Biology subjects

Datta, S.

Publications and source records attributed to Datta, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Reprogrammed E. coli for secretion of thermophilic cellulase cocktail for seawater-compatible lignocellulosic bioprocessing

The development of efficient cellulase systems is crucial for sustainable lignocellulosic biorefining. In this study, we engineered Escherichia coli to co-express and secrete a thermophilic cellulase cocktail consisting of a Bacillus licheniformis processive endoglucanase (H1AD14), a Chaetomium thermophilum cellobiohydrolase (G0SAE6), and a glucose-tolerant engineered {beta}-glucosidase B8CYA8tm (V169C/E173L/I246A B8CYA8) from Halothermothrix orenii. Fusion with the AnsB secretion tag enabled extracellular yields of 0.2-0.4 g/L for each enzyme, bypassing costly purification while retaining activity. The secretion was confirmed via immunoblotting using anti-His antibody, and catalytic activity was validated through enzymatic assays. The absence of E. coli native periplasmic maltose-binding protein (detected with anti-MBP antibody) in the extracellular medium ruled out cell lysis, confirming protein secretion. Using the Golden Gate assembly, we constructed and systematically evaluated synergistic enzyme combinations for hydrolytic performance. By optimizing secretion conditions, including media, inducer concentration, and incubation temperature, the total yield of secreted enzyme cocktail increased from 0.31 g/L to 0.74 g/L. The secreted cocktail effectively hydrolysed diverse lignocellulosic substrates and exhibited 100 % activity in seawater, demonstrating potential for freshwater-independent biorefining. The work addresses key economic and environmental challenges in biomass conversion by integrating secretion engineering, thermostability, and seawater tolerance into a single scalable system.

bioengineering↗

bioRxiv2025

A Chemical Mechanistic Path Leads the Way to Cellular Argpyrimidine

Argpyrimidine (APY) is a methylglyoxal-derived advanced glycation end-product (AGE) that has been associated with multiple diseases. As APY forms without an enzyme, it remains exceptionally difficult to pinpoint where APY is likely to be found, both on individual proteins and in cells. In this study, we used a peptide model system and mass spectrometry analysis to investigate the chemical mechanism through which APY arises from methylglyoxal (MGO), a biologically relevant glycating agent. Consistent with other proposed APY formation mechanisms, our results identify AGE species with a mass change of [M+144], presumably including tetrahydropyrimidine (THP), as a direct precursor to APY. However, our results rule out previously proposed reductone or oxidative decarboxylation mechanisms. Instead, we show that a formal oxidation step is not required, and that formate is released instead of CO2. We further show the potential for a nearby residue such as Tyr to assist in the APY formation mechanism by acting as a general base. These experiments also reveal that phosphorylated Tyr or Ser residues can also promote equivalent levels of APY formation, despite introducing additional negative charges that we previously showed to impede glycation. Guided by these mechanistic insights and a newly defined role for phosphorylated residues on glycation substrates, we performed quantitative bottom-up proteomics analysis for MGO-treated cells. Gene ontology analysis for AGE-modified proteins revealed enrichment of phosphorylation-related terms (e.g. kinase activity or protein phosphorylation) for APY, while other Arg post-translational modifications did not. Collectively, these data define a chemical mechanistic path to APY and suggest significant crosstalk between cellular phosphorylation and glycation events including APY formation.

biochemistry↗

bioRxiv2025

A novel mechanism of morphogenetic transition in Schizosaccharomyces pombe dependent on the MAPK Spc1 and the transcription factor Atf1 associated with sensing of optimal growth environment

Fission yeast Schizosaccharomyces pombe are rod shaped eukaryotic cells that grow by tip elongation and divide medially by formation of cell wall septum. The coordination between cell length and cell cycle phase transitions in this simple eukaryote makes it an excellent model system for studying morphogenetic events associated with both intrinsic and extrinsic disturbances in cell cycle regulation. Cell cycle progression in S. pombe is dependent on the coordinated functions of two bZIP family transcription factors Atf1 and Pcr1. In an attempt to understand this coordination, we stumbled upon the startling observation that overexpression of Atf1 in cells lacking Pcr1 led to drastic morphogenetic alteration whereby the cells became hyper elongated. In this report we present the evidences of dependence of this phenotype on metabolic status of the cell. We also show that the phenotype is dependent on the activity of the Mitogen Activated Protein Kinase, Spc1 and that it is associated with the global gene expression alterations of cells resulting from the perturbed balance of Atf1 and Pcr1 activities. We found that change in the carbon source, alterations in iron concentration and the redox environment of the cell can affect the extent of morphogenesis, to the extent of even abolishing it at times. Our results also indicate that this phenotype has a strong association with maintenance of optimum growth conditions of the cell. Taken together, our observations reveal a completely novel mechanism of morphogenetic transition in fission yeast involving the MAPK Spc1 and its downstream effector molecule Atf1, which can be tuned by the cells metabolic environment.

microbiology↗

bioRxiv2025

AR-V7 condensates drive androgen-independent transcription in castration resistant prostate cancer

Biomolecular condensates organize cellular environments and regulate key processes such as transcription. We previously showed that full-length androgen receptor (AR-FL), a major oncogenic driver in prostate cancer (PCa), forms nuclear condensates upon androgen stimulation in androgen-sensitive PCa cells. Disrupting these condensates impairs AR-FL transcriptional activity, highlighting their functional importance. However, resistance to androgen deprivation therapy often leads to castration-resistant prostate cancer (CRPC), driven by constitutively active splice variants like AR variant 7 (AR-V7). The mechanisms underlying AR-V7s role in CRPC remain unclear. In this study, we characterized the condensate-forming ability of AR-V7 and compared its phase behavior with AR-FL across a spectrum of PCa models and in vitro conditions. Our findings indicate that cellular context can influence AR-V7s condensate-forming capacity. Unlike AR-FL, AR-V7 spontaneously forms condensates in the absence of androgen stimulation and functions independently of AR-FL in CRPC models. However, AR-V7 requires a higher concentration to form condensates, both in cellular contexts and in vitro. We further reveal that AR-V7 drives transcription via both condensate-dependent and condensate-independent mechanisms. Using an AR-V7 mutant incapable of forming condensates, while retaining nuclear localization and DNA-binding ability, we reveal that the condensate-dependent regime activates part of the oncogenic KRAS pathway in CRPC models. Genes under this condensate-dependent regime were found to harbor significantly higher numbers of AR-binding sites and exhibited boosted expression in response to AR-V7. These findings uncover a previously unrecognized role of AR-V7 condensate formation in driving oncogenic transcriptional programs and shed light on its unique contribution to CRPC progression. HighlightsO_LIAR-V7 condensates form independently of both androgens and AR-FL in CRPC models. C_LIO_LIAR-V7 mediates condensate-dependent and independent transcription C_LIO_LICondensate-dependent transcription enables boosted expression of oncogenic KRAS genes C_LIO_LICondensate-dependent genes exhibit an exponential increase in expression, with a higher number of AR binding sites potentially playing a key role in their reliance on condensate formation. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/631986v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@16b50d1org.highwire.dtl.DTLVardef@86e3b6org.highwire.dtl.DTLVardef@1cfe7f3org.highwire.dtl.DTLVardef@8532a2_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters

CGGBP1, a 20 kDa protein, has several functions associated with its DNA-binding through a C2H2 zinc finger. A range of studies have shown that GC richness, inter-strand G/C-skew and low cytosine methylation are associated with CGGBP1 occupancy. The non-preference of any sequence motif as CGGBP1 binding site suggests widespread association of CGGBP1 with DNA including at potent transcription factor binding sites (TFBSs) in promoter regions. The evolutionary advantage of such a design remains unclear. The regulatory interference by human CGGBP1 at TFBSs is supported by purifying selection in the DNA-binding domain of CGGBP1 and its requirement for gene repression as well as restriction of cytosine methylation at GC-rich TFBSs. Here we describe an evolutionary trajectory of this property of CGGBP1 by combining global gene expression and cytosine methylation analyses on human cells expressing CGGBPs from four different vertebrates (representatives of coelacanth, reptiles, aves and mammals). We discover a potent cytosine methylation restriction by human CGGBP1 at some GC-rich TFBSs in repressed promoters. Further, we combine a high-throughput analysis of GC compositional bias of these CGGBP-regulated TFBSs from available orthologous sequences from a pool of over 100 species. We show that cytosine methylation restriction by CGGBP1 is tightly linked to GC retention in a set of TFBSs. Orthology analyses demonstrate that this property of CGGBPs has evolved in higher amniotes (aves and mammals) with lineage-specific heterogeneities in lower amniotes (reptiles). CGGBP1 ChIP-seq data suggest that occupancy of CGGBP1 at these target TFBSs plays a crucial role in their low methylation, GC-biased evolution and associated functions in gene repression. HighlightsO_LIResemblances in gene repression by overexpression of CGGBP1 from higher amniotes (Homo sapiens and Gallus gallus) is enhanced upon heat stress and differs from the non-repressive effects of lower amniotic CGGBPs (Anolis carolinensis and Latimeria chalumnae). C_LIO_LIGene repression by higher amniotic CGGBP1 is associated with restriction of cytosine methylation at specific GC-rich TFBSs in 1 kb promoters of target genes. Lower amniotic CGGBPs allow TFBS cytosine methylation and C-T transitions. C_LIO_LIOrthologs of CGGBP1-repressed genes from >100 vertebrates show signs of accelerated C-T losses explicitly in the TFBSs at which higher amniotic CGGBP1 restricts cytosine methylation. Such a TFBS GC-loss difference between lower and higher amniotes is restricted to genes repressed by higher amniotic CGGBP1 at physiological temperature, not heat stress. C_LIO_LIThis higher amniote-specific cytosine methylation restriction by CGGBP1 has likely influenced the differences between GC-rich TFBS composition and their abundance in target gene promoters throughout vertebrate evolution. C_LI SummaryEvolution of transcription factor binding sites (TFBSs) depends on a variety of factors including cytosine methylation-associated C-T transition rates. Most of our understanding of TFBS evolution is based on omic-scale sequence comparisons with only circumstantial evidence for the relationship between the TFBSs and physiological adaptation. We report a TFBS landscaping function for CGGBP1 by expressing its different taxon-derived forms in human cells through profiling of global gene expression and cytosine methylation alongside a meta-analysis of C-T transition rates from over 100 vertebrae genomes. We show that CGGBP1 from higher amniotes restricts cytosine methylation and maintains GC-rich TFBSs in target gene promoters for repression. This epigenetic affection of TFBS evolution by CGGBP1 is selectively seen at genes repressed at physiological temperature only and not under heat stress when gene repression by CGGBP1 becomes largely transcription factor binding site independent. Our findings connect epigenetic mechanisms to cellular physiology through TFBS evolution linked with changes in CGGBP1.

evolutionary biology↗

bioRxiv2024

Syntaxin11 Deficiency Inhibits CRAC Channel Priming To Suppress Cytotoxicity And Gene Expression In FHLH4 Patient T Lymphocytes.

Mutations in Syntaxin11, a Q-SNARE, result in a fatal immune disorder known as familial hemophagocytic lymphohistiocytosis 4 (FHLH4) in human patients. A key diagnostic feature of FHLH4 is defective T and natural killer (NK) cell cytotoxicity. Here we show that Syntaxin11 directly binds and regulates Orai1, the pore forming subunit of calcium release activated calcium (CRAC) channels. CRAC channels enable store-operated calcium entry (SOCE) from the extracellular space and are crucial for granule exocytosis and nuclear factor of activated T cell (NFAT) dependent gene expression in activated lymphocytes. Syntaxin11 depletion strongly inhibited SOCE, CRAC currents, NFAT activation, interleukin-2 gene expression and degranulation in FHLH4 patient T lymphocytes and cell lines without affecting membrane trafficking. Remarkably, defects of cytolytic granule exocytosis as well as interleukin-2 expression could be reversed by ionomycin in patient T lymphocytes and a constitutively active, H134S, mutant of Orai1 rescued calcium entry in Syntaxin11 depleted cells. Further analyses showed that Syntaxin11 primes Orai1 for optimal on-site multimeric assembly which was Stim independent but required for gating. Priming of ion channel pore subunits is, therefore, a primary function of specific SNAREs which may have preceded their role in membrane trafficking and vesicle fusion.

cell biology↗

bioRxiv2024

The amniote-conserved DNA-binding domain of CGGBP1 restricts cytosine methylation of transcription factor binding sites in proximal promoters to regulate gene expression

CGGBP1 is a GC-rich DNA-binding protein which is important for genomic integrity, gene expression and epigenome maintenance through regulation of CTCF occupancy and cytosine methylation. It has remained unclear how CGGBP1 integrates multiple diverse functions with its simple architecture of only a DNA-binding domain tethered to a C-terminal tail with low structural rigidity. We have used truncated forms of CGGBP1 with or without the DNA-binding domain (DBD) to assay cytosine methylation and global gene expression. Proximal promoters of CGGBP1-repressed genes, although significantly GC-poor, contain GC-rich transcription factor binding motifs and exhibit base compositions indicative of low C-T transition rates due to prevention of cytosine methylation. Genome-wide analyses of cytosine methylation and binding of CGGBP1 DBD show that CGGBP1 restricts cytosine methylation in a manner that depends on its DBD and its DNA-binding. The CGGBP1-repressed genes show an increase in promoter cytosine methylation alongside a decrease in transcript abundance when the DBD-deficient CGGBP1 is expressed. Our findings suggest that CGGBP1 protects transcription factor binding sites (TFBS) from cytosine methylation-associated loss and thereby regulates gene expression. By analysing orthologous promoter sequences we show that restriction of cytosine methylation is a function of CGGBP1 progressively acquired during vertebrate evolution. A superimposition of our results and evolution of CGGBP1 suggests that mitigation of cytosine methylation is majorly achieved by its N-terminal DBD. Our results position CGGBP1 DNA-binding as a major evolutionarily acquired mechanism through which it keeps cytosine methylation under check and regulates TFBS retention and gene activity.

molecular biology↗

bioRxiv2024

Whole-genome duplication in the Multicellularity Long Term Evolution Experiment

Whole-genome duplication (WGD) is widespread across eukaryotes and can promote adaptive evolution1-4. However, given the instability of newly-formed polyploid genomes5-7, understanding how WGDs arise in a population, persist, and underpin adaptations remains a challenge. Using our ongoing Multicellularity Long Term Evolution Experiment (MuLTEE)8, we show that diploid snowflake yeast (Saccharomyces cerevisiae) under selection for larger multicellular size rapidly undergo spontaneous WGD. From its origin within the first 50 days of the experiment, tetraploids persist for the next 950 days (nearly 5,000 generations, the current leading edge of our experiment) in ten replicate populations, despite being genomically unstable. Using synthetic reconstruction, biophysical modeling, and counter-selection experiments, we found that tetraploidy evolved because it confers immediate fitness benefits in this environment, by producing larger, longer cells that yield larger clusters. The same selective benefit also maintained tetraploidy over long evolutionary timescales, inhibiting the reversion to diploidy that is typically seen in laboratory evolution experiments. Once established, tetraploidy facilitated novel genetic routes for adaptation, playing a key role in the evolution of macroscopic multicellular size via the origin of evolutionarily conserved aneuploidy. These results provide unique empirical insights into the evolutionary dynamics and impacts of WGD, showing how it can initially arise due to its immediate adaptive benefits, be maintained by selection, and fuel long-term innovations by creating additional dimensions of heritable genetic variation.

evolutionary biology↗

bioRxiv2024

The B-box protein BBX13/COL15 suppresses photoperiodic flowering by attenuating the action of CONSTANS in Arabidopsis

The optimal timing of transition from vegetative to floral reproductive phase is critical for plant productivity and agricultural yields. Light plays a decisive role in regulating this transition. The B-box (BBX) family of transcription factors regulates several light-mediated developmental processes in plants, including flowering. Here, we identify a previously uncharacterized group II member of the BBX family, BBX13/COL15, as a negative regulator of flowering under long-day conditions. BBX13 is primarily expressed in the leaf vasculature, buds, and flowers. Its spatial expression pattern is similar to the major flowering time regulators CO and FT. bbx13 mutants flower early, while BBX13-overexpressors exhibit delayed flowering under long days. Genetic analyses showed that BBX13 acts upstream to CO and FT in the flowering pathway and negatively regulates their expression. We found that BBX13 physically interacts with CO and inhibits the CO-mediated transcriptional activation of FT. In addition, BBX13 directly binds to the CORE2 motif on the FT promoter, a site where CO also binds. Furthermore, our ChIP data indicates that BBX13 reduces the in vivo binding of CO on the FT promoter. Through luciferase assay, we found that BBX13 inhibits the CO-mediated transcriptional activation of FT. All these data together suggest that BBX13/COL15 represses flowering in Arabidopsis by attenuating CO activity. Summary statementBBX13, a previously uncharacterized protein in the B-Box family of transcription factors, negatively regulates flowering time in Arabidopsis thaliana. BBX13 physically and genetically interacts with CO and inhibits the CO-mediated transcriptional activation of FT.

plant biology↗

bioRxiv2024

Time course metabolomics and 13CO2 mapping establish BBX31/miP1b mediated metabolic readjustments conferring UV-B tolerance in Arabidopsis

B-box proteins (BBXs) are transcription factors that act as signal transducers in light signaling pathways. The microprotein BBX31/miP1b is known to play a positive role in promoting photomorphogenesis and stress tolerance under UV-B. However, the BBX31-mediated metabolic reprogramming to confer UV-B tolerance in plants is not well characterised. Here, we integrate metabolomics with kinetic 13CO2 tracer-based metabolic mapping, morpho-physiological and biochemical analysis to determine the metabolic rewiring in the UV tolerant genotypes. Our results suggest that BBX31 modulates the levels of photosynthetic compounds, reduces TCA cycle intermediates and enhances GS/GOGAT metabolic intermediates and secondary metabolic pathways. 13CO2 tracing studies established BBX31 modulates phenylpropanoid and GS/GOGAT pathways to divert flux towards the accumulation of UV-B protective metabolites phenylalanine, oxoproline, glutamine, and others. Although metabolomics indicated a higher accumulation of branch chain amino acids (BCAAs) under UV-B, they had negligible 13C incorporation, indicating their biosynthesis from pre-existing intermediates or via protein degradation. Further, we demonstrate that the exogenous application of phenylalanine, identified as one of the marker metabolites, confers tolerance to plants under UV-B. This study sheds light on BBX31-mediated metabolic rewiring under UV-B, which can assist targeted enrichment of metabolites and metabolic engineering to promote UV-B tolerance in plants. HighlightBBX31/miP1b modulates the levels of photosynthetic compounds, reduces TCA cycle intermediates and enhances GS/GOGAT metabolic intermediates to confer UV-B tolerance.

plant biology↗

bioRxiv2024

Select Bacterial Species Establish and Maintain Functionally Essential pH Gradient Profile within the Mosquito Larval Gut

The unique pH profile of mosquito larval midgut including the highly alkaline anterior midgut (AMG) and its significance in digestive physiology has been known for a long time. More recently, metagenomic association studies have shown that diverse assemblage of bacteria (microbiota) present in the gut influence larval nutrition, growth, development, and several other physiological processes. However, the precise functional mechanisms of these host-microbe interactions remain poorly understood. In this research, we studied the functional significance of gut associated bacteria in larval growth utilizing Aedes albopictus axenic/ gnotobiotic model. Results of our study demonstrate that, for AMG alkalinization, concurrent presence of Carbonic Anhydrase (CA) activity and live bacteria is essential and that the later could not be substituted by either cell-free bacterial culture supernatant, or bacterial cell lysate. Further, we found that the gut pH profile and presence of proteolytic activity could be observed in larvae colonized only with select members of the microbiota that are capable of secreting extracellular protease. Collectively, our findings suggest a novel and interesting evolutionary mechanism of host-microbe interaction, in which select members of the gut microbiota promote larval nutrition, growth and development by providing protease and creating ionic microenvironment optimal for its activity.

microbiology↗

bioRxiv2024

Implication of structural constrains facilitating the functional evolution of Pseudomonas aeruginosa KPR2 into a versatile α-keto acid reductase.

Protein structure and function dynamics in molecular evolution are intertwined. Theoretical concepts linking structure, function, and evolution of a protein, while often intuitive, necessitate validation through investigations in real-world systems. Our study empirically explores the implications of multiple panE2 gene copies in an organism, shedding light on the functional roles and evolutionary trajectories of Pseudomonas aeruginosas second copy of Ketopantoate reductase (PaKPR2) and its inactivity against the natural substrate Ketopantoate. Evolutionary changes in functional traits were examined around the active site through crystal structures and biochemical analysis. Primarily, apoKPR2 structures reveal a transformed active site cleft, forming a two-sided pocket, while substrate entry is regulated by a molecular gate. Despite cleft closure, molecular interaction properties and activity analysis of PaKPR2 suggest that it can be a versatile keto-acid reductase. However, detailed structural insights from the ligand-bound binary complex of PaKPR2-NADPH and PaKPR2-Ketoisoleucine reveal that the ligand-binding interactions at the active site are conserved and restricted to the molecules of appropriate shape and size that can be accommodated in the available space. Finally, a ternary complex structure, PaKPR2-NADP+-KIC, was solved to understand its functional evolution in terms of the residue microenvironment at the catalytic site. Collectively, the results give detailed visual experiences of different structural perspectives of the proteins functional evolution.

biochemistry↗

bioRxiv2023

ABI3 regulates ABI1 function to control cell length in primary root elongation zone

Post-embryonic primary root growth is effectively an interplay of several hormone signalling pathways. Here, we show that the ABA-responsive transcription factor ABI3, controls primary root growth through regulation of JA signalling molecule JAZ1 along with ABA responsive factor ABI1. In absence of ABI3, primary root elongation zone is shortened with significantly reduced cell length. Expression analyses and ChIP based assays indicate that ABI3 negatively regulates JAZ1 expression by occupying its upstream regulatory sequence and enriching repressive histone modification mark H3K27 trimethylation, thereby occluding RNAPII occupancy. Previous studies have shown that JAZ1 interacts with ABI1, the protein phosphatase 2C, that works during ABA signalling. Our results indicate that in absence of ABI3, when JAZ1 expression levels are high, ABI1 protein shows increased stability, compared to when JAZ1 is absent, or ABI3 is overexpressed. Consequently, in abi3 mutant, due to higher stability of ABI1, reduced phosphorylation of plasma membrane H+ATPase (AHA2) occurs. HPTS staining further indicated that, abi3 root cell apoplasts show reduced protonation, compared to wild type and ABI3 overexpressing seedlings. Such impeded proton extrusion, negatively affects cell length in primary root elongation zone. ABI3 therefore controls cell elongation in primary root by affecting ABI1-dependent protonation of root cell apoplasts. In summary, ABI3 controls expression of JAZ1 and in turn modulates function of ABI1 to regulate cell length in the elongation zone during primary root growth.

plant biology↗

bioRxiv2023

Reducing the vicissitudes of heterologous prochiral substrate catalysis by alcohol dehydrogenases through machine learning algorithms

Alcohol dehydrogenases (ADHs) encompass three distinctive superfamilies: medium-chain dehydrogenase (MDRs), short-chain dehydrogenase (SDRs), and iron-containing alcohol dehydrogenases. MDRs and SDRs have pivotal roles in converting pro-pharmaceutical ketones into chiral alcohols, serving as active pharmaceutical intermediate catalysts in industries. Nevertheless, the pursuit of aligning enzymes to a one enzyme-one substrate paradigm is intricate and resource-intensive. This study undertook the catalysis of 284 antibacterial ketone intermediates, yielding distinct patterns for both MDRs and SDRs. We endeavored to leverage machine learning to discriminate between compounds subjected to the influence of these superfamilies. To this end, we curated a dataset comprising 33 features, encompassing 4 descriptors for each compound. Subsequently, an ensemble of machine learning techniques, including Partial Least Squares (PLS) regression, k-Nearest Neighbors (kNN) regression, and Support Vector Machine (SVM) regression, was harnessed. Furthermore, the assimilation of Principal Component Analysis (PCA) augmented precision and accuracy, refining compound classification and intensifying differentiation and demarcation within diverse compound classes. As such, this classification strategy emerged as a potent approach for discerning substrates amenable to diverse alcohol dehydrogenases, thereby mitigating the reliance on high-throughput screening in identifying the optimal enzyme for specific substrate preferences.

biochemistry↗

bioRxiv2023

Tension sensing by FAK governs nuclear mechanotransduction, endothelial transcriptome and fate

Vascular endothelium forms a restrictive barrier to defend the underlying tissue against uncontrolled influx of circulating protein and immune cells. Mechanisms that mediate the transition from restrictive to leaky endothelium, a hallmark of tissue injury exemplified by acute lung injury (ALI), remain elusive. Using endothelial cell (EC)-Fak-/-mice, we show that FAK sensing and transmission of mechanical tension to the EC nucleus governs cell fate. In FAK- deleted EC, increased EC tension induced by Rho kinase caused tyrosine phosphorylation of nuclear envelope protein, emerin at Y74/Y95, and its localization in a nuclear cap. Activated emerin stimulated DNMT3a activity and methylation of the KLF2 promoter, impairing the restrictive EC transcriptome, including S1PR1. Inhibiting emerin phosphorylation or DNMT3a activity enabled KLF2 transcription of S1PR1, rescuing the restrictive EC phenotype in EC-Fak-/- lungs. Thus, FAK sensing of tension transmission to the nucleus is crucial for maintaining a restrictive EC fate and lung homeostasis.

cell biology↗

bioRxiv2023

asmbPLS: Adaptive Sparse Multi-block Partial Least Square for Survival Prediction using Multi-Omics Data

BackgroundAs high-throughput studies advance, more and more high-dimensional multi-omics data are available and collected from the same patient cohort. Using multi-omics data as predictors to predict survival outcomes is challenging due to the complex structure of such data. ResultsIn this article, we introduce an adaptive sparse multi-block partial least square (asmbPLS) regression method by assigning different penalty factors to different blocks in different PLS components for feature selection and prediction. We compared the proposed method with several competitive algorithms in many aspects including prediction performance, feature selection and computation efficiency. The performance and the efficiency of our method were demonstrated using both the simulated and the real data. ConclusionsIn summary, asmbPLS achieved a competitive performance in prediction, feature selection, and computation efficiency. We anticipate asmbPLS to be a valuable tool for multi-omics research. An R package called asmbPLS implementing this method is made publicly available on GitHub.

bioinformatics↗

bioRxiv2023

Administration of the glutamate-modulating drug riluzole after stress reverses its delayed effects on the amygdala

Extracellular glutamate levels are elevated across brain regions immediately after stress. Despite sharing common features in their genesis, the patterns of stress-induced plasticity that eventually take shape are strikingly different between these brain areas. While stress impairs structure and function in the hippocampus, it has the opposite effect on the amygdala. Riluzole, an FDA-approved drug known to modulate glutamate release and facilitate glutamate clearance, prevents stress-induced deficits in the hippocampus. But, whether the same drug is also effective in countering the opposite effects of stress in the amygdala remains unexplored. We addressed this question by using a rat model wherein even a single 2-hour acute immobilization stress causes a delayed build-up, 10 days later, in anxiety-like behavior, alongside stronger excitatory synaptic connectivity in the basolateral amygdala (BLA). This temporal profile - several days separating the acute stressor and its delayed impact - allowed us to test if these effects can be reversed by administering riluzole in the drinking water after acute stress. Post-stress riluzole not only prevented the delayed increase in anxiety-like behavior on the elevated plus-maze, but also reversed the increase in spine-density on BLA neurons 10 days later. Further, stress-induced increase in the frequency of miniature excitatory postsynaptic currents recorded in BLA slices, 10 days later, was reversed by the same post-stress riluzole administration. Together, these findings underscore the importance of therapeutic strategies, aimed at glutamate uptake and modulation, in correcting the delayed behavioral, physiological, and morphological effects of stress on the amygdala. Significance statementStress disorders are characterized by impaired cognitive function alongside enhanced emotionality. Consistent with this, the same stress elicits contrasting effects in the rodent hippocampus versus amygdala. This poses a therapeutic challenge - the same pharmacological intervention against stress has to counter these opposite effects. Yet, the immediate consequence of stress - enhanced extracellular glutamate - is similar across these two areas. To target this common feature, we treated rats with riluzole, a drug that prevents stress-induced glutamate surge. Although the drug was administered after the end of stress, it reversed its delayed impact on amygdalar structure and function. Since riluzole also enhances glutamate-uptake through glial-transporters and is approved for human use, these results highlight the importance of therapeutic strategies focused on neuron-astrocyte interactions.

neuroscience↗

bioRxiv2023

NTpred: A robust and precise machine learningframework for in-silico identification of Tyrosine nitration sites in protein sequences

Post-translational modifications (PTMs) either enhance a proteins activity in various sub-cellular processes, or degrade their activity which leads towards failure of intracellular processes. Tyrosine nitration (NT) modification degrades proteins activity that initiate and propagate various diseases including Neurodegenerative, Cardiovascular, Autoimmune diseases, and Carcinogenesis. Identification of NT modification support development of novel therapies and drug discoveries for associated diseases. Identification of NT modification in biochemical labs is expensive, time consuming, and error-prone. To supplement this process, several computational approaches have been proposed. However these approaches remain fail to precisely identify NT modification, due to the extraction of irrelevant, redundant and less discriminative features from protein sequences. The paper in hand presents NTpred framework competent in extracting comprehensive features from raw protein sequences using four different sequence encoders. To reap the benefits of different encoders, it generates four additional feature spaces by fusing different combinations of individual encodings. Furthermore, it eradicates irrelevant and redundant features from eight different feature spaces through a Recursive Feature Elimination process. Selected features of four individual encodings and four feature fusion vectors are used to train eight different Gradient Boosted Tree classifiers. The probability scores from the trained classifiers are utilized to generate a new probabilistic feature space, that is utilized to train a Logistic Regression classifier. On BD1 benchmark dataset, the proposed framework outperform existing best performing predictor in 5-fold cross validation and independent test evaluation with combined improvement of 13.7% in MCC and 20.1% in AUC. Similarly, on BD2 benchmark dataset, the proposed framework outperform existing best performing predictor with combined improvement of 5.3% in MCC and 1.0% in AUC.

bioinformatics↗