Structural Characterization and Expression Analysis of the SERK/SERL Gene Family in Rice (Oryza sativa)

Somatic embryogenesis (SE) is the developmental restructuring of somatic cells towards the embryogenic pathway and forms the basis of cellular totipotency in angiosperms. With the availability of full-length cDNA sequences from Knowledge-based Oryza Molecular Biological Encylopedia (KOME), we identified the leucine-rich repeat receptor-like kinase (LRR-RLK) genes from rice (Oryza sativa), which also encompasses genes involved in regulating somatic embryogenesis. Eight out of eleven of the rice SERK and SERL (SERK-like) genes have the TIGR annotation as (putative) brassinosteroid insensitive 1-associated receptor kinase (precursor). Real-time polymerase chain reaction analysis was undertaken to quantify transcript levels of these 11 genes. Most of these genes were upregulated by brassinosteroids although only a few of these displayed auxin induction. The expression profile of these genes is nearly uniform in the zygotic embryogenic tissue, but the expression pattern is more complex in the somatic embryogenic tissue. It is likely that OsSERKs and OsSERLs may be involved in somatic embryogenesis and also perform a role in morphogenesis and various other plant developmental processes. Functional validation of these somatic embryogenesis receptor-like kinase genes may help in elucidating their precise functions in regulating various facets of plant development

Characterization of three somatic embryogenesis receptor kinase genes from wheat, Triticum aestivum

We report here the isolation and characterization of three SOMATIC EMBRYOGENESIS RECEPTOR KINASE (TaSERK) genes from wheat. TaSERKs belong to a small family of receptor-like kinase genes, share a conserved structure and extensive sequence homology with previously reported plant SERK genes. TaSERK genes are in general auxin inducible and expressed during embryogenesis in cell cultures. We show here that somatic embryogenesis in Triticum aestivum is associated with high SERK expression which could be enhanced with auxin application and is calcium dependent. TaSERK transcripts could also be enhanced by epibrassinolide and abscisic acid. TaSERK1 and TaSERK2 may have a role in somatic embryogenesis, whereas TaSERK3 appears to be a brassinosteroid-associated kinase (BAK) lacking an SPP motif but shares a characteristic C-terminal domain with other SERK proteins. Also, the transcripts of all the three TaSERK genes could be induced in zygotic and somatic tissues. Although our analysis suggests them to be involved in somatic embryogenesis, they may have a broader role in acquiring embryogenic competence in wheat

OsIAA1, an Aux/IAA cDNA from rice, and changes in its expression as influenced by auxin and light

The Aux/IAA class of genes are rapidly induced by exogenous auxins and have been characterized extensively from many dicot species like Arabidopsis, Glycine max and Pisum sativum. We report here the isolation and characterization of rice (Oryza sativa L. subsp. Indica) OsIAA1 cDNA as a monocot member of the Aux/IAA gene family. The predicted amino acid sequence of OsIAA1 corresponds to a protein of ca. 26 kDa, which harbors all four characteristic domains known to be conserved in Aux/IAA proteins. The conservation of these Aux/IAA genes indicates that auxins have essentially a similar mode of action in monocots and dicots. Northern blot analysis revealed that the OsIAA1 transcript levels decrease in the excised coleoptile segments on auxin starvation, and the level is restored when auxin is supplemented; the increase in OsIAA1 transcript level was apparent within 15 to 30 min of auxin application. Auxin-induced OsIAA1 expression appears to be correlated with the elongation of excised coleoptile segments. In light-grown rice seedlings, OsIAA1 is preferentially expressed in roots and basal segment of the seedling, whereas in the etiolated rice seedlings, the OsIAA1 transcripts are most abundant in the coleoptile. A comparative analysis in light- and dark-grown seedling tissues indicates that the OsIAA1 transcript levels decrease on illumination

Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice

Auxin influences growth and development in plants by altering gene expression. Many auxin-responsive genes have been characterized in Arabidopsis in detail, but not in crop plants. Earlier, we reported the identification and characterization of the members of the GH3, Aux/IAA and SAUR gene families in rice. In this study, whole genome microarray analysis of auxin-responsive genes in rice was performed, with the aim of gaining some insight into the mechanism of auxin action. A comparison of expression profiles of untreated and auxin-treated rice seedlings identified 315 probe sets representing 298 (225 upregulated and 73 downregulated) unique genes as auxin-responsive. Functional categorization revealed that genes involved in various biological processes, including metabolism, transcription, signal transduction, and transport, are regulated by auxin. The expression profiles of auxin-responsive genes identified in this study and those of the members of the GH3, Aux/IAA, SAUR and ARF gene families were analyzed during various stages of vegetative and reproductive (panicle and seed) development by employing microarray analysis. Many of these genes are, indeed, expressed in a tissue-specific or developmental stage-specific manner, and the expression profiles of some of the representative genes were confirmed by real-time PCR. The differential expression of auxin-responsive genes during various stages of panicle and seed development implies their involvement in diverse developmental processes. Moreover, several auxin-responsive genes were differentially expressed under various abiotic stress conditions, indicating crosstalk between auxin and abiotic stress signaling

Carotenoid biosynthesis genes in rice: structural analysis, genome-wide expression profiling and phylogenetic analysis

Carotenoids, important lipid-soluble antioxidants in photosynthetic tissues, are known to be completely absent in rice endosperm. Many studies, involving transgenic manipulations of carotenoid biosynthesis genes, have been performed to get carotenoid-enriched rice grain. Study of genes involved in their biosynthesis can provide further information regarding the abundance/absence of carotenoids in different tissues. We have identified 16 and 34 carotenoid biosynthesis genes in rice and Populus genomes, respectively. A detailed analysis of the domain structure of carotenoid biosynthesis enzymes in rice, Populus and Arabidopsis has shown that highly conserved catalytic domains, along with other domains, are present in these proteins. Phylogenetic analysis of rice genes with Arabidopsis and other characterized carotenoid biosynthesis genes has revealed that homologous genes exist in these plants, and the duplicated gene copies probably adopt new functions. Expression of rice and Populus genes has been analyzed by full-length cDNA- and EST-based expression profiling. In rice, this analysis was complemented by real-time PCR, microarray and signature-based expression profiling, which reveal that carotenoid biosynthesis genes are highly expressed in light-grown tissues, have differential expression pattern during vegetative/reproductive development and are responsive to stress

An early auxin-responsive Aux/IAA gene from wheat (Triticum aestivum) is induced by epibrassinolide and differentially regulated by light and calcium

The plant hormone auxin plays a central role in regulating many aspects of plant growth and development. This largely occurs as a consequence of changes in gene expression. The Aux/IAA genes are best characterized among the early auxin-responsive genes, which encode short-lived transcriptional repressors. In most plants examined, including Arabidopsis, soybean, and rice, the Aux/IAA genes constitute a large gene family. By screening the available databases, at least 15 expressed sequence tags (ESTs) have been identified from wheat (Triticum aestivum), which exhibit high sequence identity with Aux/IAA homologues in other species. One of these Aux/IAA genes, TaIAA1, harbouring all the four conserved domains characteristic of the Aux/IAA proteins, has been characterized in detail. The expression of TaIAA1 is light-sensitive, tissue-specific, and is induced within 15-30 min of exogenous auxin application. Also, the TaIAA1 transcript levels increase in the presence of a divalent cation, Ca2+, and this effect is reversed by the calcium-chelating agent, EGTA. The TaIAA1 gene qualifies as the primary response gene because an increase in its transcript levels by auxin is unaffected by cycloheximide. In addition to auxin, the TaIAA1 gene is also induced by brassinosteroid, providing evidence that interplay between hormones is crucial for the regulation of plant growth and development

Phytochrome-mediated light signaling in plants: emerging trends

Phytochromes maximally absorb in the red and far-red region of the solar spectrum and play a key role in regulating plant growth and development. Our understanding of the phytochrome-mediated light perception and signal transduction has improved dramatically during the past decade. However, some recent findings challenge a few of the well-accepted earlier models regarding phytochrome structure and function. Identification of a serine/threonine specific protein phosphatase 2A (FyPP) and a type 5 protein phosphatases (PAPP5), and the phytochrome-mediated phosphorylation of phytochrome interacting factor 3 (PIF3), auxin inducible genes (Aux/IAA) and cryptochromes have opened new vistas in phytochrome biology. Importantly, the significance of proteolysis and chromatin-remodeling pathways in phytochrome signaling is becoming more apparent. The emerging concept of phytochrome as a master regulator in orchestrating downstream signaling components has become more convincing with the advent of global expression profiling of genes. Upcoming data also provide fresh insights into the nuclear localization, speckle formation, nucleo-cytoplasmic partitioning and organ-specificity aspects of phytochromes. This article highlights recent advances in phytochrome biology with emphasis on the elucidation of novel components of light signal transduction

Reconstructing an ancestral genotype of two hexachlorocyclohexane-degrading Sphingobium species using metagenomic sequence data.

Over the last 60 years, the use of hexachlorocyclohexane (HCH) as a pesticide has resulted in the production of >4 million tons of HCH waste, which has been dumped in open sinks across the globe. Here, the combination of the genomes of two genetic subspecies (Sphingobium japonicum UT26 and Sphingobium indicum B90A; isolated from two discrete geographical locations, Japan and India, respectively) capable of degrading HCH, with metagenomic data from an HCH dumpsite (∼450 mg HCH per g soil), enabled the reconstruction and validation of the last-common ancestor (LCA) genotype. Mapping the LCA genotype (3128 genes) to the subspecies genomes demonstrated that >20% of the genes in each subspecies were absent in the LCA. This includes two enzymes from the 'upper' HCH degradation pathway, suggesting that the ancestor was unable to degrade HCH isomers, but descendants acquired lin genes by transposon-mediated lateral gene transfer. In addition, anthranilate and homogentisate degradation traits were found to be strain (selectively retained only by UT26) and environment (absent in the LCA and subspecies, but prevalent in the metagenome) specific, respectively. One draft secondary chromosome, two near complete plasmids and eight complete lin transposons were assembled from the metagenomic DNA. Collectively, these results reinforce the elastic nature of the genus Sphingobium, and describe the evolutionary acquisition mechanism of a xenobiotic degradation phenotype in response to environmental pollution. This also demonstrates for the first time the use of metagenomic data in ancestral genotype reconstruction, highlighting its potential to provide significant insight into the development of such phenotypes

Molecular characterization and differential expression of cytokinin-responsive type-A response regulators in rice (Oryza sativa)

Background The response regulators represent the elements of bacterial two-component system and have been characterized from dicot plants like Arabidopsis but little information is available on the monocots, including the cereal crops. The aim of this study was to characterize type-A response regulator genes from rice, and to investigate their expression in various organs as well as in response to different hormones, including cytokinin, and environmental stimuli. Results By analysis of the whole genome sequence of rice, we have identified ten genes encoding type-A response regulators based upon their high sequence identity within the receiver domain. The exon-intron organization, intron-phasing as well as chromosomal location of all the RT-PCR amplified rice (Oryza sativa) response regulator (OsRR) genes have been analyzed. The transcripts of OsRR genes could be detected by real-time PCR in all organs of the light- and dark-grown rice seedlings/plants, although there were quantitative differences. The steady-state transcript levels of most of the OsRR genes increased rapidly (within 15 min) on exogenous cytokinin application even in the presence of cycloheximide. Moreover, the expression of the OsRR6 gene was enhanced in rice seedlings exposed to salinity, dehydration and low temperature stress. Conclusion Ten type-A response regulator genes identified in rice, the model monocot plant, show overlapping/differential expression patterns in various organs and in response to light. The induction of OsRR genes by cytokinin even in the absence of de novo protein synthesis qualifies them to be primary cytokinin response genes. The induction of OsRR6 in response to different environmental stimuli indicates its role in cross-talk between abiotic stress and cytokinin signaling. These results provide a foundation for further investigations on specific as well as overlapping cellular functions of type-A response regulators in rice

Involvement of G-proteins, calmodulin and tagetitoxin-sensitive RNA polymerase in light-regulated expression of plastid genes (psbA, psaA and rbcL) in rice (Oryza sativa L.)

The regulation of chloroplast gene expression by light involves multiple signaling components. In an earlier study, we demonstrated the role of calcium and phosphorylation in regulating the expression of photosynthesis-related plastid genes, psbA, psaA and rbcL, using rice as a model monocot system. This work has been extended further to examine the possible involvement of heterotrimeric GTP-binding proteins and calmodulin. Vacuum infiltration of 5-day-old etiolated rice seedlings with G-protein agonists, cholera toxin and GTPγS, increased the steady-state transcript levels of the plastid genes. The antagonists/inhibitors of calmodulin action, trifluoperazine and W7, inhibited the light-induced increase in steady-state transcript levels of these genes. The light-regulated expression of photosynthetic genes was also adversely affected by tagetitoxin, a specific inhibitor of plastid-encoded RNA polymerase. These results indicate the involvement of various signaling components in transduction of light signal that probably also recruits PEP to regulate plastid gene expression