Grad-seq identifies KhpB as a global RNA-binding protein in<i>Clostridioides difficile</i>that regulates toxin production

Lamm‐Schmidt, Vanessa; Fuchs, Manuela; Sulzer, Johannes; Gerovac, Milan; Hör, Jens; Dersch, Petra; Vogel, Jörg; Faber, Franziska

doi:10.1093/femsml/uqab004

Cited by 38 publications

(58 citation statements)

References 124 publications

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“… 2021a , b , Hör and Vogel 2021 , Lamm-Schmidt et al . 2021 , Riediger et al . 2021 ) is a promising technique for the identification of new 3′ UTR-derived sRNAs in both model and understudied or genetically intractable organisms.…”

Section: Using Grad-seq To Predict Functional 3′ Utr Fragmentsmentioning

confidence: 99%

An overview of gene regulation in bacteria by small RNAs derived from mRNA 3′ ends

Ponath

Hör

Vogel

2022

FEMS Microbiology Reviews

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Over the past two decades, small non-coding RNAs (sRNAs) that regulate mRNAs by short base pairing have gone from a curiosity to a major class of post-transcriptional regulators in bacteria. They are integral to many stress responses and regulatory circuits, affecting almost all aspects of bacterial life. Following pioneering sRNA searches in the early 2000s, the field quickly focused on conserved sRNA genes in the intergenic regions of bacterial chromosomes. Yet, it soon emerged that there might be another rich source of bacterial sRNAs: processed 3’ end fragments of mRNAs. Several such 3’ end-derived sRNAs have now been characterized, often revealing unexpected, conserved functions in diverse cellular processes. Here, we review our current knowledge of these 3’ end-derived sRNAs: their biogenesis through ribonucleases, their molecular mechanisms, their interactions with RNA-binding proteins, and their functional scope, which range from acting as specialized regulators of single metabolic genes to constituting entire non-coding arms in global stress responses. Recent global RNA interactome studies suggest that the importance of functional 3’ end-derived sRNAs has been vastly underestimated, and that this type of cross-regulation between genes at the mRNA level is more pervasive in bacteria than currently appreciated.

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Section: Using Grad-seq To Predict Functional 3′ Utr Fragmentsmentioning

confidence: 99%

An overview of gene regulation in bacteria by small RNAs derived from mRNA 3′ ends

Ponath

Hör

Vogel

2022

FEMS Microbiology Reviews

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“…Since fusobacteria lack CsrA, Hfq, and ProQ 87,88 , the use of FoxI as an RNA bait in experimental RBP discovery 30,74 promises to expand the currently known set of sRNArelated RBPs. Candidates include the KhpA/B proteins, which have been predicted to associate with sRNAs in gram-positive species [89][90][91] .…”

Section: Regarding General Transcription Signals Our Analysis Of Diff...mentioning

confidence: 99%

RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum

et al. 2021

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Fusobacterium nucleatum, long known as a constituent of the oral microflora, has recently garnered renewed attention for its association with several different human cancers. The growing interest in this emerging cancer-associated bacterium contrasts with a paucity of knowledge about its basic gene expression features and physiological responses. As fusobacterial lack all established small RNA-associated proteins, post-transcriptional networks in these bacteria are also unknown. Here, using differential RNA-seq (dRNAseq), we generate high-resolution global RNA maps for five clinically relevant fusobacterial strains -F. nucleatum subspecies nucleatum, animalis, polymorphum and vincentii as well as F. periodonticum -for early, mid-exponential growth and early stationary phase. These data are made available in an online browser, and we use these to uncover fundamental aspects of fusobacterial gene expression architecture and a suite of noncoding RNAs. Developing a vector for functional analysis of fusobacterial genes, we discover a conserved fusobacterial oxygen-induced small RNA, FoxI, which serves as a post-transcriptional repressor of the major outer membrane porin FomA. Our findings provide a crucial step towards delineating the regulatory networks enabling F. nucleatum adaptation to different environments, which may elucidate how these bacteria colonize different compartments of the human body.

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“…To facilitate the discovery of such RBPs, proteins interacting with FoxI could be identified using the sRNA as bait for pulldown experiments (76). A promising candidate for this role might be the RBP KhpB, which has been found to bind RNA in Streptococcus pneumonia and Clostridium difficile (96)(97)(98), and for which F. nucleatum harbors a homologue.…”

Section: Discussionmentioning

confidence: 99%

New genetic tools enable dissection of a global stress response in the early-branching speciesFusobacterium nucleatum

Ponath

Zhu

Cosi

et al. 2022

Preprint

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Fusobacterium nucleatum, long known as a common oral microbe, has recently garnered attention for its ability to colonize tissues and tumors elsewhere in the human body. Clinical and epidemiological research has now firmly established F. nucleatum as an oncomicrobe associated with several major cancer types. However, with the current research focus on host associations, little is known about gene regulation in F. nucleatum itself, including global stress response pathways that typically ensure the survival of bacteria outside their primary niche. This is due to the phylogenetic distance of Fusobacteriota to most model bacteria, their limited genetic tractability, and paucity of known gene functions. Here, we characterize a global transcriptional stress response network governed by the extracytoplasmic function sigma factor, σE. To this aim, we developed several new genetic tools for this anaerobic bacterium, including four different fluorescent marker proteins, inducible gene expression, scarless gene deletion, and transcriptional and translational reporter systems. Using these tools, we identified a σE response partly reminiscent of phylogenetically distant Proteobacteria but induced by exposure to oxygen. Although F. nucleatum lacks canonical RNA chaperones such as Hfq, we uncovered conservation of the non-coding arm of the σE response in form of the non-coding RNA FoxI. This regulatory small RNA (sRNA) acts as an mRNA repressor of several membrane proteins, thereby supporting the function of σE. In addition to the characterization of a global stress response in F. nucleatum, the genetic tools developed here will enable further discoveries and dissection of regulatory networks in this early-branching bacterium.

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Grad-seq identifies KhpB as a global RNA-binding protein inClostridioides difficilethat regulates toxin production

Cited by 38 publications

References 124 publications

An overview of gene regulation in bacteria by small RNAs derived from mRNA 3′ ends

An overview of gene regulation in bacteria by small RNAs derived from mRNA 3′ ends

RNA landscape of the emerging cancer-associated microbe Fusobacterium nucleatum

New genetic tools enable dissection of a global stress response in the early-branching speciesFusobacterium nucleatum

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