Biology subjects

Kirti, P. B.

Publications and source records attributed to Kirti, P. B..

5 recordsLinked to original sources

bioRxiv2021

Genome-wide identification, expression and bioinformatic analyses of GRAS transcription factor genes in rice

Our group has previously identified the activation tagging of a GRAS transcription factor (TF)gene in the gain-of-function mutant population of rice (indica rice variety BPT 5204) screened for water use efficiency (Moin et al, 2016a). This family of GRAS transcription factors has been well known for their diverse roles in gibberellin signaling, light responses, root development, gametogenesis etc. Recent studies indicated their role in biotic and abiotic responses as well. Although this family of TFs received significant attention, not many genes were identified specifically for their roles in mediating stress tolerance in rice. Only OsGRAS23 (here named as OsGRAS22) was reported to code for a TF that induces drought tolerance in rice. In the present study, we have analyzed the expression patterns of rice GRAS TF genes under abiotic (NaCl and ABA treatments) and biotic (leaf samples infected with pathogens, Xanthomonas oryzae pv. oryzae that causes bacterial leaf blight and Rhizoctonia solani that causes sheath blight) stress conditions. In addition, their expression patterns were also analyzed in thirteen different developmental stages. We studied their spatio-temporal regulation and correlated them with in-silico studies. Fully annotated genomic sequences available in rice database have enabled us to study the protein properties, ligand interactions, domain analysis and presence of cis-regulatory elements in a bioinformatics analysis. Most of the genes were induced immediately after the onset of stress particularly in the roots of ABA treated plants. OsGRAS39 was found to be very highly expressive gene under sheath blight infection and both abiotic stress treatments while OsGRAS8, OsSHR1 and OsSLR1 were also responsive. Our earlier functional characterization (Moin et al., 2016a) followed by the genome wide characterization of the GRAS gene family members in the present study clearly show that they are highly appropriate candidate genes for manipulating stress tolerance in rice and other crop plants.

plant biology↗

bioRxiv2021

Differential Regulation of Rice Transcriptome to Rhizoctonia solani infection

Sheath Blight (SB) disease in rice crop caused by the infection of the fungal pathogen Rhizoctonia solani (R. solani) is one of the severe rice diseases that can cause up to 50% yield losses. Naturally occurring rice varieties resistant to SB have not been reported yet. We have performed a Time-Series RNA-Seq analysis on a widely cultivated rice variety BPT-5204 for identifying its transcriptomic response signatures to R. solani infection at 1st, 2nd and 5th day post inoculation (dpi). In total, 428, 3225 and 1225 genes were differentially expressed in the treated rice plants post 1, 2 and 5 dpi, respectively. GO and KEGG enrichment analysis identified significant processes and pathways differentially altered in the rice plant after the fungal infection. Machine learning and network based integrative approach was used to construct Transcriptional Regulatory Networks (TRNs) of the rice plant at the three Time Points. Regulatory network analysis identified SUB1B, MYB30 and CCA1 as important regulatory hub Transcription Factors in rice during R. solani infection. Jasmonic acid signaling pathway was activated and in contrast, photosynthesis and carbon fixation processes were significantly compromised. Involvement of MAPK, CYPs, Peroxidases and PAL genes was observed in response to the fungal infection. Circadian clock was also strongly influenced by R. solani infection. Our integrative analysis identified 7 putative SB resistant genes altered in rice after R. solani infection and provided a better understanding of rice plant response to R. solani infection. One sentence summaryTime series expression analysis of rice variety BPT-5204 identifies key molecular signatures involved in rice plant response to R. solani infection.

systems biology↗

bioRxiv2020

Ribosomal Protein Large subunit RPL6 modulates salt tolerance in rice

The extra-ribosomal functions of ribosomal proteins RPL6 and RPL23a in stress-responsiveness have emanated from our previous studies on activation tagged mutants of rice screened for water-use efficiency (Moin et al., 2016a). In the present study, we functionally validated the RPL6, a Ribosomal Protein Large subunit member for salt stress tolerance in rice. The overexpression of RPL6 resulted in tolerance to moderate (150 mM) to high (200 mM) levels of salt (NaCl) in rice. The transgenic rice plants expressing RPL6 constitutively showed better phenotypic and physiological responses with high quantum efficiency, accumulation of more chlorophyll and proline contents, and an overall increase in seed yield compared with the wild type in salt stress treatments. An iTRAQ-based comparative proteomic analysis revealed the high expression of about 333 proteins among the 4,378 DEPs in a selected overexpression line of RPL6 treated with 200 mM of NaCl. The functional analysis showed that these highly expressed proteins (HEPs) are involved in photosynthesis, ribosome and chloroplast biogenesis, ion transportation, transcription and translation regulation, phytohormone and secondary metabolite signal transduction. An in silico network analysis of HEPs predicted that RPL6 binds with translation-related proteins and helicases, which coordinately affects the activities of a comprehensive signaling network, thereby inducing tolerance and promoting growth and yield in response to salt stress. Our overall findings identified a novel candidate, RPL6 whose characterization contributed to the existing knowledge on the complexity of salt tolerance mechanism in plants.

plant biology↗

bioRxiv2020

Gain of function mutagenesis through activation tagging identifies XPB2 and SEN1 helicase genes as potential targets for drought stress tolerance in rice

We have earlier reported on the development of an activation tagged gain-of-function mutant population in an indica rice variety, BPT-5204 (Moin et al. 2016). Screening of these gain of function mutants for water-use efficiency (WUE) followed by physiological analyses revealed the activation of two helicases, ATP-dependent RNA (SEN1) and DNA (XPB2) encoding unwinding proteins in two different mutant lines. In the current study, we examined the roles of these genes in stable activation tagged mutants of rice for drought stress responses. Transcript profiling of SEN1 and XPB2 showed their significant up-regulation under various stresses (particularly ABA and PEG). The SEN1 and XPB2 tagged mutants exhibited reduced leaf wilting, improved revival efficiency, high chlorophyll and proline contents, profuse tillering, high quantum efficiency and yield-related traits in response to simulated drought (PEG) and hormone (ABA) treatments with respect to their controls. These observations were further validated under greenhouse conditions by periodic withdrawal of water. Germination of the seeds of these mutant lines indicates their ABA insensitivity under high ABA concentration. Also, the associated high up-regulation of stress-specific genes suggests that their drought tolerance might have been because of the coordinated expression of several stress responsive genes in these two mutants. Altogether, our results provided a firm basis for SEN1 and XPB2 as potential candidates for manipulation of drought tolerance and improving rice performance and yield under limited water conditions.

plant biology↗

bioRxiv2020

Target of Rapamycin: function in abiotic stress tolerance in Arabidopsis and its involvement in a possible cross-talk with ribosomal proteins

The Target of Rapamycin (TOR) protein kinase reprograms cellular metabolism under various environmental stresses. The overexpression of TOR in Arabidopsis resulted in increased plant growth including yield and biomass when compared with the wild type under both controlled and limited water conditions. In the present investigation, we report that Arabidopsis plants overexpressing TOR exhibited enhanced tolerance to the osmotic and salt stress treatments. Further to determine the role of TOR in abiotic stresses other than water limiting conditions, which were observed earlier in rice, we have treated high and medium TOR expressing Arabidopsis plants, ATR-1.4.27 and ATR-3.7.32 respectively, with stress-inducing chemical agents such as Mannitol (100 mM), NaCl (150 mM), Sorbitol (200 mM) and PEG (7%). Both the lines, ATR-1.4.27 and ATR-3.7.32 exhibited enhanced tolerance to these stresses. These lines also had increased proline and total chlorophyll contents under stress conditions compared with their corresponding WT counterparts. The upregulation of several osmotic stress inducible genes in Arabidopsis transgenic lines indicated the role of TOR in modulating multi-stress tolerance. In the present investigation, we have also analyzed the transcriptional upregulation of ribosomal protein large and small subunit (RPL and RPS) genes in AtTOR overexpressing rice transgenic lines, TR-2.24 and TR-15.1 generated earlier (Bakshi et al., 2017a), which indicated that TOR also positively regulates the transcription of ribosomal proteins (RP) along with the synthesis of rRNAs. Also, the observations from phosphoproteomic analysis in SALK lines of various Arabidopsis T-DNA insertion mutants of ribosomal proteins showed differential regulation in phosphorylation of p70kDa ribosomal protein S6K1 and comparative analysis of phosphorylation sites for RSK (Ribosomal S6 Kinases) in RPL6, RPL18, RPL23, RPL24 and RPS28C proteins of Arabidopsis, Interestingly, rice showed similarity in their peptide sequences and Ser/Thr positions. These results suggest that the phosphorylation of S6K1 is controlled by loss/ inhibition of ribosomal protein function to switch on/ off the translational regulation for balanced growth and the pathways of both RPs and TOR are interlinked in a cyclic manner via phosphorylation of S6K1 as a modulatory step.

plant biology↗