Limits...
Haloquadratum walsbyi: limited diversity in a global pond.

Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D - PLoS ONE (2011)

Bottom Line: Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species.The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

View Article: PubMed Central - PubMed

Affiliation: Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany. mdyall-smith@csu.edu.au

ABSTRACT

Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.

Principal findings: Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.

Conclusions: Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

Show MeSH

Related in: MedlinePlus

CRISPR systems of Hqr. walsbyi strains C23T and HBSQ001.Three CRISPR loci are present in C23T, associated with two separate groups of Cas genes (coloured yellow and pink). No Cas genes, and only one, residual CRISPR with 5 spacers, are found in HBSQ001. The DR (direct repeat) sequences are shown beneath the CRISPRs. Shading between the leader sequence of CRISPR-2 of C23T and CRISPR-1 of HBSQ001 indicate that they are nearly identical in sequence. The relative position and orientation of ORF HB2151A is shown along with an arrow indicating where it matches (exactly) a spacer sequence in CRISPR-3 of C23T. Similarly, the spacer sequences in HBSQ001 that are closely similar to sequences in C23T are indicated by arrows, labeled spacer-related sequences, which point to their matching locations in the C23T genome. Nucleotide positions are given beneath the CRISPRs and details of the matching spacer sequences are given in Table S7.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3119063&req=5

pone-0020968-g007: CRISPR systems of Hqr. walsbyi strains C23T and HBSQ001.Three CRISPR loci are present in C23T, associated with two separate groups of Cas genes (coloured yellow and pink). No Cas genes, and only one, residual CRISPR with 5 spacers, are found in HBSQ001. The DR (direct repeat) sequences are shown beneath the CRISPRs. Shading between the leader sequence of CRISPR-2 of C23T and CRISPR-1 of HBSQ001 indicate that they are nearly identical in sequence. The relative position and orientation of ORF HB2151A is shown along with an arrow indicating where it matches (exactly) a spacer sequence in CRISPR-3 of C23T. Similarly, the spacer sequences in HBSQ001 that are closely similar to sequences in C23T are indicated by arrows, labeled spacer-related sequences, which point to their matching locations in the C23T genome. Nucleotide positions are given beneath the CRISPRs and details of the matching spacer sequences are given in Table S7.

Mentions: In prokaryotes, Cas/CRISPR systems provide a sequence-specific defense barrier against incoming foreign DNA such as viruses or plasmids, and the genes involved often display a high rate of change [19]. The two Haloquadratum strains differ radically in their Cas/CRISPR systems, as summarized in Figure 7. Strain C23T carries two complete sets of Cas genes, one preceding the crispr-1 locus, and a second, distinct set located between the flanking crispr-2 and crispr-3 loci. The DR sequence found in crispr-1 differs from that present in the other two CRISPR loci, consistent with their distinct Cas genes. There are 85 spacers spread across the three loci but crispr-1 has duplicates of two spacers, and crisprs-2 and -3 share an identical spacer, making a total of 82 unique spacers. Strain HBSQ001 has no Cas genes and only 5 complete spacers. A MITE (HqIRS37) has inserted within the spacer between the third and fourth copy of the DR (counting from the leader sequence end). The residual HBSQ001 crispr locus is closely related to crispr-2 of C23T as they share the same leader and DR sequences (labeled DR2 in Figure 7), but the lack of Cas genes in HBSQ001 means that the CRISPR system in that strain is non-functional.


Haloquadratum walsbyi: limited diversity in a global pond.

Dyall-Smith ML, Pfeiffer F, Klee K, Palm P, Gross K, Schuster SC, Rampp M, Oesterhelt D - PLoS ONE (2011)

CRISPR systems of Hqr. walsbyi strains C23T and HBSQ001.Three CRISPR loci are present in C23T, associated with two separate groups of Cas genes (coloured yellow and pink). No Cas genes, and only one, residual CRISPR with 5 spacers, are found in HBSQ001. The DR (direct repeat) sequences are shown beneath the CRISPRs. Shading between the leader sequence of CRISPR-2 of C23T and CRISPR-1 of HBSQ001 indicate that they are nearly identical in sequence. The relative position and orientation of ORF HB2151A is shown along with an arrow indicating where it matches (exactly) a spacer sequence in CRISPR-3 of C23T. Similarly, the spacer sequences in HBSQ001 that are closely similar to sequences in C23T are indicated by arrows, labeled spacer-related sequences, which point to their matching locations in the C23T genome. Nucleotide positions are given beneath the CRISPRs and details of the matching spacer sequences are given in Table S7.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3119063&req=5

pone-0020968-g007: CRISPR systems of Hqr. walsbyi strains C23T and HBSQ001.Three CRISPR loci are present in C23T, associated with two separate groups of Cas genes (coloured yellow and pink). No Cas genes, and only one, residual CRISPR with 5 spacers, are found in HBSQ001. The DR (direct repeat) sequences are shown beneath the CRISPRs. Shading between the leader sequence of CRISPR-2 of C23T and CRISPR-1 of HBSQ001 indicate that they are nearly identical in sequence. The relative position and orientation of ORF HB2151A is shown along with an arrow indicating where it matches (exactly) a spacer sequence in CRISPR-3 of C23T. Similarly, the spacer sequences in HBSQ001 that are closely similar to sequences in C23T are indicated by arrows, labeled spacer-related sequences, which point to their matching locations in the C23T genome. Nucleotide positions are given beneath the CRISPRs and details of the matching spacer sequences are given in Table S7.
Mentions: In prokaryotes, Cas/CRISPR systems provide a sequence-specific defense barrier against incoming foreign DNA such as viruses or plasmids, and the genes involved often display a high rate of change [19]. The two Haloquadratum strains differ radically in their Cas/CRISPR systems, as summarized in Figure 7. Strain C23T carries two complete sets of Cas genes, one preceding the crispr-1 locus, and a second, distinct set located between the flanking crispr-2 and crispr-3 loci. The DR sequence found in crispr-1 differs from that present in the other two CRISPR loci, consistent with their distinct Cas genes. There are 85 spacers spread across the three loci but crispr-1 has duplicates of two spacers, and crisprs-2 and -3 share an identical spacer, making a total of 82 unique spacers. Strain HBSQ001 has no Cas genes and only 5 complete spacers. A MITE (HqIRS37) has inserted within the spacer between the third and fourth copy of the DR (counting from the leader sequence end). The residual HBSQ001 crispr locus is closely related to crispr-2 of C23T as they share the same leader and DR sequences (labeled DR2 in Figure 7), but the lack of Cas genes in HBSQ001 means that the CRISPR system in that strain is non-functional.

Bottom Line: Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species.The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

View Article: PubMed Central - PubMed

Affiliation: Department of Membrane Biochemistry, Max-Planck-Institute of Biochemistry, Martinsried, Germany. mdyall-smith@csu.edu.au

ABSTRACT

Background: Haloquadratum walsbyi commonly dominates the microbial flora of hypersaline waters. Its cells are extremely fragile squares requiring >14%(w/v) salt for growth, properties that should limit its dispersal and promote geographical isolation and divergence. To assess this, the genome sequences of two isolates recovered from sites at near maximum distance on Earth, were compared.

Principal findings: Both chromosomes are 3.1 MB in size, and 84% of each sequence was highly similar to the other (98.6% identity), comprising the core sequence. ORFs of this shared sequence were completely synteneic (conserved in genomic orientation and order), without inversion or rearrangement. Strain-specific insertions/deletions could be precisely mapped, often allowing the genetic events to be inferred. Many inferred deletions were associated with short direct repeats (4-20 bp). Deletion-coupled insertions are frequent, producing different sequences at identical positions. In cases where the inserted and deleted sequences are homologous, this leads to variant genes in a common synteneic background (as already described by others). Cas/CRISPR systems are present in C23(T) but have been lost in HBSQ001 except for a few spacer remnants. Numerous types of mobile genetic elements occur in both strains, most of which appear to be active, and with some specifically targetting others. Strain C23(T) carries two ∼6 kb plasmids that show similarity to halovirus His1 and to sequences nearby halovirus/plasmid gene clusters commonly found in haloarchaea.

Conclusions: Deletion-coupled insertions show that Hqr. walsbyi evolves by uptake and precise integration of foreign DNA, probably originating from close relatives. Change is also driven by mobile genetic elements but these do not by themselves explain the atypically low gene coding density found in this species. The remarkable genome conservation despite the presence of active systems for genome rearrangement implies both an efficient global dispersal system, and a high selective fitness for this species.

Show MeSH
Related in: MedlinePlus