A Role for Initiation Codon Context in Chloroplast Translation

Esposito, Donna; Hicks, Amanda J.; Stern, David B.

doi:10.1105/tpc.010236

Cited by 14 publications

(7 citation statements)

References 54 publications

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“…But if only a few codon pairs (much less than 36) are used to code R‐S sequences in the protein, it is often inferred as a biased usage of codon contexts for the paired amino acids. This phenomenon is generally referred to as ‘codon context bias' (Bossi & Ruth, ; Murgola, Pagel & Hijazi, ; Berg & Silva, ; Esposito, Hicks & Stern, ; Moura et al , ). Such bias in a gene may influence mRNA decoding fidelity and affect overall translational selection (Bossi & Ruth, ; Buckingham, ; Irwin, Heck & Hatfield, ; Moura et al , ).…”

Section: Principles and Methods Of Quantifying Codon Usage Biasmentioning

confidence: 99%

Codon usage bias: causative factors, quantification methods and genome‐wide patterns: with emphasis on insect genomes

2012

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Codon usage bias refers to the phenomenon where specific codons are used more often than other synonymous codons during translation of genes, the extent of which varies within and among species. Molecular evolutionary investigations suggest that codon bias is manifested as a result of balance between mutational and translational selection of such genes and that this phenomenon is widespread across species and may contribute to genome evolution in a significant manner. With the advent of whole-genome sequencing of numerous species, both prokaryotes and eukaryotes, genome-wide patterns of codon bias are emerging in different organisms. Various factors such as expression level, GC content, recombination rates, RNA stability, codon position, gene length and others (including environmental stress and population size) can influence codon usage bias within and among species. Moreover, there has been a continuous quest towards developing new concepts and tools to measure the extent of codon usage bias of genes. In this review, we outline the fundamental concepts of evolution of the genetic code, discuss various factors that may influence biased usage of synonymous codons and then outline different principles and methods of measurement of codon usage bias. Finally, we discuss selected studies performed using whole-genome sequences of different insect species to show how codon bias patterns vary within and among genomes. We conclude with generalized remarks on specific emerging aspects of codon bias studies and highlight the recent explosion of genome-sequencing efforts on arthropods (such as twelve Drosophila species, species of ants, honeybee, Nasonia and Anopheles mosquitoes as well as the recent launch of a genome-sequencing project involving 5000 insects and other arthropods) that may help us to understand better the evolution of codon bias and its biological significance.

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Section: Principles and Methods Of Quantifying Codon Usage Biasmentioning

confidence: 99%

Codon usage bias: causative factors, quantification methods and genome‐wide patterns: with emphasis on insect genomes

2012

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“…Here, as throughout the manuscript, we show WT bases in normal type and mutated bases in bold. As shown in Figure 1C, for petA , the WT sequence of the initiation codon ( −1 U‐AUG) was changed to AU U to reduce the translation rate, a context allowing easy analysis of the importance of the −1 residue (Chen et al ., 1995; Esposito et al ., 2001). Then, the WT −1 uridine was changed to A ( A ‐AU U ) or C ( C ‐AU U ).…”

Section: Resultsmentioning

confidence: 99%

“…To create plasmids containing an ectopic copy of trnfM , a 450 bp Hin cII fragment from pfmetsk‐ containing either trnfM fM‐CAUAsspI, fM‐CAUUsspI or fM‐CAUGsspI was inserted into the Stu I site of the plasmid pQMAD, which contains the aadA gene (Goldschmidt‐Clermont, 1991) inserted in the Eco RV site between petA and petD . pQMAD had been altered to contain one of several mutations at the initiation region of petA (Esposito et al ., 2001).…”

Section: Methodsmentioning

confidence: 99%

“…This result raised the possibility that one or more of the −3 to −1 positions relative to the initiation codon had a functional importance. It was subsequently shown that mutation of the −1 U residue severely reduced translation when combined with an AUU initiation codon, or at elevated temperature (35°C) in the context of an AUG initiation codon (Esposito et al ., 2001). These observations, taken together with a 75% conservation of a uridine at position −1 in the chloroplast mRNAs of C.reinhardtii (the genome sequence is reported in Maul et al ., 2002), led us to consider whether the E.coli extended interaction model could also be proposed for plastid translation.…”

Section: Introductionmentioning

confidence: 99%

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In vivo evidence for the prokaryotic model of extended codon-anticodon interaction in translation initiation

et al. 2003

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contributed equally to this work Initiation codon context is an important determinant of translation initiation rates in both prokaryotes and eukaryotes. Such sequences include the Shine± Dalgarno ribosome-binding site, as well as other motifs surrounding the initiation codon. One proposed interaction is between the base immediately preceding the initiation codon (±1 position) and the nucleotide 3¢ to the tRNAf Met anticodon, at position 37. Adenine is conserved at position 37, and a uridine at ±1 has been shown in vitro to favor initiation. We have tested this model in vivo, by manipulating the chloroplast of the green alga Chlamydomonas reinhardtii, where the translational machinery is prokaryotic in nature. We show that translational defects imparted by mutations at the petA ±1 position can be suppressed by compensatory mutations at position 37 of an ectopically expressed tRNA fMet . The mutant tRNAs are fully aminoacylated and do not interfere with the translation of other proteins. Although this extended base pairing is not an absolute requirement for initiation, it may convey added speci®city to transcripts carrying non-standard initiation codons, and/or preserve translational ®delity under certain stress conditions.

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“…It engages in complementary base pairing with the 3 end of the 16S ribosomal RNA and thereby mediates translation initiation. It is important to know that, as in bacteria, the spacing between the Shine-Dalgarno sequence and the initiation codon is absolutely critical to the efficiency of translation initiation in plastids (36,47,59). The 3 UTR confers transcript stability, typically by folding into a stable stem-loop-type RNA secondary structure (165).…”

Section: Promoters and Untranslated Regionsmentioning

confidence: 99%

Engineering Plastid Genomes: Methods, Tools, and Applications in Basic Research and Biotechnology

Bock

2015

Annu. Rev. Plant Biol.

291

207

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The small bacterial-type genome of the plastid (chloroplast) can be engineered by genetic transformation, generating cells and plants with transgenic plastid genomes, also referred to as transplastomic plants. The transformation process relies on homologous recombination, thereby facilitating the site-specific alteration of endogenous plastid genes as well as the precisely targeted insertion of foreign genes into the plastid DNA. The technology has been used extensively to analyze chloroplast gene functions and study plastid gene expression at all levels in vivo. Over the years, a large toolbox has been assembled that is now nearly comparable to the techniques available for plant nuclear transformation and that has enabled new applications of transplastomic technology in basic and applied research. This review describes the state of the art in engineering the plastid genomes of algae and land plants (Embryophyta). It provides an overview of the existing tools for plastid genome engineering, discusses current technological limitations, and highlights selected applications that demonstrate the immense potential of chloroplast transformation in several key areas of plant biotechnology.

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A Role for Initiation Codon Context in Chloroplast Translation

Cited by 14 publications

References 54 publications

Codon usage bias: causative factors, quantification methods and genome‐wide patterns: with emphasis on insect genomes

Codon usage bias: causative factors, quantification methods and genome‐wide patterns: with emphasis on insect genomes

In vivo evidence for the prokaryotic model of extended codon-anticodon interaction in translation initiation

Engineering Plastid Genomes: Methods, Tools, and Applications in Basic Research and Biotechnology

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