Biology subjects

Sowdhamini, R.

Publications and source records attributed to Sowdhamini, R..

30 records · Page 2Linked to original sources

bioRxiv2022

A Dimer between Monomers and Hexamers - Oligomeric Variations in Glucosamine 6-Phosphate Deaminase Family

In bacteria that live in hosts whose terminal sugar is a sialic acid, Glucosamine 6-phosphate deaminase (NagB) catalyzes the last step in the conversion of sialic acid into Fructose-6-phosphate, which enters the glycolytic pathway. The enzyme exists as a hexamer in Gram-negative bacteria and is shown to be allosterically regulated. In Gram-positive bacteria, it exists as a monomer and lacks allosteric regulation. Our identification of a dimeric Gram-negative bacterial NagB motivated us to characterize the structural basis of the various oligomeric forms. We characterized the crystal structures of NagB from two Gram-negative pathogens, Haemophilus influenzae (Hi) and Pasturella multocida (Pm). The Hi-NagB is active as a hexamer, while Pm-NagB is active as a dimer. We confirm that this is not a crystallographic artifact by cryo-electron microscopy. Both Hi-NagB and Pm-NagB contain the C-terminal helix, and the residues in the interface involved in oligomerization are conserved. The hexamer is described as a dimer of trimers. In the Pm-NagB dimer, the dimeric interface is conserved. This would suggest that the three possible oligomeric forms of NagB are a monomer, a dimer, and a trimer of dimers. Computational modeling and MD simulations indicate that the residues at the trimeric interface have less stabilizing energy of oligomer formation than those in the dimer interface. We propose that Pm-NagB is the evolutionary link between the monomer and the hexamer forms.

biochemistry↗

bioRxiv2021

LIM domain-wide comprehensive mutagenesis reveals the role of leucine in CSRP3 protein stability

Cardiomyopathies are a severe and chronic cardiovascular burden worldwide, affecting a large cohort in the general population. Cysteine and glycine-rich protein 3 (CSRP3) is one of key proteins implicated in dominant dilated cardiomyopathy (DCM) and hypertrophic cardiomyopathy (HCM). In this study, we device a rapid in-silico screening protocol that creates a mutational landscape map for all possible allowed and disallowed substitutions in the protein of interest. This map provides the structural and functional insights on the stability of LIM domains of CSRP3. Further, the sequence analysis delineates the eukaryotic CSRP3 protein orthologs which complements the mutational map. Next, we also evaluated the effect of HCM/DCM mutations on these domains. One of highly destabilising mutations - L44P (also disease causing) and a neutral mutation - L44M were further subjected to molecular dynamics (MD) simulations. The results establish that L44P substitution affects the LIM domain structure. The present study provides a useful perspective to our understanding of the role of mutations in the CSRP3 LIM domains and their evolution. Experimentally verifying every reported mutation can become challenging both in time and resources used. This study provides a novel screening method for quick identification of key mutation sites for specific protein structures that can reduce the burden on experimental research.

bioinformatics↗

bioRxiv2021

De-novo draft genome sequence of Crocus Sativus L, Saffron, a golden condiment.

Crocus sativus L, saffron is the highest priced but low yielding plant of medicinal and culinary importance. Despite its economic status, the omic information on this plant is very scarce, with only a couple of transcriptomics and epigenetic studies. In the present study, the draft genome sequence of C. sativus has been assembled using Illumina sequencing. In fact, this is the first genome sequence from any member of family Iridaceae. Genome size of C. sativus was estimated to be 3.5 Gb and the draft genome is 3.01 Gb long with 84.24% genome coverage. In total, 8,62,275 repeats and 9,64,231 SSR markers have been identified. A total of 53,546 functional genes were annotated, out of which, 43,649 proteins were associated with GO annotation. 5726 proteins were identified as transcription factors, with MYB & MYB related family proteins being more abundant. Orthology analysis of C. sativus with 3 different monocot species of the same plant order and rice (model monocot plant) revealed 7328 proteins clusters to be conserved in all the five plant species, whereas 2510 proteins cluster were unique to C. sativus only. 10,912 unigenes of C. sativus were mapped to 387 KEGG pathways of monocot. The genes involved in the pathway of apocarotenoids biosynthesis (crocin, crocetin, picrocrocin, and safranal) were present in the draft genome.

genomics↗

bioRxiv2021

Chasing the cardiomyopathy modifier genes: Integrative computational analysis interweave the missing links in cardiomyopathy diseasome

Cardiomyopathies are progressive disease conditions that give rise to an abnormal heart phenotype and are a leading cause of heart failures in the general population. These are complex diseases that show co-morbidity with other diseases. The molecular interaction network in the localised disease neighbourhood is an important step toward deciphering molecular mechanisms underlying these complex conditions. In this pursuit, we employed network medicine techniques to systematically investigate cardiomyopathys genetic interplay with other diseases and uncover the molecular players underlying these associations. We predicted a set of candidate genes in cardiomyopathy by exploring the DIAMOnD algorithm on the human interactome. We next revealed how these candidate genes form association across different diseases and highlighted the predominant association with brain, cancer and metabolic diseases. Through integrative systems analysis of molecular pathways, heart-specific mouse knockout data and disease tissue-specific transcriptomic data, we screened and ascertained prominent candidates that show abnormal heart phenotype, including NOS3, MMP2 and SIRT1. Our computational analysis broadens the understanding of the genetic associations of cardiomyopathies with other diseases and holds great potential in cardiomyopathy research.

bioinformatics↗

bioRxiv2021

Genome-wide survey of odorant-binding proteins in the dwarf honey bee Apis florea

Odorant binding proteins (OBPs) in insects bind to volatile chemical cue and help in their binding to odorant receptors. The odor coding hypothesis states that OBPs may bind with specificity to certain volatiles and aid the insect in various behaviours. Honeybees are eusocial insects with complex behaviour that requires olfactory inputs. Here, we have identified and annotated odorant binding proteins from the genome of the dwarf honey bee, Apis florea using an exhaustive homology-based bioinformatic pipeline and analyzed the evolutionary relationships between the OBP subfamilies. Our study suggests that Minus-C subfamily may have diverged from the Classic subfamily of odorant binding proteins in insects.

bioinformatics↗

bioRxiv2021

Disulfide-rich, cyclic peptides from Clitoria ternatea protect against β-amyloid toxicity and oxidative stress in transgenic Caenorhabditis elegans

Neurotoxic aggregation of {beta}-amyloid (A{beta}) peptide is a hallmark of Alzheimers disease and increased reactive oxygen species (ROS) is known to be associated with this. Here, we report neuroprotective effects of disulfide-rich, circular peptides from Clitoria ternatea on A{beta}-induced toxicity in transgenic Caenorhabditis elegans. We show that cyclotide-rich fractions from different plant tissues delay A{beta}-induced paralysis in transgenic CL4176 strain expressing human muscle-specific A{beta}1-42 gene. It also improved A{beta}-induced defects in chemotaxis in CL2355 expressing A{beta}1-42 in neuronal cells. ROS assay suggests that this is likely mediated by inhibition of A{beta} oligomerization. Further, A{beta} deposits were reduced in the strain, CL2006 treated with the fractions. Computational docking and molecular dynamics (MD) simulation support the findings since cyclotides bind effectively and stably to different forms of A{beta} structures via hydrogen bonding and hydrophobic interactions. MD simulation further shows that cyclotides destabilize toxic amyloid assemblies. The study shows that cyclotides from C. ternatea could be a source of novel pharmacophore scaffold against neurodegenerative diseases.

plant biology↗

bioRxiv2021

DDX24, a D-E-A-D box RNA helicase, is required for muscle fiber organization and anterior pole specification essential for head regeneration in planarians.

Planarians have a remarkable ability to undergo whole-body regeneration. The timely establishment of polarity at the wound site followed by the specification of the organizing centers- the anterior pole and the posterior pole, are indispensable for successful regeneration. In planarians, polarity, pole, and positional-information determinants are predominantly expressed by muscles. The molecular toolkit that enables this functionality of planarian muscles however remains poorly understood. Here we report that SMED_DDX24, a D-E-A-D Box RNA helicase and the homolog of human DDX24, is critical for planarian head regeneration. DDX24 is enriched in muscles and its knockdown leads to defective muscle-fiber organization and failure to re-specify anterior pole/organizer. Overall, loss of DDX24 manifests into gross misregulation of many well-characterized positional-control genes and patterning-control genes, necessary for organogenesis and tissue positioning and tissue patterning. In addition, wound-induced Wnt signalling was also upregulated in ddx24 RNAi animals. Canonical WNT-{beta}CATENIN signalling is known to suppress head identity throughout bilateria, including planarians. Modulating this Wnt activity by {beta}-catenin-1 RNAi, the effector molecule of this pathway, partially rescues the ddx24 RNAi phenotype, implying that a high Wnt environment in ddx24 knockdown animals likely impedes their normal head regeneration. Furthermore, at a sub-cellular level, RNA helicases are known to regulate muscle mass and function by regulating their translational landscape. ddx24 knockdown leads to the downregulation of large subunit ribosomal RNA and the 80S ribosome peak, implying its role in ribosome biogenesis and thereby influencing the translational output. This aspect seems to be an evolutionarily conserved role of DDX24. In summary, our work demonstrates the role of a D-E-A-D box RNA helicase in whole-body regeneration through muscle fiber organization, and pole and positional-information re-specification, likely mediated through translation regulation.

developmental biology↗

bioRxiv2020

DEELIG: A Deep Learning-based approach to predict protein-ligand binding affinity

Protein-ligand binding prediction has extensive biological significance. Binding affinity helps in understanding the degree of protein-ligand interactions and has wide protein applications. Protein-ligand docking using virtual screening and molecular dynamic simulations are required to predict the binding affinity of a ligand to its cognate receptor. In order to perform such analyses, it requires intense computational power and it becomes impossible to cover the entire chemical space of small molecules. Recent developments using deep learning has enabled us to make sense of massive amounts of complex datasets where the ability of the model to "learn" intrinsic patterns in a complex plane of data is the strength of the approach. Here, we have incorporated Convolutional Neural Networks to find spatial relationships amongst data to help us predict affinity of binding of proteins in whole superfamilies towards a diverse set of ligands without the need of a docked pose or complex as input. The models were trained and validated using a detailed methodology for feature extraction. We have also tested DEELIG on protein complexes relevant to the current public health scenario. Our approach to network construction and training on protein-ligand dataset prepared in-house has yielded novel insights.

bioinformatics↗

bioRxiv2020

Molecular and functional characterization of buffalo nasal epithelial odorant binding proteins and their structural insights by in-silico and biochemical approach

The olfactory system is capable of detecting and distinguishing thousands of environmental odorants that play a key role in reproduction, social behaviours including pheromones influenced classical events. Membrane secretary odorant binding proteins (OBPs) are soluble lipocalins, localized in the nasal membrane of mammals. They bind and carry odorants within the nasal epithelium to putative olfactory transmembrane receptors (ORs). While the existence of OBPs and their significant functions are very well known in insects and laboratory mammals, there is little information about the species-specific OBPs in buffaloes. In fact, the OBP of nasal epithelium has not yet been exploited to develop a suitable technique to detect estrus which is being reported as a difficult task in buffalo. In the present study, using molecular biology and protein engineering approaches, we have cloned six novel OBP isoforms from buffalo nasal epithelium (bnOBPs). Furthermore, 3D model was developed and molecular-docking, dynamics experiments were performed by In-silico approach. In particular, we found four residues (Phe104, Phe134, Phe69 and Asn118) from OBP1a, which had strong binding affinities towards two sex pheromones, specifically oleic acid and p-cresol. We expressed this protein in Escherichia coli to examine its involvement in the sex pheromone perception from female buffalo urine and validated through fluorescence quenching studies. Interestingly, fluorescence binding experiments also showed similar strong binding affinities of OBP1a to oleic acid and p-cresol. By using structural data, the binding specificity is also verified by site-directed mutagenesis of the four residues followed by in-vitro binding assays. Our results enable to better understand the functions of different nasal epithelium OBPs in buffaloes. They also lead to improved understanding of the interaction between olfactory proteins and odorants to develop highly selective biosensing devices for non-invasive detection of estrus in buffaloes.

bioinformatics↗

bioRxiv2020

Heterogeneous distribution of mRNAs within flight muscle fibers, and implications for function

Muscle heterogeneity has been explored in terms of fiber-type distribution, structural organisation, and differences at their junctions with neurons and tendons. We amplify on such observation to additionally suggest that muscle syncytia have nonuniform protein requirements along their length, deployed for developmental and functional uses. An exploration of regionalized proteins or their mRNA across muscle syncytia has not been done. We investigated mRNA localization in regions of Drosophila melanogaster dorsal longitudinal muscle (DLM) syncytia over their entire transcriptome. Dissection of muscle regions, their RNA-seq and stringent Differential Gene Expression analysis indeed reveals statistically significant regionalization of nearly a hundred mRNA over the length of DLMs. Functions of over half of these genes require experimental verification. A preponderance of mRNA coding for catabolic and proteolytic enzymes is conspicuous among transcripts enriched in the posterior of DLMs. Our findings provide a foundation for exploring molecular processes that contribute to syncytial maturation and muscle homeostasis in a spatially non-homogenous manner.

developmental biology↗

bioRxiv2018

EcRBPome: a comprehensive database of all known E. coli RNA-binding proteins

BackgroundThe repertoire of RNA-binding proteins (RBPs) in bacteria play crucial role for their survival, and interactions with the host machinery, but there is little information, record or characterisation in bacterial genomes. As a first step towards this, we have chosen the bacterial model system Escherichia coli, and organised all RBPs in this organism into a comprehensive database named EcRBPome.\n\nResultsEcRBPome contains RBPs recorded from 166 complete E. coli proteomes available in the RefSeq database (as of May 2016). The database provides various features related to the E. coli RBPs, like their domain architectures, PDB structures, GO and EC annotations etc. It provides the assembly, bioproject and biosample details of each strain, as well as cross-strain comparison of occurrences of various RNA-binding domains (RBDs). The percentage of RBPs, the abundance of the various RBDs harboured by each strain have been graphically represented in this database and available alongside other files for user download.\n\nConclusionTo the best of our knowledge, this is the first database of its kind and we hope that it will be of great use to the biological community. Database URL: http://caps.ncbs.res.in/ecrbpome

bioinformatics↗

bioRxiv2018

hRBPome: a central repository of all known human RNA-binding proteins

BackgroundRNA-binding proteins (RBPs) have been extensively studied in humans over the past few years. Multiple reports have been made in the literature for genome-wide survey for this class of proteins in the human genome using different tools and techniques. Due to the inherent difference in the nature of the methods used in identifying human RBPs, as well as the diverse sources for data collection in each of these studies, there exists immense heterogeneity (including diversity in data formats) and poor intersection among the datasets available from the different studies.\n\nDescriptionhRBPome is a comprehensive database of human RBPs known from six different studies. We have introduced considerable uniformity in the data, by mapping the various data formats reported by the different studies to gene names. This makes comparison across studies (datasets) easier than was possible before. We also provide confidence scores to each of these known RBPs, on the basis of their presence across studies.\n\nConclusionThis database presents a set of 837 high confidence RBP genes, identified in three or more resources, out of the six studies considered. Hence, it forms a \"gold standard\" for RBPs in the human genome. It also provides information for all the human RBPs from multiple resources, known to the best of our knowledge, on a common platform. The database can be accessed from the following URL: http://caps.ncbs.res.in/hrbpome

bioinformatics↗