Viswanathan Chinnusamy

Steroidogenic acute regulatory related transfer (StART) proteins that are involved in transport of lipid molecules, play a myriad of functions in insects, mammals and plants. These proteins consist of a modular START domain of approximately 200 amino acids which binds and transfers the lipids. In the present study we have performed a genome-wide search for all START domain proteins in chickpea. The search identified 36 chickpea genes belonging to the START domain family. Through a phylogenetic tree reconstructed with Arabidopsis, rice, chickpea, and soybean START proteins, we were able to identify four transmembrane START proteins in chickpea. These four proteins are homologous to the highly conserved mammalian phosphatidylcholine transfer proteins. The multiple sequence alignment of all the transmembrane containing START proteins from Arabidopsis, rice, chickpea, and soybean revealed that the amino acid residues to which phosphatidylcholine binds in mammals, is also conserved in all these plant species, implying an important functional role and a very similar mode of actionof all these proteins across dicots and monocots. This study characterises a few of the not so well studied transmembrane START superfamily genes that may be involved in stress signalling.The expression analysis in various tissues showed that these genes are predominantly expressed in flowers and roots of chickpea. Three of the chickpea TM START genes showed induced expression in response to drought, salt, wound and heat stress, suggesting their role in stress respopnse.

Wheat is a staple food worldwide and provides 40% of the calories in the diet. Climate change and global warming pose a threat to wheat production, however, and demand a deeper understanding of how heat stress might impact wheat production and wheat biology. However, it is difficult to identify novel heat stress associated genes when the genomic information is not available. Wheat has a very large and complex genome that is about 37 times the size of the rice genome. The present study sequenced the whole transcriptome of the wheat cv. HD2329 at the flowering stage, under control (22° ± 3°C) and heat stress (42°C, 2 h) conditions using Illumina HiSeq and Roche GS-FLX 454 platforms. We assembled more than 26.3 and 25.6 million high-quality reads from the control and HS-treated tissues transcriptome sequences respectively. About 76,556 (control) and 54,033 (HS-treated) contigs were assembled and annotated de novo using different assemblers and a total of 21,529 unigenes were obtained. Gene expression profile showed significant differential expression of 1525 transcripts under heat stress, of which 27 transcripts showed very high (>10) fold upregulation. Cellular processes such as metabolic processes, protein phosphorylation, oxidations-reductions, among others were highly influenced by heat stress. In summary, these observations significantly enrich the transcript dataset of wheat available on public domain and show a de novo approach to discover the heat-responsive transcripts of wheat, which can accelerate the progress of wheat stress-genomics as well as the course of wheat breeding programs in the era of climate change.

MYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by "top-down" and "guide-gene" approaches. More than 50% of OsMYBs were strongly correlated under 50 experimental conditions with 51 hub genes via "top-down" approach. Further, clusters were identified using Markov Clustering (MCL). To maximize the clustering performance, parameter evaluation of the MCL inflation score (I) was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by "guide-gene" approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought response in rice. Thus, the co-regulatory network analysis facilitated the identification of complex OsMYB regulatory networks, and candidate target regulon genes of selected guide MYB genes. The results contribute to the candidate gene screening, and experimentally testable hypotheses for potential regulatory MYB TFs, and their targets under stress conditions.

Thermotolerance is required in crop plants in order to maintain productivity under heat stress. At the cellular level, thermotolerance is linked with the induction of heat shock proteins (HSPs), a response conserved from prokaryotes to eukaryotes. HSPs belong to six families and each family has several members, of which only a few may be involved in acquired thermotolerance. Molecular approaches may help to assign specific role to HSPs involved in thermotolerance. Thermotolerant genotypes show adaptations at various levels of organization besides showing qualitative and quantitative differences in HSPs as compared to the thermosensitive genotypes. In future, HSPs and enzymes with broader thermal kinetic windows may be the desired selection criteria at molecular level for breeding thermotolerant crop plants.

Unrevealing the molecular details of plant response and defense against abiotic stress factors such as drought, salt and temperature extremes is a crucial and challenging issue in plant research. Functional genomics and computational biology enhance pace of molecular dissection of abiotic stress response mechanisms. During the past two decades several QTLs associated with abiotic stress responses of plants have been mapped. A QTL is a chromosomal region that contains a gene or genes that influence a quantitative trait. QTL mapping approach is applied frequently to map chromosomal regions that contribute significantly to a complex trait. The availability of complete genome sequence of important model plants namely Arabidopsis and rice, QTL databases and mapping tools facilitate genomics-based strategies for gene discovery, coupled with high-throughput techniques speed-up gene discovery for abiotic stress tolerance.

: Leaf area index (LAI) of vegetation influences radiation interception, latent and sensible heat fluxes, and CO2 exchange between terrestrial ecosystems and atmosphere. LAI is used as a key input parameter in many crop growth simulation and radiative transfer models. Conventional LAI measurements are usually time-consuming, and is taken at few representative sample sites only.Alternately, non invasiveestimation of LAIfrom digital image can be an inexpensive and reliable and faster option.The present study attempts to develop an approach for estimation of LAI using top-of canopy digital colour photography over wheat canopy. Different colour based vegetation indices such as Excess Green (ExG), Excess Red (ExR),Normalized Difference(NDI) and Excess Green minus Excess Red (ExG-ExR) Indices were developed from digital images. A histogram-based threshold technique was used to separate green vegetation tissues from background soil in order to derive the canopy vertical gap fraction. The i...

Carotenoid metabolism is regulated by several genes encoding carotenoid biosynthetic pathway enzymes. In the present study, a fruit transcriptome in tomato (Solanum lycopersicum) was compared between high lycopene accumulating genotype EC-521086 and low lycopene accumulating genotype VRT-32-1 at three different stages (green, breaker and red) of fruit ripening. This analysis led to the identification of 2,558 differentially expressed genes at three stages of fruit ripening. Among these genes, 123 were carotenoid-correlated genes. Quantitative RT-PCR analysis revealed high expression of genes encoding enzymes involved in lycopene biosynthesis like IPP isomerase, phytoene synthase, phytoene desaturase, z-carotene desaturase; and comparatively lower expression of genes encoding enzymes involved in lycopene catabolism like lycopene cyclase, carotenoid e-ring hydroxylase, zeaxanthin epoxidase, violaxanthin de-epoxidase and neoxanthin synthase in EC-521086, thereby possibly explaining the...

The objective of this study was to examine the role of ethylene, aerenchyma formation and expression of xyloglucan endotransglycosylase (XET) in the waterlogging tolerance of contrasting mung bean (Vigna radiata) genotypes viz., T 44 (tolerant) and Pusa Baisakhi (susceptible), and a highly tolerant wild Vigna species Vigna luteola under pot-culture condition. Waterlogging resulted in decrease in relative water content (RWC) and chlorophyll (Chl) content in leaves, and membrane stability index (MSI) in root and leaf tissues. Waterlogging induced decline in RWC, MSI, and Chl was greater in Pusa Baisakhi (PB) than V. luteola and T 44. Ethylene production in the roots increased in all the genotypes, however, the concentration was higher in V. luteola and T 44 than Pusa Baisakhi. Though the waterlogging induced XET expression in the roots was observed in case of V. luteola and T 44, aerenchyma formation was observed only in the roots of V. luteola. PCR band products were cloned and seque...

ABSTRACT The effect of heat stress on the components of grain weight was analysed in wheat (Triticum aestivum L.) varieties differing in grain weight stability. The wheat varieties PBW154, Sonalika and Hindi62 were raised in the field (New Delhi, India; 77°12′ E, 28°40′ N, 228.6 m a.s.l.) at three dates of sowing: 19 November 1992 (DOS I), 14 December 1992 (DOS II) and 18 January 1993 (DOS III). The late-sown crop (DOS III) experienced 6–8 °C warmer temperatures during grain development than the crop sown at the normal time (DOS I). The heat susceptibility index (S) revealed that grain weight was less susceptible to heat in Sonalika and PBW154 than in Hindi62. Heat stress reduced both the grain growth duration (GGD) and the grain growth rate (GGR). The grain weight reduction in PBW154 and Sonalika was mainly due to a reduction in GGR, while that of Hindi62 was due to a reduction in GGD. In vivo studies on starch and protein synthesis in excised endosperm at 15, 25 and 35 °C revealed that both processes were more thermotolerant in Hindi62 than in PBW154. The grain starch content was stable in Hindi62 while that in PBW154 was significantly reduced under heat stress. The grain nitrogen content at maturity increased in both varieties under heat stress. It was concluded that the heat susceptibility of grain weight in Hindi62 was mainly due to a reduction in GGD, although GGR, starch and protein synthesis were more thermotolerant in developing grains of Hindi62 than in those of PBW154.Einfluss von Hitzestress auf das Kornwachstum, Stärke und Proteinsynthese in Körnern von Weizen (Triticum aestivum L.)-Sorten mit unterschiedlicher KorngewichtsstabilitätDer Einfluss von Hitzestress auf die Komponenten des Korngewichtes wurden bei Weizen (T. aestivum L.)-Sorten unterschiedlicher Korngewichtsstabilität untersucht. Weizenvarietäten viz. PBW154, Sonalika und Hindi62 wurden unter Feldbedingungen (New Delhi, India, 77°12′E, 28°40′N, 228,6 m) an drei Terminen, 19.11.1992 (DOS I), 14.12.1992 (DOS II) und 18.01.1993 (DOS III) angesät. Die späte Aussaat (DOS III) unterlag 6–8 °C wärmeren Temperaturen während der Kornentwicklung im Vergleich zu den normal Terminen angesäten Beständen. Hitzeempfindlichkeitsindex (S) zeigte, dass das Korngewicht toleranter bei Sonalika und PBW154 war im Vergleich zu Hindi62. Der Hitzestress reduzierte die Kornwachstumsdauer (GGD) und die Kornwachstumsrate (GGR). Die Reduktion im Korngewicht bei PBW154 und Sonalika war im wesentlichen eine Folge der Reduktion von GGR, während die Korngewichtsreduktion von Hindi62 eine Folge der Reduktion in GGD war. In vivo-Untersuchungen bezüglich Stärke und Proteinsynthese in separiertem Endosperm bei 15 °C, 25 °C und 35 °C zeigte, dass beide Prozesse thermotoleranter bei Hindi62 als bei PBW154 waren. Der Kornstärkegehalt war bei Hindi62 stabil, während der Kornstärkegehalt von PBW154 signifikant unter Hitzestress reduziert wurde. Der Stickstoffgehalt des Korns zur Reife nahm in beiden Varietäten unter Hitzestress zu. Es kann angenommen werden, dass die Hitzeempfindlichkeit des Korngewichtes bei Hindi62 wesentlich eine Folge der Reduktion von GGD war, obwohl GGR Stärke und Proteinsynthese thermotoleranter in den sich entwickelnden Körnern von Hindi62 im Vergleich zu PBW154 waren.

ABSTRACT Our knowledge base involving the biochemical participants of epigenetic control has expanded greatly over the last decade. The role of epigenetic marks to DNA and histones controlled by non-coding RNAs is one of the most intensely studied areas of biology today. This review covers many of the mechanisms that non-coding RNAs and other molecules use to control gene expression and eventually affect responses to the environment. In the first part of the review, we discuss the array of covalent modifications to the genome that constitute the epigenome, which consists of the histone variants, covalent modifications, and post-translational modifications that result in gene expression changes. How the histone variants and post-translational modifications including, acetylation, methylation, phosphorylation, ubiquitination and sumoylation help form the epigenome is also summarized. Our eventual understanding of how the environment controls these modifications will open incredible opportunities in agriculture, medicine and the development of practical tools for biology. In the second part of this review we discuss the growing list of environmentally-mediated epigenetic modifications, and examples of transgenerational epigenetic inheritance events, that may begin to change our views of adaptive responses to the environment and evolution.

Genetic improvement in drought tolerance in rice is the key to save water for sustainable agriculture. Drought tolerance is a complex trait and involves interplay of a vast array of genes. Several genotypes of rice have evolved features that impart tolerance to drought and other abiotic stresses. Comparative analysis of drought stress-responsive transcriptome between drought-tolerant (DT) landraces/genotypes and drought-sensitive modern rice cultivars will unravel novel genetic regulatory mechanisms involved in stress tolerance. Here, we report transcriptome analysis in a highly DT rice landrace, Nagina 22 (N22), versus a high-yielding but drought-susceptible rice variety IR64. Both genotypes exhibited a diverse global transcriptional response under normal and drought conditions. Gene ontology (GO) analysis suggested that drought tolerance of N22 was attributable to the enhanced expression of several enzyme-encoding genes. Drought susceptibility of IR64 was attributable to significant down-regulation of regulatory components that confer drought tolerance. Pathway analysis unravelled significant up-regulation of several components of carbon fixation, glycolysis/gluconeogenesis and flavonoid biosynthesis and down-regulation of starch and sucrose metabolism in both the cultivars under drought. However, significant up-regulation of α-linolenic acid metabolic pathway observed in N22 under drought appears to be in good agreement with high drought tolerance of this genotype. Consensus cis-motif profiling of drought-induced co-expressed genes led to the identification of novel cis-motifs. Taken together, the results of the comparative transcriptome analysis led to the identification of specific genotype-dependent genes responsible for drought tolerance in the rice landrace N22.

The phytohormone abscisic acid (ABA) regulates many key processes in plants, such as seed germination, seedling growth, and abiotic stress tolerance. In recent years, a minimal set of core components of a major ABA signaling pathway has been discovered. These components include a RCAR/PYR/PYL family of ABA receptors, a group of PP2C phosphatases, and three SnRK2 kinases. However, how the interactions between the receptors and their targets are regulated by other proteins remains largely unknown. In a companion paper published in this issue, we showed that ROP11, a member of the plant-specific Rho-like small GTPase family, negatively regulates multiple ABA responses in Arabidopsis. The current work demonstrated that the constitutively active ROP11 (CA-ROP11) can modulate the RCAR1/PYL9-mediated ABA signaling pathway based on reconstitution assays in Arabidopsis thaliana protoplasts. Furthermore, using luciferase complementation imaging, yeast two-hybrid assays, co-immunoprecipitation assays in Nicotiana benthamiana and bimolecular fluorescence complementation assays, we demonstrated that CA-ROP11 directly interacts with ABI1, a signaling component downstream of RCAR1/PYL9. Finally, we provided biochemical evidence that CA-ROP11 protects ABI1 phosphatase activity from inhibition by RCAR1/PYL9 and thus negatively regulates ABA signaling in plant cells. A model of how ROP11 acts to negatively regulate ABA signaling is presented.

Epigenetic mechanisms, namely histone modifications and DNA methylation induced changes in the chromatin, give rise to epigenomes, which add diversity and complexity to the genome of organisms. Epigenetic modifications play a pivotal role in genomic imprinting, paramutation, defense against transposon proliferation and regulation of gene expression. Specific combinations of histone N-tail modifications can be considered a histone code, which determines

The genes involved in the biosynthetic pathway of ectoine (2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylic acid) from Bacillus halodurans were cloned as an operon and expressed in E. coli. Analysis of the deduced ectoine biosynthesis cluster amino acid sequence revealed that the ectoine operon contain 2,389 bp, encoded by three genes; ectA, ectB and ectC that encode proteins of 189, 427 and 129 amino acids with deduced molecular masses of 21,048, 47,120 and 14,797 Da respectively. Extracts of induced cells showed two bands at 41 kDa and 17 kDa, possibly corresponding to the products of the later two genes. However the expression of ectA gene could not be ascertained by SDS-PAGE. The activity of the ectA protein was confirmed by an acylation assay. The transgenic E. coli accumulated upto 4.6 mg ectoine/l culture. This is the first report of an engineered E. coli strain carrying the ectoine genes of the alkaliphilic bacterium, B. halodurans.