Biology subjects

Subramani, S.

Publications and source records attributed to Subramani, S..

16 recordsLinked to original sources

bioRxiv2026

Functional diversification across yeast lineages of the nucleus-vacuole junction forming protein Nvj1

Nucleus-vacuole junctions (NVJs) in Saccharomyces cerevisiae serve as an inter-organellar hub for multiple cell processes, including lipid transport and biosynthesis, an intra-nuclear quality control mechanism, and piecemeal microautophagy of the nucleus. NVJs are formed by complexes between Vac8 in the vacuole membrane and Nvj1 in the nuclear envelope. Nvj1 also links the inner and outer nuclear membranes across the perinuclear lumen. Orthologs of Nvj1 had previously only been found in yeasts of the order Saccharomycetales, raising the possibility that NVJs are restricted to this clade. Using homology and synteny, we discovered scores of novel Nvj1 orthologs across 200 million years of evolution within the subphylum Saccharomycotina. Not all orthologs mediate NVJ formation when expressed in S. cerevisiae, and some lack a sequence motif necessary for this function. Furthermore, the sequence motif required for binding the oxysterol binding protein Osh1 and an associated novel sequence motif, both found only in the order Saccharomycetales, were independently lost in three different lineages. This collection suggests specific opportunities to explore evolutionary and functional adaptations of Nvj1s in ecologically and physiologically diverse yeasts.

cell biology↗

bioRxiv2025

Alternative splicing of synaptotagmin 7 regulates oligomerization and short-term synaptic plasticity

Synaptic plasticity is crucial for learning and memory. The presynaptic calcium sensor synaptotagmin 7 (syt7) regulates aspects of short-term plasticity (STP), but the underlying mechanisms remain unclear. Here, we show that alternative splicing of the syt7 juxtamembrane linker acts as a molecular switch at both biochemical and functional levels. The and {beta} variants undergo liquid-liquid phase separation to form condensates, while the {gamma} variant forms aggregates. Using iGluSnFR imaging, we found that when expressed at equal levels, these three isoforms also diverge regarding their abilities to regulate two key aspects of STP: paired-pulse facilitation and synaptic depression. STED microscopy showed that all three isoforms form active zone-associated clusters that colocalize with syt1, while MINFLUX super-resolution microscopy resolved syt7 clusters within the active zone, well-positioned to directly control synaptic vesicle dynamics. Thus, alternative splicing might fine-tune STP by differentially impacting syt7 oligomerization.

neuroscience↗

bioRxiv2025

TOR and heat shock response pathways regulate peroxisome biogenesis during proteotoxic stress

Peroxisomes are versatile organelles mediating energy homeostasis and redox balance. While peroxisome dysfunction is linked to numerous diseases, the molecular mechanisms and signaling pathways regulating peroxisomes during cellular stress remain elusive. Using yeast, we show that perturbations disrupting protein homeostasis including loss of ER or cytosolic chaperone function, impairments in ER protein translocation, blocking ER N-glycosylation, or reductive stress, cause peroxisome proliferation. This proliferation is driven by increased de novo biogenesis from the ER as well as increased fission of pre-existing peroxisomes, rather than impaired pexophagy. Notably, peroxisome biogenesis is essential for cellular recovery from proteotoxic stress. Through comprehensive testing of major signaling pathways, we determine this response to be mediated by activation of the heat shock response and inhibition of Target of Rapamycin (TOR) signaling. Finally, the effects of proteotoxic stress and TOR inhibition on peroxisomes are also captured in human fibroblasts. Overall, our findings reveal a critical and conserved role of peroxisomes in cellular response to proteotoxic stress.

cell biology↗

bioRxiv2024

Bulk and selective autophagy cooperate to remodel a fungal proteome in response to changing nutrient availability

Cells remodel their proteomes in response to changing environments by coordinating changes in protein synthesis and degradation. In yeast, such degradation involves both proteasomal and vacuolar activity, with a mixture of bulk and selective autophagy delivering many of the vacuolar substrates. Although these pathways are known to be generally important for such remodeling, their relative contributions have not been reported on a proteome-wide basis. To assess this, we developed a method to pulse-label the methylotrophic yeast Komagataella phaffii (i.e. Pichia pastoris) with isotopically labeled nutrients, which, when coupled to quantitative proteomics, allowed us to globally monitor protein degradation on a protein-by-protein basis following an environmental perturbation. Using genetic ablations, we found that a targeted combination of bulk and selective autophagy drove the vast majority of the observed proteome remodeling activity, with minimal non-autophagic contributions. Cytosolic proteins and protein complexes, including ribosomes, were degraded via Atg11-independent bulk autophagy, whereas proteins targeted to the peroxisome and mitochondria were primarily degraded in an Atg11-dependent manner. Notably, these degradative pathways were independently regulated by environmental cues. Taken together, our new approach greatly increases the range of known autophagic substrates and highlights the outsized impact of autophagy on proteome remodeling. Moreover, the resulting datasets, which we have packaged in an accessible online database, constitute a rich resource for identifying proteins and pathways involved in fungal proteome remodeling.

bioengineering↗

bioRxiv2024

Automated, image-based quantification of peroxisome characteristics with perox-per-cell

perox-per-cell automates cumbersome, image-based data collection tasks often encountered in peroxisome research. The software processes microscopy images to quantify peroxisome features in yeast cells. It uses off-the-shelf image processing tools to automatically segment cells and peroxisomes and then outputs quantitative metrics including peroxisome counts per cell and spatial areas. In validation tests, we found that perox-per-cell output agrees well with manually-quantified peroxisomal counts and cell instances, thereby enabling high-throughput quantification of peroxisomal characteristics. The software is available at https://github.com/AitchisonLab/perox-per-cell

bioinformatics↗

bioRxiv2023

Aeroplane wing, a new recessive autosomal phenotypic marker in malaria vector, Anopheles stephensi Liston

A novel and distinct mutant, with an aeroplane wing (ae) phenotype, is reported for the first time in the urban malaria vector, Anopheles stephensi. The mutant mosquitoes exhibit extended wings that are easily visible to naked eyes in both sexes. This mutant was first observed in a nutritionally stressed experimental isofemale line and characterized for its genetic inheritance and other related parameters. Meticulous and strategic genetic crosses revealed that the ae gene is an autosomal, recessive, non-sex-linked and monogenic trait with full penetrance and uniform expression in the adult stage. Cytogenetic study of the ovarian polytene chromosome revealed an inversion on the 3L chromosome (3Li) in both the ae mutant and its parent line. No significant differences in wing venation and other parameters were observed in ae mutants compared to their normal parental lines. This ae mutant would be an excellent marker that can be used by researchers to study the function of related genes within the genome. Author summaryIn the present study, we have established and describe the inheritance of an unusual novel aeroplane (ae) winged mutant in Anopheles stephensi, an urban malaria vector in India. The ae mutant lines exhibit three open-wing orientations in both the sexes of adults viz. left (LW), right (RW) and double wing (DW) during its resting phase. Through various inbreeding crosses we demonstrated the mode of inheritance of the ae gene to be autosomal, recessive and monogenic in nature. The morphometric studies of eggs and wings revealed that mutant lines are on par with their parental lines. Cytogenetic study of polytene chromosome of ae mutant revealed the presence of heterogenic inversion on the 3L chromosome arm, which might help in adaptation mechanism. We strongly believe that ae phenotypic markers have great applications bridging both basic and applied genetic research such as constructing linkage maps, identifying loci of quantitative and/or qualitative traits and as guides for insect transformation studies.

genetics↗

bioRxiv2023

Rhythm generating mechanisms in rat sino-atrial node and ventricle

The major membrane currents responsible for sinoatrial and idioventricular rhythm-generation were studied in isolated rat heart preparations, perfused in Langendorff mode. The rates of whole isolated hearts beating with sinoatrial rhythm decreased with cesium and ivabradine, both blockers of the funny current, and were not affected by nickel, at a dose which blocks T-type calcium current. The sinoatrial rhythm was completely abolished by reduction or removal of sodium from the perfusate (interventions that inhibit calcium-extrusive mode of the sodium/calcium exchanger), or by nifedipine, an L-type calcium channel blocker. Idioventricular rhythm, however, was arrested only by reduction of sodium in the perfusate. Ivabradine reduced the idioventricular rate, nickel did not cause any change, while nifedipine in some cases increased it. The inferences made based on these observations are that INCX and ICaL are obligatory rhythm-generating currents in the sinoatrial node, while INCX is the only obligatory mechanism for an idioventricular rhythm. The funny current is not an obligatory requirement for sinoatrial as well as idioventricular rhythm-generation. However, it enhances the frequency of LCRs. Our results in the isolated whole heart are in corroboration with results from isolated cells.

physiology↗

bioRxiv2022

Enrichment of phenotype among biological forms of Anopheles stephensi Liston through establishment of isofemale lines

The success of vector management programs relies on knowledge of the biology and genetic make-up of mosquitoes so that they can be interlaced with modern tools for developing suitable intervention strategies. There are many reports available for rearing varied species of mosquito vectors. However, there are limited studies addressing the development of isofemale lines among mosquitoes to homogenize the population to obtain both high-quality genome assemblies and enrichment of phenotype. Anopheles stephensi, an urban malaria vector, is one of the major invasive vectors of malaria distributed throughout the Indian subcontinent, Middle East, and has recently been expanding its range in Africa. With the existence of three biological forms, distinctly identifiable based on the number of ridges on eggs with varying vectorial competence, An. stephensi is a perfect species for developing a method for the successful establishment of isofemale lines, which can be tested for retention of the expected vectorial competence for the various forms. We describe the key steps in the establishment and validation of isofemale lines, which include monitoring the transgenerational fitness traits, morphometrics of eggs, and adult wing size during every generation. After the initial inbreeding depression, as proof of the tedious selection process, no significant morphometric differences were observed in the wings and egg size between the parental and their respective isofemale lines. We observed a significant change in the vectorial competence between the respective isofemale and parental lines enriching expected differential susceptibility towards malaria parasites by the type and intermediate forms. Interestingly, IndCh and IndInt strains showed variations in resistance to different insecticides belonging to all the four major classes. These variant lines have been characterized for their levels of homozygosity both at the phenotype and genotype levels and can be used as a standard reference or as a biological resource for other studies related to urban malaria research. Author summaryIsofemale lines can be a valuable resource for characterizing and enhancing several genotypic and phenotypic traits. This is the first detailed report of the establishment of two isofemale lines of type and intermediate biological forms in Anopheles stephensi. The work encompasses the characterization of fitness traits among the two lines through a transgenerational study. Further, isofemale colonies were established and used to characterize insecticide susceptibility and vector competence. The study provides valuable insights into the differential susceptibility status of the parental and isofemale to different insecticides belonging to the same class. Corroborating with the earlier hypothesis we exemplify the high vector competence in type form than the intermediate from using homozygous isofemale lines. Using these isofemale lines it is now possible to study host-parasite interactions and identify factors that might be responsible for altered susceptibility and increased vector competence in An. stephensi biological forms that would also pave way for developing better vector management strategies.

genetics↗

bioRxiv2022

Identification of a TNF-TNFR-like system in malaria vectors (Anopheles stephensi) likely to influence Plasmodium resistance

Identification of Plasmodium-resistance genes in malaria vectors remains an elusive goal despite the recent availability of high-quality genomes of several mosquito vectors. An. stephensi, with its three distinctly-identifiable forms at the egg stage, correlating with varying vector competence, offers an ideal species to discover functional mosquito genes implicated in Plasmodium resistance. Recently, the genomes of several strains of An. stephensi of the type-form, known to display high vectorial capacity, have been reported. Here, we report a chromosomal-level assembly of an intermediate-form of An. stephensi strain (IndInt), shown to have reduced vectorial capacity relative to a strain of type-form (IndCh). The contig level assembly with a L50 of 4 was scaffolded into chromosomes by using the genome of IndCh as the reference. The final assembly shows a heterozygous paracentric inversion, 3Li, involving 8 Mbp, which is syntenic to the extensively-studied 2La inversion implicated in Plasmodium resistance in An. gambiae involving 21 Mbp. Deep annotation of genes within the 3Li region in IndInt assembly using the state-of-the-art protein-fold prediction and other annotation tools reveals the presence of a TNF-like gene, which is the homolog of the eiger gene in Drosophila. Subsequent chromosome-wide searches revealed homologs of wengen (wgn) and grindelwald (grnd) genes in IndInt, which are known to be the receptors for eiger in Drosophila. We have identified all the genes in IndInt required for eiger-mediated signaling by analogy to TNF-TNFR system, suggesting the presence of a functionally active eiger signaling pathway present in IndInt. Comparative genomics of high-quality genome assemblies of the three type-forms with that of IndInt, reveals structurally disruptive mutations in eiger gene in all three strains of the type-form, alluding to compromised innate immunity in the type-form as the cause of high vectorial capacity in these strains. This is the first report of the presence of an intact evolutionarily-conserved TNF-TNFR signaling system in malaria vectors, with a potential role in Plasmodium resistance.

genomics↗

bioRxiv2021

The bacterial magnesium transporter MgtA reveals highly selective interaction with specific cardiolipin species

A significant challenge today within protein lipidology is to understand the relationship between cell structure, lipid membrane integrity, ion homeostasis and the embedded membrane proteins. The bacterial magnesium transporter A (MgtA) is a specialized P-type ATPase important for Mg2+ import into the cytoplasm; disrupted magnesium homeostasis is linked to intrinsic ribosome instability and nitro-oxidative stress in Salmonella strains. MgtAs function is highly dependent on anionic lipids, particularly cardiolipin, and further co-localization of cardiolipin with MgtA at the E. coli cell poles has been revealed. Here, we show that MgtA has functional specificity for cardiolipin 18:1, but it reaches maximum activity only in combination with cardiolipin 16:0, equivalent to the major components of native cardiolipin found in E. coli membranes. This is the first time it has been shown experimentally that two different lipid species from the same class, individually promoting low activity, can enhance activity in combination. Native mass spectrometry verifies the presence of two binding sites for cardiolipin and kinetic studies reveal that a cooperative relationship likely exists between the two different cardiolipin variants (cardiolipin 16:0 and cardiolipin 18:1). This is the first experimental evidence of cooperative effects between lipids of the same class, with only minor variations in their acyl chain composition, acting on a membrane protein. In summary, our results reveal that MgtA exhibits a highly complex interaction with one cardiolipin 18:1 and one cardiolipin 16:0, affecting protein activity and stability, and contributing to our understanding of the particular interactions between lipid environment and membrane proteins. Further, a better understanding of Mg2+ homeostasis in bacteria, due to its role as a virulence regulator, will provide further insights into the regulation and mechanism of bacterial infections.

biochemistry↗

bioRxiv2021

OXPHOS deficiencies affect peroxisome proliferation by downregulating genes controlled by the SNF1 signaling pathway

How environmental cues influence peroxisome proliferation, particularly through other organelles, remains largely unknown. Yeast peroxisomes metabolize all fatty acids (FA), and methylotrophic yeasts also metabolize methanol. NADH and acetyl-CoA, the products of these pathways enter mitochondria for ATP production, and for anabolic reactions. During the metabolism of FA and/or methanol, the mitochondrial oxidative phosphorylation (OXPHOS) pathway accepts NADH for ATP production and maintains cellular redox balance. Remarkably, peroxisome proliferation in Pichia pastoris was abolished in NADH shuttling and OXPHOS mutants affecting complex I or III, or by the mitochondrial uncoupler, 2,4-dinitrophenol (DNP), indicating ATP depletion causes the phenotype. We show that mitochondrial OXPHOS deficiency inhibits the expression of several peroxisomal proteins implicated in FA and methanol metabolism, as well as in peroxisome division and proliferation. These genes are regulated by the Snf1 complex (SNF1), a pathway generally activated by high AMP and low ATP. Consistent with this mechanism, in OXPHOS mutants, Snf1 is activated by phosphorylation, but Gal83, its interacting subunit, fails to translocate to the nucleus. Phenotypic defects in peroxisome proliferation observed in the OXPHOS mutants, and phenocopied by the{Delta} gal83 mutant, were rescued by deletion of three transcriptional repressor genes (MIG1, MIG2 and NRG1) controlled by SNF1 signaling. We uncovered here the mechanism by which peroxisomal and mitochondrial metabolites influence redox and energy metabolism, while also influencing peroxisome biogenesis and proliferation, thereby exemplifying interorganellar communication and interplay involving peroxisomes, mitochondria, cytosol and the nucleus. We discuss the physiological relevance of this work in view of human OXPHOS deficiencies.

cell biology↗

bioRxiv2021

Vasoconstriction in isolated goat aorta does not increase mean aortic pressure

Vasoconstriction in small arteries and arterioles is known to increase resistance to flow, while vasoconstriction in large arteries and aorta is known to decrease their compliance. Besides this general understanding, there is no systematic documentation on what happens to small artery compliance and large artery resistance during vasoconstriction and the corresponding alterations in vascular pressure. The aim of the study is to assess the effect of adrenaline on goat aortae and small arteries in terms of resistance and compliance. Isolated goat aortae and small arteries were perfused with a pulsatile pump and lumen pressure was recorded before and after addition of adrenaline. In the aortae, systolic pressure increased, diastolic pressure decreased, pulse pressure increased (p = 0.018, WSR); but the mean pressure remained the same (p = 0.357, WSR). Small artery vasoconstriction caused an increase in systolic, diastolic and mean pressures (p = 0.028, WSR). Using length, radius, and thickness data from the tissues and the tubes of the experimental set-up, electrical models were simulated to understand the biological data. The simulations allow us to infer that vasoconstriction in aorta leads to a reduction in compliance, but an increase in resistance if any, is not sufficient to change the mean aortic pressure. On the other hand, vasoconstriction in small arteries increases resistance, but a decrease in compliance if any, does not affect any of the four pressure parameters measured. Vasoconstriction in aorta decreases compliance and therefore increases pulse pressure but does not change resistance significantly enough to alter mean pressure. Key Points SummaryO_LIThe main aim of the study is to understand where exactly resistance (R) and compliance (C) components of the vasculature occur. There is no definitive evidence for the effect of large artery vasoconstriction on resistance and hence the mean arterial pressure. C_LIO_LIThe manuscript presents biological experiments studying the pressure response of goat aorta and small arteries to adrenaline (invitro) and the interpretations using equivalent electrical models. C_LIO_LIThe study shows that in aorta and large arteries, vasoconstriction does not lead to a reduction in lumen diameter sufficient to cause a rise in resistance and mean pressure as compared to small arteries. C_LIO_LIKnowledge of exact location of R and C in the arterial tree enables re-assessment of the differential action of vasoactive drugs on resistance versus compliance vessels once we resolve beat-to-beat R and C changes in response to a drug. This way antihypertensive therapy can be tailored to address the specific cause of the type of hypertension. C_LI

physiology↗

bioRxiv2020

Hidden features of the malaria vectormosquito, Anopheles stephensi ,revealed by a high-quality referencegenome

BackgroundThe mosquito Anopheles stephensi is a vector of urban malaria in Asia that recently invaded Africa. Studying the genetic basis of vectorial capacity and engineering genetic interventions are both impeded by limitations of a vectors genome assembly. The existing assemblies of An. stephensi are draft-quality and contain thousands of sequence gaps, potentially missing genetic elements important for its biology and evolution. ResultsTo access previously intractable genomic regions, we generated a reference-grade genome assembly and full transcript annotations that achieve a new standard for reference genomes of disease vectors. Here, we report novel species-specific transposable element families and insertions in functional genetic elements, demonstrating the widespread role of TEs in genome evolution and phenotypic variation. We discovered 29 previously hidden members of insecticide resistance genes, uncovering new candidate genetic elements for the widespread insecticide resistance observed in An. stephensi. We identified 2.4 Mb of the Y-chromosome and seven new male-linked gene candidates, representing the most extensive coverage of the Y-chromosome in any mosquito. By tracking full length mRNA for >15 days following blood feeding, we discover distinct roles of previously uncharacterized genes in blood metabolism and female reproduction. The Y-linked heterochromatin landscape reveals extensive accumulation of long-terminal repeat retrotransposons throughout the evolution and degeneration of this chromosome. Finally, we identify a novel Y-linked putative transcription factor that is expressed constitutively through male development and adulthood, suggesting an important role throughout male development. ConclusionCollectively, these results and resources underscore the significance of previously hidden genomic elements in the biology of malaria mosquitoes and will accelerate development of genetic control strategies of malaria transmission.

genomics↗

bioRxiv2020

A near-chromosome level genome assembly of Anopheles stephensi

Malaria remains a major healthcare risk to growing economies like India and a chromosome-level reference genome of Anopheles stephensi is critical for successful vector management and an understanding of vector evolution. We report a chromosome-level assembly of an Indian strain from draft genomes of two strains using a homology-based iterative approach. The resulting assembly with an L50 of 9 had long enough scaffolds for building 90% of the three chromosomes using physical markers. The sequencing of individuals reveals a genetic diversity ten times higher than what is reported. Based on the developmental transcriptome and orthology of the 54 olfactory receptors (ORs) to those of other Anopheles species, we identify olfactory receptors with the potential for host recognition in the genus Anopheles. A comparative analysis of the genomes suggests limited inter-chromosomal gene flow and chromosomal arm switching with a potential role in adaptive radiation within the genus Anopheles.

genomics↗

bioRxiv2019

Phenylephrine induces relaxation of longitudinal strips from small arteries of goat legs

Alpha adrenergic stimulation is known to produce vasoconstriction. We have earlier shown that, in spiral strips of small arteries Phenylephrine (PE) caused vasorelaxation under high nitric oxide (NO) environment. However on further experimentation it was realized that the PE-induced vasorelaxant response occurred only with longitudinal strips of small arteries even under normal NO environment while circular strips showed contraction with PE even under high NO environment. Such PE-induced vasorelaxation of longitudinal strips was blocked by Phentolamine, an alpha-adrenergic receptor blocker. On delineation of specific receptor subtype, PE-induced relaxation was found to be mediated through alpha 1D receptor. However, this phenomenon is specific to small artery, as longitudinal smooth muscle of aorta showed only contractile response to adrenergic stimulation. There is no prior report of longitudinal smooth muscle in small artery up to our knowledge. The results of this study and histological examination of vessel sections suggest the presence of longitudinal smooth muscle in small artery and their relaxant response to alpha adrenergic stimulation is a novel phenomenon.

physiology↗

bioRxiv2019

Blood pressure variability from intra-arterial recordings in humans

Systolic and diastolic blood pressures are reported as single point values by the non-invasive techniques used in clinical practice, while, in fact, they are highly varying signals. The objective of this study was to document the magnitude of variation of systolic and diastolic pressures over a few minutes by analysing intra-arterial pressure recordings made in 51 haemodynamically stable patients in an intensive care unit. Intra-arterial pressure data were acquired by a validated data acquisition system. Fast-Flush test was performed and the dynamic characteristics of the catheter transducer system namely natural frequency and damping co-efficient were calculated. Only those recordings with acceptable dynamic characteristics were included in the analysis. Power spectral calculation using the Discrete Fourier transform (DFT) of the pressure recording revealed two frequency peaks below the peak at heart rate. The lower and higher frequency peaks below the heart rate peak are referred to as Mayer and Traube waves in this study. Mayer wave peaks were observed in DFT spectra of 49 out of 51 patients. The Mayer wave frequency peaks ranged between 0.045 Hz to 0.065 Hz in 41 out of 51 patients. The frequency of Traube waves or the respiratory variations was more than 0.14 Hz. Three categories of systolic and diastolic pressure variabilities namely beat-to-beat variability, Respiratory variability (Traube wave amplitude) and Total magnitude of variation are reported for all 51 patients. The mean systolic and diastolic pressure variations (in a period of about 10 minutes) in the study sample were 21 {+/-} 9 mm Hg and 14 {+/-} 5 mm Hg respectively. Given the magnitude of systolic and diastolic pressure variations over a few minutes, the validity of reporting single point values for these pressures and using single point cut-offs for diagnosis and treatment of hypertension must be re-evaluated.

physiology↗