Biased Codon Usage: An Exploration of Its Role in Optimization of Translation

Boer, H. H.; Kastelein, Rob

doi:10.1016/b978-0-409-90027-9.50014-6

Cited by 90 publications

(73 citation statements)

References 143 publications

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“…All of these preferred codons except CCA (Pro) have a G or C in the wobble position, which may correspond to the relatively high G+C content (57%) of C. glutamicum (38). However, the results of the codon usage analysis suggest a highly biased codon usage in the three genes, and it is likely that the combined codon usage reflects the relative abundance of tRNA species (6,19).…”

Section: E--tsk-d----ea--e-rn Rfaqelaala Adngafvsdg Fgvvhraqts -Vydiamentioning

confidence: 48%

“…This is reflected by the high specific enzyme activities determined in cell extracts. In addition to the gap, pgk, and tpi genes, two more presumably highly expressed genes of C. glutamicum have been characterized:fda (57) related to the degree of codon bias (6,19,29), it was interesting to compare the combined codon usage of gap, pgk, tpi, fda, and gdh with that of C. glutamicum genes which code for enzymes involved in amino acid (threonine, lysine, isoleucine, phenylalanine, or tryptophan) biosynthesis and which I therefore consider to be moderately expressed. As shown in Table 3, the former group of genes is in fact significantly more highly biased than the latter.…”

Section: Discussionmentioning

confidence: 99%

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Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Eikmanns

1992

J Bacteriol

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To investigate a possible chromosomal clustering of glycolytic enzyme genes in Corynebacterium glutamicum, a 6.4-kb DNA 27,198). The amino acid sequences of the three enzymes show up to 62% (GAPDH), 48% (PGK), and 44% (TPI) identity in comparison with respective enzymes from other organisms. The gap, pgk, tpi, and ppc genes were cloned into the C. glutamicum-Escherichia coli shuttle vector pEKO and introduced into C. glutamicum. Relative to the wild type, the recombinant strains showed up to 20-fold-higher specific activities of the respective enzymes. On the basis of codon usage analysis of gap, pgk, tpi, and previously sequenced genes from C. glutamicum, a codon preference profile for this organism which differs significantly from those of E. coli and Bacillus subtilis is presented.

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Section: E--tsk-d----ea--e-rn Rfaqelaala Adngafvsdg Fgvvhraqts -Vydiamentioning

confidence: 48%

Section: Discussionmentioning

confidence: 99%

Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Eikmanns

1992

J Bacteriol

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“…Various di erent bacterial host cells, plasmids and growth conditions have been tested unsuccessfully for improvement of the expression level. Rare codon usage and unfavourable tRNA distribution could be reasons for the lack of high expression by this system [6]. Although the usage of rare codons may not account solely for low levels of expression it is evident that an mRNA with an unbalanced codon frequency will have di erent elongation rates for di erent regions of the sequence and di erent codons.…”

Section: Expression and Puri®cationmentioning

confidence: 99%

“…Although the usage of rare codons may not account solely for low levels of expression it is evident that an mRNA with an unbalanced codon frequency will have di erent elongation rates for di erent regions of the sequence and di erent codons. The likelihood that a particular tRNA binds to the ribosomal A site depends strictly on the distribution of all other tRNAs and any disturbance of this distribution will have an in¯uence on the speed of the elongation step [6]. The occurrence of a rare codon may stall the translation process long enough to terminate transcription prematurely.…”

Section: Expression and Puri®cationmentioning

confidence: 99%

Heterologous expression of human transketolase

Schenk

Duggleby

Nixon

1998

The International Journal of Biochemistry & Cell Biology

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Transketolase belongs to the family of thiamin diphosphate dependent enzymes. The aim of this study was to establish a bacterial expression system for human transketolase in order to investigate the functional characteristics of mammalian transketolases. The level of recombinant human enzyme expressed in Escherichia coli was modest. Puri®cation of recombinant transketolase and separation from the E. coli enzyme has been greatly simpli®ed by means of a non-cleavable hexa-histidine tag. The highest speci®c activity was 13.5 U/mg and the K m values were 0.27 20.02 and 0.51 20.05 mM for the substrates D-xylulose 5-phosphate and D-ribose 5-phosphate, respectively. Binding of cofactors to the apoenzyme showed the expected hysteresis. Without preincubation, the K m values for thiamin diphosphate and for Mg 2+ were, respectively, 4.120.8 and 2.5 20.4 mM, but after 1 h of preincubation these values were 85 216 nM and 0.74 20.23 mM. The kinetic constants are similar to those of the native enzyme puri®ed from human erythrocytes. Despite the modest expression level the reported system is well suited to a variety of functional studies. #

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“…First, all codons in the native hIL-7 sequence were changed to those favoring high level expression using E. coli codon bias (18). These changes do not alter the native IL-7 amino acid sequence, and this strategy has been shown to increase recombinant IL-2 production in E. coli (19).…”

Section: Design and Construction Of A Synthetic Rhil-7 Genementioning

confidence: 99%

Disulfide Bond Assignment in Human Interleukin-7 by Matrix-assisted Laser Desorption/Ionization Mass Spectroscopy and Site-directed Cysteine to Serine Mutational Analysis

Cosenza¹,

Sweeney²,

Murphy³

1997

Journal of Biological Chemistry

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Interleukin-7 (IL-7) is a proteinaceous biological response modifier that has a bioactive tertiary structure dependent on disulfide bond formation. Disulfide bond assignments in human (h)IL-7 are based upon the results of matrix-assisted laser desorption/ionization (MALDI) mass spectroscopy and Cys to Ser mutational analyses. A gene encoding the hIL-7 was synthesized incorporating Escherichia coli codon usage bias and was used to express biologically active protein as determined by stimulation of precursor B-cell proliferation. MALDI mass spectroscopic analysis of trypsin-digested hIL-7 was performed and compared with the anticipated results of a simulated tryptic digestion. Many of the anticipated hIL-7 tryptic fragments were detected including one with a molecular mass equivalent to the sum of two polypeptides linked through a disulfide bond respectively. In single disulfide bond-forming mutants of hIL-7, the ability to stimulate cell proliferation was abolished in the presence of 2 mM dithiothreitol. The results presented strongly suggest that only a single disulfide bond is required for hIL-7 to form a tertiary structure capable of stimulating precursor B-cell proliferation.

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Biased Codon Usage: An Exploration of Its Role in Optimization of Translation

Cited by 90 publications

References 143 publications

Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Identification, sequence analysis, and expression of a Corynebacterium glutamicum gene cluster encoding the three glycolytic enzymes glyceraldehyde-3-phosphate dehydrogenase, 3-phosphoglycerate kinase, and triosephosphate isomerase

Heterologous expression of human transketolase

Disulfide Bond Assignment in Human Interleukin-7 by Matrix-assisted Laser Desorption/Ionization Mass Spectroscopy and Site-directed Cysteine to Serine Mutational Analysis

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