Comparative genomics reveals diversified CRISPR-Cas systems of globally distributed Microcystis aeruginosa, a freshwater bloom-forming cyanobacterium.

Chen Yang,Tao Li,Feibi Lin,Jindong Zhao,Qi Li

doi:10.3389/fmicb.2015.00394

Abstract

Microcystis aeruginosa is one of the most common and dominant bloom-forming cyanobacteria in freshwater lakes around the world. Microcystis cells can produce toxic secondary metabolites, such as microcystins, which are harmful to human health. Two M. aeruginosa strains were isolated from two highly eutrophic lakes in China and their genomes were sequenced. Comparative genomic analysis was performed with the 12 other available M. aeruginosa genomes and closely related unicellular cyanobacterium. Each genome of M. aeruginosa containing at least one clustered regularly interspaced short palindromic repeat (CRISPR) locus and total 71 loci were identified, suggesting it is ubiquitous in M. aeruginosa genomes. In addition to the previously reported subtype I-D cas gene sets, three CAS subtypes I-A, III-A and III-B were identified and characterized in this study. Seven types of CRISPR direct repeat have close association with CAS subtype, confirming that different and specific secondary structures of CRISPR repeats are important for the recognition, binding and process of corresponding cas gene sets. Homology search of the CRISPR spacer sequences provides a history of not only resistance to bacteriophages and plasmids known to be associated with M. aeruginosa, but also the ability to target much more exogenous genetic material in the natural environment. These adaptive and heritable defense mechanisms play a vital role in keeping genomic stability and self-maintenance by restriction of horizontal gene transfer. Maintaining genomic stability and modulating genomic plasticity are both important evolutionary strategies for M. aeruginosa in adaptation and survival in various habitats.

Highlights

Water eutrophication has become a major environmental problem all over the world as it induces the expansion and persistence of Harmful Algal Blooms (HABs) (Heisler et al, 2008; Smith and Schindler, 2009)
Genome Assembly and General Features of M. aeruginosa Genomes Primary assembly of TAIHU98 used long reads by Newbler and resulted in 395 contigs, and paired-end reads were used to assemble them into 50 contigs within 6 scaffolds
We identified a total of 1726 unique spacers in all clustered regularly interspaced short palindromic repeat (CRISPR) loci of the M. aeruginosa genomes and compared them with available databases to search for possible proto-spacers from bacteria, plasmids, viruses or metagenome data (Figure 5A)

Summary

Introduction

Water eutrophication has become a major environmental problem all over the world as it induces the expansion and persistence of Harmful Algal Blooms (HABs) (Heisler et al, 2008; Smith and Schindler, 2009). Microcystis species are dominant freshwater bloomforming cyanobacterium and produce a range of toxic organic compounds that can affect human and animal health through drinking and recreational water (Paerl et al, 2001; Westrick et al, 2010). Of this genus, M. aeruginosa is the most typical and notorious species, mainly because of the production of microcystins, which have been the chief agent in numerous cases of animal and human poisoning (Briand et al, 2003; Soares et al, 2006). Genome comparison between non-toxic and toxic strains of M. aeruginosa revealed that they share less than half of their genes, and suggested numerous genes had been gained during evolution (Yang et al, 2013)

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