@Article{Shah_Alkhnbashi_Behler-Compr_searc_for-2019,
  author =	 {Shah, Shiraz A. and Alkhnbashi, Omer S. and Behler, Juliane 
                  and Han, Wenyuan and She, Qunxin and Hess, Wolfgang R. and 
                  Garrett, Roger A. and Backofen, Rolf},
  title =	 {Comprehensive search for accessory proteins encoded with 
                  archaeal and bacterial type {III} {CRISPR}-cas gene 
                  cassettes reveals 39 new cas gene families},
  journal =	 {RNA Biol},
  year =	 {2019},
  volume =	 {16},
  number =	 {4},
  pages =	 {530-542},
  user =	 {backofen},
  pmid =	 {29911924},
  doi = 	 {10.1080/15476286.2018.1483685},
  issn = 	 {1555-8584},
  issn = 	 {1547-6286},
  abstract =	 {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 .}
}