Transcription termination and antitermination of bacterial CRISPR arrays

Abstract
Data availability
Article and author information
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Abstract

A hallmark of CRISPR-Cas immunity systems is the CRISPR array, a genomic locus consisting of short, repeated sequences ('repeats') interspersed with short, variable sequences ('spacers'). CRISPR arrays are transcribed and processed into individual CRISPR RNAs that each include a single spacer, and direct Cas proteins to complementary sequence in invading nucleic acid. Most bacterial CRISPR array transcripts are unusually long for untranslated RNA, suggesting the existence of mechanisms to prevent premature transcription termination by Rho, a conserved bacterial transcription termination factor that rapidly terminates untranslated RNA. We show that Rho can prematurely terminate transcription of bacterial CRISPR arrays, and we identify a widespread antitermination mechanism that antagonizes Rho to facilitate complete transcription of CRISPR arrays. Thus, our data highlight the importance of transcription termination and antitermination in the evolution of bacterial CRISPR-Cas systems.

Data availability

Raw ChIP-seq data are available from EBI ArrayExpress/ENA using accession number E-MTAB-7242. Raw sequencing data for conjugation experiments involving V. cholerae are available from EBI ArrayExpress/ENA using accession number E-MTAB-9631.

The following data sets were generated

1. Stringer AM
2. Wade JT
(2018) Nus factors prevent premature transcription termination of bacterial CRISPR arrays
EMBL-EBI ArrayExpress, E-MTAB-7242.

https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-7242/
1. Stringer AM
2. Wade JT
(2020) Transcription Termination and Antitermination of Bacterial CRISPR Arrays
EMBL-EBI ArrayExpress, E-MTAB-9631.

https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9631/

Article and author information

Author details

Anne M Stringer

Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, United States

Competing interests
The authors declare that no competing interests exist.
Gabriele Baniulyte

Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-0235-7938
Erica Lasek-Nesselquist

Bioinformatics Core Facility, Wadsworth Center, New York State Department of Health, Albany, United States

Competing interests
The authors declare that no competing interests exist.
Kimberley D Seed

Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-0139-1600
Joseph T Wade

Division of Genetics, Wadsworth Center, New York State Department of Health, Albany, United States

For correspondence
joseph.wade@gmail.com

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-9779-3160

Funding

National Institute of General Medical Sciences (R01GM122836)

Joseph T Wade

National Institute of Allergy and Infectious Diseases (R21AI126416)

Joseph T Wade

National Institute of Allergy and Infectious Diseases (R01AI127652)

Kimberley D Seed

Burroughs Wellcome Fund (Investigators in the Pathogenesis of Infectious Disease Award)

Kimberley D Seed

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.