Biology subjects

Kateriya, S.

Publications and source records attributed to Kateriya, S..

9 recordsLinked to original sources

bioRxiv2026

Unusual photochemical characteristics of a novel BLUF-like protein from fungus

Blue light using Flavin (BLUF) proteins are microbial photoreceptors that are involved in various physiological responses. Their occurrence and biochemical properties in fungi remain poorly understood. Here, we investigated a putative BLUF photoreceptor from the corn-smut fungus Mycosarcoma maydis (MmBLUF). Domain analysis, multiple sequence alignment of BLUF core regions, and structural modelling indicated conserved canonical BLUF fold and flavin-pocket residues. However, when heterologously expressed, UV-visible and fluorescence spectroscopy revealed different spectral behaviour than canonical BLUF protein. Further, we tested the role of extended N-terminus in modulation of chromophore binding by expressing N-terminus truncated protein variants. Our results suggest that the unusual spectral behaviour is not linked to the truncation construct (extended N-terminus), which also showed similar spectral features, indicating that the extended N-terminus is unlikely to account for an unusual photodynamics characteristics. Our findings support MmBLUF as a structurally conserved putative fungal BLUF-like photoreceptor with different photochemical properties. Further studies are required to establish its chromophore identity, photocycle and function of this unusual BLUF-like domain from fungal system.

biochemistry↗

bioRxiv2026

Network Topology reveals disrupted AMPA receptor stabilization leads to an impaired LTD in epileptic synapses

Cognitive comorbidities in epilepsy patients may be the result of synaptic alterations and impaired synaptic signalling. Electrophysiological evidence demonstrates that epileptic synapses undergo a GluN2B-dependent metaplastic shift, where a low-frequency stimulation protocol unexpectedly induced long-term potentiation (LTP) rather than long-term depression (LTD). However, the downstream postsynaptic structural cascade responsible for this functional impairment remains unresolved. To elucidate the molecular architecture driving this shift, this study employed an in silico protein-protein interaction network approach using Cystoscape. A baseline intersection network of LTD and epilepsy-associated genes were constructed, anchored with GRIN2B, and topologically ranked to identify hub proteins. This analysis identified a core module biased toward synaptic potentiation, dominated by the kinase CAMK2A, AMPA receptor subunits, and auxiliary Transmembrane AMPA Receptor Regulatory Proteins (TARPs) and CNIH2. These provided a structural basis for the prolonged receptor retention and delayed deactivation kinetics characteristic of epileptic synapses. Mapping the LTD-execution machinery against this interactome revealed that calcineurin was topologically segregated and lacks direct connectivity from the central AMPA receptor complex. Further studies would be required to test and confirm the involvement of these proteins. To experimentally validate these in silico findings, human transcriptomic data from cortical and hippocampal tissues of drug-resistant epilepsy patients was also analyzed which confirmed the significant upregulation of CNIH2 and CACNG2 in both tissue types. The cross-validation with patient transcriptomic data, demonstrated that the epileptic synapse undergoes a pathological shift. Hence, the upregulation of the auxiliary proteins functionally overpowers the established LTD machinery and prevents LTD consolidation.

neuroscience↗

bioRxiv2026

In silico characterization of unique fungal modular rhodopsin expands the horizon of novel optobiological and biomedical applications

Microbial modular rhodopsins, in which light-sensing rhodopsin domains are fused with effector modules, have emerged as promising tools for optogenetic regulation in algae and other systems. However, the diversity and potential regulatory roles of fungal modular rhodopsins remain largely unexplored. Here, we performed a comprehensive in-silico analysis to identify previously uncharacterized fungal modular-rhodopsins that pair a conserved light-sensing core with diverse effector domains, including RPEL-motif, NADP-binding Rossmann fold domain, MCM (Mini-Chromosome Maintenance) domain, and GC-cAT (Carnitine O-Acetyltransferase) modules. In Aureobasidium pullulans, the representative modular rhodopsin (ApRh-RPEL) contains RPEL-motif associated with actin-related and transcriptional regulatory processes, suggesting light-driven fungal signaling pathway involved in transcriptional and cellular regulation, respectively. Rhodopsins fused with NADP-binding Rossmann fold and MCM domains further indicate possible applications in light-programmable metabolic and cell-cycle signaling. Genome mining additionally revealed that A. pullulans harbours a diverse but underexplored array of biosynthetic gene clusters (BGCs), raising the intriguing possibility that light perception may regulate secondary metabolite pathways. Supporting this, multisource protein-protein interaction network analysis links ApRh-RPEL to enzymes involved in terpenoid and sphingolipid biosynthesis, indicating potential cross-talk between light-sensing module and metabolic regulation. These findings outline a computationally derived model in which fungal modular rhodopsins (ApRh-RPEL) function as opto-synthetic regulators of biosynthetic processes. Structural predictions confirmed conserved Schiff-base lysine and retinal-binding pocket, highlighting functional diversity across fungal rhodopsins. Together, these findings expand the optogenetic toolkit and provide a framework for engineering light-driven signaling in fungi, with applications in optobiological and biomedical applications.

bioinformatics↗

bioRxiv2025

Intraflagellar transport-20 coiled-coil domain mediates the channelrhodopsins trafficking to the cilia in Chlamydomonas reinhardtii

The primary cilium is a microtubule-based organelle essential for cellular signaling, whose assembly depends on intraflagellar transport (IFT). IFT20, a unique IFT-B component, localizes to both Golgi and cilium/flagellum, and plays a role in ciliary membrane protein trafficking. Here, we analyzed IFT20-mediated ciliary membrane trafficking of channelrhodopsin-1 (ChR1) in Chlamydomonas reinhardtii. IFT20 and ChR1 was found to be co-localized throughout the cilia of C. reinhardtii wild-type strain. In bbs1 mutants, IFT20 exhibited distribution along the flagellar length and basal body region. In contrast, ChR1 was found to be accumulating in the distal region of the cilia. Further, protein interaction network analysis reveals that IFT20 serves as a central adaptor, interfacing ancillary ciliary trafficking components, including Arf, the IFT complex, and BBSome subunits. The Arf co-localized with IFT20 in the cilia of the wild-type strain, suggesting a potential interaction. The fluorescence spectroscopic analysis shows that upon GTP binding, IFT20 undergoes concentration-dependent fluorescence quenching. From the far-UV CD spectroscopic analysis, it was observed that recombinant IFT20 has a predominantly helical structure, which does not change upon GTP binding. These findings extend the mechanistic understanding of ciliary membrane protein delivery in C. reinhardtii and reveal a conserved role of IFT20 in photoreceptor trafficking.

cell biology↗

bioRxiv2025

Molecular plasticity in the flavin binding pocket of BLUF domain evolves first light-gated endonuclease in bacterial system

The bacterium Rubellimicrobium mesophilum possesses a BLUF coupled endonuclease III (BLUF-EndoIII) with potential endonuclease activity. Interestingly, the crucial amino acid residues (tyrosine, histidine and tryptophan) responsible for BLUF photocycle and photodynamics are evolutionarily replaced by phenylalanine (Y5F), asparagine (H27N) and alanine (W87A) residues, respectively. In present communication, we have studied the impact of this evolutionary plasticity on the BLUF photodynamics and associated endonuclease activity. The results obtained showed that the evolutionary plasticity in the BLUF domain influenced various functional aspects of BLUF domain including FAD binding, domain stability, recovery kinetics, and spectral characteristics. The impact of amino acid plasticity on the C-terminal endonuclease (EndoIII) domain was also studied. The evolutionary plasticity induced changes in the flavin binding pocket of the BLUF domain elevated the light-gated endonuclease activity associated with EndoIII domain. The molecular docking analysis and spectroscopic studies also confirmed the substrate-binding ability of the BLUF-EndoIII. The elevated endonuclease activity suggested that the amino acid residues, which are crucial for BLUF photocycle are indeed dispensable and there might exists another electron transfer pathway for BLUF domain activation and regulation of associated endonuclease domain. Considering the role of endonucleases in bacterial defense, the understanding of the BLUF photodynamics, mechanism of signal transfer to the downstream endonuclease domain and associated endonuclease activity might elucidate the first naturally occurring light-gated endonuclease in bacterial system.

biochemistry↗

bioRxiv2024

Phototropin localization and interactions regulate photophysiological processes in Chlamydomonas reinhardtii

Phototropin, a blue-light sensing serine/threonine kinase, plays a pivotal role in regulating diverse photophysiological processes in both plants and algae. In Chlamydomonas reinhardtii, phototropin (CrPhot) localizes to the eyespot and flagella, coordinating key cellular functions such as phototaxis, photosynthesis, gametogenesis, and chlorophyll biosynthesis. While previous research has identified phototropin interactions with signaling proteins such as channelrhodopsins and light-harvesting complex proteins, many aspects of its interaction network and regulatory mechanisms remain unresolved. In this study, we explored novel interacting protein partners of phototropin and their roles in modulating its regulatory functions in Chlamydomonas reinhardtii. Employing a suite of intraflagellar transport (IFT) mutants of C. reinhardtii such as IFT172, IFT52, IFT88, IFT139, kinesin/dynein, CEP290 etc., we elucidate that phototropin localization within the flagella and eyespot is IFT-mediated. Our study highlights interaction of phototropin with other photoreceptors-channelrhodopsins (ChR1 and ChR2), chlamyopsin 6, LOV-histidine kinases (LOV-HK1, LOV-HK2) and signaling protein-14-3-3. CRISPR-Cas9 knockouts of phototropin showed reduced ChR1, 14- 3-3 levels and exhibited impaired photomotility. Moreover, two LOV-domain containing histidine kinases, LOV-HK1 and LOV-HK2, were identified in C. reinhardtii. Gene expression of LOV-HK1 and LOV-HK2 were found to be elevated in UV-light in C. reinhardtii and their genes expression was found to be altered in phototropin CRISPR-Cas9 knockouts. This study provides new insights into phototropin signalosome and highlights molecular mechanisms governing its function. The research outcomes advances our understanding of phototropin trafficking and signal modulation in Chlamydomonas reinhardtii, and sets the stage for further exploration into the broader physiological roles of phototropin in cellular responses. Graphical abstractPhototropin, a blue-light receptor in Chlamydomonas reinhardtii, localizes to the flagella and eyespot, mediates phototaxis and photosynthesis. Its trafficking is mediated by intraflagellar transport (IFT) machinery, with mutations in IFT components (kinesin, dynein, IFT172, IFT52, IFT88, IFT139, CEP290) disrupting phototropin localization. Phototropin interacts with other photoreceptors like channelrhodospins (ChR1/2), chlamyopsin 6, LOV-histidine kinases (LOV-HK1, LOV-HK2) and signaling proteins (14-3-3), coordinating light-driven responses. These findings underscore the details of phototropin trafficking and phototropin signaling impacting light-induced physiological processes in C. reinhardtii. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/630506v1_ufig1.gif" ALT="Figure 1000"> View larger version (51K): org.highwire.dtl.DTLVardef@29f6b3org.highwire.dtl.DTLVardef@10382aeorg.highwire.dtl.DTLVardef@1786f0dorg.highwire.dtl.DTLVardef@1c2ed65_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights* Phototropin localizes in eyepot and flagella in Chlamydomonas reinhardtii. * Intraflagellar transport (IFT) mutants of C. reinhardtii suggest role of different IFT proteins in phototropin trafficking and localization. * Phototropin interacts with other photoreceptors (ChR1 & ChR2, COP6, LOV-HK1 & LOV-HK2) and signaling proteins (14-3-3), contributing to various physiological processes. * CRISPR-Cas9 knockouts of phototropin showed reduced 14-3-3 protein content and photomotility response in C. reinhardtii.

plant biology↗

bioRxiv2024

Clonal spheroids capture functional and genetic heterogeneity of head and neck cancer

Head and neck cancer squamous cell carcinoma (HNSCC) cells exhibit both structural and functional diversity, making them valuable models for understanding tumor heterogeneity at clinical levels. In this study, we generated single-cell-derived spheroids (SCDS) from HNSCC cell lines and patient tumor cells using scaffold- and non-scaffold-based methods to assess this variability. A distinct structural variability among these SCDS, categorized as hypo- and hyperproliferative spheroids based on size, was observed. Hyperproliferative spheroids demonstrated heightened proliferative and tumorigenic potential and increased sensitivity to cisplatin and radiation, while hypoproliferative spheroids exhibited enhanced migratory capabilities. Single-cell RNA sequencing (scRNA-seq) of hypo- and hyperproliferative spheroids provided insights into the transcriptional landscape of HNSCC cells, validating the observed structural and functional heterogeneities within primary tumors. These functionally and genetically characterized spheroids offer valuable tools for the development of next-generation therapeutics. Statement of SignificanceEstablishment and characterization of single-cell-derived spheroids from head and neck cancer cells, employing scaffold and non-scaffold materials, demonstrate functional and genetic heterogeneity. Single-cell analysis reveals correlations between genetic diversity and spheroid functionality. These characterized spheroids offer potential for advancing therapeutics development.

cancer biology↗

bioRxiv2024

Pathways in the brain, heart, and lung influenced by SARS-CoV-2 NSP6 and SARS-CoV-2 regulated miRNAs: an in silico study hinting cancer incidence

The influence of SARS-CoV-2 non-structural protein in the hosts tissue-specific complexities remains a mystery and needs more in-depth attention because of COVID-19 recurrence and long COVID. Here we investigated the influence of SARS-CoV-2 transmembrane protein NSP6 (Non-structural protein 6) in three major organs - the brain, heart, and lung in silico. To elucidate the interplay between NSP6 and host proteins, we analyzed the protein-protein interaction network of proteins regulated after SARS-CoV-2 infection and that are interacting with NSP6 interacting proteins. Pathway enrichment analyses provided global insights into biological pathways governed by differentially regulated genes in the three tissues after COVID-19 infection. Many drugs targeting hub genes of tissue-specific protein interactome were found that could be candidates for COVID-19 management. MiRNA-gene network for the tissue-specific regulated proteins was also deduced and comparing gene list targeted by SARS-CoV-2 regulated miRNAs, we found three and two common genes in the brain and lung respectively. Among the five common proteins revealed as potential therapeutic targets across the three tissues, Galectin3 (LGALS3) that was upregulated in the heart and brain after COVID-19 infection is reported to be influencing all the ten hallmarks of cancer positively and is found in multiple cancers. COVID-19 infection also causes myocardial inflammation and heart failure (HF). HF is observed to be increasing cancer incidence. Our bioinformatics and systems study hints probable effect of COVID-19 infection in cancer incidence and warrants in-depth studies in this direction and cancer surveillance especially with the present scenario of long COVID-19 and recurrent COVID-19 infections. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/578752v2_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@f10223org.highwire.dtl.DTLVardef@c34b64org.highwire.dtl.DTLVardef@18aaf59org.highwire.dtl.DTLVardef@1fe0b35_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2023

COVID-19 ORF3a Viroporin Influenced Common and Unique Cellular Signalling Cascades in Lung, Heart and Brain Choroid Plexus Organoids with Additional Enriched MicroRNA Network Analyses for Lung and Brain Tissues

Tissue specific implications of SARS-CoV-2 encoded accessory proteins are not fully understood. SARS-CoV-2 infection can severely affect three major organs - the heart, lung, and brain. We analysed SARS-CoV-2 ORF3a interacting host proteins in these three major organs. Further we identified common and unique interacting host proteins, their targeting miRNAs (lung and brain), and delineated associated biological processes reanalysing RNA-seq data from the brain (COVID-19 infected/uninfected Choroid Plexus Organoids study), lung tissue from COVID-19 patients/healthy subjects, and cardiomyocyte cells based transcriptomics analyses. Our in silico studies showed ORF3a interacting proteins could vary depending upon tissues. Number of unique ORF3a interacting proteins in brain, lung and heart were 10, 7 and 1 respectively. Though common pathways influenced by SARS-CoV-2 infection were more, unique 21 brain and 7 heart pathways were found. One unique pathway for heart was negative regulation of calcium ion transport. Reported observations of COVID-19 patients with the history of hypertension taking calcium channel blockers (CCBs) or dihydorpyridine CCBs had elevated rate of intubation or increased rate of intubation/death respectively. Also likelihood of hospitalization of chronic CCB users with COVID-19 was more in comparison to long term Angiotensin Converting Enzyme inhibitors/Angiotensin Receptor Blockers users. Further studies are necessary to confirm this. miRNA analysis of ORF3a interacting proteins in brain and lung revealed, 2 of 37 brain miRNAs and 1 of 25 lung miRNAs with high degree and betweenness indicating their significance as hubs in the interaction network. Our study could help in identifying potential tissue specific COVID-19 drug/drug repurposing targets.

bioinformatics↗