Institutional Publications
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Item Engineered diazotrophs with host-inducible nitrogen supply systems: Transforming rice farming through innovative nitrogen biofertilizers(John Wiley & Sons, 2026) Sengupta, Ahana; Sahoo, Rudra Narayan; Sinharoy, SenjutiNitrogen pollution represents a critical challenge in the 21st century, highlighting the urgent need for sustainable alternatives to industrial nitrogen fixation. Diazotrophic bacteria, which uniquely convert dinitrogen (N2) into bioavailable forms, offer a promising solution through biological nitrogen fixation (BNF). These bacteria typically perform nitrogen fixation under nitrogen-limited conditions. Over the past 50 years, extensive research has elucidated the molecular mechanisms and regulatory pathways governing BNF. Recent microbiome studies have revealed that wild rice accessions harbor a greater abundance of diazotrophic bacteria, whereas a substantial proportion of these beneficial microbes have been lost in modern cultivated varieties. Advancements in synthetic biology have enabled the engineering of nitrogen‑exporting diazotrophs, potentially reducing dependence on industrial nitrogen fertilizers. This review emphasizes the importance of targeted research to develop customized diazotrophic microbes in conjunction with synthetic microbial community that can serve as nitrogen exporters for rice. Furthermore, it highlights the necessity of identifying rice cultivars that are particularly responsive to these microbial interventions. Finally, it provides a comprehensive roadmap addressing key challenges and opportunities in deploying BNF to supplement plant nitrogen nutrition and advance sustainable agriculture.Item Organized peripheral vascular strand development in nodules is controlled by a bHLH/HLH heterodimer(John Wiley & Sons, 2026) Srivastava, Deevita; Bhadu, Vikash; Sahoo, Rudra Narayan; Ghosh, Asim Kumar; Upadhyay, Priya; Bhardwaj, Akanksha; Udvardi, Michael K; Ranjan, Aashish; Sinharoy, SenjutiThe Leguminosae family can develop root nodules with symmetrical peripheral vascular-strands (PVSs). Medicago truncatula forms indeterminate nodules with PVSs. The PVSs elongate directly from the root toward the nodule apex, maintaining a symmetrical organization and facilitating the formation of the cylindrical nodule structure. By combining genetic, biochemical, and genomic tools, we have shown that two basic Helix-Loop-Helix groups of transcription factors, MtbHLH1 (renamed Nodule Vascular bundle Development 1 (NVD1)) and NVD2, control the development of symmetrical PVSs in M. truncatula. In nvd1 nodules, PVSs drift toward the infection zone, generating aberrantly shaped nodules. NVD1 activates its expression along with NVD2, a transcriptional regulator. NVD1 functions downstream of auxin signaling. Transcriptome sequencing of nvd1 and nvd2 nodules, combined with visualization of auxin and cytokinin (CK) signal outputs, revealed disrupted auxin and CK signaling in nvd nodules. Furthermore, ectopic expression of the auxin biosynthetic enzyme (MtYUCCA8) under pMtNVD1 and pMtNVD2 resulted in defective PVSs. Mutant nvd2 nodules display asymmetric PVSs. NVD2 regulates the transcriptional activity of NVD1 by forming heterodimers with it. The formation of symmetrical PVSs depends on the balanced presence of NVD1 and NVD2. Our findings highlight the pivotal role of the NVD1-NVD2 interaction in shaping the development of symmetrical PVSs.Item Conserved hinge regions in SYMRK enable release of Malectin-like Domain for symbiont passage during rhizobia-legume symbiosis(Oxford University Press, 2026) Chakrabarti, Dipanjan; Paul, Anindita; Molla, Firoz; Bhattacharyya, S; Das, Sagnik; Chakraborty, Sampurna; Ghosh, Dona; Biswas, Alokmoy; Kundu, Anindya; Sinharoy, Senjuti; DasGupta, MaitrayeeSymbiosis Receptor Kinase (SYMRK), a malectin-like-domain/leucine-rich-repeat receptor-like-kinase (MLD-LRR-RLK), is the upstream most component in the Common-Symbiosis-Signalling-Pathway. We highlight two Proline residues that were distinctly acquired by SYMRK orthologues in its hinge-regions to constitute a signalling module for allowing progress of symbionts across transcellular barriers during rhizobia-legume symbiosis. Within the Ectodomain hinge (EctoD-hinge) all MLD-LRR-RLKs have a conserved W1xnGDPCxnW2x4C motif, where SYMRK orthologues within legumes have a distinct signature with a Proline preceding W2 enabling cleavage of SYMRK ectodomain for releasing MLD. Within the kinase hinge (KD-hinge) at gatekeeper+1 position, a conserved Glutamate in MLD-LRR-RLKs is replaced by Proline in all SYMRK orthologues that enabled its dual-specific kinase activity for ensuring ectodomain cleavage. Substitution of either Proline restricted cortical progression of symbionts forming infection patches in the nodule apex without affecting epidermal invasion and nodule organogenesis. This halt was entirely overcome by ectopic expression of free MLD demonstrating the released MLD to have an active role in progress of symbionts. Overall, we show that conservation of distinct Prolines in hinge-regions of SYMRK orthologues in legumes generates a signalling module involving dimerization and optimal phosphorylation of SYMRK for releasing MLD as an active transducer of symbiosis signalling.Item RSD-mediated suppression of NIN and NLP2 transcription is crucial for symbiotic nitrogen fixation(John Wiley & Sons, 2026) Bhardwaj, Akanksha; Gupta, Megha; Bhattacharjee, Oindrila; Raul, Bikash; Ghosh, Asim Kumar; Nagalla, L. V. Sairam; Yadav, Prashant; Bandyopadhyay, Kaustav; Ranjan, Aashish; Sinharoy, SenjutiIndeterminate nodules establish a developmental gradient along their longitudinal axis, separating cell differentiation from symbiotic nitrogen fixation (SNF). The apex contains differentiating cells, while the differentiated leghemoglobin-rich cells of the nitrogen-fixation zone shield the rhizobial nitrogenase complex from oxygen to facilitate SNF. By combining biochemical, genetic, and genomic approaches, we demonstrate the pivotal role of the Regulator of Symbiosome Differentiation (RSD), a transcriptional repressor, in the transition from symbiosome development to SNF. Interacting Protein of DMI3 (IPD3) activates RSD expression in the invasion zone (ZII) and interzone (IZ). RSD interacts with Nodule Inception (NIN), and NIN-like protein 2 (NLP2) through a novel protein-protein interaction domain. RSD determines cell fate in ZII and the IZ by suppressing several targets of NIN and NLP2, including Leghemoglobins, Nodule-specific Cysteine-Rich genes, and Symbiotic Cysteine-rich Receptor-like Kinase. Our findings underscore the critical role of RSD-mediated suppression of transcription in facilitating the transition from bacteroid differentiation to SNF.Item Trans-QTL alliance of HKT1 and PHL7 modulate salinity stress tolerance and enhance crop yield endurance(John Wiley & Sons, 2026) Mohanty, Jitendra K.; Yadav, Antima; Narnoliya, Laxmi; Thakro, Virevol; Rathore, Deepanshi; Tripathi, Shailesh; Sinharoy, Senjuti; Agarwal, Pinky; Parida, Swarup K.Salinity stress can cause significant yield losses in crops because of its major impact on reproductive success. The complexity of salinity stress responses, particularly their tissue- and cell-specific regulation, continues to challenge the translation of molecular insights into tangible crop yield improvements. In the present study, the authors deployed a genomic strategy combining a genome-wide association study, regional association analysis, QTL mapping, fine mapping, and map-based cloning to delineate a pair of novel CaPHL7 and CaHKT1 alleles that regulate yield under salinity stress. The selected contrasting accessions, developed near-isogenic lines (NILs), overexpressed chickpea lines and complemented Arabidopsis lines collectively underscore the functional significance of the identified alleles in relaying yield endurance under salinity stress conditions. Functional characterisation of the genes revealed the intricate transcriptional regulation of CaHKT1 by CaPHL7, which influences the degree of salinity stress tolerance. Furthermore, in our efforts to enhance yield endurance, we discovered a novel regulatory role for the phosphorus (P) starvation-responsive gene (PHL7) in legumes, facilitating salinity stress adaptation. This study provides the first functional validation of a trans-QTL regulatory model in chickpea, where CaPHL7, located on one chromosome, transcriptionally activates CaHKT1 on a separate chromosome. The regulatory mechanism plays a key role in excluding sodium from the transpiration stream, thereby protecting reproductive processes from salinity-induced damage and mitigating yield penalties. This inter-locus regulation explains yield stability and offers useful insights that may be considered in future efforts to enhance salt resilience in chickpea.Item TAIL-PCR for the recovery of Tnt1 flanking sequences in chickpea: a tool for functional genomics studies(Springer Nature Publishing AG, 2026) Chauhan, Chetan; Ranjan, Shubhashish; Jangid, Vinod Kumar; Sinharoy, Senjuti; Senthil-Kumar, MuthappaThermal asymmetric interlaced polymerase chain reaction (TAIL-PCR) is a powerful technique for amplifying genomic regions flanking Tnt1-retortransposon insertions in plants. Here, we present a TAIL-PCR protocol for amplifying Tnt1-flanking genomic sequences in chickpea using Tnt1-transformed hairy roots as the starting material. The amplified products can be cloned and sequenced for the precise mapping of Tnt1-integration sites in the chickpea genome. This method enables the functional characterization of chickpea genes governing root-specific traits and can be easily adapted for flanking sequence tag recovery in chickpea Tnt1-mutant populations.Item Discovery of diverse chimeric peptides in a eukaryotic proteome sets the stage for experimental validation of the mosaic translation hypothesis(Elsevier B.V., 2025) Çakır, Umut; Gabed, Noujoud; Koroglu, Yunus Emre; Kaya, Selen; Sinharoy, Senjuti; Benedito, Vagner A.; Brunet, Marie; Roucou, Xavier; Kryvoruchko, Igor S.The high complexity of eukaryotic organisms enabled their evolutionary success, driven by the diversification of their proteomes. Various mechanisms contributed to this process. Alternative splicing had the largest known impact among these mechanisms. Earlier, we hypothesized that along with alternative splicing, a different but conceptually similar mechanism creates novel versions of existing proteins in all eukaryotes. However, this mechanism operates at the level of translation, where amino acid sequence novelty arises through multiple programmed ribosomal frameshifting events occurring within the same transcript. This mechanism, which is termed mosaic translation, is very difficult to demonstrate even with the most up-to-date molecular tools. Thus, it remained unnoticed so far. Using a subset of mass spectrometry proteomic data from various organs of the model plant Medicago truncatula, we took the first step toward experimental validation of this hypothesis. Our original in silico approach resulted in the discovery of two candidates for mosaic proteins (homologs of EF1α and RuBisCo) and 154 candidates for chimeric peptides. Chimeric peptides and polypeptides are produced in the course of one ribosomal frameshifting event and may correspond to parts of mosaic proteins. In addition, our analysis reveals the possibility of translation of chimeric peptides from five ribosomal RNA transcripts, ten long non-coding RNA transcripts, and one transfer RNA transcript. These findings are novel and will form the basis for future experimental validation. We also present multiple lines of indirect evidence supporting the validity of our in silico data.Item Induced post-invasive defenses in the nonhost plant Parthenium hysterophorus L. prevent root cortical colonization by Macrophomina phaseolina and impart resistance to dry root rot(Elsevier B.V., 2025) Mirchandani, Rishabh; Kandpal, Manu; Ranjan, Aashish; Sinharoy, Senjuti; Senthil-Kumar, MuthappaDry root rot (DRR) of chickpea is caused by the broad-range necrotrophic fungus Macrophomina phaseolina. Chickpea germplasm does not provide durable resistance to DRR, which is particularly devastating under drought. Even moderately resistant chickpea varieties become susceptible under combined stress. We hypothesized that nonhost resistance (NHR) is durable even under combined stress. Using the blotter paper assay and stereomicroscopic observations, we identified the asterid weed Parthenium hysterophorus as a potential nonhost of M. phaseolina among 82 potential nonhosts. Epidermal necrotic lesions were prevented in P. hysterophorus. In planta fungal load was 0.195 and 0.007 ng/ng total DNA in chickpea and P. hysterophorus, respectively. M. phaseolina could not colonize the P. hysterophorus root while up to 6 cortical cell layers were colonized in chickpea. Further, NHR was durable under combined stress. Dual RNA sequencing revealed that M. phaseolina actively attempted to infect the nonhost and activated specific genes in the xenobiotics degradation pathway. P. hysterophorus also showed an active defense response with1958 and 2294 differentially expressed genes at 2 and 4 DAI, respectively, with 363 upregulated at both time points. Differential expression of cell wall synthesis, phytohormone signaling, and other defense response pathways likely contributes to NHR. Few genes in the phenylpropanoid biosynthesis pathways in P. hysterophorus were also upregulated, possibly because these metabolites are linked to the distinct changes in the fungus during nonhost infection. We therefore conclude that P. hysterophorus exhibits post-invasive NHR to M. phaseolina and that general defense, phytohormone signaling and secondary metabolic pathways contribute to NHR.Item Genome sequencing of Mesorhizobium Spp. NI-7, an efficient nitrogen-fixing microsymbiont of chickpea with potential to unravel the molecular mechanisms of symbiotic nitrogen fixation in legumes(Springer Nature Publishing AG, 2024) Srivastava, Deevita; Ghosh, Asim K; Ranjan, Aashish; Sinharoy, SenjutiRoot nodule symbiosis is a major pillar of sustainable agriculture. The newly formed symbiotic organ in the legume root harbours rhizobacteria, which can fix atmospheric nitrogen into a bioavailable and reduced form, ammonia. Previously, we reported the isolation of an efficient Mesorhizobium spp. NI-7, from the interior of chickpea nodules. Here, we report the draft genome sequence of the Mesorhizobium spp. NI-7 and the comparative genomics among different Mesorhizobium strains that have adopted symbiosis during chickpea domestication. The draft genome of Mesorhizobium spp. NI-7 consists of a single 4.28 Mbp chromosome and a 359 Kbp plasmid. The 16 S rDNA sequence based phylogenetic analysis highlighted that Mesorhizobium spp. NI-7 belongs to a diverse Mesorhizobium clade that evolved during the domestication of chickpea. Comparative genomics among several Mesorhizobium strains identified 2193 common orthologous groups and several unique orthologous groups among the different Mesorhizobium pairs. The draft genome contains the essential nitrogen fixation genes along with the genes required for the nutrient exchange from the plant to the symbiont. Additionally, part of the symbiotic NOD-factor operon and Type III secretion system were also detected in the Mesorhizobium spp. NI-7 draft genome. The comparative genomics among the Mesorhizobium strains identified a subset of rhizobial genes that would have evolved during chickpea-Mesorhizobium adaptation to the Indian sub-continent. These genes are unique targets that can be validated in the future to understand the chickpea and Mesorhizobium adaptation. In summary, the draft genome sequencing of Mesorhizobium spp. NI-7 will equip the plant-microbe community with a chickpea-compatible Mesorhizobium strain isolated from India, suitable for both fundamental and advanced research on nodulation in chickpea, as well as for promoting sustainable agriculture in a comprehensive manner.Item Editorial: Plant-rhizobia symbiosis and nitrogen fixation in legumes(Frontiers Media S.A., 2024) Sinharoy, Senjuti; Tian, Chang-Fu; Montiel, Jesu´sNitrogen (N) is essential for life, but eukaryotes lack the ability to access this element, as only prokaryotic enzymes can convert N to ammonia. The Haber-Bosch process revolutionized agriculture by enabling synthetic N-fertilizer production, but its overuse and mismanagement created significant environmental challenges (Rockstrom et al., 2009; Richardson et al., 2023). Biological Nitrogen Fixation (BNF) by diazotrophic bacteria and symbiotic nitrogen fixation (SNF) by N-fixing plants offer age-old solutions to the N-problem (Adams et al., 2018).