CRISPR adaptive immune systems of Archaea

Abstract

CRISPR adaptive immune systems were analyzed for all available completed genomes of archaea, which included representatives of each of the main archaeal phyla. Initially, all proteins encoded within, and proximal to, CRISPR-cas loci were clustered and analyzed using a profile–profile approach. Then cas genes were assigned to gene cassettes and to functional modules for adaptation and interference. CRISPR systems were then classified primarily on the basis of their concatenated Cas protein sequences and gene synteny of the interference modules. With few exceptions, they could be assigned to the universal Type I or Type III systems. For Type I, subtypes I-A, I-B, and I-D dominate but the data support the division of subtype I-B into two subtypes, designated I-B and I-G. About 70% of the Type III systems fall into the universal subtypes III-A and III-B but the remainder, some of which are phyla-specific, diverge significantly in Cas protein sequences, and/or gene synteny, and they are classified separately. Furthermore, a few CRISPR systems that could not be assigned to Type I or Type III are categorized as variant systems. Criteria are presented for assigning newly sequenced archaeal CRISPR systems to the different subtypes. Several accessory proteins were identified that show a specific gene linkage, especially to Type III interference modules, and these may be cofunctional with the CRISPR systems. Evidence is presented for extensive exchange having occurred between adaptation and interference modules of different archaeal CRISPR systems, indicating the wide compatibility of the functionally diverse interference complexes with the relatively conserved adaptation modules.

Knowledge-based discovery for designing CRISPR-CAS systems against invading mobilomes in thermophiles

“…Using CRISPRstrand server, Alkhnbashi et al (2014) predicted the repeat orientations of multiple mature RNA species (crRNAs) for the identification and characterization of protospacers on genome invaders and regulatory motifs in the leader sequences of CRISPR arrays. Vestergaard et al (2014) also classified the cas subtypes based on cas-protein occurrences for archaea. Phylogenetic analysis of this study also revealed that many functions of the identified cas proteins could be derived from distantly related genomes, plasmids and phages that was agreed to earlier findings (Nelson et al 1999;Zivanovic et al 2002;Boucher et al 2003;Marraffini and Sontheimer 2009;Chellapandi and Ranjani 2011;Spilman et al 2013).…”

“…Phylogenetic analysis of this study also revealed that many functions of the identified cas proteins could be derived from distantly related genomes, plasmids and phages that was agreed to earlier findings (Nelson et al 1999;Zivanovic et al 2002;Boucher et al 2003;Marraffini and Sontheimer 2009;Chellapandi and Ranjani 2011;Spilman et al 2013). Euryarchaea are more diverse phylogenetically than crenarchaea because of they are generally heterotophic in nature and frequent a wide range of natural environments (Vestergaard et al 2014). It suggested that many of their natural habitats are relatively rich in bacteria, rendering their CRISPR systems more susceptible to exchange between archaea and bacteria.…”

“…RNA-directed defense mechanisms in the genomes of thermophilic bacteria and archaea have evolved like a prokaryotic genome to cope with the constant threat of genome invaders (Chellapandi and Ranjani 2011;Makarova et al 2012;Weinberger et al 2012;Vestergaard et al 2014). The existence of this pathway in these genomes has been hypothesized to parallel the eukaryotic RNAi pathway known as Clustered regularly interspaced short palindromic repeats-CRISPR-associated sequences (CRISPR-CAS) system or prokaryotic RNAi (pRNAi) (Lillestol et al 2006;Makarova et al 2006;Tomoyasu et al 2008).…”

“…Among 25 gene families in the CAS system, eight gene families (cas1, cas2, cas4, cas6, cas7) have reported for the nuclease activity, nine families (cas5) for Repeat-Associated Mysterious Proteins (RAMP) and two families (cas3) for DNA/RNA polymerase/helicase activity (Makarova et al 2006;Quax et al 2013;Vestergaard et al 2014). However, the functions of several other cas gene families remain obscure.…”

“…Although CRISPR-CAS related information available in the CRISPR database, a detailed knowledge and annotation would be required to understanding its existence and hypothetical molecular mechanism in recently sequenced thermophiles (Vestergaard et al 2014). In this perspective, the present study was intended to analyze their molecular diversity of structural components in the CRISPR-CAS systems, and to design and construction of their acquired defense pathways against genome invaders by using knowledge-based genome-wide survey and phylogenybased functional annotation.…”