Biology subjects

Sharma, G.

Publications and source records attributed to Sharma, G..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Comprehensive Functional Self-Antigen Screening to Assess Cross-Reactivity in a Promiscuous Engineered T-cell Receptor

T cell receptor therapeutics are an emerging modality of biologic and cell-based medicines with the unique ability to target intracellular antigens and finely discriminate between healthy and infected or mutated cells. An obstacle to the development of new T cell receptor therapeutics is the difficulty in engineering these proteins for enhanced therapeutic efficacy while avoiding introduction of unexpected off-target autoreactivity. In this study, we apply a functional high-throughput screening assay, Tope-seq, to detecting cross-reactive epitopes in libraries of >5 x 105 unique peptide-coding sequences. We retrospectively analyze an affinity-enhanced engineered T cell receptor, which previously failed clinical trials due to severe off-target toxicity caused by epitope cross-reactivity, by comprehensive functional testing against all genome-coded self-antigens. Using the Tope-seq methodology, we were able to identify the epitope mediating off-target reactivity at a significance threshold of p < 0.01 in first-pass bulk screening. We also identified other potential cross-reactive epitopes of the engineered TCR of-interest, suggesting that the need for assessing promiscuity in TCR based therapeutics is larger than previously appreciated.

immunology↗

bioRxiv2025

Functional and structural characterization of a combination of pan-sarbecovirus antibodies with potent antiviral activity

Sarbecoviruses, a subgenus of coronaviruses, include strains with zoonotic spillover risk as exemplified by recent outbreaks (SARS-CoV-1, SARS-CoV-2). Monoclonal antibodies targeting conserved spike protein regions (RBD class 4, S2 fusion machinery) exhibit broad sarbecovirus neutralization, but their utility has been impacted by immune selection leading to escape and suboptimal neutralization. Using structure-conditioned machine-learning protein design we optimized two broadly neutralizing sarbecovirus antibodies to rescue the activity of a class 4 anti-RBD antibody against Omicron variants and improve the neutralization profile of an anti-S2 stem antibody, resulting in the identification of the lead candidates PRO-37587 and GB-0669. Both antibodies displayed remarkable resilience to SARS-CoV-2 evolution. Structural analyses elucidated the mechanistic basis of their broad neutralization profiles. In combination, these antibodies exhibited improved SARS-CoV-2 neutralization in vitro and in vivo and a higher barrier to resistance. These findings support further evaluation of such antibody combination as countermeasure against current and emerging sarbecoviruses.

microbiology↗

bioRxiv2025

Sensory Appendage Protein triggers alarm to pyrethroid in Indian malarial vector Anopheles culicifacies

Sensory appendage proteins (SAPs) serve as molecular arms of odorant-binding protein family members and mediate chemical communication from the external to the internal environment of the insect body. We recently reported that SAP members might have an important role in blood-feeding and/or insecticide resistance-associated behavioral physiologies, but the mechanism remains unclear. Here we show how SAP contributes (i) to the host attraction during navigation for blood-feeding, and (ii) triggers an alert via integrated actions of eyes and peripheral sensory organs to circumvent the toxic effect of insecticide in the susceptible strain of An. culicifacies. Among the six identified SAP members, AcSAP1 and AcSAP2 are abundantly expressed in the olfactory and legs, and their expression is significantly modulated at night in naive adult female mosquitoes. We noticed that AcSAP1 silencing significantly impairs the host-attraction properties of the mosquitoes. Its strong binding affinity to the synthetic pyrethroid prompted us to evaluate the AcSAP1 response to insecticide exposure. Confocal microscopy and molecular profiling data reveal a heightened modulation in the expression of AcSAP1 in eyes, and other peripheral sensory organs including the olfactory (****p<0.00001), legs (**p < 0.004), wings (***p < 0.0004). These findings collectively suggest a crucial role of AcSAP1 in facilitating mosquito navigation, and/or insecticide avoidance. Unraveling the basis of SAP interactions with peripheral sensory systems could pave the way for the development of novel vector control tools.

animal behavior and cognition↗

bioRxiv2024

Same strain, two genomes: Creating a consensus circular genome of Myxococcus xanthus DZ2 revealed the diversity of a large polyploid prophage region within the close-related myxobacterial strains

One of the well-known myxobacterial model organism, i.e., Myxococcus xanthus DZ2 strain has three reported assemblies of which two complete assemblies (MxDZ2_Tam and MxDZ2_Nan) have been reported in the last three years for the same strain procured from same culture collection stock. Raw assemblies of this same strain were reported circular and differed by 6.4 kb, raising questions about their accuracy. Therefore, our computational analysis, removing duplicate ends, aligning genomes to the origin of replication, and circularization, revealed a minimal size difference of only 32 bp, with MxDZ2_Tam being slightly larger. Further comparative analysis identified 40 sequence variations: 38 indels and 2 substitutions, with 24 variations concerning 18 coding genes. Eight of these 24 variations triggered frameshift mutations, seven of them encountered a premature stop codon followed by a second ORF and the remaining three had a premature stop codon followed by a non-coding region. 78% of these variations were detected in the regions which had repeated bases, especially guanine and cytosine, which is one of the well-known sequencing limitations. Although PacBio HiFi technology, used for the complete assemblies, boasts a low error rate, it remains higher than the 454-platform used for the earlier MxDZ2_Kirby assembly. Using MxDZ2_Kirby as a reference, we determined that most variations were specific to MxDZ2_Nan, while MxDZ2_Tam showed greater consistency with MxDZ2_Kirby. Based on these findings, we constructed a consensus truly circular genome for the same M. xanthus DZ2 strain. Additionally, we monitored divergence between M. xanthus DZ2 and its close relative M. xanthus DK1622 in the number of Mx-alpha regions, which are linked to interspecies and intraspecies antagonism via the toxin gene sitA. Further comparative genome analysis across 61 myxobacteria revealed the presence of Mx-alpha regions in five other organisms, though only M. xanthus DZ2 and DZF1 contained all three Mx-alpha regions. Overall, this study underscores the need for meticulous validation of sequencing-based genome assemblies and their variations along with highlighting the genomic diversity within M. xanthus strains based on a large polyploid prophage region, known as Mx-alpha. ImportanceSequencing an organism is an efficient way to investigate its physiology and function. Through this study, we focused on resolving differences between two genome assemblies of the same strain, i.e., M. xanthus DZ2, procured from the same culture collection and assembled via two different organisations. We identified 40 differences between these two, which led to inconsistencies in how some proteins were predicted and annotated. By comparing these assemblies with a third draft genome, we created a more accurate and reliable consensus truly circular genome for this strain. We also investigated a particular region of the genome, known as Mx Alpha, that contains genes for toxin-antitoxin systems, which play a role in helping the bacteria recognize and interact with related strains. These findings provide new insights into the diversity of this region in Myxococcus and its phylum Myxococcota relatives, shedding light on how these bacteria interact within their communities.

bioinformatics↗

bioRxiv2024

Comparative genomic insight into the myxobacterial carbohydrate-degrading potential and their ecological impact.

Myxobacteria are an intriguing group of social-behavior-depicting microbes with unique physiological characteristics such as fruiting body formation, gliding motility, and predation, encompassing the largest genomes (>9 Mb) within the Eubacteria kingdom. These soil-dwelling organisms are crucial for lignocellulosic biomass degradation, which has both ecological and industrial significance. While previous studies have demonstrated polysaccharide deconstruction abilities in a few myxobacterial species, we aim to elucidate the distribution of their Carbohydrate Active Enzymes (CAZymes) domains per organism, with a focus on proteins involved in the catabolism of critical polysaccharides such as cellulose, lignin, xylan, starch, pectin, fructan, chitin, and dextran, across 61 high-quality sequenced myxobacterial genomes. Our findings reveal that 3.5% of the total genes at the median level have domains related to CAZyme functions across different myxobacterial families. Notably, family Archangiaceae (4.4%) and Myxococcaceae (3.7%) members exhibit the most significant genomic diversity and potential for degrading multiple substrates within lignocellulosic biomass. These plentiful CAZymes probably enable these majorly soil-harboring myxobacteria to break down various carbohydrate substrates into simpler biological molecules, which not only allow these organisms to sustain in poor-nutrient environments but also enable them to be critical players in carbon cycling and organic matter decomposition. We conclude that myxobacteria have an unexplored genomic potential that may play an integral role in the degradation of recalcitrant plant biomass, potentially influencing soil health and composition. This study further suggests the critical ecological importance of these CAZymes in sustaining the balance of terrestrial ecosystems and diverse industrial applications. ImportancePolysaccharides are the most abundant polymers making up the Earths biomass. Polysaccharide degradation is well-known to be carried out by diverse microorganisms; however, there is more to be explored concerning the novel organisms that can degrade these biomolecules efficiently along with understanding the newer mechanisms and reactions carried out in this process. Soil-dwelling myxobacteria, model organisms for our study, are unique and under-studied social-behavior-depicting microbes. In this research, we investigated their genetic potential to encode carbohydrate-active enzymes involved in breaking down various substrates, including lignocellulosic biomass which is predominantly present in their habitat. We further emphasized their potential to be utilized in industrial applications amongst the paper-pulp, food-beverage, textile, and biofuel industries.

microbiology↗

bioRxiv2024

Metabolic regulation of RNA methylation by the m6A-reader IGF2BP3

The interplay of RNA modifications - deposited by "writers", removed by "erasers" and identified by RNA binding proteins known as "readers" - forms the basis of the epitranscriptomic gene regulation hypothesis. Recent studies have identified the oncofetal RNA-binding protein IGF2BP3 as a "reader" of the N6-methyladenosine (m6A) modification and crucial for regulating gene expression. Yet, how its function as a reader overlaps with its critical oncogenic function in leukemia remains an open question. Here, we report the novel finding that the reader IGF2BP3 reprograms cellular metabolism, resulting in an altered ability of the "writers" to modify the epitranscriptome. In leukemia cells, IGF2BP3 supports increased glycolytic flux and one-carbon metabolism, leading to increased production of S-adenosyl methionine (SAM), a key substrate for methylation reactions within the cell. IGF2BP3 directly regulates the translation of MAT2B, the regulatory subunit of the methionine-adenosyltransferase complex, which is the final enzyme in a pathway leading to SAM production. This, in turn, results in increased m6A modifications on RNA, resulting in positive feedback regulation. This novel mechanism illustrates how metabolism mutually acts with epitranscriptomic modifications, underscoring the pervasive impact of IGF2BP3 in gene regulatory mechanisms governing a broad range of cancer-specific processes.

cancer biology↗

bioRxiv2024

An envelope stress response governs long-chain fatty acid metabolism via a small RNA to maintain redox homeostasis in Escherichia coli

Long-chain fatty acids (LCFAs) are a tremendous source of energy for several bacteria but are complex to use because they induce redox stress. We previously showed that LCFA degradation impedes oxidative protein folding in the Escherichia coli envelope, an issue that arises due to the insufficiency of ubiquinone, a lipid-soluble electron carrier in the electron transport chain (ETC). To maintain redox homeostasis, E. coli activates the CpxAR two-component system; however, the nature of feedback imparted by this envelope stress response (ESR) remained unknown. Here, we show that contrary to the well-recognized remedial mode of Cpx restoring envelope integrity by upregulating protein quality control factors, in LCFA-grown cells, it uses a preventive measure to maintain homeostasis. Cpx increases ubiquinone availability for oxidative protein folding by suppressing LCFA metabolism and directly increasing ubiquinone levels. Further, rather than using its conventional mode of imparting regulation via CpxR working as a transcriptional regulator, during LCFA metabolism, Cpx mainly uses its non-coding arm to counteract envelope redox stress. The Cpx-regulated small RNA CpxQ represses fad genes involved in LCFA transport and {beta}-oxidation, downregulates components of glyoxylate shunt, gluconeogenesis, and ETC, and increases ubiquinone content. Corroborating with its role in repressing LCFA metabolism and maintaining redox homeostasis, CpxQ overexpression impairs growth of E. coli in LCFAs and CpxQ deletion renders LCFA-grown E. coli hypersensitive to a thiol agent. Our foremost work studying the interconnection between LCFA metabolism, redox stress, and ESR in E. coli provides a rationale for investigating similar networks in other LCFA-utilizing bacteria. Significance StatementLong-chain fatty acids (LCFAs) are energy-rich nutrients for Escherichia coli; however, their utilization hampers disulfide bond (DSB) formation in secreted proteins, an essential process that occurs in the envelope compartment. Here, we show that an envelope stress response manipulates LCFA metabolism in E. coli and uses a small RNA (sRNA) to restore homeostasis. Several bacteria with a huge impact on human health use host-derived LCFAs during infection. Because many virulence factors require DSB formation, the present study offers a basis to examine whether sRNAs play a role in governing envelope redox balance during LCFA metabolism in pathogens. The sRNA-mediated control is likely an ideal strategy both for rapid response to and quick recovery from LCFA-induced stress.

microbiology↗

bioRxiv2024

DecoyFinder: Identification of Contaminants in Sets of Homologous RNA Sequences

MotivationRNA structure is essential for the function of many non-coding RNAs. Using multiple homologous sequences, which share structure and function, secondary structure can be predicted with much higher accuracy than with a single sequence. It can be difficult, however, to establish a set of homologous sequences when their structure is not yet known. We developed a method to identify sequences in a set of putative homologs that are in fact non-homologs. ResultsPreviously, we developed TurboFold to estimate conserved structure using multiple, unaligned RNA homologs. Here, we report that the positive predictive value of TurboFold is significantly reduced by the presence of contamination by non-homologous sequences, although the reduction is less than 1%. We developed a method called DecoyFinder, which applies machine learning trained with features determined by TurboFold, to detect sequences that are not homologous with the other sequences in the set. This method can identify approximately 45% of non-homologous sequences, at a rate of 5% misidentification of true homologous sequences. AvailabilityDecoyFinder and TurboFold are incorporated in RNAstructure, which is provided for free and open source under the GPL V2 license. It can be downloaded at http://rna.urmc.rochester.edu/RNAstructure.html

bioinformatics↗

bioRxiv2024

A unique bacterial family strikes again!

In a recent study, Rolf Muller and colleagues identified a novel myxobacterial family Pendulisporaceae, encompassing four new strains with biosynthetic gene clusters (BGCs) largely distinct from known families. These strains, sourced from 1980s soil samples, display unique genomic and chemical features, suggesting significant biotechnological and pharmaceutical potential. This study underscores the value of exploring underrepresented microbial taxa for novel natural products, highlighting the potential of the family Pendulisporaceae as a source of new antimicrobial and therapeutic agents.

microbiology↗

bioRxiv2024

Afterload-induced Decreases in Fatty Acid Oxidation Develop Independently of Increased Glucose Utilization

BackgroundMetabolic substrate utilization in HFpEF (heart failure with preserved ejection fraction), the leading cause of heart failure worldwide, is pivotal to syndrome pathogenesis and yet remains ill defined. Under resting conditions, oxidation of free fatty acids (FFA) is the predominant energy source of the heart, supporting its unremitting contractile activity. In the context of disease-related stress, however, a shift toward greater reliance on glucose occurs. In the setting of obesity or diabetes, major contributors to HFpEF pathophysiology, the shift in metabolic substrate use toward glucose is impaired, sometimes attributed to the lower oxygen requirement of glucose oxidation versus fat metabolism. This notion, however, has never been tested conclusively. Furthermore, whereas oxygen demand increases in the setting of increased afterload, myocardial oxygen availability remains adequate for fatty acid oxidation (FAO). Therefore, a "preference" for glucose has been proposed. Methods and ResultsPyruvate dehydrogenase complex (PDC) is the rate-limiting enzyme linking glycolysis to the TCA cycle. As PDK4 (PDC kinase 4) is up-regulated in HFpEF, we over-expressed PDK4 in cardiomyocytes, ensuring that PDC is phosphorylated and thereby inhibited. This leads to diminished use of pyruvate as energy substrate, mimicking the decline in glucose oxidation in HFpEF. Importantly, distinct from HFpEF-associated obesity, this model positioned us to abrogate the load-induced shift to glucose utilization in the absence of systemic high fat conditions. As expected, PDK4 transgenic mice manifested normal cardiac performance at baseline. However, they manifested a rapid and severe decline in contractile performance when challenged with modest increases in afterload triggered either by L-NAME or surgical transverse aortic constriction (TAC). This decline in function was not accompanied by an exacerbation of the myocardial hypertrophic growth response. Surprisingly, metabolic flux analysis revealed that, after TAC, fractional FAO decreased, even when glucose/pyruvate utilization was clamped at very low levels. Additionally, proteins involved in the transport and oxidation of FFA were paradoxically downregulated after TAC regardless of genotype. ConclusionsThese data demonstrate that cardiomyocytes in a setting in which glucose utilization is robustly diminished and prevented from increasing do not compensate for the deficit in glucose utilization by up-regulating FFA use.

cell biology↗

bioRxiv2024

The RNA binding ubiquitination ligase MEX3B regulates bFGF-dependent neuronal proliferation.

BackgroundE3 ubiquitin ligases, integral components of the proteasomal degradation cascade, are critical for regulating the cellular proteome via canonical proteasome-mediated protein degradation; however, the non-canonical functions of these ligases in neuronal development are poorly understood. Our study focuses on a special class of E3 ubiquitin ligases known as RNA Binding Ubiquitin Ligases (RBUL) that harbour RNA-binding domains; allowing them to acquire all the properties of RNA-binding proteins (RBPs) and regulate transcriptional or post-transcriptional changes associated with the control of gene expression in cellular phenotypes. We aim to identify one such RUBL in the context of the highly dynamic yet stringently controlled process of neural proliferation and neural fate determination. ResultsMEX3B protein is a member of the MEX3 family and a part of the RBUL class of E3 ligases. It is differentially expressed in Neural Progenitor Cells (NPCs) upon differentiation. Mex3b RNA and protein were found to have temporally opposing expression patterns in presence of basic fibroblast growth factor (bFGF), a key signalling protein involved in neuronal proliferation. MEX3B is required for maintenance of the proliferative state of NPCs, whereas, its knockdown promotes transition from proliferative to differentiation state even in presence of bFGF that restricts differentiation. Furthermore, the knockdown of MEX3B protein results in the appearance of morphological hallmarks associated with early stages of neuronal differentiation including increase in neurite length and complexity. MEX3B interacts with the pro-proliferative transcription activator REST and the long non-coding RNA, HOTAIR. The study suggests the existence of a bFGF-dependent, combinatorial axis involving Mex3b, REST and HOTAIR, for the maintenance of NPC proliferative states. ConclusionMEX3B, containing RNA binding motifs, is a unique E3 ligase that is necessary for bFGF-dependent proliferation. Mex3b protein invokes its non-canonical function of an RNA binding protein to form a tripartite complex with the transcription activator REST and HOTAIR lncRNA to define the proliferative state of NPCs. The study highlights a unique feature of special E3 ligases in neuronal proliferation during brain development that was previously overlooked.

neuroscience↗

bioRxiv2024

Comparative genomics studies provide insights into the taxonomic classification and secondary metabolic potential of five bioactive Streptomyces species isolated from the North-Western Himalaya

The linear genome of genus Streptomyces members has the potential to encode diverse and novel biosynthetic gene clusters of invaluable antimicrobial and therapeutic significance. The use of limited taxonomic markers makes the precise identification of these miracle microbes very challenging. In the ongoing omics era, genome sequencing and in-silico analysis of these potential antibiotic producers provide deeper insights into their taxonomy, functional capabilities, and potential for antibiotic production. Here this study presents a multifaceted approach for proper taxonomic identification and genomic and bioinformatic analysis of five bioactive Streptomyces species collected from different sampling sites in the high-altitude oligotrophic North-Western Himalaya, Kashmir, India. We used polyphasic taxonomic classification approaches, such as phylogenetic markers (16S rDNA and gyrase B), average nucleotide identity (ANI) estimation, and digital DNA-DNA hybridization (dDDH), which revealed accurate taxonomic placement of five Streptomyces species, named as, Streptomyces violarus ASQP_29, S. rhizosphaerihabitans ASQP_78, S. fulvoviolaceus ASQP_80, S. mirabilis ASQP_98, and S. thajiwasiensis ASQP_92. Amongst these, one notable finding is the discovery of a novel species proposed as Streptomyces thajiwasiensis sp. nov. ASQP_92. In addition, our study presents the first genome announcement report and analysis for S. rhizosphaerihabitans ASQP_78. Genomic annotation highlighted the presence of an exceptionally high number of poorly characterized genes and hypothetical proteins, indicating their potential for undiscovered biotechnological applications. Clusters of orthologous groups (COG) and gene ontology (GO) analysis provided insights into their varied functional roles in metabolism, signaling, information storage and secondary metabolite biosynthesis. Domain-based functional characterization further detailed their involvement in various biological processes particularly in antibiotic biosynthesis, transport, and resistance. Biosynthetic gene clusters (BGC) analysis demonstrated their diverse metabolite biosynthetic capabilities and identified both unique and conserved BGCs emphasizing the species-specific roles in bioactive metabolite production and the potential of orphan BGCs in novel drug discovery. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/596145v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@15ac69corg.highwire.dtl.DTLVardef@a52f89org.highwire.dtl.DTLVardef@d3f8d6org.highwire.dtl.DTLVardef@75cce7_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract:C_FLOATNO Genomic analysis and taxonomic affiliations of five bioactive Streptomyces species isolated from high altitudes of the North Western Himalaya C_FIG

microbiology↗

bioRxiv2024

Biological activities and metabolic profile of endophytic Bacillus haynesii from Momordica charantia

Endophytes share a complex intimate relationship due to which they are capable of synthesizing metabolites that are either similar or derivative of host bioactive compounds. Such endophytes especially from medicinal plants can be prospected for commercial-scale production of the therapeutic compound. Thus, the study evaluates the antioxidant and anti-inflammatory potential of Momordica charantia fruit endophyte Bacillus haynesii R2MCFF61, and determines its metabolite profile through LC-Q-TOF-MS for the bioactive compounds produced. B. haynesii R2MCFF61 showed significant antioxidant and anti-inflammatory potential with increased DPPH scavenging activity in the standard compound and inhibition of protein denaturation respectively. The metabolic profile of this endophyte showed 23 compounds, mostly consisting of metabolites from lipid, phenylpropanoid and triterpenoid pathways. B. haynesii R2MCFF61 showed production of cucurbitane-triterpenoids namely Momordicoside K, 19-dimethoxycucurbita-5(10),6,22(E),24-tetraen-3{beta}-ol and 23(E)-7{beta}-methoxycucurbita-5,23,25-trien-3{beta}-ol. These compounds are mainly produced by M. charantia fruit and their production by its endophyte is reported for the first time. Thus, these results indicate the promising therapeutic potential of B. haynesii R2MCFF61 which can be utilized as a low-cost sustainable source of these bioactive compounds.

microbiology↗

bioRxiv2024

Nanodisc reconstitution and characterization of amyloid-β precursor protein C99

Amyloid precursor protein (APP) plays a pivotal role in the pathology of Alzheimers disease. Since the fragmentation of the membrane-bound APP that results in the production of amyloid-beta peptides is the starting point for amyloid toxicity in AD, it is important to investigate the structure and dynamics of APP in a near-native lipid-bilayer environment. However, the reconstitution of APP into a stable/suitable membrane-mimicking lipid environment is a challenging task. In this study, the 99-residue C-terminal domain of APP is successfully reconstituted into polymer nanodiscs and characterized using size-exclusion chromatography, mass spectrometry, solution NMR, and magic-angle spinning solid-state NMR. In addition, the feasibility of using lipid-solubilizing polymers for isolating and characterizing APP in native E. coli membrane environment is demonstrated.

biochemistry↗

bioRxiv2024

Whole genome sequencing and comparative genomic studies of Priestia filamentosa JURBA-X for its drought-tolerance, plant-growth promotion, and fluorescent characteristics

Priestia filamentosa JURBA-X is a nonmotile, endospore-forming, and Gram-positive bacterium isolated from a rhizosphere soil sample of groundnut fields in Andhra Pradesh, India, during summer. JURBA-X exhibits chains of filamentous morphology with vibrant yellow fluorescence. It shows tolerance to drought stress, phosphate solubilization, siderophore production, and antibacterial activity. 16s rRNA and single-copy orthologous DNA gyrase subunit B-based phylogenies suggested its closeness with Priestia filamentosa spp., leading to its classification as P. filamentosa JURBA-X. The whole genome was assembled into 5,113,908 bp, distributed across 55 contigs with a GC content of 36.59% and 5,352 protein-coding genes. Genome-genome distance and average nucleotide identity confirmed its designation as a novel strain within P. filamentosa. Assignment of genes/proteins in diverse functions such as drought tolerance, plant growth promotion (PGP), lantibiotics, polyketides, vitamin synthesis, siderophores production, and phosphate solubilization highlight its potential utilization in agriculture as a PGPR and industrial production of antimicrobial agent, vitamins, and biopolymers. Our research concluded that the fluorescence exhibited by JURBA-X is potentially attributed to the production of resistomycin, which might have been horizontally transferred from Streptomyces resistomycificus as inferred by the homology of resistomycin (rem) biosynthesis cluster genes.

microbiology↗

bioRxiv2024

Putative origin of Myxococcus fulvus 124B02 plasmid, pMF1, from a chromosomal segment in another Myxococcus species

Myxobacteria or order Myxococcales (old nomenclature) or phylum Myxococcota (new terminology) are fascinating organisms well known for their diverse peculiar physiological, taxonomic, and genomic properties. Researchers have long sought to identify plasmids within these organisms, yet thus far, only two organisms from different families have been found to harbor a plasmid. This study delves into the origin and evolution of one of these plasmids, i.e., pMF1 present in M. fulvus 124B02 in the suborder Cystobacterineae and family Myxococcaceae. Here we first reannotated the pMF1 plasmid genome sequence and identified two additional genes which were not annotated till now. We further reported that all pMF1 plasmid genes depict homology with M. stipitatus CYD1 draft genome (contig 28) and a chromosomal segment of M. stipitatus DSM14675 in a syntenic manner, suggesting the presence of plasmid-like structure in M. stipitatus CYD1 but integrated as part of its chromosome. To comprehend the relationship among these three species, we conducted phylogenetic analyses using 16S and concatenated housekeeping genes and GGDC analysis, which confirmed that M. stipitatus CYD1 is a distinct and novel species within the genus Myxococcus. Overall, this study sheds light on the putative origin of the pMF1 plasmid, which likely originated from a closely related yet distinct species, possibly through the partition from its chromosome as a segment. ImportanceMyxobacteria are not well-known to have plasmids. Till now, only two organisms have been shown to have plasmids, raising a pertinent question about how these plasmids evolved randomly within the phylum Myxococcota. The study presented in this manuscript delves into the origin and evolution of the pMF1 plasmid found in Myxococcus fulvus 124B02, a member of the suborder Cystobacterineae and family Myxococcaceae. Our research addresses the intriguing topic of plasmid identification and evolution within Myxobacteria, which are a group of fascinating organisms that have garnered significant interest due to their diverse physiological, taxonomic, and genomic properties.

genomics↗

bioRxiv2024

Effect of environmental conditions on the wing morphometric variation in Aedes aegypti (Diptera: Culicidae) in India

Aedes aegypti an efficient vector of different arboviral diseases, is a major concern for public health globally. Originating from Africa, this vector has now invaded most of the parts of the world, which shows its thriving adaptability against diverse ecological conditions. In India too, Ae. aegypti has been found almost everywhere and along with Ae. albopictus, it contributed more than 0.2 million cases of dengue in the year 2022. Due to heterogeneous environmental settings in India, this vector has shown various intraspecific variations including its behavioral, genetic, and physiological characteristics. Thus, the present study hypothesized that there will be some differences in wing morphometrics across the country for this species. Considering this, we have sampled adults and immatures of Ae. aegypti from 11 distinct locations, representing six varied climatic regions of India. The immatures were reared to adult and the right wing was used to score the morphometric variations. A significant variation in wing size and shape was observed. The Himalayan region (Srinagar CS: 1.92 {+/-} 0.08 mm) supports the shortest (CS: 2.04 {+/-} 0.09 mm) wing size mosquitoes while the Deccan Peninsular region (Nagpur CS: 4.48 {+/-} 0.06 mm) exhibits the largest (CS: 4.46 {+/-} 0.10 mm) wing size mosquito. After excluding the allometric effect, the semi-desert region (Kota) showed the greatest wide variety of wing shapes corresponding to a larger morphospace in CVA analysis. In addition, region-wise wing size was found positively correlated with temperature (64%) and altitude (82%) but no directional trend was detected for wing shape characteristics. Conclusively, the study suggests the existence of varied population structures of Ae. aegypti in India based on wing morphometric analysis. This finding will be helpful towards focused actions and early measures to reduce the impact of these diseases carrying mosquitoes on public health.

zoology↗

bioRxiv2023

A Synthetic Cytotoxic T cell Platform for Rapidly Prototyping TCR Function

Current tools for functionally profiling T cell receptors with respect to cytotoxic potency and cross-reactivity are hampered by difficulties in establishing model systems to test these proteins in the contexts of different HLA alleles and against broad arrays of potential antigens. We have implemented and validated a granzyme-activatable sensor of T cell cytotoxicity in a novel universal prototyping platform which enables facile recombinant expression of any combination of TCR-, peptide-, and class I MHC-coding sequences and direct assessment of resultant responses. This system consists of an engineered cell platform based on the immortalized natural killer cell line, YT-Indy, and the MHC-null antigen-presenting cell line, K562. These cells were engineered using contemporary gene-editing techniques to furnish the YT-Indy/K562 pair with appropriate protein domains required for recombinant TCR expression and function in a non-T cell chassis, integrate a fluorescence-based target-centric early detection reporter of cytotoxic function, and deploy a set of protective genetic interventions designed to preserve antigen-presenting cells for subsequent capture and downstream characterization. Our data show successful reconstitution of the surface TCR complex in the YT-Indy cell line at biologically relevant levels. We also demonstrate successful induction and highly sensitive detection of antigen-specific response in multiple distinct model TCRs, with significant responses (p < 0.05 and Cohens d >1.9) in all cases. Additionally, we monitored destruction of targets in co-culture and found that our survival-optimized system allowed for complete preservation after 24-hour exposure to cytotoxic effectors. With this bioplatform, we anticipate investigators will be empowered to rapidly express and characterize T cell receptor responses, generate new knowledge regarding the patterns of T cell receptor recognition, and optimize novel therapeutic T cell receptors for improved cytotoxic potential and reduced cross-reactivity to undesired antigenic targets.

immunology↗