Title: On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

Abstract

Cas1 integrase is the key enzyme of the clustered regularly interspaced short palindromic repeat (CRISPR)-Cas adaptation module that mediates acquisition of spacers derived from foreign DNA by CRISPR arrays. In diverse bacteria, thecas1gene is fused (or adjacent) to a gene encoding a reverse transcriptase (RT) related to group II intron RTs. An RT-Cas1 fusion protein has been recently shown to enable acquisition of CRISPR spacers from RNA. Phylogenetic analysis of the CRISPR-associated RTs demonstrates monophyly of the RT-Cas1 fusion, and coevolution of the RT and Cas1 domains. Nearly all such RTs are present within type III CRISPR-Cas loci, but their phylogeny does not parallel the CRISPR-Cas type classification, indicating that RT-Cas1 is an autonomous functional module that is disseminated by horizontal gene transfer and can function with diverse type III systems. To compare the sequence pools sampled by RT-Cas1-associated and RT-lacking CRISPR-Cas systems, we obtained samples of a commercially grown cyanobacterium—Arthrospira platensis. Sequencing of the CRISPR arrays uncovered a highly diverse population of spacers. Spacer diversity was particularly striking for the RT-Cas1-containing type III-B system, where no saturation was evident even with millions of sequences analyzed. In contrast, analysis of the RT-lacking type III-D system yielded a highly diverse poolmore » but reached a point where fewer novel spacers were recovered as sequencing depth was increased. Matches could be identified for a small fraction of the non-RT-Cas1-associated spacers, and for only a single RT-Cas1-associated spacer. Thus, the principal source(s) of the spacers, particularly the hypervariable spacer repertoire of the RT-associated arrays, remains unknown.IMPORTANCEWhile the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures ofArthrospira platensis, a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic. While the majority of CRISPR-Cas immune systems adapt to foreign genetic elements by capturing segments of invasive DNA, some systems carry reverse transcriptases (RTs) that enable adaptation to RNA molecules. From analysis of available bacterial sequence data, we find evidence that RT-based RNA adaptation machinery has been able to join with CRISPR-Cas immune systems in many, diverse bacterial species. To investigate whether the abilities to adapt to DNA and RNA molecules are utilized for defense against distinct classes of invaders in nature, we sequenced CRISPR arrays from samples of commercial-scale open-air cultures ofArthrospira platensis, a cyanobacterium that contains both RT-lacking and RT-containing CRISPR-Cas systems. We uncovered a diverse pool of naturally occurring immune memories, with the RT-lacking locus acquiring a number of segments matching known viral or bacterial genes, while the RT-containing locus has acquired spacers from a distinct sequence pool for which the source remains enigmatic.« less

Authors:

Silas, Sukrit ^[1]; Makarova, Kira S. ^[2]; Shmakov, Sergey ^[3]; Páez-Espino, David ^[4]; Mohr, Georg ^[5]; Liu, Yi ^[1]; Davison, Michelle ^[6]; Roux, Simon ^[7]; Krishnamurthy, Siddharth R. ^[8]; Fu, Becky Xu Hua ^[1]; Hansen, Loren L. ^[1]; Wang, David ^[8]; Sullivan, Matthew B. ^[7]; Millard, Andrew ^[9]; Clokie, Martha R. ^[10]; Bhaya, Devaki ^[6]; Lambowitz, Alan M. ^[5]; Kyrpides, Nikos C. ^[11]; Koonin, Eugene V.  ^[2];

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Fire, Andrew Z. ^[1]

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+ Show Author Affiliations

1. Stanford Univ., CA (United States)
2. National Inst. of Health (NIH), Bethesda, MD (United States)
3. Skolkovo Inst. of Science and Technology (Russia); National Inst. of Health (NIH), Bethesda, MD (United States)
4. USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)
5. Univ. of Texas, Austin, TX (United States)
6. Carnegie Inst. for Science, Stanford, CA (United States)
7. The Ohio State Univ., Columbus, OH (United States)
8. Washington Univ., St. Louis, MO (United States)
9. Univ. of Warwick (United Kingdom)
10. Univ. of Leicester (United Kingdom)
11. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)

Publication Date:

Tue Jul 11 00:00:00 EDT 2017

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE

OSTI Identifier:

1626121

Grant/Contract Number:  

AC02-05CH11231; R01-GM37706; R01-GM37949

Resource Type:

Accepted Manuscript

Journal Name:

mBio (Online)

Additional Journal Information:

Journal Name: mBio (Online); Journal Volume: 8; Journal Issue: 4; Journal ID: ISSN 2150-7511

Publisher:

American Society for Microbiology

Country of Publication:

United States

Language:

English

Subject:

59 BASIC BIOLOGICAL SCIENCES; Microbiology; CRISPR; RNA spacer acquisition; cyanobacteria; deep sequencing; horizontal gene transfer; host-parasite relationship; phylogeny; reverse transcriptase