Evidence for the adaptive evolution of the carbon fixation gene<i>rbcL</i>during diversification in temperature tolerance of a clade of hot spring cyanobacteria

Miller, Scott R.

doi:10.1046/j.1365-294x.2003.01831.x

Cited by 21 publications

(18 citation statements)

References 47 publications

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“…For example, adaptations to temperature (Miller and Castenholz, 2000;Allewalt et al, 2006) may be based on adaptive nucleotide substitutions (Miller, 2003;Ward et al, 2011a). The metagenomic diversity with respect to the Roseiflexus sp.…”

Section: Differences Between Metagenomes and Isolate Genomesmentioning

confidence: 99%

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

et al. 2011

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Phototrophic microbial mat communities from 60 1C and 65 1C regions in the effluent channels of Mushroom and Octopus Springs (Yellowstone National Park, WY, USA) were investigated by shotgun metagenomic sequencing. Analyses of assembled metagenomic sequences resolved six dominant chlorophototrophic populations and permitted the discovery and characterization of undescribed but predominant community members and their physiological potential. Linkage of phylogenetic marker genes and functional genes showed novel chlorophototrophic bacteria belonging to uncharacterized lineages within the order Chlorobiales and within the Kingdom Chloroflexi. The latter is the first chlorophototrophic member of Kingdom Chloroflexi that lies outside the monophyletic group of chlorophototrophs of the Order Chloroflexales. Direct comparison of unassembled metagenomic sequences to genomes of representative isolates showed extensive genetic diversity, genomic rearrangements and novel physiological potential in native populations as compared with genomic references. Synechococcus spp. metagenomic sequences showed a high degree of synteny with the reference genomes of Synechococcus spp. strains A and B 0 , but synteny declined with decreasing sequence relatedness to these references. There was evidence of horizontal gene transfer among native populations, but the frequency of these events was inversely proportional to phylogenetic relatedness.

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Section: Differences Between Metagenomes and Isolate Genomesmentioning

confidence: 99%

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

et al. 2011

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“…The highly conservative nature of rbcL is probably the reason for the lack of enthusiasm for the evolutionary analysis of this gene, and in particular for the study of putative positive selection acting on rbcL . The only exception to this trend was the analysis of the rbcL evolution in the thermotolerant cyanobacteria genus Synechococcus , which has shown an increase in the number of hydrophobic residues in the rbcL s of more thermotolerant strains – a pattern observed for many thermostable proteins [13]. However, the dataset of eight sequences used in Synechococcus study could be too small to detect positive selection using likelihood molecular phylogenetic analysis [14].…”

Section: Introductionmentioning

confidence: 99%

Widespread positive selection in the photosynthetic Rubisco enzyme

2007

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Background: Rubisco enzyme catalyzes the first step in net photosynthetic CO 2 assimilation and photorespiratory carbon oxidation and is responsible for almost all carbon fixation on Earth. The large subunit of Rubisco is encoded by the chloroplast rbcL gene, which is widely used for reconstruction of plant phylogenies due to its conservative nature. Plant systematicists have mainly used rbcL paying little attention to its function, and the question whether it evolves under Darwinian selection has received little attention. The purpose of our study was to evaluate how common is positive selection in Rubisco among the phototrophs and where in the Rubisco structure does positive selection occur.

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“…The amino acid replacements in RbcL at the interface of subunits are correlated with the loss and gain of pyrenoids in the unicellular green alga lineage [19]. In addition, positive Darwinian selection of rbcL has been detected in cyanobacteria [20] and various taxonomic groups of land plants [21]–[23].…”

Section: Introductionmentioning

confidence: 99%

Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton

et al. 2009

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BackgroundHeterophyllous aquatic plants show marked phenotypic plasticity. They adapt to environmental changes by producing different leaf types: submerged, floating and terrestrial leaves. By contrast, homophyllous plants produce only submerged leaves and grow entirely underwater. Heterophylly and submerged homophylly evolved under selective pressure modifying the species-specific optima for photosynthesis, but little is known about the evolutionary outcome of habit. Recent evolutionary analyses suggested that rbcL, a chloroplast gene that encodes a catalytic subunit of RuBisCO, evolves under positive selection in most land plant lineages. To examine the adaptive evolutionary process linked to heterophylly or homophylly, we analyzed positive selection in the rbcL sequences of ecologically diverse aquatic plants, Japanese Potamogeton.Principal FindingsPhylogenetic and maximum likelihood analyses of codon substitution models indicated that Potamogeton rbcL has evolved under positive Darwinian selection. The positive selection has operated specifically in heterophyllous lineages but not in homophyllous ones in the branch-site models. This suggests that the selective pressure on this chloroplast gene was higher for heterophyllous lineages than for homophyllous lineages. The replacement of 12 amino acids occurred at structurally important sites in the quaternary structure of RbcL, two of which (residue 225 and 281) were identified as potentially under positive selection.Conclusions/SignificanceOur analysis did not show an exact relationship between the amino acid replacements and heterophylly or homophylly but revealed that lineage-specific positive selection acted on the Potamogeton rbcL. The contrasting ecological conditions between heterophyllous and homophyllous plants have imposed different selective pressures on the photosynthetic system. The increased amino acid replacement in RbcL may reflect the continuous fine-tuning of RuBisCO under varying ecological conditions.

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Evidence for the adaptive evolution of the carbon fixation generbcLduring diversification in temperature tolerance of a clade of hot spring cyanobacteria

Cited by 21 publications

References 47 publications

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

Community ecology of hot spring cyanobacterial mats: predominant populations and their functional potential

Widespread positive selection in the photosynthetic Rubisco enzyme

Molecular Adaptation of rbcL in the Heterophyllous Aquatic Plant Potamogeton

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