Related Experiment Video
Updated: Mar 21, 2026
12:33
Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing
Published on: July 28, 2017
13.5K
Codon Adaptation of Plastid Genes.
Haruo Suzuki1, Brian R Morton2
1Graduate School of Science and Engineering, Yamaguchi University, Yamaguchi, Japan.
Plos One
|May 20, 2016
Summary
Codon adaptation, a bias in gene translation, is widespread across diverse plastid genomes. Selection favors specific "adaptive codons" due to shared ancestry, with varying strength across lineages.
Area of Science:
- Genomics
- Molecular Biology
- Evolutionary Biology
Background:
- Codon adaptation, or codon usage bias, enhances gene translation efficiency under selective pressure.
- Previous studies indicated codon adaptation in a few highly expressed plastid genes.
- This research expands the analysis to all fully sequenced plastid genomes.
Purpose of the Study:
- To investigate codon usage bias across a comprehensive range of plastid genomes.
- To identify the prevalence and characteristics of codon adaptation in plastids.
- To compare codon adaptation patterns across different evolutionary lineages.
Main Methods:
- Analysis of codon usage bias in fully sequenced plastid genomes from diverse taxa.
- Identification of 'adaptive codons' favored by selection.
- Estimation of the relative strength of selection across various lineages.
Main Results:
- Codon adaptation is prevalent in most plastid genomes, with exceptions in species lacking photosynthesis.
- Selection consistently favors the same set of adaptive codons across taxa, suggesting a common origin.
- Selection strength varies, being strong in Stramenopiles and Chlorophyta, but weaker in Rhodophyta, Euglenozoa, and Embryophyta.
Conclusions:
- Codon adaptation is a widespread phenomenon in plastids, mirroring patterns seen in eubacterial genomes.
- The consistent use of adaptive codons points to shared ancestry from the initial endosymbiont.
- Understanding codon adaptation is crucial for comprehending gene expression and evolution in plastids.
Related Concept Videos
02:19Export of Mitochondrial and Chloroplast Genes
4.4K
A eukaryotic cell can have up to three different types of genetic systems: nuclear, mitochondrial, and chloroplast. During evolution, organelles have exported many genes to the nucleus; this transfer is still ongoing in some plant species. Approximately 18% of the Arabidopsis thaliana nuclear genome is thought to be derived from the chloroplast’s cyanobacterial ancestor, and around 75% of the yeast genome derived from the mitochondria’s bacterial ancestor. This export has occurred...
4.4K
02:16Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
17.4K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
17.4K
01:18Protein Transport to the Inner Chloroplast Membrane
2.5K
Proteins targeted to the inner chloroplast membrane, or plastid proteins, are transported by two general pathways: the stop-transfer and the re-insertion or post-import pathways. Most plastid proteins carry N-terminal transit sequences and internal import sequences targeting it to the specific chloroplast subcompartment. Proteins targeted by the stop-transfer pathway have internal hydrophobic sequences that inhibit their translocation into the stroma. As a result, these precursors are arrested...
2.5K
02:05Gene Evolution - Fast or Slow?
8.3K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
8.3K
01:11Protein Transport to the Outer Chloroplast Membrane
2.5K
Chloroplast outer membrane proteins encoded by the nucleus are synthesized in the cytosol. Soon after synthesis, they bind cytosolic factors such as 14-3-3 protein and the Hsp70 chaperones that keep these precursors in an unfolded state until their translocation.
Two models describe the mechanism of precursor recognition and entry across the outer membrane through the TOC complex. Model 1 suggests the newly synthesized precursor binds to the TOC receptor 159 and forms a complex.
Two models describe the mechanism of precursor recognition and entry across the outer membrane through the TOC complex. Model 1 suggests the newly synthesized precursor binds to the TOC receptor 159 and forms a complex.
2.5K
01:28Plasmids
3.8K
Plasmids are extrachromosomal DNA molecules found in bacteria, archaea, and some eukaryotic microbes like yeast. These small, circular DNA structures typically contain fewer than 30 genes, although some may exist linearly. Plasmids vary in their number within a cell, known as copy number. Single-copy plasmids are present in one copy per cell and multi-copy plasmids are present in multiple copies, reaching over 100 copies per cell.Plasmids usually replicate independently of the chromosomal DNA...
3.8K