of the rice <i>OsDUF872</i> family

<p>With the advance of sequencing technology, the number of sequenced plant genomes has been rapidly increasing. However, many plant proteins in public databases are recognised as proteins with domains of unknown function (DUF). DUF872 is such a protein family that consists of plant proteins with unknown function. In this study, we analysed three DUF872 members (OsDUF872.1, OsDUF872.1 and OsDUF872.3) in rice Nipponbare with three distinct motifs. Real-time polymerase chain reaction showed that the expression patterns of the three corresponding OsDUF872 protein-encoding genes varied in 15 different rice tissues. The expression of <i>OsDUF872.2</i> was significantly (<i>P</i> < 0.01) upregulated under salt, cold and heat stress conditions. Overexpression of OsDUF872.2 in <i>Escherichia coli</i> significantly improved the resistance to heat. These results improve our understanding of these poorly-studied proteins and provide information for future studies on other proteins of unknown function.</p