U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SRX24110602: GSM8180908: R. torques VIII-239 mucin o-glycans biol rep 1; [Ruminococcus] torques VIII-239; RNA-Seq
1 ILLUMINA (Illumina HiSeq 4000) run: 22.2M spots, 6.7G bases, 2Gb downloads

External Id: GSM8180908_r1
Submitted by: University of Michigan
Study: Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron
show Abstracthide Abstract
Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques—a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)— degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong fucosidase, sialidase and b1,4-galactosidase activities. There was a lack of detectable sulfatase and weak ß1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which may contribute to its association with IBD. Overall design: Ruminococcus torques VIII-239 was grown in 3 biological replicate cultures to mid-log phase under anaerobic conditions at 37ºC on YCFA medium containing either glucose or mucin O-glycans. RNA was isolated and rRNA depleted. RNA-seq analysis was performed to identify differentially regulated genes on these substrates.
Sample: R. torques VIII-239 mucin o-glycans biol rep 1
SAMN40699864 • SRS20897721 • All experiments • All runs
Library:
Name: GSM8180908
Instrument: Illumina HiSeq 4000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: Samples were treated with 500 uL buffer (200 mM NaCl, 200 mM Tris, 20 mM EDTA at pH 8), 210 uL of 20% SDS, and 500 uL phenol:choloroform:isoamyl alcohol (125:24:1, pH 4.3) and was bead beat for 3 minutes. Samples were precipitated with isopropanol, purified with the RNeasy Mini Kit,treated with DNase (NEB), and re-purified wtih the RNeasy Mini Kit. rRNA was depleted with the MICROBEExpress Bacterial mRNA Enrichment Kit (ThermoFisher). Samples were multiplexed for sequencing on the Illumina NovaSeq X platform at the University of Michigan Sequencing Core.
Runs: 1 run, 22.2M spots, 6.7G bases, 2Gb
Run# of Spots# of BasesSizePublished
SRR2850944622,170,9186.7G2Gb2024-06-19

ID:
32419496

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...