Biology subjects

Adhya, S.

Publications and source records attributed to Adhya, S..

5 recordsLinked to original sources

bioRxiv2026

Repetitive extragenic palindrome (REP) elements are local, context-dependent, dual 3'UTR regulators in Escherichia coli

Repetitive extragenic palindromes (REPs) are the most abundant repetitive noncoding elements in the E. coli genome. Despite their abundance, the primary function of REPs has remained unclear. At different times, REPs have been proposed to contribute to chromosome organization, mRNA decay regulation, and transcription termination, among other functions. Here, we show that the model REP, REP325, does not measurably compact the chromosome but instead acts as a 3UTR-associated transcription regulator within the yjdMN operon, functioning both as a partially Rho-dependent terminator that limits transcription into the downstream yjdN gene and as an mRNA stabilizer that protects the upstream yjdM transcript from degradation. This dual role in controlling both transcriptional readthrough and susceptibility to decay provides a framework that reconciles several previously conflicting observations about REP function. Our genome-wide RNA-seq analysis further reveals that REPs with more canonical sequence and hairpin structures are more often associated with upstream-biased expression in tandem gene pairs, and that REPs positioned between convergent genes correlate with elevated expression of both genes. The large variance in expression patterns in both gene pair configurations is consistent with context-dependent termination and degradation blocking. Similarly, REPs do not uniformly affect mRNA half-lives. Because REP locations vary between E. coli strains, REPs likely contribute to regulatory diversity by tuning gene expression without altering protein-coding sequences or promoter regions, opening new avenues for modulating gene expression through REP-mediated transcription regulation.

biophysics↗

bioRxiv2026

A {lambda} Phage Platform for Successful Therapeutic Display of Protein Antigens

We have developed a vector platform for delivery of foreign peptides by genetic modification of the temperate lambda ({lambda}) bacteriophage. This delivery platform is capable of displaying peptides or proteins on either terminus of the structural {lambda} head protein D, present in [~]420 copies per phage particle, and {lambda} side tail fiber (Stf), present at 12 copies per phage particle. Proteins and peptides can be easily fused for display through the low-cost and high-efficiency methods of recombineering and {lambda} prophage induction for recombinant phage preparation described here. To improve this vector technology for use in antigen selection and immunotherapy, we introduced several mutations in the bacterial host and resident prophage {lambda} that improve engineering, induction, phage stability, yield, fusion protein accommodation capacity, and longevity in animal systems. We tested the ability of this {lambda} display system to identify useful antigens and generate antibodies in a mouse model. We report its success as a new technology for both applications: the selection and delivery of therapeutic peptides and proteins.

bioengineering↗

bioRxiv2025

circEPSTI1 Enables Dengue Innate Immune Evasion by Sponging miR-942-5p, a Repressor of AKT1 and the Viral Genome

Circular RNAs (circRNAs) have recently been identified as crucial regulators of gene expression in various diseases. Their role in dengue remains unexplored. In this study, circEPSTI1 induction was observed in peripheral blood mononuclear cells (PBMCs) and plasma of dengue patients. The induction of circEPSTI1 is interferon-dependent and enhances DENV infection by sponging the expression of miR-942-5p. The antiviral role of miR-942-5p is mediated by bidirectional inhibition through targeting conserved genomic sequences of the DENV genome of different subtypes across NS1, NS3, and NS5 and the host AKT1 signaling pathway. RNA-seq analysis of DENV-infected circEPSTI1 knockdown A549 cells identified SERPINE1 and AKT1 signaling pathways to be dysregulated significantly. circEPSTI1 relieves the inhibition of miR-942-5p over DENV genomic RNA and the host SERPINE1 to activate AKT1 signaling. The activation of AKT1 signaling facilitates cell survival and enhances DENV replication. The expression of SERPINE1 and circEPSTI1 was upregulated in Dengue patients, and pharmaceutical inhibition of SERPINE1 through Tiplaxtinin inhibits the DENV replication by reducing the expression of circEPSTI1. Overall, our result demonstrates the therapeutic potential of Tiplaxtinin by targeting the circ-EPSTI1-miR-942-5p-SERPINE1-AKT axis in dengue treatment.

immunology↗

bioRxiv2021

Separate physiological roles of specific and non-specific DNA binding of HU protein in Escherichia coli

Conserved in bacteria, the histone-like protein HU is crucial for genome organization and expression of many genes. It binds DNA regardless of the sequence and exhibits two binding affinities in vitro, low-affinity to any B-DNA (non-specific) and high-affinity to DNA with distortions like kinks and cruciforms (structure-specific), but the physiological relevance of the two binding modes needed further investigation. We validated and defined the three conserved lysine residues, K3, K18, and K83, in Escherichia coli HU as critical amino acid residues for both non-specific and structure-specific binding and the conserved proline residue P63 additionally for only the structure-specific binding. By mutating these residues in vivo, we showed that two DNA binding modes of HU play separate physiological roles. The DNA structure-specific binding, occurring at specific sites in the E. coli genome, promotes higher-order DNA structure formation, regulating the expression of many genes, including those involved in chromosome maintenance and segregation. The non-specific binding participates in numerous associations of HU with the chromosomal DNA, dictating chromosome structure and organization. Our findings underscore the importance of DNA structure in transcription regulation and promiscuous DNA-protein interactions in a dynamic organization of a bacterial genome.

molecular biology↗

bioRxiv2019

Single molecule tracking reveals the role of transitory dynamics of nucleoid-associated protein HU in organizing the bacterial chromosome

HU is the most conserved nucleoid-associated protein in eubacteria and has been implicated as a key player in global chromosome organization. The mechanism of HU-mediated nucleoid organization, however, remains poorly understood. Using single molecule tracking coupled with genetic manipulations, we characterized the dynamics of HU in live Escherichia coli cells. We found that native HU dimers bind and unbind chromosomal DNAs weakly and transitorily across the entire nucleoid volume but remain nucleoid-localized, reminiscent of random diffusion in a liquid phase-separated, membrane-less "macro-compartment" distinct from the remaining cytosol. Mutating three key surface lysine residues of HU nearly entirely abolished the weak and transitory interactions of HU with DNA and led to severe cell growth and DNA segregation defects, suggesting the importance of HUs interactions with chromosomal DNA mediated by the positively charged surface. A conserved proline residue important for recognizing bent and cruciform DNAs such as that in recombination intermediates, similarly abolished HUs rapid and transitory DNA interaction dynamics but had little impact on its apparent binding stability with nonspecific chromosomal DNAs. Interestingly, the proline residue appeared to be important for HU{beta} dimer formation as mutating this residue makes HU{beta} behave similarly to HU2 dimers. Finally, we find that while prior evidence has found HU capable of depositing nucleoid-associated noncoding RNAs onto cruciform DNA structures, deletion of these specific naRNAs or inhibition of global transcription had a relatively minor effect on HU dynamics irrespective altered nucleoid compaction. Our results suggest a model of chromosome organization mediated by weak, transient interactions of HU, a substantial deviation from nucleoid-like proteins such as histones. Such collective sum of the numerous weak, transitory binding events of HU with nonspecific chromosome DNAs could generates a "force" to maintain a dynamic, fluid nucleoid with enough flexibility to rapidly facilitate global topological processes such as replication or nucleoid segregation.

biophysics↗