Biology subjects

Grasis, J. A.

Publications and source records attributed to Grasis, J. A..

4 recordsLinked to original sources

bioRxiv2026

Infection Tunes the Dynamics of Adenoviral E1A Disordered Regions

Intrinsically Disordered Proteins and protein regions (IDPs) are abundant in many viral proteomes and play diverse roles in the viral infectious cycles. The adenovirus Early Protein 1A (E1A) is one such viral IDP. E1A acts as a molecular hub that regulates viral infection by mediating interactions between viral and multiple host proteins. Like other IDPs, E1A exists in a flexible ensemble of conformations. Despite a demonstrated link between ensemble structure and function in E1A, no real-time measurement of its ensemble has been performed. Here, we use live cell FRET microscopy to measure the local ensemble structure of E1A in human cells, both in healthy cells and in cells infected with adenovirus. We found specific disordered regions undergo significant changes to their ensemble in infected cells. Furthermore, infection also alters the propensity of these regions to partition between the cytoplasm and nucleus, a hallmark of E1A function during infection. Our results showcase that the structural ensembles of viral IDPs are responsive to infection, and suggest that these may play a role in regulating infection progression. SignificanceIntegral to many viral proteomes are intrinsically disordered proteins and protein regions (IDPs), which target and rewire cellular pathways to ensure infection progression. During this process, the physical and chemical composition of the cell changes dramatically: metabolism is rewired, viral proteins are produced en masse, and as a result, the chemical composition of the host proteome is significantly altered. IDPs are known to be structurally sensitive to even mild changes in their environment, and their structural changes can result in a change to function. Here, using live cell FRET microscopy, we show that the structure and spatial localization of an adenovirus IDP, E1A, is altered in cells infected by the virus. Beyond a possible functional role for structural sensitivity in viral IDP function, our findings suggest that host IDPs may also be structurally altered by infection, with downstream functional consequences.

biophysics↗

bioRxiv2024

Filamentous bacteriophages induce proinflammatory responses in intestinal epithelial cells

Bacteriophages are the dominant members of the human enteric virome and can shape bacterial communities in the gut; however, our understanding of how they directly impact health and disease is limited. Previous studies have shown that specific bacteriophage populations are expanded in patients with Crohns disease (CD) and ulcerative colitis (UC), suggesting that fluctuations in the enteric virome may contribute to intestinal inflammation. Based on these studies, we hypothesized that a high bacteriophage burden directly induces intestinal epithelial responses. We found that filamentous inoviruses M13 and Fd induced dose-dependent IL-8 expression in the human intestinal epithelial cell line HT-29 to a greater degree than their lytic counterparts T4 and {phi}X174 did. We also found that M13, but not Fd, reduced bacterial internalization in HT-29 cells. This led us to investigate the mechanism underlying M13-mediated inhibition of bacterial internalization by examining the antiviral and antimicrobial responses in these cells. M13 upregulated Type I and III IFN expression and augmented short-chain fatty acid (SCFA)-mediated LL-37 expression in HT-29 cells. Taken together, our data establish that inoviruses directly affect human intestinal epithelial cells. These results provide new insights into the complex interactions between bacteriophages and the intestinal mucosa, which may underlie disease pathogenesis.

microbiology↗

bioRxiv2023

Temperate gut phages are prevalent, diverse, and predominantly inactive

Large-scale metagenomic and data mining efforts have uncovered an expansive diversity of bacteriophages (phages) within the human gut1-3. These insights include broader phage populational dynamics such as temporal stability4, interindividual uniqueness5,6 and potential associations to specific disease states7,8. However, the functional understanding of phage-host interactions and their impacts within this complex ecosystem have been limited due to a lack of cultured isolates for experimental validation. Here we characterise 125 active prophages originating from 252 diverse human gut bacterial isolates using seven different induction conditions to substantially expand the experimentally validated temperate phage-host pairs originating from the human gut. Importantly, only 17% of computationally predicted prophages were induced with common induction agents and these exhibited distinct gene patterns compared to non-induced predictions. Active Bacteroidota prophages were among the most prevalent members of the gut virome, with extensive use of diversity generating retroelements and exhibiting broad host ranges. Moreover, active polylysogeny was present in 52% of studied gut lysogens and led to coordinated prophage induction across diverse conditions. This study represents a substantial expansion of experimentally validated gut prophages, providing key insights into their diversity and genetics, including a genetic pathway for prophage domestication and demonstration that differential induction was complex and influenced by divergent prophage integration sites. More broadly, it highlights the importance of experimental validation alongside genomic based computational prediction to enable further functional understanding of these commensal viruses within the human gut.

microbiology↗

bioRxiv2021

hafeZ: Active prophage identification through read mapping

SummaryBacteriophages that have integrated their genomes into bacterial chromosomes, termed prophages, are widespread across bacteria. Prophages are key components of bacterial genomes, with their integration often contributing novel, beneficial, characteristics to the infected host. Likewise, their induction--through the production and release of progeny virions into the surrounding environment--can have considerable ramifications on bacterial communities. Yet, not all prophages can excise following integration, due to genetic degradation by their host bacterium. Here, we present hafeZ, a tool able to identify active prophages (i.e. those undergoing induction) within bacterial genomes through genomic read mapping. We demonstrate its use by applying hafeZ to publicly available sequencing data from bacterial genomes known to contain active prophages and show that hafeZ can accurately identify their presence and location in the host chromosomes. Availability and ImplementationhafeZ is implemented in Python 3.7 and freely available under an open-source GPL-3.0 license from https://github.com/Chrisjrt/hafeZ. Bugs and issues may be reported by submitting them via the hafeZ github issues page. Contactcturkington@ucmerced.edu or chrisjrt1@gmail.com

bioinformatics↗