Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families
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Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families. / Shah, Shiraz A.; Alkhnbashi, Omer S.; Behler, Juliane; Han, Wenyuan; She, Qunxin; Hess, Wolfgang R.; Garrett, Roger A.; Backofen, Rolf.
In: RNA Biology, Vol. 16, No. 4, 2019, p. 530-542.Research output: Contribution to journal › Journal article › Research › peer-review
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T1 - Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families
AU - Shah, Shiraz A.
AU - Alkhnbashi, Omer S.
AU - Behler, Juliane
AU - Han, Wenyuan
AU - She, Qunxin
AU - Hess, Wolfgang R.
AU - Garrett, Roger A.
AU - Backofen, Rolf
PY - 2019
Y1 - 2019
N2 - A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in Synechocystis confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.
AB - A study was undertaken to identify conserved proteins that are encoded adjacent to cas gene cassettes of Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats – CRISPR associated) interference modules. Type III modules have been shown to target and degrade dsDNA, ssDNA and ssRNA and are frequently intertwined with cofunctional accessory genes, including genes encoding CRISPR-associated Rossman Fold (CARF) domains. Using a comparative genomics approach, and defining a Type III association score accounting for coevolution and specificity of flanking genes, we identified and classified 39 new Type III associated gene families. Most archaeal and bacterial Type III modules were seen to be flanked by several accessory genes, around half of which did not encode CARF domains and remain of unknown function. Northern blotting and interference assays in Synechocystis confirmed that one particular non-CARF accessory protein family was involved in crRNA maturation. Non-CARF accessory genes were generally diverse, encoding nuclease, helicase, protease, ATPase, transporter and transmembrane domains with some encoding no known domains. We infer that additional families of non-CARF accessory proteins remain to be found. The method employed is scalable for potential application to metagenomic data once automated pipelines for annotation of CRISPR-Cas systems have been developed. All accessory genes found in this study are presented online in a readily accessible and searchable format for researchers to audit their model organism of choice: http://accessory.crispr.dk.
KW - accessory
KW - ancillary
KW - archaea
KW - auxillary
KW - bacteria
KW - CARF
KW - cas
KW - CRISPR
KW - csx1
KW - csx3
KW - helicase
KW - nuclease
KW - protease
KW - type III
U2 - 10.1080/15476286.2018.1483685
DO - 10.1080/15476286.2018.1483685
M3 - Journal article
C2 - 29911924
AN - SCOPUS:85048840591
VL - 16
SP - 530
EP - 542
JO - R N A Biology
JF - R N A Biology
SN - 1547-6286
IS - 4
ER -
ID: 209706071