Genetic diversity and its consequences for light adaptation in Prochlorococcus

When different cells thrive across diverse environments, their genetic differences can reveal what genes are essential to survival in a particular environment. Prochlorococcus, a cyanobacterium that dominates the open ocean, offers an opportunity to explore such differences. Its diversity is examined here, beginning with an overview and comparison of 12 fully sequenced Prochlorococcus genomes. The Prochlorococcus core genome, that set of genes shared by all cultured Prochlorococcus, appears to be well defined by the set shared by these isolates. The flexible genome, that set of genes found in some isolates but not shared by all Prochlorococcus, was found to be much larger and open-ended. Most laterally-acquired genes were found to be located in highly variable islands such as those described in previous studies of Prochlorococcus. Those lateral gene transfer events can also be placed on the Prochlorococcus phylogenetic tree: each Prochlorococcus isolate possesses a significant number of genes that even its closest sequenced cousin does not. A particular gene family may define a Prochlorococcus ecotype if those genes are possessed by all members of that ecotype, and if their presence gives that ecotype a selective advantage in some circumstance, thus contributing to the determination of its niche. One gene family is conspicuous for appearing in many copies per genome in one Prochlorococcus clade, referred to as eNATL. The sequenced strains belonging to this clade each possess over 40 copies of genes encoding high light inducible proteins (HLIPs), compared to only 9-24 in the other Prochlorococcus genomes. Other studies suggest these genes may be involved in resistance to sudden increases in light intensity, among other stresses. This becomes especially interesting as recent field studies also found that eNATL cells may survive changes in light intensity more easily than other lowlight adapted Prochlorococcus. Here, the effects of light shocks on an eNATL strain and on other Prochlorococcus strains are studied. eNATL cultures do recover from light shock conditions that are lethal to other low light-adapted Prochlorococcus. Measurements of bulk in vivo chlorophyll fluorescence, fluorescence per cell, and variable fluorescence, along with preliminary gene expression data, suggest that the early, rapid response of high light-adapted cells and of eNATL cells distinguish them from other low light-adapted cells, possibly explaining their subsequent survival. The possible role of HLIPs in this response is discussed. The discussion of HLIPs and eNATL is based on the complete sequences of only two eNATL genomes, both sampled from the same part of the ocean at the same time. That dataset is expanded by the inclusion of Global Ocean Survey environmental shotgun reads, from which are identified several thousand HLIP genes. Past work has shown that HLIPs are divided into two distinct clades: the core, freshwater cyanobacteria-like HLIPs and the flexible, phage-like, island-bound copies. That distinction is examined in the metagenomic data, demonstrating that the separate types are consistently found in distinct chromosomal neighborhoods.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Biology.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2011

Author dc:creator

• Kettler, Gregory C. (Gregory Carl)

Advisor dc:contributor.advisor

• Sallie W. Chisholm.

• Biology.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/68428

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/68428