Tyson GW, Banfield JF.. Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses. Environ Microbiol 10: 200-207

Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA.
Environmental Microbiology (Impact Factor: 6.24). 02/2008; 10(1):200-7. DOI: 10.1111/j.1462-2920.2007.01444.x
Source: PubMed

ABSTRACT Recent experimental evidence has demonstrated that bacteria acquire resistance to viruses by incorporation of short transcribed nucleotide sequences into regions of clustered regularly interspaced short palindromic repeats (CRISPR). We have analysed community genomic data from acidophilic microbial biofilms and discovered that evolution of the CRISPR regions in two distinct Leptospirillum group II bacteria occurs fast enough to promote individuality in otherwise nearly clonal populations. Comparative genomics strongly indicates very recent lateral transfer of the CRISPR locus between these populations, followed by significant loss of spacer sequences and locus expansion by unidirectional heterogeneous addition of new spacer sequences. Diversification of the CRISPR region is inferred to be a population-level response to the rapidly changing selective pressure of phage predation. Results reinforce the importance of phage-host interactions in shaping microbial ecology and evolution over very short time scales.

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    • "As an example, E. coli contains a CRISPR-Cas system that is efficiently silenced by H-NS [26], which could be interpreted as inactivation conferring a selective advantage. On the other side of the scale, in an analysis of acid mine drainage, extreme CRISPR diversity was observed where no two sampled individual cells had the same spacers [27]. The viruses in the acid mine drainage used recombination to diversify rapidly, making any but the most recent spacers lack a target [28]. "
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    ABSTRACT: Viruses are a common threat to cellular life, not the least to bacteria and archaea who constitute the majority of life on Earth. Consequently, a variety of mechanisms to resist virus infection has evolved. A recent discovery is the adaptive immune system in prokaryotes, a type of system previously thought to be present only in vertebrates. The system, called CRISPR-Cas, provide sequence-specific adaptive immunity and fundamentally affect our understanding of virus-host interaction. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize and clear infections. There has been rapid advancement in our understanding of this immune system and its applications, but there are many aspects that await elucidation making the field an exciting area of research. This review provides an overview of the field and highlights unresolved issues. Copyright © 2015. Published by Elsevier B.V.
    Biochimie 04/2015; 437. DOI:10.1016/j.biochi.2015.03.025 · 3.12 Impact Factor
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    • "There are two primary characteristics of CRISPRs that make them suitable for such a purpose. First, due to the evolutionary arms race between foreign elements (e.g., phages) and the host bacteria, the associated rapidly changing selection pressures may cause CRISPRs to evolve quite quickly (Karginov & Hannon, 2010; Tyson & Banfield, 2008). Thus, through the acquisition of new and deletion of old spacers, differences useful for typing and subtyping (in Salmonella, this refers to strain identification and differentiation at the serovar and sub-serovar level) could arise even between closely related strains. "
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    ABSTRACT: Evolutionary studies of clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated (cas) genes can provide insights into host-pathogen co-evolutionary dynamics and the frequency at which different genomic events (e.g., horizontal vs. vertical transmission) occur. Within this study, we used whole genome sequence (WGS) data to determine the evolutionary history and genetic diversity of CRISPR loci and cas genes among a diverse set of 427 Salmonella enterica ssp. enterica isolates representing 64 different serovars. We also evaluated the performance of CRISPR loci for typing when compared to whole genome and multilocus sequence typing (MLST) approaches. We found that there was high diversity in array length within both CRISPR1 (median = 22; min = 3; max = 79) and CRISPR2 (median = 27; min = 2; max = 221). There was also much diversity within serovars (e.g., arrays differed by as many as 50 repeat-spacer units among Salmonella ser. Senftenberg isolates). Interestingly, we found that there are two general cas gene profiles that do not track phylogenetic relationships, which suggests that non-vertical transmission events have occurred frequently throughout the evolutionary history of the sampled isolates. There is also considerable variation among the ranges of pairwise distances estimated within each cas gene, which may be indicative of the strength of natural selection acting on those genes. We developed a novel clustering approach based on CRISPR spacer content, but found that typing based on CRISPRs was less accurate than the MLST-based alternative; typing based on WGS data was the most accurate. Notwithstanding cost and accessibility, we anticipate that draft genome sequencing, due to its greater discriminatory power, will eventually become routine for traceback investigations.
    PeerJ 04/2014; 2:e340. DOI:10.7717/peerj.340 · 2.10 Impact Factor
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    • "Given that this newly described bacterial defense system has been found in approximately half of all bacterial species studied, resistance mechanisms that target foreign genetic material in the cell may be less constrained than mechanisms targeting phage adsorption. Furthermore, these molecular defense mechanisms can now be productively studied using sequence-based technologies (Tyson & Banfield, 2008) to establish an idea of the relative importance of the different categories of bacterial resistance mechanisms. The prevalence of these mechanisms will undoubtedly shed light into bacteria–phage interactions in the environment. "
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    ABSTRACT: Phages are considered the most abundant and diverse biological entities on Earth and are notable not only for their sheer abundance, but also for their influence on bacterial hosts. In nature, bacteria–phage relationships are complex and have far-reaching consequences beyond particular pairwise interactions, influencing everything from bacterial virulence to eukaryotic fitness to the carbon cycle. In this review, we examine bacteria and phage distributions in nature first by highlighting biogeographic patterns and nonhost environmental influences on phage distribution, then by considering the ways in which phages and bacteria interact, emphasizing phage life cycles, bacterial responses to phage infection, and the complex patterns of phage host specificity. Finally, we discuss phage impacts on bacterial abundance, genetics, and physiology, and further aim to clarify distinctions between current theoretical models and point out areas in need of future research.
    Advances in applied microbiology 01/2014; 89:135–183. DOI:10.1016/B978-0-12-800259-9.00004-4 · 2.24 Impact Factor
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