Biology subjects

Guo, M. S.

Publications and source records attributed to Guo, M. S..

6 recordsLinked to original sources

bioRxiv2026

GapR is a nucleoid-associated protein that stiffens and overtwists DNA to promote transcription and replication

GapR is an -proteobacterial nucleoid-associated protein reported to either directly regulate transcription of AT-rich DNA or to regulate transcription indirectly through sensing DNA topology and modulating topoisomerase activity. We use single-DNA micromechanics, biolayer interferometry (BLI), and computational analysis to study GapR transcriptional regulation. Micromechanics experiments show that GapR overtwists DNA and shortens its contour length. GapR binding also substantially increases DNA bending persistence length and twist stiffness, while promoting duplex DNA melting at higher forces. Nonequilibrium binding experiments show GapR-DNA complexes to be extremely stable, with essentially no dissociation on hour-long time scales. Strikingly, our BLI experiments show that GapR has high affinity for AT-rich DNA while our micromechanics show that GapR binding is enhanced by pre-twisting of DNA, validating GapR affinity for both forms. By analyzing published GapR binding data, we differentiate between AT-rich and overtwisted DNA binding, revealing that overtwisted DNA primarily determines GapR localization. Lastly, we show that these two binding modes exert opposite effects on transcription. AT-rich binding stimulates initiation, likely by promoting RNA polymerase progression, while overtwisted DNA binding represses transcription, possibly by stabilizing local overtwist at promoters. We propose that GapR binding promotes a conformation of DNA ideal for efficient replication and transcription progression. 3 Key pointsO_LIGapR is a DNA structuring protein that binds AT-rich and overtwisted, positively supercoiled DNA C_LIO_LIGapR binding stiffens DNA, limits plectoneme formation, and melts undertwisted DNA at higher force C_LIO_LIGapR binding modes exert opposing effects on transcription initiation while promoting elongation C_LI

molecular biology↗

bioRxiv2024

Post-translational modifications on protein VII are important during the early stages of adenovirus infection.

Due to the importance of post-translational modification (PTM) in cellular function, viruses have evolved to both take advantage of and be susceptible to such modification. Adenovirus encodes a multifunctional protein called protein VII, which is packaged with the viral genome in the core of virions and disrupts host chromatin during infection. Protein VII has several PTMs whose addition contributes to the subnuclear localization of protein VII. Here, we used mutant viruses that abrogate or mimic these PTMs on protein VII to interrogate their impact on protein VII function during adenovirus infection. We discovered that acetylation of the lysine in positions 2 or 3 (K2 or K3) is deleterious during early infection as mutation to alanine led to greater intake of protein VII to the nucleus and enhanced early gene expression. Furthermore, we determined that protein VII is acetylated at alternative residues late during infection which may compensate for the mutated sites. Lastly, due to the role of the early viral protein E1A in viral gene activation, we investigated the interaction between protein VII and E1A and demonstrated that protein VII interacts with E1A through a chromatin-mediated interaction. Together, these results emphasize that the complexity of virus-host interactions is intimately tied to post-translational modification. ImportanceAdenoviruses are a ubiquitous human pathogen that cause a variety of diseases, such as respiratory infections, gastroenteritis, and conjunctivitis. While often viewed as a self-limiting infection in healthy individuals, adenoviruses are particularly harmful for immunocompromised patients. Here, we investigate the functional role of post-translational modifications (PTMs) on an essential adenovirus core protein, protein VII, describing how they regulate its function during early and late stages of infection. Our study focuses on how specific PTMs on protein VII influence transcription, localization, and interactions with other proteins, highlighting how PTMs are employed by viruses to alter protein function.

microbiology↗

bioRxiv2024

The muscarinic acetylcholine receptor in dermal papilla cells regulates hair growth

The role of cholinergic system in hair biology is poorly understood. In M4 muscarinic receptor (mAChR) knockout mice, the hair follicles have a prolonged telogen phase and fail to produce hair shafts. Here, we reported that hair growth was regulated by cholinergic system via mAChRs. Dermal papilla cells expressed different cholinergic biomarkers. Inhibiting AChE or activating mAChR in dermal papilla cells, culture vibrissae and skin epidermis promoted the hair growth. In cultured papilla cells treated with bethanechol, an agonist of mAChR, an activation of Wnt/{beta}-catenin signalling was illustrated by various indicative biomarkers, including phosphorylation of GSK-3{beta} and mRNA expression of various molecules for Wnt/{beta}- catenin signalling. Activation of Wnt/{beta}-catenin signalling was mediated by PI3K/AKT and ERK signalling upon the stimulation of bethanechol. In addition, an increase in hair shaft elongation was observed in mouse vibrissae upon the treatment of bethanechol, suggesting the cholinergic role in hair growth.

neuroscience↗

bioRxiv2023

Adenovirus protein VII binds the A-box of HMGB1 to repress interferon responses.

Viruses hijack host proteins to promote infection and dampen host defenses. Adenovirus encodes the multifunctional protein VII that serves both to compact viral genomes inside the virion and disrupt host chromatin. Protein VII binds the abundant nuclear protein high mobility group box 1 (HMGB1) and sequesters HMGB1 in chromatin. HMGB1 is an abundant host nuclear protein that can also be released from infected cells as an alarmin to amplify inflammatory responses. By sequestering HMGB1, protein VII prevents its release, thus inhibiting downstream inflammatory signaling. However, the consequences of this chromatin sequestration on host transcription are unknown. Here, we employ bacterial two-hybrid interaction assays and human cell biological systems to interrogate the mechanism of the protein VII-HMGB1 interaction. HMGB1 contains two DNA binding domains, the A- and B-boxes, that bend DNA to promote transcription factor binding while the C-terminal tail regulates this interaction. We demonstrate that protein VII interacts directly with the A-box of HMGB1, an interaction that is inhibited by the HMGB1 C-terminal tail. By cellular fractionation, we show that protein VII renders A-box containing constructs insoluble, thereby acting to prevent their release from cells. This sequestration is not dependent on HMGB1s ability to bind DNA but does require post-translational modifications on protein VII. Importantly, we demonstrate that protein VII inhibits expression of interferon {beta}, in an HMGB1- dependent manner, but does not affect transcription of downstream interferon- stimulated genes. Together, our results demonstrate that protein VII specifically harnesses HMGB1 through its A-box domain to depress the innate immune response and promote infection.

microbiology↗

bioRxiv2022

Differential Roles of positive and negative supercoiling in compacting the E. coli genome

This study aims to explore whether and how positive and negative supercoiling contribute to the three-dimensional (3D) organization of the bacterial genome. We used recently published Escherichia coli GapR ChIP-seq and TopoI ChIP-seq (also called EcTopoI-seq) data, which marks positive and negative supercoiling sites, respectively, to study how positive and negative supercoiling correlates with the corresponding contact frequencies obtained from chromosome conformation capture sequencing (Hi-C and 5C). We found that supercoiled chromosomal loci have overall higher Hi-C contact frequencies than sites that are not supercoiled, with positive supercoiling surprisingly corresponding to higher spatial contacts than negative supercoiling. Additionally, Hi-C contact frequencies alone could identify positive, but not negative, supercoiling with high accuracy. The majority of positive and negative supercoils coincide with highly active transcription units, with a minor group likely associated with replication and other genomic processes. Our results suggest that both positive and negative supercoiling enhance chromosome interactions, but positive supercoils contribute more than negative supercoils to bring distant chromosomal loci closer in space. Based on these results, we propose new physical models of how the E. coli chromosome is organized differentially by positive and negative supercoils.

bioinformatics↗

bioRxiv2021

High-resolution, genome-wide mapping of positive supercoiling in chromosomes

Supercoiling impacts DNA replication, transcription, protein binding to DNA, and the three-dimensional organization of chromosomes. However, there are currently no methods to directly interrogate or map positive supercoils, so their distribution in genomes remains unknown. Here, we describe a method, GapR-seq, based on the chromatin immunoprecipitation of GapR, a bacterial protein that preferentially recognizes overtwisted DNA, for generating high-resolution maps of positive supercoiling. Applying this method to E. coli and S. cerevisiae, we find that positive supercoiling is widespread, associated with transcription, and particularly enriched between convergently-oriented genes, consistent with the "twin-domain" model of supercoiling. In yeast, we also find positive supercoils associated with centromeres, cohesin binding sites, autonomously replicating sites, and the borders of R-loops (DNA-RNA hybrids). Our results suggest that GapR-seq is a powerful approach, likely applicable in any organism, to investigate aspects of chromosome structure and organization not accessible by Hi-C or other existing methods.

molecular biology↗