Biology subjects

Banerjee, S.

Publications and source records attributed to Banerjee, S..

At least 235 records · Page 13Linked to original sources

bioRxiv2020

Real-Time Microfluidics-Magnetic Tweezers connects conformational stiffness with energy landscape by a single experiment

Proteins are versatile biopolymers whose functions are determined by their structures. Understanding the structural dynamicity, with respect to energy landscape, is essential to describe their biological functions. The ability to study the dynamical properties of a single protein molecule is thus crucial, but ensuring that multiple physical properties can be simultaneously extracted within a single experiment on the exact same protein molecule in real-time has hitherto been infeasible. Here, we present magnetic tweezers technology that surmounts this limitation, providing real-time dynamic information about changes in several molecular properties ({Delta}G0, conformation, and mean first passage time of unfolding and refolding) from a single experiment, by remeasuring the very same protein molecule in varying chemical condition. We illustrate the versatility of the method by studying electrolyte-dependent conformational flexibility and the energy landscape of substrate protein L under force. Changing salt concentrations reshapes the energy landscape by two specific ways: it speeds-up refolding kinetics while slowing down unfolding kinetics. From the same trajectory, we calculate the stiffness of the protein polymer, a quantity that varies with salt concentration. The data is described within the framework of a modified electrolyte FJC model that we propose and study here. The observed correlation between{Delta} G0, kinetics and polymer elasticity connect protein chain physics and the energy landscape, while the experimental methodology we describe of getting energy landscape from a single experiment could have wide-ranging applications.

biophysics↗

bioRxiv2020

Mitochondria Controlled mTORC1 Activation Compartmentalizes Translation Initiation Factor eIF4E to Augment Intracellular Trafficking and Extracellular Export of miRNA in Mammalian Cells

Defective intracellular trafficking and export of miRNAs has been observed in senescent mammalian cells having impaired mitochondrial potential. Similar to what happens in senescent cells, Uncoupling Protein 2 mediated depolarization of mitochondrial membrane potential results in progressive sequestration of miRNAs with polysomes and lowered release of miRNAs through extracellular vesicles. Supporting importance of mitochondrial membrane potential on miRNAs fate determination, impaired miRNA-trafficking process in growth retarded human cells has been found to be reversed in presence of Genipin an inhibitor of Uncoupling Protein 2. Mitochondrial detethering of endoplasmic reticulum in mitochondria depolarized cells, found to be responsible for defective compartmentalization of translation initiation factor eIF4E to ER attached polysomes. It causes retarded translation process of target mRNAs with rER attached polysomes to ensure reduced intracellular trafficking and extracellular export of miRNAs. We have identified a reduced activity of mTORC1 complex in mitochondria defective cells to cause reduced phosphorylation of eIF4E-BP1 to cause retarded eIF-4E targeting to ER attached polysome. Cumulatively, these data suggest intricate involvement of mitochondrial membrane potential and dynamics to determine stability of miRNAs in mammalian cells by affecting sub-cellular locations and export of miRNPs by affecting mTORC1 complex, the regulator of the protein translational machinery. Significance statementHow the reduced mitochondrial activity in growth retarded cells causes defective miRNA export is an open question. Mitochondrial defects induces a retarded subcellular miRNP trafficking in human cells to cause an upregulation in cellular miRNA content by reducing extracellular vesicle-mediated export of miRNA. We have identified a defective compartmentalization of translation initiation factor eIF4E in mitochondria-ER detethered mammalian cells to cause the retarded intracellular miRNA movement and export Activity of mTORC1 complex, a key regulator of protein translation in mammalian cells, is found to be responsible for ER-compartmentalization of eIF4E. mTORC1 activity reduction in growth retarded and mitochondria detethered cells influences the cell fate by acting on miRNA-mRNA axis. This is a unique way how mitochondrial activity is linked with protein translation and gene repression control in mammalian cells.

molecular biology↗

bioRxiv2020

An evolutionarily conserved metallophosphodiesterase is a determinant of lifespan in Drosophila

Evolutionarily conserved genes usually have a critical role to play during organismal aging and longevity. Here, we show that a previously uncharacterized Class III metallophosphoesterase in Drosophila, an ortholog of the MPPED1 and MPPED2 proteins in mammals, is necessary for optimal lifespan. dMPPED is the product of the gene CG16717 and hydrolyzed a variety of phosphodiester substrates in a metal-dependent manner. dMPPED was expressed widely during development and in the adult fly. Deletion of the gene in flies dramatically reduced lifespan, without affecting development or fecundity. Longevity was restored on ubiquitous expression of the protein, and neuronal expression of both wild type and the catalytically inactive form of dMPPED was also able to restore normal lifespan. Overexpression of the protein, both ubiquitously and neuronally in wild type flies extended lifespan by ~ 20%. RNA-seq analysis of dMPPEDKO flies revealed mis-regulation of innate immune pathways, a number of transcription factors and genes earlier reported to affect aging and lifespan. Importantly, neuronal expression of mammalian MPPED2 was able to rescue lifespan in dMPPEDKO flies, but not extend lifespan in wild type flies. This reports the first description of the biological role of an evolutionarily conserved metallophosphoesterase that may serve as a scaffolding protein in diverse signaling pathways to modulate longevity in the fly.

developmental biology↗

bioRxiv2020

Hypoxia driven oncometabolite L-2HG maintains "stemness"-differentiation balance and facilitates immune suppression in pancreatic cancer

2-hydroxyglutarate (2-HG) has gained considerable importance in glioma and blood cancers that have mutations in the IDH1/2 gene. In the current study we show for the first time that pancreatic tumors produce 2HG in the absence of IDH1/2 mutation. Our study shows that hypoxic pancreatic tumors that have activated lactate dehydrogenase (LDH) activity, produce the L-isoform of 2HG. Metabolic mass spectrometric analysis along with chiral derivatization showed that pancreatic cancer cells as well as stromal cells secrete the L-isomeric form of 2-hydroxyglutarate (L-2HG) when exposed to hypoxic environment. Serum analysis of human pancreatic cancer patients also showed similar accumulation of L-2HG. Our results showed that this abnormally accumulated L-2HG regulates self-renewal by increasing expression of genes associated with stemness (Sox-2, CD133) and by decreasing expression of differentiation genes (Pdx-1, HB9, NKX6.1). Further analysis showed that secreted L-2HG mediates cross talk with immune T-cells and hampers their proliferation and migration thereby suppressing the anti-tumor immunity. In vivo targeting of LDH enzyme with inhibitor (GSK2837808A) showed decrease in L-2HG as well as subsequent tumor regression and sensitization to immune-checkpoint therapy. Present study shows for the first time that hypoxia mediated accumulation of L-2HG drives self-renewal in pancreatic cancer by shifting critical balance of gene expression towards stemness and promotes immune suppression by impairing T cell activation in this disease. Additionally, it indicates that targeting LDH can sensitize pancreatic tumors to anti-PD1 therapy by decreasing L-2HG and reverting their immune evasive function.

cancer biology↗

bioRxiv2020

Reverse regression increases power for detecting trans-eQTLs

Trans-acting expression quantitative trait loci (trans-eQTLs) are genetic variants affecting the expression of distant genes. They account for [≥]70% expression heritability and could therefore facilitate uncovering mechansisms underlying the origination of complex diseases. However, unlike cis-eQTLs, identifying trans-eQTLs is challenging because of small effect sizes, tissue-specificity, and the severe multiple-testing burden. Trans-eQTLs affect multiple target genes, but aggregating evidence over individual SNP-gene associations is hampered by strong gene expression correlations resulting in correlated p-values. Our method Tejaas predicts trans-eQTLs by performing L2-regularized reverse multiple regression of each SNP on all genes, aggregating evidence from many small trans-effects while being unaffected by the strong expression correlations. Combined with a novel non-linear, unsupervised k-nearest-neighbor method to remove confounders, Tejaas predicted 18851 unique trans-eQTLs across 49 tissues from GTEx. They are enriched in open chromatin, enhancers and other regulatory regions. Many overlap with disease-associated SNPs, pointing to tissue-specific transcriptional regulation mechanisms. Tejaas is available under GPL at https://github.com/soedinglab/tejaas.

genetics↗

bioRxiv2020

Mutational spectra of SARS-CoV-2 orf1ab polyprotein and Signature mutations in the United States of America

Pandemic COVID-19 outbreak has been caused due to SARS-COV2 pathogen, resulting millions of infection and death worldwide, USA being on top at the present moment. The long, complex orf1ab polyproteins of SARS-COV2 play an important role in viral RNA synthesis. To assess the impact of mutations in this important domain, we analyzed 1134 complete protein sequences of orf1ab polyprotein from NCBI Virus database from affected patients across various states of USA from December 2019 to 25th April, 2020. Multiple sequence alignment using Clustal Omega followed by statistical significance was calculated. Four significant mutations T265I (nsp 2), P4715L (nsp 12) and P5828L and Y5865C (both at nsp 13) were identified in important non-structural proteins, which function either as replicase or helicase. A comparative analysis shows 265T>I, 5828P>L and 5865Y>C are unique to USA and not reported from Europe or Asia; while one, 4715P>L is predominant in both Europe and USA. Mutational changes in amino acids are predicted to alter structure and function of corresponding proteins, thereby it is imperative to consider the mutational spectra while designing new antiviral therapeutics targeting viral orf1ab.

bioinformatics↗

bioRxiv2020

Stroma secreted IL6 selects for stem-like population and alters pancreatic tumor microenvironment by reprogramming metabolic pathways

Pancreatic adenocarcinoma is a devastating disease with an abysmal survival rate of 9%. A robust fibro-inflammatory and desmoplastic stroma, characteristic of pancreatic cancer, contributes to the challenges in developing viable therapeutic strategies in this disease. Apart from constricting blood vessels and preventing efficient drug delivery to the tumor, the stroma also contributes to aggressive biology of the cancer along with its immune-evasive microenvironment. In this study, we show that in pancreatic tumors, the developing stroma increases tumor initiation frequency in pancreatic cancer cells in vivo by enriching for CD133+ aggressive "stem-like" cells. Additionally, the stromal fibroblasts secrete IL6 as the major cytokine, increases glycolytic flux in the pancreatic tumor cells and increases lactate efflux in the microenvironment via activation of the STAT signaling pathway. We also show that the secreted lactate favors activation of M2 macrophages in the tumor microenvironment, which excludes CD8+ T-cells in the tumor. Our data additionally confirms that treatment of pancreatic tumors with anti-IL6 antibody results in tumor regression as well as decreased CD133+ population within the tumor. Furthermore, inhibiting the lactate efflux in the microenvironment reduces M2 macrophages, and makes pancreatic tumors more responsive to anti-PD1 therapy. This suggests that stromal IL6 driven metabolic reprogramming plays a significant role in the development of an immune evasive microenvironment. In conclusion, our study shows that targeting the metabolic pathways affected by stromal IL6 can make pancreatic tumors amenable to checkpoint inhibitor therapy.

cancer biology↗

bioRxiv2020

Weight Sensitivity of Temporal SNR Metrics in multi-echo fMRI

PurposeIn multi-echo fMRI (ME-fMRI), various weighting schemes have been proposed for the combination of the data across echoes. Here we introduce a framework that facilitates a deeper understanding of the weight dependence of temporal SNR measures in ME-fMRI. Theory and MethodsWe examine two metrics that have been used to characterize ME-fMRI performance: temporal SNR (tSNR) and multi-echo temporal (metSNR). Both metrics can be described using the generalized Rayleigh quotient (GRQ) and are predicted to be relatively insensitive to the weights when there is a high degree of similarity between a metric-specific matrix in the GRQ numerator and a metricindependent covariance matrix in the GRQ denominator. The application of the GRQ framework to experimental data is demonstrated using a resting-state fMRI dataset acquired with a multi-echo multi-band EPI sequence. ResultsIn the example dataset, similarities between the covariance matrix and the metSNR and tSNR numerator matrices are highest in grey matter (GM) and cerebrospinal fluid (CSF) voxels, respectively. For representative GM and CSF voxels that exhibit high matrix similarity values, the metSNR and tSNR values, respectively, are both within 4% of their optimal values across a range of weighting schemes. However, there is a fundamental tradeoff, with a high degree of weight sensitivity in the tSNR and metSNR metrics for the representative GM and CSF voxels, respectively. Geometric insight into the observed weight dependencies is provided through a graphical interpretation of the GRQ. ConclusionA GRQ framework can provide insight into the factors that determine the weight sensitivity of tSNR and metSNR measures in ME-fMRI.

neuroscience↗

bioRxiv2020

Decoding the lethal effect of SARS-CoV-2 (novel coronavirus) strains from global perspective: molecular pathogenesis and evolutionary divergence

BackgroundCOVID-19 is a disease with global public health emergency that have shook the world since its first detection in China in December, 2019. Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) is the pathogen responsible behind this pandemic. The lethality of different viral strains is found to vary in different geographical locations but the molecular mechanism is yet to be known. MethodsAvailable data of whole genome sequencing of different viral strains published by different countries were retrieved and then analysed using Multiple Sequence Alignment and Pair-wise Sequence Alignment leading to Phylogenetic tree construction. Each location and the corresponding genetic variations were screened in depth. Then the variations are analysed at protein level giving special emphasis on Non Synonymous amino acid substitutions. The fatality rates in different countries were matched against the mutation number, rarity of the nucleotide alterations and functional impact of the Non Synonymous changes at protein level, separately and in combination. FindingsAll the viral strains have been found to evolve from the viral strain of Taiwan (MT192759) which is 100% identical with the ancestor SARS-CoV-2 sequences of Wuhan (NC 045512.2; submitted on 5th Jan, 2020). Transition from C to T (C>T) is the most frequent mutation in this viral genome and mutations A>T, G>A, T>A are the rarest ones, found in countries with maximum fatality rate i.e Italy, Spain and Sweden. 20 Non Synonymous mutations are located in viral genome spanning Orf1ab polyprotein, Surface glycoprotein, Nucleocapsid protein etc. The functional effect on the structure and function of the protein can favourably or unfavourably interact with the host body. InterpretationThe fatality outcome depends on three important factors (a) number of mutation (b) rarity of the allelic variation and (c) functional consequence of the mutation at protein level. The molecular divergence, evolved from the ancestral strain (S) lead to extremely lethal (E), lethal(L) and non lethal (N) strains with the involvement of an Intermediate strain(I).

bioinformatics↗

bioRxiv2020

Exploration of endo-xylanase from novel strain of Bacillus velezensis AG20 isolated from the cave of Meghalaya

Cave sets the example of extreme ecological niche and habitat for diversified microorganisms. Present study involved in the isolation of endoxylanase producing novel strain Bacillus velezensis AG20 from the Krem Phyllut cave, Meghalaya, India. Culture dependent studies, molecular phylogentics, RNA secondary folding pattern based on 16S rDNA substantiated the identity of this novel strain. Bacillus velezensis AG20 revealed the superbug quality having resistance against various class of broad-spectrum antibiotics. Bacillus velezensis AG20 revealed biofilm formation over the cell surface in FESEM. Highest cell biomass and xylanase production supported in TB medium, further purified partially to 5.3 fold with 21% yield. Molecular weight of the purified xylanase found to be 45 kDa. Enzyme kinetics and pattern of hydrolysis revealed the evidence for the selection of linear birchwood xylan with Vmax = 21.0 {+/-} 3.0 U/ml, Km = 1.25 mg/ml, Kcat = 1.75/s at optimum pH 7 and temperature 50{degrees}C also found significant statistically in Taguchis orthogonal design. Conversely, ruled out any exoacting activity against synthetic pNP-xylopyranoside substrate. Endo-xylanase isolated from Bacillus velezensis AG20 was moderately thermostable over temperatures 50 and 60{degrees}C. Time dependent hydrolysis of agro-waste sugar cane bagasse depicted the production of xylooligosaccharides (XOS) predominantly xylobiose, xylotriose and xylotetrose. Purified mixed XOS hold their prebiotic potential by promoting the growth of probiotics Bifidobacterium and Lactobacillus as well as high stability (~90%) against systemic fluids. Mixed XOS (300 g/ml) displayed anti-proliferation activities by reducing the growth of HT-29 and Caco-2 cells significantly 90% and 75%, respectively, after 48 h. IMPORTANCEExtremophiles dwelling inside the caves have laden with the extraordinary capabilities of bioconversion by nature. The pristine ecological niche inside the cave, absence of proper light and air, supports the livelihood of novel microorganisms. In India, Meghalaya is hoisting longest caves in the East Khasi Hills, providing conducive environment for novel bacterial strains. With the prime objective of isolating novel bacterial strains that produce extracellular xylanase our studies have been carried out. Considering the present industrial demand for nutraceutical, prebiotics, anti-proliferating agents and biofuels by the conversion of lignocellulosic biomass (LCB), novel enzymes are required. Xylanases from bacterial origin play a significant role in conversion of LCB into oligosaccharides. Therefore, exploration and characterization of xylanase producing novel isolate from cave may pave the new arena for the production of prebiotic and anti-inflammatory oligosaccharides from agro-waste.

microbiology↗

bioRxiv2020

Homeostatic scaling is driven by a translation-dependent degradation axis that recruits miRISC remodelling

Homeostatic scaling in neurons has been attributed to the individual contribution of either translation or degradation; however there remains limited insight towards understanding how the interplay between the two processes effectuates synaptic homeostasis. Here, we report that a co-dependence between protein synthesis and degradation mechanisms drives synaptic homeostasis whereas abrogation of either prevents it. Coordination between the two processes is achieved through the formation of a tripartite complex between translation regulators, the 26S proteasome and the miRNA-induced-silencing-complex (miRISC) components such as Argonaute, MOV10 and Trim32 on actively translating transcripts or polysomes. The components of this ternary complex directly interact with each other in an RNA-dependent manner. Disruption of polysomes abolishes this ternary interaction, suggesting that translating RNAs facilitate the combinatorial action of the proteasome and the translational apparatus. We identify that synaptic downscaling involves miRISC remodeling which entails the mTORC1-dependent translation of Trim32, an E3 ligase and the subsequent degradation of its target, MOV10 via the phosphorylation of p70 S6 kinase. We find that the E3 ligase Trim32 specifically polyubiquitinates MOV10 for its degradation during synaptic downscaling. MOV10 degradation alone is sufficient to invoke downscaling by enhancing Arc translation through its 3 UTR and causing the subsequent removal of post-synaptic AMPA receptors. Synaptic scaling was occluded when we depleted Trim32 and overexpressed MOV10 in neurons, suggesting that the Trim32-MOV10 axis is necessary for synaptic downscaling. We propose a mechanism that exploits a translation-driven protein degradation paradigm to invoke miRISC remodeling and induce homeostatic scaling during chronic network activity.

neuroscience↗

bioRxiv2020

Detection and skeletonization of single neurons and tracer injections using topological methods

Neuroscientific data analysis has traditionally relied on linear algebra and stochastic process theory. However, the tree-like shapes of neurons cannot be described easily as points in a vector space (the subtraction of two neuronal shapes is not a meaningful operation), and methods from computational topology are better suited to their analysis. Here we introduce methods from Discrete Morse (DM) Theory to extract the tree-skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections. Since individual neurons are topologically trees, it is sensible to summarize the collection of neurons using a consensus tree-shape that provides a richer information summary than the traditional regional connectivity matrix approach. The conceptually elegant DM approach lacks hand-tuned parameters and captures global properties of the data as opposed to previous approaches which are inherently local. For individual skeletonization of sparsely labelled neurons we obtain substantial performance gains over state-of-the-art non-topological methods (over 10% improvements in precision and faster proofreading). The consensus-tree summary of tracer injections incorporates the regional connectivity matrix information, but in addition captures the collective collateral branching patterns of the set of neurons connected to the injection site, and provides a bridge between single-neuron morphology and tracer-injection data.

neuroscience↗

bioRxiv2020

Nutrient-dependent trade-offs between ribosomes and division protein synthesis control bacterial growth and cell shape

Cell size control emerges from a regulated balance between the rates of cell growth and division. In bacteria, simple quantitative laws connect cellular growth rate to ribosome abundance. However, it remains poorly understood how translation regulates bacterial cell size and shapes under growth perturbations. Here we develop a whole-cell model for growth dynamics in rod-shaped bacteria that links ribosomal abundance with cell geometry, division control, and the extracellular environment. Our study reveals that cell size maintenance under nutrient perturbations requires a balanced trade-off between ribosomes and division protein synthesis. Deviations from this trade-off relationship are predicted under translational perturbations, leading to distinct modes of cell morphological changes, in agreement with single-cell experimental data on Escherichia coli. Furthermore, by calibrating our model with experimental data, we predict how combinations of nutrient-, translational- and shape perturbations can be chosen to optimize bacterial growth fitness and antibiotic resistance.

systems biology↗

bioRxiv2020

miR-142 regulates IL-6 signalling during host immune response to Staphylococcus epidermidis infection in zebrafish

Host immune responses to Staphylococcus epidermidis, a frequent cause of nosocomial infections, are not well understood. We have established a novel bath immersion model of this infection in zebrafish larvae. S.epidermidis infection activates Tlr-2 signalling pathway by upregulation of tlr-2. Macrophages play a primary role in the host immune response and are involved in clearance of infection in the larvae. There is marked inflammation characterised by heightened NF-{kappa}B signalling and elevation of several pro-inflammatory cytokines. Infected larvae show rapid upregulation of il-1b and tnf-a transcripts and relatively slower elevation of il-6 transcription. The IL-6 signalling pathway is additionally subject to amplification by elevation of IL-6 signal transducer (il-6st) levels, which negatively correlates with miRNA dre-miR-142-5p expression. Enhanced IL-6 signalling is protective to the host in this model as inhibition of the signalling pathway resulted in increased mortality upon S.epidermidis infection. Our study describes the host immune responses to S.epidermidis infection, identifies a likely role for miR-142-5p - il-6st interaction in modulating this response and establishes the importance of IL-6 signalling in this infection model.

immunology↗

bioRxiv2020

Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder-decoder deep networks

Understanding of neuronal circuitry at cellular resolution within the brain has relied on tract tracing methods which involve careful observation and interpretation by experienced neuroscientists. With recent developments in imaging and digitization, this approach is no longer feasible with the large scale (terabyte to petabyte range) images. Machine learning based techniques, using deep networks, provide an efficient alternative to the problem. However, these methods rely on very large volumes of annotated images for training and have error rates that are too high for scientific data analysis, and thus requires a significant volume of human-in-the-loop proofreading. Here we introduce a hybrid architecture combining prior structure in the form of topological data analysis methods, based on discrete Morse theory, with the best-in-class deep-net architectures for the neuronal connectivity analysis. We show significant performance gains using our hybrid architecture on detection of topological structure (e.g. connectivity of neuronal processes and local intensity maxima on axons corresponding to synaptic swellings) with precision/recall close to 90% compared with human observers. We have adapted our architecture to a high performance pipeline capable of semantic segmentation of light microscopic whole-brain image data into a hierarchy of neuronal compartments. We expect that the hybrid architecture incorporating discrete Morse techniques into deep nets will generalize to other data domains.

neuroscience↗

bioRxiv2020

Loop 1 of APOBEC3C regulates its antiviral activity against HIV-1

APOBEC3 deaminases (A3s) provide mammals with an anti-retroviral barrier by catalyzing dC-to-dU deamination on viral ssDNA. Within primates, A3s have evolved diversely via gene duplications and fusions. Human APOBEC3C (hA3C) efficiently restricts the replication of viral infectivity factor (vif)-deficient Simian immunodeficiency virus (SIV{Delta}vif), but for unknown reasons, it inhibits HIV-1{Delta}vif weakly. In catarrhines (Old World monkeys and apes), the A3C loop 1 displays the conserved amino acid pair WE, while the corresponding consensus sequence in A3F and A3D is the largely divergent pair RK, which is also the inferred ancestral sequence for the last common ancestor of A3C|D|F in primates. Here, we report that modifying the WE residues in hA3C loop 1 to RK leads to stronger interactions with ssDNA substrate, facilitating catalytic function, which resulted in a drastic increase in both deamination activity and the ability to restrict HIV-1 and LINE-1 replication. Conversely, the modification hA3F_WE resulted only in a marginal decrease in HIV-1{Delta}vif inhibition. The two series of ancestral gene duplications that generated A3C, A3D-CTD and A3F-CTD allowed neo/subfunctionalization: A3F-CTD maintained the ancestral RK residues in loop 1, while strong evolutionary pressure selected for the RK[->]WE modification in catarrhines A3C, possibly allowing for novel substrate specificity and function. AUTHOR SUMMARYThe restriction factors of the APOBEC3 (A3) family of cytidine deaminases inhibit the replication of Vif-deficient retroviruses mainly by mutating their viral genomes. While there are seven A3 proteins (A3A-A3H) found in humans only A3G and A3F potently inhibit HIV-1 replication. A3C in general and its retroviral restriction capacity have not been widely studied probably due to its weak anti-HIV-1 activity, however, it displays a strong antiviral effect against SIV. Understanding the role of A3C is important because it is highly expressed in CD4+ T cells, is upregulated upon HIV-1 infection, and is distributed cell-wide. In this study, we report that replacing two residues in loop 1 of A3C protein with conserved positively-charged amino acids enhance the substrate DNA binding, which markedly facilitates its deamination-dependent antiviral activity against HIV-1 as well as increasing the restriction of LINE-1 retroelements. Furthermore, our evolutionary analysis demonstrates that the pressure that caused the loss of potential loop 1 residues occurred only in A3C but not in primate homologues. Overall, our study highlights the possibility of A3C acting as a super restriction factor, however, this was likely evolutionarily selected against to achieve a balance between anti-viral/anti-LINE-1 activity and genotoxicity.

microbiology↗

bioRxiv2020

Intratumor Heterogeneity and Evolution of Colorectal Cancer

Intratumor heterogeneity (ITH) enable us to understand the evolution of cancer. ITH and evolution of colorectal cancer (CRC) has not been well studied. In this prospective study, we recruited different stages of 68 CRC patients with primary tumor at right-sided colon, left-sided colon and rectum. We performed high-depth whole exome sequencing of 206 multi-region tumor samples including primary tumors, lymph node metastasis (LN) and extranodal tumor deposits (ENTD). Our result showed extreme ITH with Darwinian pattern of CRC evolution, evolution pattern of left-sided CRC was more complex and divergent than right-sided CRC and both LN and ENTD were of polyclonal in origin. Extensive ITH was found in driver mutations in KRAS and PIK3CA genes, suggesting major limitations of single biopsies in clinical diagnosis for the CRC patients. In conclusion, our study showed the Darwinian pattern of CRC evolution with differences in evolution pattern between right-sided and left-sided CRC patients.

genetics↗

bioRxiv2020

Size regulation of multiple organelles competing for a shared subunit pool

How cells regulate the size of intracellular structures and organelles, despite continuous turnover in their component parts, is a longstanding question. Recent experiments suggest that size control of many intracellular assemblies is achieved through the depletion of a limiting subunit pool in the cytoplasm. While the limiting pool model ensures organelle size scaling with cell size, it does not provide a mechanism for robust size control of multiple co-existing structures. Here we propose a kinetic theory for size regulation of multiple structures that are assembled from a shared pool of subunits. We demonstrate that a negative feedback between the growth rate and the size of individual structures underlies size regulation of a wide variety of intracellular assemblies, from cytoskeletal filaments to three-dimensional organelles such as centrosomes and the nucleus. We identify the feedback motifs for size control in these structures, based on known molecular interactions, and quantitatively compare our theory with available experimental data. Furthermore, we show that a positive feedback between structure size and growth rate can lead to bistable size distributions arising from autocatalytic growth. In the limit of high subunit concentration, autocatalytic growth of multiple structures leads to stochastic selection of a single structure, elucidating a mechanism for polarity establishment.

biophysics↗