Biology subjects

Acharya, D.

Publications and source records attributed to Acharya, D..

17 recordsLinked to original sources

bioRxiv2026

A dsRNA Virus Converts Early Endosomes into Stable Replication Organelles Through Maturation Arrest and Retrograde Transport

Infectious bursal disease virus (IBDV) and infectious pancreatic necrosis virus (IPNV) are major animal pathogens that impose a heavy burden on the poultry and aquaculture industries. Yet, major aspects of their unique replication program remain unknown. IBDV is unusual among double-stranded RNA viruses in that it replicates in association with host endosomes. We previously demonstrated this association to be orchestrated by the viral protein VP3 and the early endosomal lipid phosphatidylinositol 3-phosphate [PtdIns(3)P], suggesting an essential role for VP3 in forming birnaviruses specialized replication compartments. Here, combining high-resolution fluorescence and correlative light-electron microscopy with diverse molecular and biochemical analyses, we define how the IBDV protein VP3 targets and remodels host endosomes, and establish that endosome-associated replication is conserved in members of the Birnaviridae family. We show that IBDV VP3 targets early endosomes via the PtdIns(3)P effector Early Endosomal Antigen 1 (EEA1) to arrest their maturation and prompt their association with the Golgi complex via ESCPE-1-mediated retrograde transport. We further show that IPNV also exploits endosomal membranes for replication in a PtdIns(3)P dependent manner, although for this virus VP3 engages endosomes through an EEA1-independent mechanism yet to be determined. This work uncovers how birnaviruses exploit a single viral protein to orchestrate endosome remodeling and intracellular trafficking to establish specialized replication compartments while revealing both conserved and host-adapted features of birnaviruses replication.

cell biology↗

bioRxiv2026

Genomic 8-oxoguanine is associated with transcriptionally active chromatin and elevated gene expression in Plasmodium falciparum

Epigenetic regulation is central to the developmental progression and pathogenicity of the unicellular eukaryotic parasite Plasmodium falciparum; yet, the contribution of DNA base modifications remains poorly understood. One such modification, 8-oxoguanine (8-oxoG), which was initially identified as an oxidative lesion and a marker of DNA damage, has since emerged as a transcriptional regulator in advanced eukaryotes. Given that P. falciparum encounters a highly oxidative environment in human blood, we investigated the potential gene regulatory role of 8-oxoG during its intra-erythrocytic developmental cycle (IDC). Using immunodetection assays, we first confirmed the presence of 8-oxoG in P. falciparum genomic DNA and observed a gradual increase in 8-oxoG abundance from ring to schizont stages. We then optimized oxidative DNA immunoprecipitation sequencing (OxiDIP-seq) for the highly AT-rich parasite genome and generated genome-wide 8-oxoG profiles across four IDC timepoints, which revealed reproducible enrichment of 8-oxoG at discrete genomic loci, with more than 50% of the peaks stable across developmental stages. Notably, 8-oxoG accumulated at putative G-quadruplex-forming sequences in the parasite genome and preferentially localized within exonic regions of protein-coding genes, exhibiting a marked enrichment near STOP codons and within 3' untranslated regions. This in turn correlated with significantly higher steady-state transcript levels of 8-oxoG-marked genes, with stage-specific changes in 8-oxoG enrichment closely matching transcriptional activity. Furthermore, 8-oxoG-marked loci were preferentially associated with active and poised histone post-translational modifications, while showing no evidence of altered nucleosome occupancy. Collectively, these findings demonstrate that 8-oxoG is a widespread and non-random DNA modification in P. falciparum and suggest that it may function as an epigenetic mark associated with transcriptionally permissive chromatin and gene activation during parasite blood-stage development.

genomics↗

bioRxiv2026

Dual-compartment engagement of STAR-family proteins SAM68 and QKI by LINC00941 sustains oncogenic fitness in RAS-driven lung cancer

Long non-coding RNAs (lncRNAs) are increasingly recognised as effectors of oncogenic signalling, yet the transcriptional programmes through which driver mutations regulate lncRNA expression remain poorly defined. Here we identify LINC00941 as a direct transcriptional target of FOSL1, an AP-1 transcription factor downstream of the KRAS-MAPK pathway, establishing the first FOSL1-regulated lncRNA in lung adenocarcinoma (LUAD). LINC00941 is significantly upregulated in LUAD across multiple independent cohorts, and its depletion via siRNAs, shRNAs, and antisense oligonucleotides (ASOs) induces proliferative arrest and stress-induced premature senescence, accompanied by transcriptomic suppression of cell cycle and DNA damage response (DDR) genes. Mechanistically, LINC00941 operates through a dual-compartment mechanism engaging two STAR-family RNA-binding proteins in distinct subcellular contexts. In the nucleus, LINC00941 binds SAM68 through its 700-1300 nucleotide region and shields it from proteasomemediated degradation, thereby sustaining SAM68-dependent PARP1 activation and DDR competency; RNF123 is identified as a candidate E3 ligase mediating SAM68 turnover in the absence of LINC00941. In the cytoplasm, LINC00941 sequesters QKI, preventing its nuclear translocation; LINC00941 depletion releases QKI to the nucleus, driving alternative splicing dysregulation including validated NUMB exon 12 exclusion, and QKI co-depletion rescues the anti-proliferative phenotype both in vitro and in xenograft models. Multi-cohort survival analysis across three independent LUAD datasets (n=649) identifies LINC00941 as an independent prognostic factor for poor overall survival. Gymnotic ASO-mediated targeting of LINC00941 significantly suppresses xenograft tumour growth without systemic toxicity, providing preclinical proof-of-concept for therapeutic tractability. Together, these findings establish LINC00941 as a compartment-specific oncogenic scaffold within the KRAS-FOSL1 transcriptional axis and a tractable therapeutic target in LUAD.

cancer biology↗

bioRxiv2026

Herpes simplex virus infection promotes ALS pathology through ICP0-mediated PML body disruption

Transactive response DNA binding protein 43 kDa (TDP-43) pathology, is a central molecular hallmark of amyotrophic lateral sclerosis (ALS). However, the underlying triggers are incompletely understood. Here, we show that infection with herpes simplex virus (HSV) induces molecular hallmarks of ALS in various in vitro and in vivo models and is associated with an increased risk of ALS in human population data. German healthcare provider data (n = 238,440) and herpesvirus serology of an ALS patient and control cohort (n = 1,100) showed that HSV infection elevated the ALS risk by 210% and odds by [~]65%, respectively. On a molecular level, HSV infection promoted TDP-43 pathology in neuronal cell models, human iPSC-derived motoneurons and cerebral organoids, mice, and human tissue sections. This effect was triggered by HSV-1 or 2, but not by several other related herpesviruses. Mechanistically, the infected cell protein 0 (ICP0) of HSV-1/2 drives TDP-43 pathology by disturbance of promyelocytic leukemia nuclear bodies (PML-NBs), thereby abrogating TDP-43 SUMO2/3ylation. Taken together, we reveal a previously unrecognized association between HSV infection and ALS and clarify the underlying molecular mechanism that drives TDP-43 pathology. Our data may guide future studies into therapeutic and prophylactic interventions against ALS.

neuroscience↗

bioRxiv2025

Brain Network Analysis in Alzheimer's Disease and Mild Cognitive Impairment using High-Density Diffuse Optical Tomography

Dementia is associated with altered resting state connectivity, measures of which could aid in its early detection and monitoring. High-density diffuse optical tomography (HD-DOT) is well-suited to detect these alterations at scale due to its numerous practical advantages, but it has not yet been applied to dementia. In this study, we investigated resting state functional connectivity across the prefrontal cortex in individuals with Mild Cognitive Impairment (MCI, n = 22), Alzheimers Disease (AD, n = 21), and in healthy controls (n = 22). A graph theoretical approach was taken to characterise both global and local patterns of connectivity over a five-minute resting period. We found that individuals with AD and MCI exhibited denser and stronger networks, with shorter path lengths, as well as a loss of consistent key network hubs with worsening cognitive impairment. These results indicate that networks in dementia are more globally connected, albeit in a disorganised manner, perhaps reflecting the recruitment of additional connections for short-term stability which may be ultimately damaging in the long-term. Following the demonstration of HD-DOTs capacity to detect differences between healthy ageing and dementia, this work opens up new possibilities for the use of optical imaging in the study of this clinical population and HD-DOTs potential for scalable clinical use.

neuroscience↗

bioRxiv2025

TGFb Regulated Small GTPase RHOV interact with PEAK1 and drive MYC Expression to Promote Cellular Proliferation, Migration and Etoposide resistance

1.Non-small cell lung cancer (NSCLC) remains a leading cause of cancer-related mortality, driven by tumor heterogeneity, metastasis, and therapeutic resistance. While Rho GTPases are well-established regulators of oncogenic processes, the role of the atypical GTPases in NSCLC remains unexplored. Here, we identified RHOV as one of the commonly upregulated Rho GTPases in NSCLC. Analysis of four independent patient cohorts revealed that elevated RHOV expression serves as a robust and independent prognosticator of NSCLC patients specifically early-stage disease. Functionally, RHOV knockdown significantly inhibited cell proliferation, whereas its overexpression enhanced proliferation. Similarly, RHOV depletion suppressed cell migration by disrupting cytoskeletal dynamics, while its overexpression promoted migratory capacity. Mechanistically, we demonstrated that RHOV is a direct transcriptional target of the TGF{beta}-SMAD3 signaling pathway. RNA-seq analysis identified MYC as a critical downstream mediator of RHOV; RHOV knockdown reduced MYC expression, impairing mitochondrial oxidative phosphorylation and inducing ROS-mediated DNA damage--a phenotype rescued by MYC overexpression. Furthermore, RHOV inhibition sensitized NSCLC cells to etoposide but not doxorubicin. immunoprecipitation coupled with LC-MS revealed PEAK1 as a key interactor of RHOV. The RHOV-PEAK1 complex proved essential for NSCLC proliferation, as PEAK1 silencing abolished RHOV- driven MYC upregulation and tumor growth. This axis sustains MYC levels and activates PI3K/MAPK signaling. Intriguingly, PEAK1 depletion elevated TGF-{beta} levels, which suppressed RHOV expression, establishing a negative feedback loop wherein PEAK1 maintains RHOV by inhibiting TGF-{beta} signaling. Collectively, our findings establish RHOV as a prognostic biomarker and a driver of NSCLC progression via the RHOV-PEAK1-MYC axis, highlighting its potential as a therapeutic target. HighlightsO_LIRHOV upregulation predicts poor NSCLC survival, particularly in early-stage disease. C_LIO_LIThe RHOV-PEAK1 interaction is crucial for NSCLC growth and cell migration. C_LIO_LIRHOV inhibition sensitizes NSCLC cells to Etoposide treatment. C_LIO_LIRHOV expression is sustained via a PEAK1-TGF{beta} negative feedback loop. C_LI

cancer biology↗

bioRxiv2025

Mapping functional hemodynamic and metabolic responses to dementia: a broadband spectroscopy pilot study

SignificanceBroadband near-infrared spectroscopy (bNIRS) can simultaneously monitor several chromophores including the oxidative state of cytochrome c-oxidase (oxCCO), an oxygen metabolism biomarker whose activity is altered in Alzheimers disease. Being a portable and non-invasive neuromonitoring technique, bNIRS could thus provide accessibility to brain-specific biomarkers and aid in the dementia diagnostic pathway. AimWe use bNIRS recorded functional haemodynamic and oxCCO changes to assess their relevance in Alzheimers disease dementia as potential biomarkers. ApproachUsing a visual-stimulus paradigm, we recorded functional changes in oxy-, deoxy-haemoglobin and oxCCO in three similarly aged cohorts: healthy controls (n=5), individuals with mild cognitive impairment (n=7) and individuals with Alzheimers dementia (n=7). We then selected features from these functional responses to find the best correlation with clinical cognitive markers (cognitive and behavioural test scores and clinical diagnosis) using canonical correlation analysis. ResultsWe found individual variations in peak amplitude and time-to-peak for all the stimulus-evoked bNIRS signals across the three cohorts. Canonical correlation analysis showed a strong correlation between bNIRS features and the clinical cognitive markers (r=0.902). However, repeating the same analysis by excluding the bNIRS oxCCO features leads to a significantly lower correlation (r=0.687) with the clinical markers. ConclusionsoxCCO could be a crucial biomarker, partly explaining cognitive differences with dementia. bNIRS uniquely provides a portable and non-invasive technique to monitor several chromophores simultaneously including oxCCO with potential future applications in tracking dementia progression.

bioengineering↗

bioRxiv2025

MRPL47 Deficiency Drives Mitochondrial Dysfunction via ROS/p38-MAPK/CDKN1A Signaling in Non-Small Cell Lung Cancer

Mitoribosomes play a pivotal role in cellular energy metabolism by synthesizing proteins involved in oxidative phosphorylation (OXPHOS) system. Dysregulation of mitoribosomes has been linked to Cancer, yet there have been no studies demonstrating the genetics and epigenetic landscape of mitoribosomal proteins (MRPs). In this study, we conducted a comprehensive analysis of expression, copy number variations, mutations, data from TCGA NSCLC patients to elucidate the genetic mechanism regulating MRPs in NSCLC. Consequently, we identified MRPL47, a significantly amplified and overexpressed mitoribosomal gene. We also found significant correlation of MRPL47 expression and copy number with patients survival. Functionally, we showed that inhibition of MRPL47 was associated with reduced cell proliferation and migration. Furthermore, silencing MRPL47 impaired the enzymatic activity of electron chain complex I & III leading to a defective OXPHOS system and elevated mitochondrial ROS level. Further, we showed ROS-mediated increase in CDKN1A through the p38 MAPK pathway. The increased CDKN1A level induced G1 cell cycle arrest by inhibiting E2F activity. RNA sequencing analysis further confirmed that MRPL47 hinders cell growth by inhibiting E2F pathway. Additionally, we found that MRPL47 selectively regulates mitochondrial translation of specific OXPHOS proteins rather than influencing all mitochondrial proteins. Altogether, these findings suggest that MARPL47, is amplified and overexpressed in NSCLC and plays a critical role in tumor progression by regulating ROS signaling pathways.

cancer biology↗

bioRxiv2024

GJB3, a gap junction gene, supports cell growth by mediating cystine uptake and regulating cellular stress pathways in SLC7A11 low adenocarcinomas

Gap junctions are specialized intercellular connections that directly connect the cytoplasm of two cells via protein structure called connexins. Despite extensive research on many cell surface proteins, Gap junction proteins are understudied in cancer. In this study, we used TCGA data to identify genetic and epigenetic changes associated with Gap junction proteins. The analysis identified GJB3 as a key gene with differential methylation and expression patterns, with notable overexpression in COAD and LUAD, correlating significantly with patient survival outcomes. GJB3 knockdown studies revealed reduced cell proliferation and migration. Transcriptomic analysis revealed that GJB3 knockdown induced a cellular stress response, characterized by activation of starvation and autophagy pathways. Western blot analysis confirmed these findings, showing increased phosphorylation of eIF2 and activation of the GCN2-eIF2-ATF4 signaling axis subsequent autophagy induction. We also found that sustained autophagy induced apoptosis mediated cell death. Metabolic profiling revealed a significant decrease in cystine levels in GJB3-deficient cells. We demonstrated that GJB3 plays a crucial role in cystine uptake, especially in cells with low SLC7A11 expression. Furthermore, we showed that GJB3 can be targeted using specific antibodies, establishing it as a potential therapeutic strategy for GJB3-dependent cancers. These findings highlight the significance of GJB3 in cancer progression and its potential as a therapeutic target, offering new insights into its epigenetic regulation and functional role in cellular stress and survival mechanisms.

cancer biology↗

bioRxiv2024

MDA5 ISGylation is crucial for immune signaling to control viral replication and pathogenesis

The posttranslational modification (PTM) of innate immune sensor proteins by ubiquitin or ubiquitin-like proteins is crucial for regulating antiviral host responses. The cytoplasmic dsRNA receptor melanoma differentiation-associated protein 5 (MDA5) undergoes several PTMs including ISGylation within its first caspase activation and recruitment domain (CARD), which promotes MDA5 signaling. However, the relevance of MDA5 ISGylation for antiviral immunity in an infected organism has been elusive. Here, we generated knock-in mice (MDA5K23R/K43R) in which the two major ISGylation sites, K23 and K43, in MDA5 were mutated. Primary cells derived from MDA5K23R/K43R mice exhibited abrogated endogenous MDA5 ISGylation and an impaired ability of MDA5 to form oligomeric assemblies leading to blunted cytokine responses to MDA5 RNA-agonist stimulation or infection with encephalomyocarditis virus (EMCV) or West Nile virus. Phenocopying MDA5-/- mice, the MDA5K23R/K43R mice infected with EMCV displayed increased mortality, elevated viral titers, and an ablated induction of cytokines and chemokines compared to WT mice. Molecular studies identified human HERC5 (and its functional murine homolog HERC6) as the primary E3 ligases responsible for MDA5 ISGylation and activation. Taken together, these findings establish the importance of CARD ISGylation for MDA5-mediated RNA virus restriction, promoting potential avenues for immunomodulatory drug design for antiviral or anti-inflammatory applications. Significance StatementThe work by many groups demonstrated the important role of ubiquitination in modulating the activity of innate immune sensors. In contrast, little is still known about the significance of ISGylation in immune receptor regulation. In this study, we generated knock-in mice in which the two major ISGylation sites of the RNA sensor MDA5 were mutated. Cells from these MDA5-ISGylation-defective mice showed impaired MDA5 oligomerization and antiviral signaling as compared to WT mice. Virus-infected MDA5 knock-in mice displayed ablated antiviral responses, uncontrolled viral replication, and higher mortality. Our study identified HERC5 as the E3 ligase responsible for MDA5 ISGylation and activation. These data may offer opportunities for immune-based antiviral design or ways to alleviate inflammatory diseases associated with overzealous MDA5 activation.

immunology↗

bioRxiv2024

Studies on Human-Coronavirus protein-protein interaction network from the perspective of viral adaptation in a novel host

Host-pathogen interaction is the best example of an evolutionary arms race where pathogen and host continuously coevolve to survive and exert negative effects on each other. The adaptability of both host and pathogen is critical for this association. In this study, we explored the association of severe acute respiratory syndrome (SARS) coronaviruses (CoVs) with their human host from the genomic and evolutionary perspectives based on a comparative analysis of SARS and MERS coronaviruses. We observed that human proteins that are part of the SARS-CoV2-human association are enriched in hubs and bottlenecks. Again, these proteins take part in more protein complexes and show slower evolutionary rates compared to the human proteins associated with the two other coronaviruses, SARS-CoV and MERS-CoV. Moreover, the human proteins involved in the interaction with SARS-CoV2 are mostly longer proteins harboring long intrinsically disordered stretches and a higher level of disordered protein binding sites. Codon usage analysis revealed that the novel coronavirus is least adapted to codons used in housekeeping and lung-specific genes, compared to the other two coronaviruses. We conclude that the signatures showed by the SARS-CoV2-human protein interaction network revealed the viruss association with vital human proteins and pathways, via interactions mediated by protein complexes and intrinsically disordered protein binding sites, which may have assisted the higher infectivity of SARS-CoV2 in its human host than the other two less-virulent human coronaviruses, despite having a lower optimization to its hosts codons.

evolutionary biology↗

bioRxiv2021

A secondary metabolite drives intraspecies antagonism in a gut symbiont that is inhibited by peptidoglycan acetylation

The mammalian microbiome encodes numerous secondary metabolite biosynthetic gene clusters, yet their role in microbe-microbe interactions is unclear. Here, we characterized two polyketide synthase gene clusters (fun and pks) in the gut symbiont Limosilactobacillus reuteri. The pks, but not the fun cluster, encodes antimicrobial activity. Forty-one out of 51 L. reuteri strains tested are sensitive to Pks products, which was independent of strains host origin. The sensitivity to Pks was also established in intraspecies competition experiments in gnotobiotic mice. Comparative genome analyses between Pks-resistant and sensitive strains identified an acyltransferase gene (act) that is unique to Pks-resistant strains. Subsequent cell wall analysis of the wild-type and the act mutant strains showed that Act acetylates cell wall components. The pks mutants lost their competitive advantage and act mutants lost their Pks resistance in vivo. Thus, our findings provide insight into how closely related gut symbionts can compete and co- exist in the gastrointestinal tract.

microbiology↗

bioRxiv2021

Complete protection by a single dose skin patch delivered SARS-CoV-2 spike vaccine

SARS-CoV-2 has infected over 160 million people and resulted in more than 3.3 million deaths, and we still face many challenges in the rollout of vaccines. Here, we use the high-density microarray patch to deliver a SARS-CoV-2 spike subunit vaccine directly to the skin. We show the vaccine, dry-coated on the patch is thermostable, and delivery of spike via HD-MAP induced greater cellular and antibody immune responses, with serum able to potently neutralize clinically relevant isolates including those from the B.1.1.7 and B.1.351 lineages. Finally, a single dose of HD-MAP-delivered spike provided complete protection from a lethal virus challenge, demonstrating that HD-MAP delivery of a SARS-CoV-2 vaccine is superior to traditional needle-and-syringe vaccination and has the potential to greatly impact the ongoing COVID-19 pandemic.

microbiology↗

bioRxiv2021

A SARS-CoV-2 targeted siRNA-nanoparticle therapy for COVID-19

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in humans. Despite several emerging vaccines, there remains no verifiable therapeutic targeted specifically to the virus. Here we present a highly effective siRNA therapeutic against SARS-CoV-2 infection using a novel lipid nanoparticle delivery system. Multiple small-interfering RNAs (siRNAs) targeting highly conserved regions of the SARS-CoV-2 virus were screened and three candidate siRNAs emerged that effectively inhibit virus by greater than 90% either alone or in combination with one another. We simultaneously developed and screened two novel lipid nanoparticle formulations for the delivery of these candidate siRNA therapeutics to the lungs, an organ that incurs immense damage during SARS-CoV-2 infection. Encapsulation of siRNAs in these LNPs followed by in vivo injection demonstrated robust repression of virus in the lungs and a pronounced survival advantage to the treated mice. Our LNP-siRNA approaches are scalable and can be administered upon the first sign of SARS-CoV-2 infection in humans. We suggest that an siRNA-LNP therapeutic approach could prove highly useful in treating COVID-19 disease as an adjunctive therapy to current vaccine strategies.

synthetic biology↗

bioRxiv2020

ISG15-dependent Activation of the RNA Sensor MDA5 and its Antagonism by the SARS-CoV-2 papain-like protease

Activation of the RIG-I-like receptors, RIG-I and MDA5, establishes an antiviral state by upregulating interferon (IFN)-stimulated genes (ISGs). Among these is ISG15 whose mechanistic roles in innate immunity still remain enigmatic. Here we report that ISGylation is essential for antiviral IFN responses mediated by the viral RNA sensor MDA5. ISG15 conjugation to the caspase activation and recruitment domains of MDA5 promotes the formation of higher-order assemblies of MDA5 and thereby triggers activation of innate immunity against a range of viruses including coronaviruses, flaviviruses and picornaviruses. The ISG15-dependent activation of MDA5 is antagonized through direct de-ISGylation mediated by the papain-like protease (PLpro) of SARS-CoV-2, a recently emerged coronavirus that causes the COVID-19 pandemic. Our work demonstrates a crucial role for ISG15 in the MDA5-mediated antiviral response, and also identifies a novel immune evasion mechanism of SARS-CoV-2, which may be targeted for the development of new antivirals and vaccines to combat COVID-19.

immunology↗

bioRxiv2020

Chemically-informed Analyses of Metabolomics Mass Spectrometry Data with Qemistree

Untargeted mass spectrometry is employed to detect small molecules in complex biospecimens, generating data that are difficult to interpret. We developed Qemistree, a data exploration strategy based on hierarchical organization of molecular fingerprints predicted from fragmentation spectra, represented in the context of sample metadata and chemical ontologies. By expressing molecular relationships as a tree, we can apply ecological tools, designed around the relatedness of DNA sequences, to study chemical composition.

bioinformatics↗

bioRxiv2017

The optimization of mRNA expression level by its intrinsic properties -- insights from codon usage pattern and structural stability of mRNA

The deviation from the uniform usage of synonymous codons is termed codon usage bias. A lot has been explained from the translational viewpoint for the observed phenomenon. To understand codon usage bias from the transcriptional perspective, we present here a holistic picture of this phenomenon in Saccharomyces cerevisiae, using both wild type and computationally mutated mRNAs. Although in wild type, both codon usage bias and mRNA stability positively regulate the gene (mRNA) expression level and are positively correlated with each other, any deviation from natural situation breaks such equilibrium. Computational examination of mRNA sequences with different sets of synonymous codon composition reveals that in mutated condition, the mRNA expression becomes reduced. Furthermore, constraining codon usage pattern to wild type and carrying out randomization of codons resulted in less stable mRNA. Further, we realized a Boolean Expression explaining the gene expression under various conditions of bias and mRNA stability. These studies suggest that selection of codons is favored for regulation of gene expression through potential formation of messenger RNA structures which contribute to folding stability. The naturally occurring codon composition is responsible for optimization of gene expression, and under such composition, the mRNA structure having highest stability is selected by nature.

bioinformatics↗