Comprehensive molecular insights into the stress response dynamics of rice (Oryza sativa L.) during rice tungro disease by RNA-seq-based comparative whole transcriptome analysis

The nucleotide derivatives (p)ppGpp, comprising ppGpp and pppGpp, are important signalling molecules thatcontrol various facets of gene regulation and protein synthesis in Escherichia coli. Their synthesis is catalysedby RelA (in response to amino acid limitation) and by SpoT (in response to the limitation of carbon source orfatty acids). SpoT is also a hydrolase for degradation of both ppGpp and pppGpp, while GppA catalyses theconversion of pppGpp to ppGpp. Here we provide evidence to show that pppGpp exerts heightened toxicitycompared to that by ppGpp. Thus, gppA spoT double mutants exhibited lethality under conditions in which thesingle mutants were viable. The extent of RelA-catalysed (p)ppGpp accumulation in the gppA spoT strain wassubstantially greater than that in its isogenic gppA? derivative. The data is interpreted in terms of a model inwhich toxicity of pppGpp in the gppA spoT mutants is mediated by its activation of RelA so as to result in avicious cycle of (p)ppGpp synthesis.

Identification and validation of a virus-inducible ta-siRNA-generating TAS4 locus in tomato.

Trans-acting small interfering RNAs (ta-siRNAs) are a class of endogenous small RNA, associated with posttranscriptional gene silencing. Their biogenesis requires an initial microRNA (miRNA)-mediated cleavage of precursor RNA. Around 20 different ta-siRNA-producing loci (TASs), whose sequences are conserved, are reported in plants. In tomato, two TAS gene families have been identified, which are found to target auxin response factor gene and bacterial spot disease resistance protein Bs4 gene. Using high-throughput computational and experimental approach, we identified a new locus-producing ta-siRNA in tomato. We have also identified the putative miRNA regulating the production of ta-siRNA from this locus. The ta-siRNAs generated from TAS4 were up-regulated upon infection with a DNA virus. The potential targets of ta-siRNAs were predicted to be variety of proteins including MYB transcription factors and cell cycle regulators for some of the ta-siRNAs produced.

Begomovirus research in India: A critical appraisal and the way ahead.

Begomoviruses are a large group of whitefly-transmitted plant viruses containing single-stranded circular DNA encapsidated in geminate particles. They are responsible for significant yield losses in a wide variety of crops in India. Research on begomoviruses has focussed on the molecular characterization of the viruses, their phylogenetic analyses, infectivities on host plants, DNA replication, transgenic resistance, promoter analysis and development of virus-based gene silencing vectors. There have been a number of reports of satellite molecules associated with begomoviruses. This article aims to summarize the major developments in begomoviral research in India in the last approximately 15 years and identifies future areas that need more attention.