Biology subjects

Sheahan, M. L.

Publications and source records attributed to Sheahan, M. L..

4 recordsLinked to original sources

bioRxiv2025

Antagonism by the Type VI secretion system of Bacteroides fragilis is controlled by a TetR family regulator and released small molecule

Antagonistic systems of bacteria are often tightly regulated. The human gut Bacteroidales harbor three distinct antagonistic Type VI secretion systems (T6SS), one of which is present only in Bacteroides fragilis, known as the GA3 T6SS. Although this is the best studied of the three T6SSs, little is known about how it is regulated. The gene upstream of the GA3 T6SS locus encodes a TetR family transcriptional regulator (TetRGA3), which we show represses expression of the GA3 T6SS locus. The gene immediately upstream and divergently transcribed from tetRGA3, designated here as lgsGA3, encodes a product of the -oxoamine synthase family of pyridoxal phosphate-dependent enzymes with structural homology to the CqsA autoinducer synthase of the CAI-1 quorum sensing system of Vibrio spp. When lgsGA3 is deleted, transcription of the GA3 T6SS locus is repressed in a TetR-dependent manner. Strains synthesizing LgsGA3 produce a molecule present in the supernatant that likely serves as the TetRGA3 ligand, overcoming TetR transcriptional repression of the GA3 T6SS. We show that GA3 T6SS-specific immunity genes present on two acquired immunity defense islands are also regulated by LgsGA3 coordinating expression of GA3 T6SS antagonism with protection from competitors GA3 T6SS toxins. Production and firing of the GA3 T6SS and subsequent antagonism occurs in bacteria deleted for lgsGA3 when grown with bacteria containing this gene or their supernatants. These data show that the GA3 T6SS is regulated by a small molecule acting through TetRGA3 allowing the bacteria to coordinate antagonistic and protective systems. Significance statementThere are numerous external and intrinsic signals that dictate when bacteria become aggressive and when they activate their defensive systems. We show that B. fragilis strains with a GA3 T6SS synthesize a small molecule released from bacterial cells that acts through TetR family regulators to coordinate transcription of both the antagonistic GA3 T6SS and arrays of immunity genes to competitors GA3 T6SS toxins. Bacteria can respond to this molecule when released from non-kin bacteria, allowing them to sense and respond to a threat from a nearby competitor. The coordinated regulation of the GA3 T6SS and arrays of immunity genes is the second example of regulatory crosstalk between the GA3 T6SS and genes of MGEs through TetR family regulators.

microbiology↗

bioRxiv2024

Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes

While human autopsy samples have provided insights into pulmonary immune mechanisms associated with severe viral respiratory diseases, the mechanisms that contribute to a clinically favorable resolution of viral respiratory infections remain unclear due to the lack of proper experimental systems. Using mice co-engrafted with a genetically matched human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining successful resolution of SARS-CoV-2 infection in human lung tissues. Viral infection is rapidly cleared from fLX following a peak of viral replication, histopathological manifestations of lung disease and loss of AT2 program, as reported in human COVID-19 patients. Infection resolution is associated with the activation of a limited number of hematopoietic subsets, including inflammatory monocytes and non-canonical double-negative T-cells with cytotoxic functions, which are highly enriched in viral RNA and dissipate upon infection resolution. Activation of specific human fibroblast and endothelial subsets also elicit robust antiviral and monocyte chemotaxis signatures, respectively. Notably, systemic depletion of human CD4+ cells, but not CD3+ cells, abrogates infection resolution in fLX and induces persistent infection, supporting evidence that peripheral CD4+ monocytes are important contributors to SARS-CoV-2 infection resolution in lung tissues. Collectively, our findings unravel a comprehensive picture of the immunological events defining effective resolution of SARS-CoV-2 infection in human lung tissues, revealing markedly divergent immunological trajectories between resolving and fatal COVID-19 cases.

immunology↗

bioRxiv2023

A ubiquitous mobile genetic element disarms a bacterial antagonist of the gut microbiota

DNA transfer is ubiquitous in the gut microbiota, especially among species of Bacteroidales. In silico analyses have revealed hundreds of mobile genetic elements shared between these species, yet little is known about the phenotypes they encode, their effects on fitness, or pleiotropic consequences for the recipients genome. Here, we show that acquisition of a ubiquitous integrative and conjugative element encoding an antagonistic system shuts down the native contact-dependent antagonistic system of Bacteroides fragilis. Despite inactivating the native antagonism system, mobile element acquisition increases fitness of the B. fragilis transconjugant over its progenitor by arming it with a new weapon. This DNA transfer causes the strain to change allegiances so that it no longer targets ecosystem members containing the same element yet is armed for communal defense.

microbiology↗

bioRxiv2023

A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut

Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry cryptic plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from ones mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.

microbiology↗