Abstract：
:Two alternative hypotheses attribute different benefits to codon-anticodon adaptation. The first assumes that protein production is rate limited by both initiation and elongation and that codon-anticodon adaptation would result in higher elongation efficiency and more efficient and accurate protein production, especially for highly expressed genes. The second claims that protein production is rate limited only by initiation efficiency but that improved codon adaptation and, consequently, increased elongation efficiency have the benefit of increasing ribosomal availability for global translation. To test these hypotheses, a recent study engineered a synthetic library of 154 genes, all encoding the same protein but differing in degrees of codon adaptation, to quantify the effect of differential codon adaptation on protein production in Escherichia coli. The surprising conclusion that "codon bias did not correlate with gene expression" and that "translation initiation, not elongation, is rate-limiting for gene expression" contradicts the conclusion reached by many other empirical studies. In this paper, I resolve the contradiction by reanalyzing the data from the 154 sequences. I demonstrate that translation elongation accounts for about 17% of total variation in protein production and that the previous conclusion is due to the use of a codon adaptation index (CAI) that does not account for the mutation bias in characterizing codon adaptation. The effect of translation elongation becomes undetectable only when translation initiation is unrealistically slow. A new index of translation elongation ITE is formulated to facilitate studies on the efficiency and evolution of the translation machinery.
journal_name
Geneticsjournal_title
Geneticsauthors
Xia Xdoi
10.1534/genetics.114.172106subject
Has Abstractpub_date
2015-02-01 00:00:00pages
573-9issue
2eissn
0016-6731issn
1943-2631pii
genetics.114.172106journal_volume
199pub_type
杂志文章相关文献
GENETICS文献大全abstract：:Loss of heterozygosity (LOH) can be a driving force in the evolution of mitotic/somatic diploid cells, and cellular changes that increase the rate of LOH have been proposed to facilitate this process. In the yeast Saccharomyces cerevisiae, spontaneous LOH occurs by a number of mechanisms including chromosome loss and ...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.108.089250
更新日期：2008-07-01 00:00:00
abstract：:The X and Y chromosomes of Drosophila melanogaster each contain a cluster of several hundred ribosomal RNA genes (rDNA). A nontranscribed spacer region separates adjacent rRNA genes and contains tandem copies of 240 bp repeats that include the initiation site for RNA polymerase I transcription. We show here that Droso...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1990-06-01 00:00:00
abstract：:We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local ancestry of admixed i...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.113.160697
更新日期：2014-03-01 00:00:00
abstract：:Deficiencies encompassing part or all of the X heterochromatin of Drosophila melanogaster have been linked to three abnormalities in male meiosis and spermatogenesis: X-Y nondisjunction, skewed sperm recovery ratios favoring sperm with reduced chromatin content, and sterility in males carrying either a Y-autosome tran...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1987-07-01 00:00:00
abstract：:Two protocols are presented that allow the selection of mutations mapping to micronuclear chromosome 5 in Tetrahymena thermophilia. One protocol involves crossing mutagenized diploid cells directly to a strain nullisomic for chromosome 5 and screening the monosomic progeny for a mutant phenotype. The second protocol f...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1984-03-01 00:00:00
abstract：:The linkage disequilibrium pattern analysis is a method that allows one to detect present and past events of selection. We applied it to our data on the inversions of Drosophila mediopunctata and to published data of Drosophila subobscura, which are systems probably under complex modes of selection. The method gave me...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1991-11-01 00:00:00
abstract：:The transmission profiles of sperm mtDNA introduced into fertilized eggs were examined in detail in F1 hybrids of mouse interspecific crosses by addressing three aspects. The first is whether the leaked paternal mtDNA in fertilized eggs produced by interspecific crosses was distributed stably to all tissues after the ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-02-01 00:00:00
abstract：:The Saccharomyces cerevisiae nuclear gene RPM2 encodes a component of the mitochondrial tRNA-processing enzyme RNase P. Cells grown on fermentable carbon sources do not require mitochondrial tRNA processing activity, but still require RPM2, indicating an additional function for the Rpm2 protein. RPM2-null cells arrest...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2000-03-01 00:00:00
abstract：:Regulatory networks provide control over complex cell behavior in all kingdoms of life. Here we describe a statistical model, based on representing proteins as collections of domains or motifs, which predicts unknown molecular interactions within these biological networks. Using known protein-protein interactions of S...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2001-11-01 00:00:00
abstract：:Clustering individuals to subpopulations based on genetic data has become commonplace in many genetic studies. Inference about population structure is most often done by applying model-based approaches, aided by visualization using distance-based approaches such as multidimensional scaling. While existing distance-bas...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.115.182626
更新日期：2016-04-01 00:00:00
abstract：:Predictions for the rate of inbreeding (DeltaF) in populations with discrete generations undergoing selection on best linear unbiased prediction (BLUP) of breeding value were developed. Predictions were based on the concept of long-term genetic contributions using a recently established relationship between expected c...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2000-09-01 00:00:00
abstract：:The mutational origin and subsequent evolution of de novo genes, which are hypothesized to be genes of recent origin that are not obviously related to ancestral coding sequence, are poorly understood. However, accumulating evidence suggests that such genes may often function in male reproduction. Here we use testis-de...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.106.069245
更新日期：2007-06-01 00:00:00
abstract：:In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and t...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.105.041509
更新日期：2005-11-01 00:00:00
abstract：:The cdc19+ gene encodes an essential member of the MCM family of replication proteins in Schizosaccharomyces pombe. We have examined the structure and function of the Cdc19p protein using molecular and genetic approaches. We find that overproduction of wild-type Cdc19p in wild-type cells has no effect, but cdc19-P1 mu...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1997-11-01 00:00:00
abstract：:Directed open reading frame (ORF) disruption and a serial selection technique in Escherichia coli and the extremely thermophilic archaeon Sulfolobus solfataricus allowed the identification of otherwise cryptic crucial and noncrucial viral open reading frames in the genome of the archaeal virus SSV1. It showed that the...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1999-08-01 00:00:00
abstract：:We describe a method for co-estimating r = C/mu (where C is the per-site recombination rate and mu is the per-site neutral mutation rate) and Theta = 4N(e)mu (where N(e) is the effective population size) from a population sample of molecular data. The technique is Metropolis-Hastings sampling: we explore a large numbe...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2000-11-01 00:00:00
abstract：:To further understand how the nematode Caenorhabditis elegans defends itself against pathogen attack, we analyzed enhanced pathogen resistance (epr) mutants obtained from a forward genetic screen. We also examined several well-characterized sterile mutants that exhibit an Epr phenotype. We found that sterility and pat...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.107.083923
更新日期：2008-02-01 00:00:00
abstract：:Low-coverage next-generation sequencing methodologies are routinely employed to genotype large populations. Missing data in these populations manifest both as missing markers and markers with incomplete allele recovery. False homozygous calls at heterozygous sites resulting from incomplete allele recovery confound man...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.115.182071
更新日期：2016-02-01 00:00:00
abstract：:We describe here a family of P elements that we refer to as type I repressors. These elements are identified by their repressor functions and their lack of any deletion within the first two-thirds of the canonical P sequence. Elements belonging to this repressor class were isolated from P strains and were made in vitr...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1993-09-01 00:00:00
abstract：:fl(2)d, the Drosophila homolog of Wilms'-tumor-1-associated protein (WTAP), regulates the alternative splicing of Sex-lethal (Sxl), transformer (tra), and Ultrabithorax (Ubx). Although WTAP has been found in functional human spliceosomes, exactly how it contributes to the splicing process remains unknown. Here we atte...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.107.081679
更新日期：2008-02-01 00:00:00
abstract：:We propose a novel approximate-likelihood method to fit demographic models to human genomewide single-nucleotide polymorphism (SNP) data. We divide the genome into windows of constant genetic map width and then tabulate the number of distinct haplotypes and the frequency of the most common haplotype for each window. W...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.108.099275
更新日期：2009-05-01 00:00:00
abstract：:Seed dormancy and germination in higher plants are partially controlled by the plant hormones abscisic acid (ABA) and gibberellic acid (GA). ABA establishes dormancy during embryo maturation, whereas GA breaks dormancy and induces germination. Previous attempts to identify GA response genes were confounded because GA ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1998-06-01 00:00:00
abstract：:A method is proposed for estimating the intensity of overdominant selection scaled by the effective population size, S = 2Ns, from allele frequencies. The method is based on the assumption that, with strong overdominant selection, allele frequencies are nearly at their deterministic equilibrium values and that, to a f...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2000-12-01 00:00:00
abstract：:Determining the patterns of DNA sequence variation in the human genome is a useful first step toward identifying the genetic basis of a common disease. A haplotype map (HapMap), aimed at describing these variation patterns across the entire genome, has been recently developed by the International HapMap Consortium. In...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.104.029603
更新日期：2004-09-01 00:00:00
abstract：:Dauer formation in Caenorhabditis elegans is induced by chemosensation of high levels of a constitutively secreted pheromone. Seven genes defined by mutations that confer a dauer-formation constitutive phenotype (Daf-c) can be congruently divided into two groups by any of three criteria. Group 1 genes (daf-11 and daf-...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1993-08-01 00:00:00
abstract：:Thyroid hormone has pleiotropic effects on cochlear development, and genomic variation influences the severity of associated hearing deficits. DW/J-Pou1f1dw/dw mutant mice lack pituitary thyrotropin, which causes severe thyroid hormone deficiency and profound hearing impairment. To assess the genetic complexity of pro...
journal_title：Genetics
pub_type： 杂志文章
doi：10.1534/genetics.111.130633
更新日期：2011-10-01 00:00:00
abstract：:This study attempted to assay the zygotic contribution of X chromosome genes to the genetic control of embryonic morphogenesis in Drosophila melanogaster. A systematic screen for X-linked genes which affect the morphology of the embryo was undertaken, employing the phenotype of whole mount embryos as the major screeni...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1988-01-01 00:00:00
abstract：:A scheme for rapidly mapping chromosome rearrangements relative to the physical map of Caenorhabditis elegans is described that is based on hybridization patterns of cloned DNA on meiotic nuclei, as visualized by fluorescent in situ hybridization. From the nearly complete physical map, DNA clones, in yeast artificial ...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：1993-05-01 00:00:00
abstract：:The Thomas Hunt Morgan Medal is awarded to an individual Genetics Society of America member for lifetime achievement in the field of genetics. It recognizes the full body of work of an exceptional geneticist. The 2016 recipient is Nancy Kleckner, who has made many significant contributions to our understanding of chro...
journal_title：Genetics
pub_type： 历史文章,杂志文章
doi：10.1534/genetics.116.197608
更新日期：2016-12-01 00:00:00
abstract：:We have characterized Unstable factor for orange1 (Ufo1), a dominant, allele-specific modifier of expression of the maize pericarp color1 (p1) gene. The p1 gene encodes an Myb-homologous transcriptional activator of genes required for biosynthesis of red phlobaphene pigments. The P1-wr allele specifies colorless kerne...
journal_title：Genetics
pub_type： 杂志文章
doi：
更新日期：2003-03-01 00:00:00
