Biology subjects

Ramachandran, V.

Publications and source records attributed to Ramachandran, V..

At least 19 recordsLinked to original sources

bioRxiv2026

Purification and characterization of recombinant Rtt109, a fungus-specific histone acetyltransferase, from Candida albicans

Epigenetic regulation of chromatin dynamics via histone acetylation is one of several mechanisms by which eukaryotes regulate gene expression, DNA replication and repair, and maintain genome stability. This function is performed by histone acetyltransferases (HATs). Rtt109 is one such cytoplasmically localized HAT required for H3K56 acetylation found exclusively in fungi. Using recombinantly expressed Candida albicans Rtt109 and its chaperones, Vps75 and Asf1, we show that it can acetylate a 20-residue N-terminal H3 peptide in a coupled HAT assay only in the presence of Vps75, but not in the presence of Asf1 in vitro. This appears to be due to the fact that Rtt109-Vps75 is a high affinity stable complex, as estimated by biolayer interferometry (BLI) and gel filtration studies. The HAT activity of the Rtt109-Vps75 complex necessarily requires a flexible 118-160 residue loop of Rtt109 but not the C-terminal domain of Vps75. These results are comparable with what has been observed for the Saccharomyces cerevisiae Rtt109 homolog. In silico screening of 1,350,000 molecules from Life Chemicals Databases identified some likely inhibitors of C. albicans Rtt109 and six of them tested for binding to Rtt109 using BLI. The best ligand, F2368-0266, was used to study its effect on steady state enzyme kinetics, and found to be a competitive inhibitor of the peptide substrate but not of acetyl-CoA. Given the importance of Rtt109 in regulating virulence attributes such as hyphal morphogenesis and GPI biosynthesis in Candida albicans, and its effect on fungal pathogenesis, these results have significant clinical implications.

biochemistry↗

bioRxiv2026

A molecular grammar for programmable multiphase protein-RNA vesicles

Protein-RNA phase separation gives rise to biomolecular condensates with rich internal organization, yet the molecular rules that connect sequence-encoded interactions and composition to the emergent architecture of these condensates remain poorly defined. Here, using large-scale residue-level coarse-grained simulations, we identify a molecular grammar that governs the formation and stability of multiphase protein-RNA condensates. We show that asymmetries in protein-protein and protein-RNA interactions, together with protein stoichiometry, chain length, and condensate density, collectively determine whether condensates adopt homogeneous, layered, biphasic, or vesicle-like morphologies. Across a broad parameter space, these rules yield hollow multiphase vesicles with dense shells surrounding dilute interiors. Remarkably, vesicular condensates form spontaneously from well-mixed initial conditions, without requiring flux-driven oversaturation or extreme charge imbalance, distinguishing this mechanism from previously proposed routes to condensate hollowing. Our results establish minimal and general design principles for programming internal condensate architecture solely through sequence and composition, and provide a framework for engineering membrane-free vesicles and multilayered condensates with tunable permeability, encapsulation, and responsiveness.

biophysics↗

bioRxiv2025

What's next for Indian Ornithology? 101 key research questions

India has a rich history of ornithology, and bird research in this field has expanded considerably in recent decades, spurred by a growing number of birdwatchers and ornithologists. Despite this progress, critical gaps remain. This paper highlights key areas where further research is needed and identifies pressing questions that will shape Indian ornithology in the coming years. Drawing from diverse inputs, we present a curated list of 101 research questions spanning across the various disciplines in ornithology - Natural History, Physiology and Disease Ecology, Behaviour, Population and Community Ecology, Habitat Ecology, Macroecology and Biogeography, Population Genetics and Evolution, Applied/Economic Ornithology and Conservation. The list was compiled through a multi-stage process, starting with a public open call for questions, followed by review and curation by a smaller panel of subject specialists. Each question was independently scored by a panel of experts based on three criteria: generality, novelty, and relevance. To account for variation in scoring styles, scores were normalised using Z-scores. The top 101 research questions were then selected based on these standardised scores. Each question is accompanied by an annotation that describes the significance of the question, and highlights opportunities to address it. While our list of research questions highlights significant research priorities, it is not intended to be exhaustive. Rather, it reflects the perspectives of those involved in its curation, who deemed these questions particularly relevant and impactful towards advancing Indian ornithology. We expect these questions to spark new project ideas among students, researchers, and citizen scientists, while guiding funders, managers, and policymakers toward priority research areas.

ecology↗

bioRxiv2025

Molecular Drivers of RNA Phase Separation

RNA molecules are essential in orchestrating the assembly of biomolecular condensates and membraneless compartments in cells. Many condensates form via the association of RNA with proteins containing specific RNA binding motifs. However, recent reports indicate that low-complexity RNA sequences can self-assemble into condensate phases without protein assistance. Divalent cations significantly influence the thermodynamics and dynamics of RNA condensates, which exhibit base-specific lower-critical solution temperatures (LCST). The precise molecular origins of these temperatures remain elusive. In this study, we employ atomistic molecular simulations to elucidate the molecular driving forces governing the temperature-dependent phase behavior of RNA, providing new insights into the origins of LCST. Using RNA tetranucleotides and their chemically modified analogs, we map RNA condensates equilibrium thermodynamic profiles and structural ensembles across various temperatures and ionic conditions. Our findings reveal that magnesium ions promote LCST behavior by inducing local order-disorder transitions within RNA structures. Consistent with experimental observations, we demonstrate that the thermal stability of RNA condensates follows the Poly(G) > Poly(A) > Poly(C) > Poly(U) order shaped by the interplay of base-stacking and hydrogen bonding interactions. Furthermore, our simulations show that ionic conditions and post-translational modifications can fine-tune RNA self-assembly and modulate condensate physical properties. Author SummaryRNA molecules are essential for organizing membraneless compartments that play critical roles in cellular processes. While many of these condensates form through interactions between RNA and proteins, recent studies have shown that certain RNA sequences can self-assemble into condensates without protein assistance. This ability is influenced by the sequence composition of RNA and the presence of ions like magnesium. Using detailed molecular simulations we carried out systematic study to reveal how temperature and ionic conditions affect RNA condensation. We discovered that magnesium ions play a key role in driving RNA molecules to condense at lower temperatures by promoting structural changes within the RNA. Our findings also revealed that the stability of RNA condensates varies depending on the RNA sequence, with guanine-rich sequences being the most stable. Additionally, we demonstrated how chemical modifications and ionic conditions can fine-tune the properties of RNA condensates. This study provides new insights into how RNA forms condensates and highlights potential strategies to control their behavior, which could have implications for understanding cellular organization and developing new therapies.

biophysics↗

bioRxiv2024

Nucleoprotein phase-separation affinities revealed via atomistic simulations of short peptide and RNA fragments

Liquid-liquid phase separation of proteins and nucleic acids into condensate phases is a versatile mechanism for ensuring compartmentalization of cellular biochemistry. RNA molecules play critical roles in these condensates, particularly in transcriptional regulation and stress responses, exhibiting a wide range of thermodynamic and dynamic behaviors. However, deciphering the molecular grammar that governs the stability and dynamics of protein-RNA condensates remains challenging due to the multicomponent and heterogeneous nature of these biomolecular mixtures. In this study, we employ atomistic simulations of twenty distinct mixtures containing minimal RNA and peptide fragments to dissect the phase-separating affinities of all twenty amino acids in the presence of RNA. Our findings elucidate chemically specific interactions, hydration profiles, and ionic effects that synergistically promote or suppress protein-RNA phase separation. We map a ternary phase diagram of interactions, identifying four distinct groups of residues that promote, maintain, suppress, or disrupt protein-RNA clusters.

biophysics↗

bioRxiv2024

State of India's Birds 2023: A framework to leverage semi-structured citizen science for bird conservation

Birds and their habitats are threatened with extinction around the world. Regional assessments of the State of Birds are a vital means to prioritize data-driven conservation action by informing national and global policy. Such evaluations have traditionally relied on data derived from extensive, long-term, systematic surveys that require significant resources, limiting their feasibility to a few regions in the world. In the absence of such structured long-term datasets, semi-structured datasets have recently emerged as a promising alternative in other regions around the world. Semi-structured data are generated and uploaded by birdwatchers to citizen science platforms like eBird. Such data contain inherent biases because birdwatchers are not required to adhere to a fixed protocol. An evaluation of the status of birds from semi-structured data is therefore a difficult task that requires careful curation of data and the use of robust statistical methods to reduce errors and biases. In this paper, we present a methodology that was developed for this purpose, and was applied to produce the comprehensive State of Indias Birds (SoIB) 2023 report. SoIB 2023 assessed the status of 942 bird species in India by evaluating each species based on three metrics: 1) long-term change: change in abundance between the year 2022 and the year-interval pre-2000; 2) current annual trend: mean annual change in abundance from 2015 to 2022; and 3) distribution range size. We found evidence that 204 species have declined in the long term, and 142 species are currently declining. We present and discuss important insights about Indias birds that can guide research and conservation action in the region. We hope that the detailed methodology described here can act as a blueprint to produce State of Birds assessments from semi-structured citizen science datasets and springboard conservation action in many other regions where structured data is lacking but strong communities of birders exist. Open Research StatementThe primary data are already publicly available on eBird (Sullivan et al. 2014), and other data are already published in a GitHub repository (stateofindiasbirds 2024).

ecology↗

bioRxiv2024

MicroRNA-374b regulates SARS-CoV-2 viral protein mediated endothelial to mesenchymal transition by targeting c-FLIP

The pathophysiological consequences of COVID-19 disease are still unclear, however, endothelial cell (EC) dysfunction has been observed to play a key role in disease progression and severity. Many reports suggests that SARS-CoV-2 mediated endothelial dysfunction is the result of intracellular signaling initiated by the binding of the spike protein to ACE2, which can modify endothelial cell phenotype. Recent reports suggests endothelial to mesenchymal transition (Endo MT) as a process heavily involved in lung fibrosis of COVID 19 patients. EndoMT is involved in many chronic and fibrotic diseases and appears to be regulated by complex molecular mechanisms and different signaling pathways, in particular microRNAs (miRNAs), which constitute a crucial mediator of EndoMT. MicroRNAs (miRNAs), small endogenous RNA molecules that regulate several physiological processes including endothelial homeostasis, and vascular diseases, can be perturbed by infecting viruses. Based on these facts, this study was designed to decipher the role of miR-374b, which was found to be significantly downregulated upon profiling of SARS-CoV-2 viral protein stimulated endothelial cells. Gene profiling of endothelial cells revealed c-FLIP (CFLAR) to be among the most significantly upregulated gene. In silico target prediction analysis using targetscan revealed c-FLIP as the major target of miR-374b. Further it was identified that miR-374b can reverse c-FLIP mRNA and protein levels in SARS-CoV-2 viral protein stimulated endothelial cells under conditions of miR-374b overexpression. Since vascular dysfunction involve, under many circumstances, loss of vascular tone due to mesenchymal transition of endothelial cells, we next checked if fibrotic events are initiated downstream of c-FLIP pathway. Further mechanistic studies involving identification of the expression pattern of mesenchymal markers in SARS-CoV-2 viral protein stimulated endothelial cells in presence or absence of miR-374b provide evidence for the important role of miR-374b in regulating SARS CoV-2 mediated EndoMT and fibrotic events downstream of c-FLIP pathway and may highlight possible new therapeutic approaches targeted at the damaged endothelium.

molecular biology↗

bioRxiv2023

Mapping energy landscapes of homopolymeric RNAs via simulated tempering and deep unsupervised learning

Conformational dynamics plays crucial roles in RNA functions about sensing and responding to environmental signals. The liquid-liquid phase separation of RNAs and the formation of stress granules partly relies on RNAs conformational plasticity and its ability to engage in multivalent interactions. Recent experiments with homopolymeric and low-complexity RNAs have revealed significant differences in phase separations due to differences in base chemistry of RNA units. We hypothesize that differences in RNA phase-transition dynamics can be traced back to the differences in conformational dynamics of single RNA chains. In the present contribution, we utilize atomistic simulations with numerous unsupervised learning to map temperature dependence conformational free energy landscapes for homopolymeric RNA chains. These landscapes reveal a variety of metastable excited states influenced by the nature of base chemistry. We shed light on the distinct contributions of the polyphosphate backbone versus base chemistry in shaping conformational ensembles of different RNAs. We demonstrate that the experimentally observed temperature-driven shifts in metastable state populations align with experimental phase diagrams for homopolymeric RNAs. The work establishes a microscopic framework to reason about base-specific RNA propensity for phase separation. We believe our work will be valuable for designing novel RNA sensors for biological and synthetic applications.

biophysics↗

bioRxiv2023

Host-pathogen-vector continuum in a changing landscape: Drivers of Bartonella prevalence and evidence of historic spillover in a tropical multi-host community

Small mammals and their ectoparasites present a unique system to investigate the eco-epidemiology of multi-host vector-borne pathogens and identify specific bacterial spillover determinants. We applied ecological and evolutionary analyses in a rainforest-human-use mosaic to investigate Bartonella spp. across small mammal and ectoparasite communities. We observed substantial overlap among small mammal communities in different habitat types, predominantly driven by habitat generalists. Most ectoparasites were generalists, infecting multiple hosts. We observed high Bartonella prevalence at both study sites -a forest-plantation mosaic (47.4%) and a protected area (28.8%). Seven of the ten ectoparasite species sampled were also positive for Bartonella, following prevalence trends in their hosts. A generalised linear model revealed an independent association between aggregated ectoparasite load in hosts and Bartonella prevalence, implicating ectoparasites in transmission. Bartonella lineages from small mammals were host-specific, while ectoparasites carried Bartonella associated with other small mammal hosts, indicating the potential for cross-species transmission. Phylogenetic ancestral trait reconstruction of Bartonella haplotypes suggest historic spillover events in the small mammal community, validating the potential for contemporary spillover events. These results highlight the necessity to disentangle the complex relationship between hosts, ectoparasites, and pathogens to understand the zoonotic implications of undetected spillover events in such multi-host communities.

ecology↗

bioRxiv2023

Barley cultivars shape the abundance, phenotype, genotype and gene expression of their associated microbiota by differential root exudate secretion

Plant associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley cultivars. Distinct differences were observed between the plant-associated microbiomes of the two cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites, and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.

microbiology↗

bioRxiv2023

Frugivory and seed predation of fishtail palm (Caryota mitis Lour.) on the remote oceanic island of Narcondam, India

Oceanic islands, due to their evolutionary history and isolation, hold a disproportionately high proportion of endemic species. However, their evolutionary history also makes them vulnerable to extinctions, with most known extinctions occurring on islands. Plant-animal interactions are particularly important on islands, as island systems generally have low redundancy and are more vulnerable to disruption either via extinction or by invasive species. Here, we examined the fruit removal and seed predation of a keystone palm, Caryota mitis, on the remote oceanic island of Narcondam. The island endemic Narcondam hornbill (Rhyticeros narcondami), was the sole seed disperser of the Caryota mitis (90 hours; N = 15 trees), indicating a lack of redundancy in seed dispersal of the palm on this island. While the invasive rodent, Rattus cf. tiomanicus was the sole predator of the Caryota mitis seeds in the forest (N = 15 individual fruiting palms, 416 trap nights). Overall, 17.1% of the seeds placed (N = 375 seeds) were removed. Seeds placed under and away from the canopy, and at different densities (2 plots with 10 seeds each; 1 plot with 5 seeds, respectively), showed similar removal rates. This is indicative of ambient seed predation and the lack of safe sites for the regeneration of Caryota mitis, with potential deleterious effects on the subsequent stages of the "seed dispersal cycle". Here, from a data deficient site, we provide baseline information on the plant-frugivore interaction of a keystone palm and the potential impacts by an invasive rodent.

ecology↗

bioRxiv2022

Factors governing attachment of Rhizobium leguminosarum to legume roots

Primary attachment of rhizobia to host legume roots depends on pH and is the first physical interaction during nodulation. Genome-wide insertion sequencing, luminescence-based attachment assays and proteomic analysis demonstrate primary attachment of Rhizobium leguminosarum biovar viciae 3841 to Pisum sativum (pea) roots is more complex than previously thought. In total, 115 proteins are needed for initial attachment under one or more test conditions (acid, neutral or alkaline pH), with 22 required under all conditions. These include cell-surface filamentous hemagglutinin adhesin (RL4382) and its transporter (RL4381), transmembrane protein RL2400, RL3752 (PssA, glycosyl transferase) affecting capsular polysaccharide and transcriptional regulator RL4145 (PckR). RNASeq was used to determine targets of RL4145 (PckR) and regulator RL3453. The 54 proteins required for attachment at pH 7.0 were investigated for nodulation phenotypes. Glucomannan biosynthesis protein A (GmsA) is needed at pH 6.5 and pH 7.0. Membrane proteins DgkA and ImpA are required specifically at pH 6.5, and RpoZ at pH 7.5. Sonicated cell surface fractions inhibited root attachment at alkaline pH but no overlap between proteins identified by proteomic and INseq analysis, suggests there is no single rhicadhesin needed for alkaline attachment. Our results demonstrate the complexity of primary root attachment and diversity of mechanisms involved.

microbiology↗

bioRxiv2022

Mosaic chromosomal alterations in blood across ancestries via whole-genome sequencing

Mosaic mutations in blood are common with increasing age and are prognostic markers for cancer, cardiovascular dysfunction and other diseases. This group of acquired mutations include megabase-scale mosaic chromosomal alterations (mCAs). These large mutations have mainly been surveyed using SNP array data from individuals of European (EA) or Japanese genetic ancestry. To gain a better understanding of mCA rates and associated risk factors in genetically diverse populations, we surveyed whole genome sequencing data from 67,390 individuals, including 20,132 individuals of African ancestry (AA), and 7,608 of Hispanic ancestry (HA) with deep (30X) whole genome sequencing data from the NHLBI Trans Omics for Precision Medicine (TOPMed) program. We adapted an existing mCA calling algorithm for application to WGS data, and observed higher sensitivity with WGS data, compared with array-based data, in uncovering mCAs at low mutant cell fractions. As in previous reports, we observed a strong association with age and a non-uniform distribution of mCAs across the genome. The presence of autosomal (but not chromosome X) mCAs was associated with an increased risk of both lymphoid and myeloid malignancies. After adjusting for age, we found that individuals of European ancestry have the highest rates of autosomal mCAs, mirroring the higher rate of leukemia in this group. Our analysis also uncovered higher rates of chromosome X mCAs in AA and HA compared to EA, again after adjusting for age. Germline variants in ATM and MPL showed strong associations with mCAs in cis, including ancestry specific variants. And rare variant gene-burden analysis confirmed the association of putatively protein altering variants in ATM and MPL with mCAs in cis. Individual rare variants in DCPS, ADM17, PPP1R16B, and TET2 were all associated with autosomal mCAs and rare variants in OR4C16 were associated with chromosome X mCAs in females. There was significant enrichment of co-occurrence of CHIP mutations and mCAs both altering cancer associated genes TET2, DNMT3A, JAK2, CUX1, and TP53. Overall, our study demonstrates that rates of mCAs differ across populations and that rare inherited germline variants are strongly associated with mCAs across genetically diverse populations. These results strongly motivate further studies of mCAs in under-represented populations to better understand the causes and consequences of this class of somatic variation.

genomics↗

bioRxiv2022

Novel inhibitors against COVID-19 main protease suppressed viral infection

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19, can cause severe disease with high mortality rates, especially among older and vulnerable populations. Despite the recent success of vaccines and approval of first-generation anti-viral inhibitor against SARS-CoV-2, an expanded arsenal of anti-viral compounds that limit viral replication and ameliorate disease severity is still urgently needed in light of the continued emergence of viral variants of concern (VOC). The main protease (Mpro) of SARS-CoV-2 is the major non-structural protein required for the processing of viral polypeptides encoded by the open reading frame 1 (ORF1) and ultimately replication. Structural conservation of Mpro among SARS-CoV-2 variants make this protein an attractive target for the anti-viral inhibition by small molecules. Here, we developed a structure-based in-silico screening of approximately 11 million compounds in ZINC15 database inhibiting Mpro, which prioritized 9 lead compounds for the subsequent in vitro validation in SARS-CoV-2 replication assays using both Vero and Calu-3 cells. We validated three of these compounds significantly inhibited SARS-CoV-2 replication in the micromolar range. In summary, our study identified novel small-molecules significantly suppressed infection and replication of SARS-CoV-2 in human cells.

pathology↗

bioRxiv2022

Genomic expression responses in sensu stricto Saccharomyces yeast to DNA damage induced by methyl methanesulfonate

BackgroundOne way single-celled eukaryotes respond to DNA damage stress is by modifying their gene expression, facilitating genomic repair. Gene expression responses to DNA damage induced by methyl methanesulfonate (MMS) have been studied in the model organism Saccharomyces cerevisiae. However, lacking are investigations of the MMS stress responses in evolutionarily-related sensu stricto Saccharomyces species, including Saccharomyces cerevisiae. MethodsNext-generation Illumina RNA-sequencing was to characterize the entire transcriptomes of four evolutionarily-related species of yeast, S. cerevisiae, S. paradoxus, S. mikatae, and S. bayanus, under control and experimental (MMS) conditions. Subsequent genomic studies included gene set enrichment analysis, promoter analysis, and concentration gradient studies. ResultsS. mikitae and S. paradoxus grew well in light of MMS while S. bayanus showed no growth. While there was fair overlap in induced and repressed genes, overall each species had unique expression responses. S. paradoxus and S. bayanus showed the most distinct changes with the former greatly inhibiting a large segment of its genome while the latter induced such segments. Gene set enrichment analysis revealed significantly modulated biologic, cellular, and molecular processes in each species. Promoter analysis revealed sets of induced/repressed transcription factors for genes highly modulated in the stress response. Concentration gradient studies of S. cerevisiae showed linear increase in gene expression of RAD54, DIN7, and IRC19 in response to increasing concentrations of MMS. ConclusionOverall, we depict the transcriptome changes of four evolutionarily-related sensu stricto yeast species and several functional genomic analyses to provide a novel understanding of their responses to MMS.

genomics↗

bioRxiv2021

Genome-scale metabolic modelling of lifestyle changes in Rhizobium leguminosarum

Biological nitrogen fixation in rhizobium-legume symbioses is of major importance for sustainable agricultural practices. To establish a mutualistic relationship with their plant host, rhizobia transition from free-living bacteria in soil to growth down infection threads inside plant roots and finally differentiate into nitrogen-fixing bacteroids. We reconstructed a genome-scale metabolic model for Rhizobium leguminosarum and integrated the model with transcriptome, proteome, metabolome and gene essentiality data to investigate nutrient uptake and metabolic fluxes characteristic of these different lifestyles. Synthesis of leucine, polyphosphate and AICAR is predicted to be important in the rhizosphere, while myo-inositol catabolism is active in undifferentiated nodule bacteria in agreement with experimental evidence. The model indicates that bacteroids utilize xylose and glycolate in addition to dicarboxylates, which could explain previously described gene expression patterns. Histidine is predicted to be actively synthesized in bacteroids, consistent with transcriptome and proteome data for several rhizobial species. These results provide the basis for targeted experimental investigation of metabolic processes specific to the different stages of the rhizobium-legume symbioses. ImportanceRhizobia are soil bacteria that induce nodule formation on plant roots and differentiate into nitrogen-fixing bacteroids. A detailed understanding of this complex symbiosis is essential for advancing ongoing efforts to engineer novel symbioses with cereal crops for sustainable agriculture. Here, we reconstruct and validate a genome-scale metabolic model for Rhizobium leguminosarum bv. viciae 3841. By integrating the model with various experimental datasets specific to different stages of symbiosis formation, we elucidate the metabolic characteristics of rhizosphere bacteria, undifferentiated bacteria inside root nodules, and nitrogen-fixing bacteroids. Our model predicts metabolic flux patterns for these three distinct lifestyles, thus providing a framework for the interpretation of genome-scale experimental datasets and identifying targets for future experimental studies.

systems biology↗

bioRxiv2020

The critical ecological role of an endemic, large-bodied frugivore on a small tropical island

Endozoochory, a mutualistic interaction between plants and frugivores, is one of the key processes responsible for maintenance of tropical biodiversity. Islands, which have a smaller subset of plants and frugivores when compared with mainland communities, offer an interesting setting to understand the organization of plant-frugivore communities vis-a-vis the mainland sites. We examined the relative influence of functional traits and phylogenetic relationships on the plant-seed disperser interactions on an island and a mainland site. The island site allowed us to investigate the organization of the plant-seed disperser community in the natural absence of key frugivore groups (bulbuls and barbets) of Asian tropics. The endemic Narcondam Hornbill, was the most abundant frugivore on the island and played a central role in the community. Species strength, a measure of relevance of frugivores for plants, of frugivores was positively associated with their abundance. Among plants, figs had the highest species strength and played a central role in the community. Island-mainland comparison revealed that the island plant-seed disperser community was more asymmetric, connected and nested as compared to the mainland community. Neither phylogenetic relationships or functional traits (after controlling for phylogenetic relationships) were able to explain the patterns of interactions between plants and frugivores on the island or the mainland pointing towards the diffused nature of plant-frugivore interactions. The diffused nature is a likely consequence of plasticity in foraging behavior and trait convergence that contribute to governing the interactions between plants and frugivores.

ecology↗

bioRxiv2020

Lifestyle adaptations of Rhizobium from rhizosphere to symbiosis

By analyzing successive lifestyle stages of a model Rhizobium-legume symbiosis using mariner-based transposon insertion sequencing (INSeq), we have defined the genes required for rhizosphere growth, root colonization, bacterial infection, N2-fixing bacteroids and release from legume (pea) nodules. While only 27 genes are annotated as nif and fix in Rhizobium leguminosarum, we show 603 genetic regions (593 genes, 5 tRNAs and 5 RNA features) are required for the competitive ability to nodulate pea and fix N2. Of these, 146 are common to rhizosphere growth through to bacteroids. This large number of genes, defined as rhizosphere-progressive, highlights how critical successful competition in the rhizosphere is to subsequent infection and nodulation. As expected, there is also a large group (211) specific for nodule bacteria and bacteroid function. Nodule infection and bacteroid formation require genes for motility, cell envelope restructuring, nodulation signalling, N2 fixation, and metabolic adaptation. Metabolic adaptation includes urea, erythritol and aldehyde metabolism, glycogen synthesis, dicarboxylate metabolism and glutamine synthesis (GlnII). There are separate lifestyle adaptations specific to rhizosphere growth (17) and root colonization (23), distinct from infection and nodule formation. These results dramatically highlight the importance of competition at multiple stages of a Rhizobium-legume symbiosis. SignificanceRhizobia are soil-dwelling bacteria that form symbioses with legumes and provide biologically useable nitrogen as ammonium for the host plant. High-throughput DNA sequencing has led to a rapid expansion in publication of complete genomes for numerous rhizobia, but analysis of gene function increasingly lags gene discovery. Mariner-based transposon insertion sequencing (INSeq) has allowed us to characterize the fitness contribution of bacterial genes and determine those functionally important in a Rhizobium-legume symbiosis at multiple stages of development.

microbiology↗