Evidence map›Paper›PMID 42765828›Full record

ArticleMicrobiologyOpen2026

Interrogating the Escherichia coli Epitranscriptome Via CRISPR Interference and Nanopore Native RNA Sequencing.

Miranda E Pitt, Jianshu Zhang, An N T Nguyen, Michael B Hall, Leila Jebeli, Leo A Featherstone, Garry S A Myers, Nichollas E Scott, Lachlan J M Coin

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in MicrobiologyOpen, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors.

Miranda E PittAustralian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.ORCID https://orcid.org/0000-0002-8255-4036
Jianshu ZhangDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID https://orcid.org/0009-0008-0871-5197
An N T NguyenDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID https://orcid.org/0000-0003-4893-6636
Michael B HallDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID https://orcid.org/0000-0003-3683-6208
Leila JebeliEnteric Diseases Group, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.ORCID https://orcid.org/0000-0003-4240-9528
Leo A FeatherstoneDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID https://orcid.org/0000-0002-8878-1758
Garry S A MyersAustralian Institute for Microbiology and Infection, University of Technology Sydney, Sydney, New South Wales, Australia.
Nichollas E ScottDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID https://orcid.org/0000-0003-2556-8316
Lachlan J M CoinDepartment of Microbiology and Immunology at The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia.ORCID https://orcid.org/0000-0002-4300-455X

Funding

ARC Discovery Project Grant DP210100362Australian Research Council Future Fellowship FT200100270University of Melbourne Early Career Researcher 2021ECR152University of Melbourne Start up fund
6 · The paper itself

Abstract

Epitranscriptomics has recently gained significant momentum due to technological advances and translational applications; however, studies on bacterial RNA modifications remain limited. Bacterial RNA is notoriously prone to degradation, and methodologies to investigate the epitranscriptome are challenging. Prior research has shown RNA modifications modulate antimicrobial resistance, virulence and pathogenicity. This research employed CRISPR interference to knock down five known Escherichia coli rRNA modification genes (rlmF, rlmJ, rluD, rsmF and rsmG) in three E. coli strains. These isolates were investigated for growth delays, changes in the proteome and the influence on mRNA modifications via native RNA sequencing. CRISPRi adequately silenced the majority of RNA modification genes in E. coli (> 80% reduction). Significant growth delays were associated with rlmF, rluD and rsmF repression. Unique protein pathways corresponding with RNA modification loss were found for rlmJ (TreB, XylF), rluD (CysH, HycB, PutP, TrpB), rsmF (EvgA) and rsmG (OppC). Known rRNA modification sites for rluD (Ψ) and rsmG (m7G) were detected from analysis of nanopore electrical signal; however, only a weak signal was apparent for m6A (rlmF, rlmJ) and m5C (rsmF) modifications. The inhibition of rRNA modifications resulted in mRNA modification changes, including for genes ompC, cspC, dbhA, dbhB and secY. Our work provides an approach for unravelling the epitranscriptome of E. coli to gain insight into its functional role.

Indexed as

Escherichia coliRNA, BacterialClustered Regularly Interspaced Short Palindromic RepeatsEpitranscriptomeEpitranscriptomicsEscherichia coli ProteinsGene Expression Regulation, BacterialNanopore SequencingRNA MethylationRNA Processing, Post-TranscriptionalSequence Analysis, RNAEscherichia coli ProteinsRNA, BacterialbacteriaCRISPR interferenceepitranscriptomicsnanopore RNA sequencingproteomicsRNA modifications

Identifiers

PMID42765828
PMCPMC13592227

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.