Biology subjects

Ravichandran, A.

Publications and source records attributed to Ravichandran, A..

10 recordsLinked to original sources

bioRxiv2026

Toward resolving gravitational effects on microbial growth with computer simulations

As the duration of space flights increases, so does the need to optimize off-planet microbial growth. Microbes can both be unintentionally brought into space and cause human disease or be intentionally harnessed for on-site bioengineering functions. However, optimizing microbial growth is challenging due to an insufficient understanding of how microbial communities are affected by the extraterrestrial environment. To address this gap, we have modified a previously developed model for cell growth in microgravity. By improving the functional form used for cell growth as well as the code usability, we enable further research into how microbial communities are influenced by gravity. Applying this model to isolate individual effects of gravity on cell growth indicates that a lack of gravity-driven flow decreases cell growth in microgravity, while the absence of sedimentation increases cell growth in microgravity. These opposite effects likely contribute to the system-dependent effects of microgravity observed experimentally.

biophysics↗

bioRxiv2026

Investigating the activity of Varicella Zoster Virus (VZV) SUMO-targeted Ubiquitin Ligase ORF61

Varicella Zoster Virus (VZV) is a dsDNA virus that infects dermal cells and causes characteristic cutaneous lesions. The virus undergoes neurotropism and later causes secondary cycles of infection. In the host nucleus, Promyelocytic Leukaemia Nuclear Bodies (PML-NBs) spontaneously form around the VZV genome to repress viral gene expression. VZV encodes for a ubiquitin E3 ligase ORF61 to disperse PML-NBs and alleviate repression. ORF61 functions as a ubiquitin E3 ligase with a conserved RING domain at the N-terminal end. It carries three SUMO-interacting motifs (SIMs) that mediate interactions with SUMOylated proteins within PML bodies. The mechanism by which ORF61 disperses PML-NBs is poorly understood. To understand how ORF61 interacts with SUMOylated proteins, we investigated its interaction with SUMO and studied its SUMO-Targeted Ubiquitin Ligase (STUbL) activity. Our studies reveal that ORF61 co-opts the E2D family for ubiquitination activity. A specific network of interactions between the E2 enzyme, ORF61, and Ub facilitates polyubiquitination. ORF61 can synthesize branched polyubiquitin chains of K11, K48, and K63 linkages. The C-terminal SIM in ORF61 is a high-affinity binder of SUMO chains. Utilizing the SIM, ORF61 targets specific lysines on SUMO chains for ubiquitination. These studies provide crucial insights into the functional mechanism of viral STUbL ORF61.

biochemistry↗

bioRxiv2024

Should elephants graze or browse? The nutritional and functional consequences of dietary variation in a mixed-feeding megaherbivore

Unlike specialist browsers and grazers, the diets of mixed-feeding megaherbivores like elephants are complex and broad, comprising numerous plant species of variable nutritional quality. Here, we revisit an unresolved debate on whether browse is more nutritious than grasses for elephants, as browse is thought to have greater crude protein content. We first analyzed carbon isotopes in 102 fecal samples of Asian elephants to quantify the contribution of browsing and grazing to their diet in Nagarahole National Park, southern India. We show that elephants are predominantly browsers in the grass-scarce Nagarahole forests, in contrast with predominant grazing reported in the nearby grass-abundant savannas of the Nilgiri Biosphere Reserve. We then compared the forage quality of high-browsing and high-grazing diets by analyzing these samples for two proxies of crude protein content (CP): nitrogen content (N%) and Carbon-to-Nitrogen ratio (C:N). Interestingly, high-browsing diets did not have higher N% or lower C:N (proxies for high CP) than low-browsing (high-grazing) diets. To explore the generality of this finding, we analyzed nutritional differences (i.e., CP and fibre content values) between browse and grass across 141 plant species consumed by Asian elephants. We show that woody browse and non-legume browse, which are major components of elephant browse, do not have appreciably higher CP than grasses. Our findings suggest that browsing and grazing broadly have similar nutritional value for such bulk-feeding mixed feeders. Finally, based on the observed habitat-wide variation in browsing, we provide a new framework for assessing how elephants shape woody vegetation across the forests and savannas of Asia, with important implications for conservation and carbon cycling.

ecology↗

bioRxiv2023

Bacterial deamidases modulate ubiquitin structure and dynamics to dysregulate ubiquitin signaling

The deamidases secreted by Burkholderia pseudomallei and Enteropathogenic Ecoli modify the residue 40 in ubiquitin from a Glutamine (Q) to Glutamate (E), triggering several downstream processes to cause cell cycle arrest and activate immune responses. Deamidation hampers the activity of ubiquitin and its interaction with ubiquitin chain receptors by an unknown mechanism. Here, we study the effect of deamidation on ubiquitin structure and dynamics. We report the crystal structure of the deamidated ubiquitin, supported by NMR and molecular dynamics simulations. The structure reveals a new intra-molecular salt bridge between the deamidated region and the C-terminal tail of ubiquitin. The salt bridge perturbs the dynamics of the ubiquitin tail to reduce affinity for ubiquitin receptors like the p62 ubiquitin-associated domain. The salt bridge disrupts the transition to catalytically active E2~Ub closed conformation. Consequently, RING E3s fail to interact with E2~Ub, reducing ubiquitination activity. Our findings reveal that deamidation-induced intramolecular salt bridges in ubiquitin modulate conformational ensembles to inactivate ubiquitination.

biochemistry↗

bioRxiv2022

The proteasomal degradation signal FAT10 modulates substrate stability to accelerate degradation

The proteasome controls levels of most cellular proteins, and its activity is regulated under stress, quiescence, and inflammation. However, factors determining the proteasomal degradation activity remain poorly understood. Proteasome substrates are conjugated with small proteins (tags) like ubiquitin and Fat10 to target them to the proteasome. It is unclear if the structural plasticity of proteasome-targeting tags influences substrate degradation. The tag Fat10 is activated during inflammation, and ambiguously, Fat10 and its substrates undergo rapid proteasomal degradation. We report that the rapid degradation of Fat10 substrates depends on its structural plasticity. While the ubiquitin tag is recycled at the proteasome, Fat10 is degraded with the substrate, and the mechanical unfolding kinetics of Fat10 regulates substrate degradation. Our studies reveal that long-range salt bridges are absent in the Fat10 structure, creating a plastic protein with partially unstructured regions suitable for proteasome engagement. Such a malleable structure also provides low resistance to mechanical unfolding and expedites proteasomal degradation. We also uncovered that the Fat10 plasticity destabilizes substrates significantly and creates partially unstructured regions in the substrate to enhance degradation. NMR-relaxation-derived order parameters and temperature dependence of chemical shifts identify the Fat10-induced partially unstructured regions in the substrate. They correlated excellently to the regions where Fat10 contacts the substrate, suggesting that the tag-substrate collision destabilizes the substrate. These results highlight a strong dependence of proteasomal degradation on the structural plasticity and thermodynamic properties of the proteasome-targeting tag.

biochemistry↗

bioRxiv2020

Transcriptomic analysis of Lentinus squarrosulus to provide insights into its biodegradation ability.

Basidiomycetes are of special interest in biotechnological research for their versatile potential in degradation of lignocellulosic biomass. This study accordingly reports analysis of transcriptome of a white-rot Basidiomycete L.squarrosulus grown in simple potato dextrose broth supplemented with aromatic compound, reactive black dye to gain an insight into the degradation ability of the fungus. RNA was sequenced using Illumina NextSeq 500 to obtain 6,679,162 high quality paired end reads that were assembled de novo using CLC assembly cell to generate 25,244 contigs.Putative functions were assigned for the 10,494 transcripts based on sequence similarities through BLAST2GO 5.2 and Function annotator. Functional assignments revealed enhanced oxidoreductase activity through the expression of diverse biomass degrading enzymes and their corresponding co-regulators. CAZyme analysis through dbCAN and CUPP revealed the presence of 6 families of polysaccharide lyases, 51 families of glycoside hydrolases, 23 families of glycoside transferases, 7 families of carbohydrate esterases and 10 families of Auxiliary activities.Genes encoding the ligninolytic enzymes and auxiliary activities among the transcript sequences were identified through gene prediction by AUGUSTUS and FGENESH. Biochemical analysis of a couple of biomass degrading enzymes substantiated the functional predictions. In essence, L.squarrosulus grown in a simple medium devoid of lignocellulosic substrate demonstrated presence of a repertoire of lignocellulose degrading enzymesimplying that source of lignocellulose is not required for expression of these biomass degrading enzymes. The study hereby underlines the significance of L.squarrosulus in biomass degradation and its future functional exploitation in biomass conversion applications.

molecular biology↗

bioRxiv2018

Chronology of motor-mediated microtubule streaming

We introduce a computer-based simulation model for coarse-grained, effective motor-mediated interaction between microtubule pairs to study the time-scales that compose cytoplasmic streaming. We characterise microtubule dynamics in two-dimensional systems by chronologically arranging five distinct processes of varying duration that make up streaming, from microtubule pairs to collective dynamics. The structures found were polarity sorted due to the propulsion of antialigned microtubules. This also gave rise to the formation of large polar-aligned domains, and streaming at the domain boundaries. Correlation functions, mean squared displacements, and velocity distributions reveal a cascade of processes ultimately leading to microtubule streaming and advection, spanning multiple microtubule lengths. The characteristic times for the processes span over three orders of magnitude from fast single-microtubule processes to slow collective processes. Our approach can be used to directly test the importance of molecular components, such as motors and crosslinking proteins between microtubules, on the collective dynamics at cellular scale.

biophysics↗

bioRxiv2018

A novel Versatile Peroxidase from Lentinus squarrosulus (MH172167)towards enhanced delignification and digestibility of crop residues

Scarcity of quality feed is a major constraint concerning livestock productivity with recalcitrant lignin hindering utilization of crop residues as quality animal feed. Degradation of lignin in nature is contributed by white-rot fungi through their enriched ligninolytic system. Versatile Peroxidase plays a key role in ligninolysis through its capability to oxidize diverse class of aromatics without mediators. In this study, wild isolates of wood rotting fungi were screened for potential peroxidases oxidizing manganese and aromatic compounds. The strain identified as Lentinus squarrosulus (TAMI004, BankIt2098576 MH172167) was monitored for enzyme activity in solid state and submerged fermentation. L. squarrosulus demonstrated predominant Versatile Peroxidase activity amongst the screened wild isolates displaying hybrid characteristic of manganese oxidation and manganese independent reactions on aromatic compounds. The manganese oxidizing peroxidase activity evidenced in submerged fermentation was 12 IU/L whereas in solid state fermentation it was 131 IU/L. This ability to act through manganese mediated and independent reactions on phenolics reveals its biotechnological and industrial significance. Treatment of common crop residues with crude extract of L. squarrosulus rich in Versatile Peroxidase obtained from both Solid state and submerged fermentations showed a decrease in their Neutral Detergent Fiber, Acid Detergent Fiber and Acid Detergent Lignin content showing biodegradation, substantiating the ligninolytic ability and more prominently increase in their digestibility. To the best of our knowledge, this is the first report describing Versatile Peroxidase from Lentinus squarrosulus with potential to augment the ruminant digestibility of crop residues.\n\nImportanceVersatile Peroxidase of White-rot fungi, a relatively less studied lignolytic enzyme, is very efficient in depolymerization of lignin macromolecule through its multivalent catalytic sites. Lignin degradation is very appealing from the application perspective as attack on lignin exposes the energy affluent polysaccharides for utilization in extensive biotechnological applications. Reports on relevance of Versatile Peroxidase for these purposes are still emerging, however the role of ligninolytic enzymes especially Versatile Peroxidase in enriching ruminant feed is yet unturned. Here, this work demonstrates the potential of Versatile Peroxidase from a novel species Lentinus squarrosulus in delignification thereby upgrading the digestibility and nutritive value of crop residues. The observations validate the importance of the enzyme in improvement of crop residues for feeding ruminants in the current scenario where, livestock productivity is severely impacted by lack of quality feed and demand for alternate feed resources is intensifying.

microbiology↗

bioRxiv2018

Occidiofungin, an actin binding antifungal with in vivo efficacy in a vulvovaginal candidiasis infection

Current antifungal treatment options are plagued with rapidly increasing occurrence of resistance, high degree of toxicity and a limited spectrum of activity. The need to develop a novel antifungal with a unique target, wider spectrum of activity, and reduced toxicity to the host, is urgent. We have identified and characterized one such compound named occidiofungin that is produced by the soil bacterium Burkholderia contaminans MS14. This study identifies the primary cellular target of the antifungal, which was determined to be actin. Actin binding metabolites are generally characterized by their ability to inhibit polymerization or depolymerization of actin filaments, which presumably accounts for their severe toxicity. Occidiofungin, instead, has a subtler effect on actin dynamics that triggers apoptotic cell death. We were able to demonstrate the effectiveness of the antifungal in treating a vulvovaginal yeast infection in a murine model. This discovery puts occidiofungin in a unique class of actin-binding antifungal compounds with minimal reported toxicity to the host. The results of this study are important for the development of a novel class of antifungals that could fill the existing gap in treatment options for fungal infections.\n\nAuthor summaryWidespread resistance to antifungal compounds currently in use has been alarming. Identification and development of a new class of antifungals with a novel cellular target is desperately needed. This study describes the assays carried out to determine the molecular target and evaluate efficacy of one such novel antifungal compound called occidiofungin. Occidiofungin modified with a functional alkyne group enabled affinity purification assays and localization studies in yeast. These studies led to the identification of the actin binding property of occidiofungin. Actin-binding by secondary metabolites often exhibit severe host toxicity, but this does not appear to be the case for occidiofungin. We have previously been able to administer occidiofungin to mice at concentrations in the range of 5 mg/kg without any serious complications. We were able to demonstrate the effectiveness of the antifungal in treating a vaginal fungal infection in a murine model. The results outlined in this manuscript establish that occidiofungin is an efficacious compound with a novel molecular target, putting it in a completely new class of antifungals.

microbiology↗

bioRxiv2018

A rapid microwave method for isolation of genomic DNA and identification of white rot fungi.

White rot fungi (WRF) produce lignolytic enzymes comprised by laccases and peroxidases responsible for mineralization of recalcitrant lignin. Because of the so-called lignin modifying enzymes(LMEs), these fungi have potential applications in biodegradation and bioremediation processes. Increased demand for lignolytic enzymes to exploit their various applications has sparked interest in identifying and characterizing new novel strains of WRF. Despite this undisputed biotechnological significance, molecular identification of WRF, remains a daunting task for researchers as genomic DNA isolation is a tedious process, unsuccessful many a times because of their rigid and resistant cell walls. A rapid, effective and efficient method to identify the innumerable fungal strains within no time is the need of the hour. The fungal mycelia of various unknown as well as know isolates of WRF, after alternative washing with TE buffer and sterile water were suspended in TE buffer. Fungi in solution were then exposed to microwave. The crude extract contained genomic DNA which was extracted and amplified using ITS primers for further identification. Based on sequencing results the identity of known cultures was confirmed, while the unknown cultures were identified as Clitopilus scyphoides (AGUM004, BankIt2098576 MH172163); Ganoderma rasinaceum (AGUM007, BankIt2098576 MH172163); Schizophyllum sp (KONA001 BankIt2098576 MH172164; AGUM011 BankIt2098576 MH172165and AGUM021 BankIt2098576 MH172166respectively), Coprinellus disseminatus (BANG001, BankIt2098576 MH172167) and Lentinus squarrosulus (TAMI004, BankIt2098576 MH172167). The microwave method described for isolating quality DNA of WRF without further purification steps proved a novel method requiring less than ten minutes and minimized the chances of the presence of PCR inhibitors.\n\nIMPORTANCEWhite rot fungi which decay wood, possess selective lignin degrading enzymes responsible for degrading a wide variety of environmental pollutants, xenobiotic compounds in addition to mineralizing chemicals that are insoluble and recalcitrant. Lignolytic enzymes hold potential towards replacing conventional chemical processes and their increased demand in the market has ignited interest in identifying and characterizing new strains of WRF. A rapid, efficient method capable of quickly identifying fungal isolates is a constraint. The microwave method is a novel quick method for isolating superior quality DNA. Its adoption circumvents the initial purification steps and /or interference of PCR inhibitors, which are encompassed in the use of conventional methods. The microwave method thus permits the thorough amplification of the ITS region thereby aiding in the easy identification of unknown species. Use of the microwave method will permit researchers to obtain DNA from fungi very quickly for further application in molecular studies.

molecular biology↗