Codon bias in Escherichia coli: the influence of codon context on mutation and selection

Berg, Otto G.; Silva, Pedro J. N.

doi:10.1093/nar/25.7.1397

Cited by 73 publications

(51 citation statements)

References 41 publications

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“…The processivity errors for the set of all E. coli proteins (27) were calculated by using the k cat ͞K m values for the RFs in Tables 1 and 2, previously reported RF1 and RF2 concentrations (15), and tRNA isoacceptor levels reported by Dong et al (28). Assuming that all ternary complexes have the same k cat ͞K m value (2.2⅐10 7 M Ϫ1 ⅐s Ϫ1 ) for their cognate interactions with the ribosome (29), the expected frequency of false stops in E. coli proteins is approximately proportional to sequence length, reaching about 20% for proteins of 1,500 aa.…”

Section: Discussionmentioning

confidence: 99%

The accuracy of codon recognition by polypeptide release factors

Freistroffer

Kwiatkowski

Buckingham

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

152

150

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The precision with which individual termination codons in mRNA are recognized by protein release factors (RFs) has been measured and compared with the decoding of sense codons by tRNA. An Escherichia coli system for protein synthesis in vitro with purified components was used to study the accuracy of termination by RF1 and RF2 in the presence or absence of RF3. The efficiency of factor-dependent termination at all sense codons differing from any of the three stop codons by a single mutation was measured and compared with the efficiency of termination at the three stop codons. RF1 and RF2 discriminate against sense codons related to stop codons by between 3 and more than 6 orders of magnitude. This high level of accuracy is obtained without energy-driven error correction (proofreading), in contrast to codon-dependent aminoacyl-tRNA recognition by ribosomes. Two codons, UAU and UGG, stand out as hotspots for RF-dependent premature termination.protein synthesis ͉ translational processivity ͉ premature termination S ixty-one of the 64 base triplets in the genetic code are sense codons, which are translated in bacteria to the 20 standard amino acids in proteins by about 50 aminoacyl-tRNAs. The remaining three codons usually signal termination of translation and the release of completed proteins from ribosomes by release factors RF1 and RF2. Efficient translation requires both rapid binding to their respective codons of cognate aminoacyl-tRNAs, in ternary complex with elongation factor EF-Tu and GTP, and fast termination of protein synthesis at stop signals by RFs. In addition to fast signal processing, codon translation must attain a high level of accuracy so that nonacceptable amino acid replacements in nascent proteins do not impair cell growth and viability. Similarly, misrecognition by RFs of sense codons as stop signals leads to truncated proteins, an energetically costly event, the frequency of which also must be contained.Pauling was among the first to reflect on the errors that must occur during protein synthesis because of the limited maximum differences in interaction standard free energies between different pairs of amino acids, and he concluded that amino acid substitutions theoretically should occur at frequencies in the percent range (1). Though later shown to be overly pessimistic (2), these predictions led to theoretical studies showing that enzymatic selection can, under certain conditions, be more accurate than the instrinsic selectivity of a single step.The accuracy (A) of simple enzyme selection schemes, defined as the probability of correct product formation divided by the probability of an error at equal concentrations of cognate and noncognate substrates, is limited by the standard free energy difference between the transition state leading to product formation and ground state for cognate (⌬G c ) and noncognate (⌬G nc ) substrates by the inequality. The precision of codon translation depends on differences in H-bond energies between cognate and noncognate tRNAcodon interactions, though other i...

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Section: Discussionmentioning

confidence: 99%

The accuracy of codon recognition by polypeptide release factors

Freistroffer

Kwiatkowski

Buckingham

et al. 2000

Proc. Natl. Acad. Sci. U.S.A.

152

150

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“…On the other hand, for processivity errors, i.e. drop-off, false stops or frameshifts, the cost will be proportional to the length of protein produced before the error; in this case, there will be a negative gradient in the usage of error-prone sequences (5). Clearly, gradients in codon usage will also lead to an apparent dependence on gene length for the average usage.…”

Section: Methodsmentioning

confidence: 99%

“…TTT|T or A|AAG, where slippage of the ribosome could occur forwards or backwards respectively. In the case of Phe, the bias and the negative gradient of has been interpreted as an avoidance of frameshift sensitive sites in a forward direction (5). Similarly, may show an avoidance of backward frameshifting.…”

Section: Potential Frameshift Sitesmentioning

confidence: 99%

“…This suggests that there is a positive selection on codons that are translated more efficiently, either faster or more accurately. The strength of the codon bias to some extent also depends on gene length (2) and on the context of bases surrounding each codon (3)(4)(5). Average codon bias also varies within each gene, increasing in the first 100 codons (6,7), leveling off and remaining constant until it again declines in the last 20 codons (8).…”

Section: Introductionmentioning

confidence: 99%

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Gradients in nucleotide and codon usage along Escherichia coli genes

Hooper

Berg

2000

Nucleic Acids Research

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The usage of codons and nucleotide combinations varies along genes and systematic variation causes gradients in usage. We have studied such gradients of nucleotides and nucleotide combinations and their immediate context in Escherichia coli. To distinguish mutational and selectional effects, the genes were subdivided into three groups with different codon usage bias and the gradients of nucleotide usage were studied in each group. Some combinations that can be associated with a propensity for processivity errors show strong negative gradients that become weaker in genes with low codon bias, consistent with a selection on translational efficiency. One of the strongest gradients is for third position G, which shows a pervasive positive gradient in usage in most contexts of surrounding bases.

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“…Phe, Pro). Differences in codon bias and nucleotide content among the urease genes of WH7805 could reflect differences in their expression levels (Berg & Silva, 1997;Wilbanks & Glazer, 1993), although there is no direct evidence of the relative expression levels of the urease genes in WH7805. Differences in base composition might also reflect genome-scale influences driven by the opposite orientation of ureDABC versus ureEFG (Freeman et at., 1998).…”

Section: Partial Purification Of the Wh7805 Urease Enzymementioning

confidence: 99%

The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amiohydrolase, EC 3.5.1.5) to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme

Collier¹,

Brahamsha²,

Palenik³

1999

Microbiology

119

101

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Cyanobacteria assigned to the genus Synechococcus are an important component of oligotrophic marine ecosystems, where their growth may be constrained by IOW availability of fixed nitrogen. Urea appears to be a major nitrogen resource in the sea, but little molecular information exists about its utilization by marine organisms, including Synechococcus. Oligonucleotide primers were used to amplify a conserved fragment of the urease (urea amidohydrolase, EC 3.5.1.5) coding region from cyanobacteria. A 5 7 kbp region of the genome of the unicellular marine cyanobacterium Synechococcus sp. strain WH7805 was then cloned, and genes encoding three urease structural subunits and four urease accessory proteins were sequenced and identified by homology. The WH7805 urease had a predicted subunit composition typical of bacterial ureases, but the organization of the WH7805 urease genes was unique. Biochemical characteristics of the WH7805 urease enzyme were consistent with the predictions of the sequence data. Physiological data and sequence analysis both suggested that the urease operon may be nitrogenregulated by the ntcA system in WH7805. Inactivation of the large subunit of urease, ureC, prevented WH7805 and Synechococcus WH8102 from growing on urea, demonstrating that the urease genes cloned are essential to the ability of these cyanobacteria to utilize urea as a nitrogen source.Keywords : nitrogen assimilation, cyanobacterium, ammonium, nitrate, phytoplankton INTRODUCTIONThe unicellular cyanobacteria assigned to the genus Synechococcus (Waterbury & Rippka, 1989) are an important component of the phytoplankton in many marine and freshwater planktonic ecosystems (Fogg, 1987;Waterbury et al., 1986). They contribute most significantly to total primary production in their most oligotrophic habitats (Chisholm, 1992;Fogg, 1987 ; . The GenBank accession numbers for the sequences reported in this paper are AF065139 and AF056189. Joint, 1986), such as those large oceanic regions where nitrogen availability is thought to limit primary productivity. The nitrogen utilized by the cyanobacteria and other primary producers in these regions appears to derive largely from the planktonic food-web-driven recycling of nitrogen from biomass into ammonium and urea (Dugdale 8c Goering, 1967;Fogg, 1987;Hayward, 1991 ;Price & Harrison, 1988). Urea, which is generally present in marine waters at levels of 0-1-1 pM (Antia et al., 1991), is formed by bacterial degradation of nucleic and amino acids and excreted by many animals as a waste product (McCarthy, 1980;Walsh, 1997). Urea is also the single dominant component of the diverse group of organic nitrogenous compounds known collectively as dissolved organic nitrogen that is present in the oligotrophic oceans at a total concentration of about 5 pM (Antia et al., 1991). For all phytoplankton that have been examined except the Chlorophytes, urease is the enzyme responsible for decomposing urea (Leftley & Syrett, 1973). Urease (urea amidohydrolase, EC 3.5.1.5) is a nickel-requiring metalloenzyme ...

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Codon bias in Escherichia coli: the influence of codon context on mutation and selection

Cited by 73 publications

References 41 publications

The accuracy of codon recognition by polypeptide release factors

The accuracy of codon recognition by polypeptide release factors

Gradients in nucleotide and codon usage along Escherichia coli genes

The marine cyanobacterium Synechococcus sp. WH7805 requires urease (urea amiohydrolase, EC 3.5.1.5) to utilize urea as a nitrogen source: molecular-genetic and biochemical analysis of the enzyme

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