Nomenclature for membrane-bound light-harvesting complexes of cyanobacteria

Chen, Min; Zhang, Yinan; Blankenship, Robert E.

doi:10.1007/s11120-007-9255-0

Cited by 30 publications

(13 citation statements)

References 46 publications

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“…Two major accessory light-harvesting and protection systems exist in cyanobacteria, PBPs (reviewed in ref. 37), and accessory chlorophyll-binding proteins (CBPs) (38)(39)(40). Like other ''alternative Chl'' cyanobacteria, A. marina does not construct the supramolecular PBP assemblies, the PBSs.…”

Section: Resultsmentioning

confidence: 99%

Niche adaptation and genome expansion in the chlorophyll d -producing cyanobacterium Acaryochloris marina

Swingley

Chen

Cheung³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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201

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Acaryochloris marina is a unique cyanobacterium that is able to produce chlorophyll d as its primary photosynthetic pigment and thus efficiently use far-red light for photosynthesis. Acaryochloris species have been isolated from marine environments in association with other oxygenic phototrophs, which may have driven the niche-filling introduction of chlorophyll d. To investigate these unique adaptations, we have sequenced the complete genome of A. marina. The DNA content of A. marina is composed of 8.3 million base pairs, which is among the largest bacterial genomes sequenced thus far. This large array of genomic data is distributed into nine single-copy plasmids that code for >25% of the putative ORFs. Heavy duplication of genes related to DNA repair and recombination (primarily recA) and transposable elements could account for genetic mobility and genome expansion. We discuss points of interest for the biosynthesis of the unusual pigments chlorophyll d and ␣-carotene and genes responsible for previously studied phycobilin aggregates. Our analysis also reveals that A. marina carries a unique complement of genes for these phycobiliproteins in relation to those coding for antenna proteins related to those in Prochlorococcus species. The global replacement of major photosynthetic pigments appears to have incurred only minimal specializations in reaction center proteins to accommodate these alternate pigments. These features clearly show that the genus Acaryochloris is a fitting candidate for understanding genome expansion, gene acquisition, ecological adaptation, and photosystem modification in the cyanobacteria.comparative microbial genomics ͉ photosynthesis ͉ oxygenic phototrophs ͉ evolution

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Section: Resultsmentioning

confidence: 99%

Niche adaptation and genome expansion in the chlorophyll d -producing cyanobacterium Acaryochloris marina

Swingley

Chen

Cheung³

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

201

184

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“…S6). Some of these proteins, such as CBPIV, have previously been annotated as PsbC homologs (25), because all CBP proteins are thought to have a common evolutionary origin with the psbC gene (24). Because of the vast enrichment of cyanobacterial protein sequences, the increase from two to six known CBPVI sequences augments phylogenetic resolution (bootstrap support of 85%), allowing us to more confidently assert that there is a separate and distinct CBPVI subfamily.…”

Section: Prochlorococcus Marinus Mit 9215mentioning

confidence: 99%

“…These proteins are analogous in function to eukaryotic LHCs. Because of the growing number of proteins and names, an overarching nomenclature has been proposed to name this protein family the chlorophyll binding proteins (CBPs), which are characterized by six transmembrane helices and the ability to bind chlorophyll (24).…”

Section: Prochlorococcus Marinus Mit 9215mentioning

confidence: 99%

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Shih

Latifi

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

744

883

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The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels. To explore the molecular basis of their different phenotypes and biochemical capabilities, we sequenced the genomes of 54 phylogenetically and phenotypically diverse cyanobacterial strains. Comparison of cyanobacterial genomes reveals the molecular basis for many aspects of cyanobacterial ecophysiological diversity, as well as the convergence of complex morphologies without the acquisition of novel proteins. This phylum-wide study highlights the benefits of diversity-driven genome sequencing, identifying more than 21,000 cyanobacterial proteins with no detectable similarity to known proteins, and foregrounds the diversity of lightharvesting proteins and gene clusters for secondary metabolite biosynthesis. Additionally, our results provide insight into the distribution of genes of cyanobacterial origin in eukaryotic nuclear genomes. Moreover, this study doubles both the amount and the phylogenetic diversity of cyanobacterial genome sequence data. Given the exponentially growing number of sequenced genomes, this diversity-driven study demonstrates the perspective gained by comparing disparate yet related genomes in a phylum-wide context and the insights that are gained from it.

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“…The LH system in Prochlorococcus involves membrane-bound, chlorophyll-binding proteins (Pcbs) encoded by the pcb genes [14]–[18]. Some marine Synechococcus contain pcb -like genes that are induced under conditions of iron limitation and can be identified as a phylogenetically distinct group that includes the functionally characterized iron-stress-induced gene isiA ; this gene is sometimes referred to as pcbD or pcbC/isiA and here is called isiA -like [6], [19]–[21]. We can therefore define three functionally distinct types of LH genes in marine oxyphotobacteria: (1) the PBS genes of Synechococcus ; (2) the pcb genes of Prochlorococcus ; and (3) the iron-stress-induced genes ( isiA -like) present in some marine Synechococcus .…”

Section: Introductionmentioning

confidence: 99%

Biogeography of Photosynthetic Light-Harvesting Genes in Marine Phytoplankton

2009

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BackgroundPhotosynthetic light-harvesting proteins are the mechanism by which energy enters the marine ecosystem. The dominant prokaryotic photoautotrophs are the cyanobacterial genera Prochlorococcus and Synechococcus that are defined by two distinct light-harvesting systems, chlorophyll-bound protein complexes or phycobilin-bound protein complexes, respectively. Here, we use the Global Ocean Sampling (GOS) Project as a unique and powerful tool to analyze the environmental diversity of photosynthetic light-harvesting genes in relation to available metadata including geographical location and physical and chemical environmental parameters.MethodsAll light-harvesting gene fragments and their metadata were obtained from the GOS database, aligned using ClustalX and classified phylogenetically. Each sequence has a name indicative of its geographic location; subsequent biogeographical analysis was performed by correlating light-harvesting gene budgets for each GOS station with surface chlorophyll concentration.Conclusion/SignificanceUsing the GOS data, we have mapped the biogeography of light-harvesting genes in marine cyanobacteria on ocean-basin scales and show that an environmental gradient exists in which chlorophyll concentration is correlated to diversity of light-harvesting systems. Three functionally distinct types of light-harvesting genes are defined: (1) the phycobilisome (PBS) genes of Synechococcus; (2) the pcb genes of Prochlorococcus; and (3) the iron-stress-induced (isiA) genes present in some marine Synechococcus. At low chlorophyll concentrations, where nutrients are limited, the Pcb-type light-harvesting system shows greater genetic diversity; whereas at high chlorophyll concentrations, where nutrients are abundant, the PBS-type light-harvesting system shows higher genetic diversity. We interpret this as an environmental selection of specific photosynthetic strategy. Importantly, the unique light-harvesting system isiA is found in the iron-limited, high-nutrient low-chlorophyll region of the equatorial Pacific. This observation demonstrates the ecological importance of isiA genes in enabling marine Synechococcus to acclimate to iron limitation and suggests that the presence of this gene can be a natural biomarker for iron limitation in oceanic environments.

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Nomenclature for membrane-bound light-harvesting complexes of cyanobacteria

Cited by 30 publications

References 46 publications

Niche adaptation and genome expansion in the chlorophyll d -producing cyanobacterium Acaryochloris marina

Niche adaptation and genome expansion in the chlorophyll d -producing cyanobacterium Acaryochloris marina

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing

Biogeography of Photosynthetic Light-Harvesting Genes in Marine Phytoplankton

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