Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises

Irastortza-Olaziregi, Mikel; Amster‐Choder, Orna

doi:10.3389/fmicb.2020.624830

Cited by 59 publications

(51 citation statements)

References 312 publications

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“…Amidst the heterogeneous RNA pool, translation takes place concurrently during transcription and mRNA decay in bacteria (Irastortza-Olaziregi and Amster-Choder, 2021).…”

Section: Introductionmentioning

confidence: 99%

Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

Herzel

Stanley²,

Taggart³

et al. 2021

Preprint

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Bacterial mRNAs have short life cycles, in which transcription is rapidly followed by translation and degradation within seconds to minutes. The resulting diversity of mRNAs impacts their functionality but has remained unresolved. Here we quantitatively map the 3’ status of cellular RNAs in Escherichia coli during steady-state growth and report a large fraction of molecules (median>60%) that are fragments of canonical full-length mRNAs. The majority of RNA fragments are decay intermediates following endonuclease cleavage by RNase E and yet-unknown nucleases, whereas nascent RNAs contribute to a smaller fraction. Despite the prevalence of decay intermediates in total RNA, they are underrepresented in the pool of ribosome-associated transcripts and can thus distort quantifications for the abundance of full-length, functional mRNAs. The large heterogeneity within mRNA molecules in vivo highlights the importance in discerning functional transcripts and provides a lens for studying the dynamic life cycle of mRNAs.

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“…Amidst the heterogeneous RNA pool, translation takes place concurrently during transcription and mRNA decay in bacteria (Irastortza-Olaziregi and Amster-Choder, 2021).…”

Section: Introductionmentioning

confidence: 99%

Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

Herzel

Stanley²,

Taggart³

et al. 2021

Preprint

View full text Add to dashboard Cite

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“…It is noteworthy that the archaeal domain of life encompasses highly diverse organisms, of which only a few model organisms have been studied so far. As documented for the bacterial world ( Irastortza-Olaziregi and Amster-Choder, 2020 ; Johnson et al, 2020 ), expressome formation might occur in some archaeal species but not in others.…”

Section: Is Transcription Coupled To Translation In Archaea?mentioning

confidence: 81%

Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World

et al. 2021

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The lack of a nucleus is the defining cellular feature of bacteria and archaea. Consequently, transcription and translation are occurring in the same compartment, proceed simultaneously and likely in a coupled fashion. Recent cryo-electron microscopy (cryo-EM) and tomography data, also combined with crosslinking-mass spectrometry experiments, have uncovered detailed structural features of the coupling between a transcribing bacterial RNA polymerase (RNAP) and the trailing translating ribosome in Escherichia coli and Mycoplasma pneumoniae. Formation of this supercomplex, called expressome, is mediated by physical interactions between the RNAP-bound transcription elongation factors NusG and/or NusA and the ribosomal proteins including uS10. Based on the structural conservation of the RNAP core enzyme, the ribosome, and the universally conserved elongation factors Spt5 (NusG) and NusA, we discuss requirements and functional implications of transcription-translation coupling in archaea. We furthermore consider additional RNA-mediated and co-transcriptional processes that potentially influence expressome formation in archaea.

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“…However, we observed a complex transcription pattern with multiple possible RNA variants. Given that transcription and translation are coupled in E. coli, new questions about the translation efficiency and transcript stability of the transcript variants emerge (58)(59)(60)(61). Furthermore, highquality long-read RNA-seq data can be used to analyse degradation or processing patterns to gain new insights into mRNA decay in prokaryotes.…”

Section: Discussionmentioning

confidence: 99%

Insights into rRNA processing and modification mapping in Archaea using Nanopore-based RNA sequencing

Gruenberger

Ferreira-Cerca

Grohmann

2021

Preprint

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High-throughput sequencing dramatically changed our view of transcriptome architectures and allowed for ground-breaking discoveries in RNA biology. Recently, sequencing of full-length transcripts based on the single-molecule sequencing platform from Oxford Nanopore Technologies (ONT) was introduced and is widely employed to sequence eukaryotic and viral RNAs. However, experimental approaches implementing this technique for prokaryotic transcriptomes remain scarce. Here, we present an experimental and bioinformatic workflow for ONT RNA-seq in the bacterial model organism Escherichia coli, which can be applied to any microorganism. Our study highlights critical steps of library preparation and computational analysis and compares the results to gold standards in the field. Furthermore, we comprehensively evaluate the applicability and advantages of different ONT-based RNA sequencing protocols, including direct RNA, direct cDNA, and PCR-cDNA. We find that cDNA-seq offers improved yield and accuracy without bias in quantification compared to direct RNA sequencing. Notably, cDNA-seq can be readily used for simultaneous transcript quantification, accurate detection of transcript 5′ and 3′ boundaries, analysis of transcriptional units and transcriptional heterogeneity. In summary, we establish Nanopore RNA-seq to be a ready-to-use tool allowing rapid, cost-effective, and accurate annotation of multiple transcriptomic features thereby advancing it to become a standard method for RNA analysis in prokaryotes.

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Coupled Transcription-Translation in Prokaryotes: An Old Couple With New Surprises

Cited by 59 publications

References 312 publications

Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

Ubiquitous mRNA decay fragments in E. coli redefine the functional transcriptome

Coupling of Transcription and Translation in Archaea: Cues From the Bacterial World

Insights into rRNA processing and modification mapping in Archaea using Nanopore-based RNA sequencing

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