Genomic islands and the ecology and evolution of Prochlorococcus

Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
Science (Impact Factor: 31.48). 04/2006; 311(5768):1768-70. DOI: 10.1126/science.1122050
Source: PubMed

ABSTRACT Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer, and some are differentially expressed under light and nutrient stress. Furthermore, genome fragments directly recovered from ocean ecosystems indicate that these islands are variable among cooccurring Prochlorococcus cells. Genomic islands in this free-living photoautotroph share features with pathogenicity islands of parasitic bacteria, suggesting a general mechanism for niche differentiation in microbial species.

Download full-text


Available from: Matthew B Sullivan, Jun 16, 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The high light-inducible polypeptides (HLIPs) are critical for survival under high light (HL) conditions in Synechocystis PCC 6803. In this article, we determined the localization of all four HLIPs in thylakoid protein complexes and examined effects of hli gene deletion on the photosynthetic protein complexes. The HliA and HliB proteins were found to be associated with trimeric photosystem I (PSI) complexes and the Slr1128 protein, whereas HliC was associated with PsaL and TMP14. The HliD was associated with partially dissociated PSI complexes. The PSI activities of the hli mutants were 3- to 4-fold lower than that of the wild type. The hli single mutants lost more than 30% of the PSI trimers after they were incubated in intermediate HL for 12 h. The reduction of PSI trimers were further augmented in these cells by the increase of light intensity. The quadruple hli deletion mutant contained less than one-half of PSI trimers following 12-h incubation in intermediate HL. It lost essentially all of the PSI trimers upon exposure to HL for 12 h. Furthermore, a mutant lacking both PSI trimers and Slr1128 showed growth defects similar to that of the quadruple hli deletion mutant under different light conditions. These results suggest that the HLIPs stabilize PSI trimers, interact with Slr1128, and protect cells under HL conditions.
    Plant physiology 08/2008; 147(3):1239-50. DOI:10.1104/pp.108.121087 · 7.39 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Microarrays are useful tools for detecting and quantifying specific functional and phylogenetic genes in natural microbial communities. In order to track uncultivated microbial genotypes and their close relatives in an environmental context, we designed and implemented a 'genome-proxy' microarray that targets microbial genome fragments recovered directly from the environment. Fragments consisted of sequenced clones from large-insert genomic libraries from microbial communities in Monterey Bay, the Hawaii Ocean Time-series station ALOHA, and Antarctic coastal waters. In a prototype array, we designed probe sets to 13 of the sequenced genome fragments and to genomic regions of the cultivated cyanobacterium Prochlorococcus MED4. Each probe set consisted of multiple 70-mers, each targeting an individual open reading frame, and distributed along each approximately 40-160 kbp contiguous genomic region. The targeted organisms or clones, and close relatives, were hybridized to the array both as pure DNA mixtures and as additions of cells to a background of coastal seawater. This prototype array correctly identified the presence or absence of the target organisms and their relatives in laboratory mixes, with negligible cross-hybridization to organisms having <or= approximately 75% genomic identity. In addition, the array correctly identified target cells added to a background of environmental DNA, with a limit of detection of approximately 0.1% of the community, corresponding to approximately 10(3) cells ml(-1) in these samples. Signal correlated to cell concentration with an R(2) of 1.0 across six orders of magnitude. In addition, the array could track a related strain (at 86% genomic identity to that targeted) with a linearity of R(2) = 0.9999 and a limit of detection of approximately 1% of the community. Closely related genotypes were distinguishable by differing hybridization patterns across each probe set. This array's multiple-probe, 'genome-proxy' approach and consequent ability to track both target genotypes and their close relatives is important for the array's environmental application given the recent discoveries of considerable intrapopulation diversity within marine microbial communities.
    Environmental Microbiology 02/2008; 10(2):506-21. DOI:10.1111/j.1462-2920.2007.01471.x · 6.24 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Genome reduction has been considered the hallmark of endosymbiotic bacteria, such as endocellular mutualists or obligatory pathogens until it was found exactly the same in several free-living bacteria. In endosymbiotic bacteria genome reduction is mainly attributed to degenerative processes due to small population size. These cannot affect the free-living bacteria with reduced genomes because they are known to have very large population sizes. It has been proposed that selection for simplification drove genome reduction in these free-living bacteria. For at least one of them (Prochlorococcus), genome reduction is associated with accelerated evolution and we suggest an alternative hypothesis based on increase in mutation rate as the primary cause of genome reduction in free-living bacteria.
    Genetica 12/2007; 134(2):205-10. DOI:10.1007/s10709-007-9226-6 · 1.75 Impact Factor