Dataset Information

GC3 biology in corn, rice, sorghum and other grasses.

ABSTRACT: BACKGROUND: The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates but not in all plants, or in invertebrates or cold-blooded vertebrates. RESULTS: Here we demonstrate that in certain organisms the amount of GC at the wobble position (GC3) can be used to distinguish two classes of genes. We highlight the following features of genes with high GC3 content: they (1) provide more targets for methylation, (2) exhibit more variable expression, (3) more frequently possess upstream TATA boxes, (4) are predominant in certain classes of genes (e.g., stress responsive genes) and (5) have a GC3 content that increases from 5'to 3'. These observations led us to formulate a hypothesis to explain GC3 bimodality in grasses. CONCLUSIONS: Our findings suggest that high levels of GC3 typify a class of genes whose expression is regulated through DNA methylation or are a legacy of accelerated evolution through gene conversion. We discuss the three most probable explanations for GC3 bimodality: biased gene conversion, transcriptional and translational advantage and gene methylation.

SUBMITTER: Tatarinova TV

PROVIDER: S-EPMC2895627 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

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GC3 biology in corn, rice, sorghum and other grasses.

Tatarinova Tatiana V TV Alexandrov Nickolai N NN Bouck John B JB Feldmann Kenneth A KA

BMC genomics 20100516

<h4>Background</h4>The third, or wobble, position in a codon provides a high degree of possible degeneracy and is an elegant fault-tolerance mechanism. Nucleotide biases between organisms at the wobble position have been documented and correlated with the abundances of the complementary tRNAs. We and others have noticed a bias for cytosine and guanine at the third position in a subset of transcripts within a single organism. The bias is present in some plant species and warm-blooded vertebrates ...[more]

PMID: 20470436

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Project description:Invasive plant species often dominate native species in competition, augmenting other potential advantages such as release from natural enemies. Resource pre-emption may be a particularly important mechanism for establishing dominance over competitors of the same functional type. We hypothesized that competitive success of an exotic grass against native grasses is mediated by establishing an early size advantage. We tested this prediction among four perennial C4 warm-season grasses: the exotic weed Johnsongrass (Sorghum halepense), big bluestem (Andropogon gerardii), little bluestem (Schizachyrium scoparius) and switchgrass (Panicum virgatum). We predicted that a) the competitive effect of Johnsongrass on target species would be proportional to their initial biomass difference, b) competitive effect and response would be negatively correlated and c) soil fertility would have little effect on competitive relationships. In a greenhouse, plants of the four species were grown from seed either alone or with one Johnsongrass neighbor at two fertilizer levels and periodically harvested. The first two hypotheses were supported: The seedling biomass of single plants at first harvest (50 days after seeding) ranked the same way as the competitive effect of Johnsongrass on target species: Johnsongrass < big bluestem < little bluestem/switchgrass, while Johnsongrass responded more strongly to competition from Johnsongrass than from native species. At final harvest, native plants growing with Johnsongrass attained between 2-5% of their single-plant non-root biomass, while Johnsongrass growing with native species attained 89% of single-plant non-root biomass. Fertilization enhanced Johnsongrass' competitive effects on native species, but added little to the already severe competitive suppression. Accelerated early growth of Johnsongrass seedlings relative to native seedlings appeared to enable subsequent resource pre-emption. Size-asymmetric competition and resource-pre-emption may be a critical mechanism by which exotic invasive species displace functionally similar native species and alter the functional dynamics of native communities.

Dataset Information

GC3 biology in corn, rice, sorghum and other grasses.

Publications

GC3 biology in corn, rice, sorghum and other grasses.

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