The Roles of Compensatory Evolution and Constraint in Aminoacyl tRNA Synthetase Evolution.


:Mitochondrial protein translation requires interactions between transfer RNAs encoded by the mitochondrial genome (mt-tRNAs) and mitochondrial aminoacyl tRNA synthetase proteins (mt-aaRS) encoded by the nuclear genome. It has been argued that animal mt-tRNAs have higher deleterious substitution rates relative to their nuclear-encoded counterparts, the cytoplasmic tRNAs (cyt-tRNAs). This dynamic predicts elevated rates of compensatory evolution of mt-aaRS that interact with mt-tRNAs, relative to aaRS that interact with cyt-tRNAs (cyt-aaRS). We find that mt-aaRS do evolve at significantly higher rates (exemplified by higher dN and dN/dS) relative to cyt-aaRS, across mammals, birds, and Drosophila. While this pattern supports a model of compensatory evolution, the level at which a gene is expressed is a more general predictor of protein evolutionary rate. We find that gene expression level explains 10-56% of the variance in aaRS dN/dS, and that cyt-aaRS are more highly expressed in addition to having lower dN/dS values relative to mt-aaRS, consistent with more highly expressed genes being more evolutionarily constrained. Furthermore, we find no evidence of positive selection acting on either class of aaRS protein, as would be expected under a model of compensatory evolution. Nevertheless, the signature of faster mt-aaRS evolution persists in mammalian, but not bird or Drosophila, lineages after controlling for gene expression, suggesting some additional effect of compensatory evolution for mammalian mt-aaRS. We conclude that gene expression is the strongest factor governing differential amino acid substitution rates in proteins interacting with mitochondrial versus cytoplasmic factors, with important differences in mt-aaRS molecular evolution among taxonomic groups.


Mol Biol Evol


Adrion JR,White PS,Montooth KL




Has Abstract


2016-01-01 00:00:00














  • Methods for Estimating Demography and Detecting Between-Locus Differences in the Effective Population Size and Mutation Rate.

    abstract::It is known that the effective population size (Ne) and the mutation rate (u) vary across the genome. Here, we show that ignoring this heterogeneity may lead to biased estimates of past demography. To solve the problem, we develop new methods for jointly inferring past changes in population size and detecting variatio...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Zeng K,Jackson BC,Barton HJ

    更新日期:2019-02-01 00:00:00

  • Human long noncoding RNAs are substantially less folded than messenger RNAs.

    abstract::Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary...

    journal_title:Molecular biology and evolution

    pub_type: 信件


    authors: Yang JR,Zhang J

    更新日期:2015-04-01 00:00:00

  • Origin of Nogo-A by domain shuffling in an early jawed vertebrate.

    abstract::Unlike mammals, fish are able to regenerate axons in their central nervous system. This difference has been partly attributed to the loss/acquisition of inhibitory proteins during evolution. Nogo-A--the longest isoform of the reticulon4 (rtn4) gene product--is commonly found in mammalian myelin where it acts as a pote...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Shypitsyna A,Málaga-Trillo E,Reuter A,Stuermer CA

    更新日期:2011-04-01 00:00:00

  • Evolution of the Telomere-Associated Protein POT1a in Arabidopsis thaliana Is Characterized by Positive Selection to Reinforce Protein-Protein Interaction.

    abstract::Gene duplication is a major driving force in genome evolution. Here, we explore the nature and origin of the POT1 gene duplication in Arabidopsis thaliana. Protection of Telomeres (POT1) is a conserved multifunctional protein that modulates telomerase activity and its engagement with telomeres. Arabidopsis thaliana en...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Beilstein MA,Renfrew KB,Song X,Shakirov EV,Zanis MJ,Shippen DE

    更新日期:2015-05-01 00:00:00

  • Molecular evolution of the primate developmental genes MSX1 and PAX9.

    abstract::In primates, the craniofacial skeleton and the dentition are marked by high levels of interspecific variation. Despite this, there are few comparative species studies conducted at the molecular level to investigate this functional diversity. We have determined nucleotide sequences of MSX1 and PAX9, two developmental g...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Perry GH,Verrelli BC,Stone AC

    更新日期:2006-03-01 00:00:00

  • Divergence and Remarkable Diversity of the Y Chromosome in Guppies.

    abstract::The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Almeida P,Sandkam BA,Morris J,Darolti I,Breden F,Mank JE

    更新日期:2021-01-23 00:00:00

  • Population Parameters Underlying an Ongoing Soft Sweep in Southeast Asian Malaria Parasites.

    abstract::Multiple kelch13 alleles conferring artemisinin resistance (ART-R) are currently spreading through Southeast Asian malaria parasite populations, providing a unique opportunity to observe an ongoing soft selective sweep, investigate why resistance alleles have evolved multiple times and determine fundamental population...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Anderson TJ,Nair S,McDew-White M,Cheeseman IH,Nkhoma S,Bilgic F,McGready R,Ashley E,Pyae Phyo A,White NJ,Nosten F

    更新日期:2017-01-01 00:00:00

  • c-Myb is an evolutionary conserved miR-150 target and miR-150/c-Myb interaction is important for embryonic development.

    abstract::Human c-Myb proto-oncogene is highly expressed in hematopoietic progenitors as well as leukemia and certain solid tumor. However, the regulatory mechanisms of its expression and biological functions remain largely unclear. Recently, c-Myb has been shown to be targeted by microRNA-150 (miR-150) which thereby controls B...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Lin YC,Kuo MW,Yu J,Kuo HH,Lin RJ,Lo WL,Yu AL

    更新日期:2008-10-01 00:00:00

  • Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs.

    abstract::The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Darbellay F,Necsulea A

    更新日期:2020-01-01 00:00:00

  • Mitochondrial DNA in the sea urchin Arbacia lixula: evolutionary inferences from nucleotide sequence analysis.

    abstract::From the stirodont Arbacia lixula we determined the sequence of 5,127 nucleotides of mitochondrial DNA (mtDNA) encompassing 18 tRNAs, two complete coding genes, parts of three other coding genes, and part of the 12S ribosomal RNA (rRNA). The sequence confirms that the organization of mtDNA is conserved within echinoid...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: De Giorgi C,Lanave C,Musci MD,Saccone C

    更新日期:1991-07-01 00:00:00

  • Parallel evolution of nacre building gene sets in molluscs.

    abstract::The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently a...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Jackson DJ,McDougall C,Woodcroft B,Moase P,Rose RA,Kube M,Reinhardt R,Rokhsar DS,Montagnani C,Joubert C,Piquemal D,Degnan BM

    更新日期:2010-03-01 00:00:00

  • Gene regulatory divergence among species estimated by altered developmental patterns in interspecific hybrids.

    abstract::Disturbances in the schedules of gene expression in developing interspecific fish hybrids have been used to draw inferences about the extent of gene regulatory divergence between species and about the degree to which this gene regulatory divergence is correlated with structural gene divergence, as estimated by genetic...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章,评审


    authors: Parker HR,Philipp DP,Whitt GS

    更新日期:1985-05-01 00:00:00

  • HLA Heterozygote Advantage against HIV-1 Is Driven by Quantitative and Qualitative Differences in HLA Allele-Specific Peptide Presentation.

    abstract::Pathogen-mediated balancing selection is regarded as a key driver of host immunogenetic diversity. A hallmark for balancing selection in humans is the heterozygote advantage at genes of the human leukocyte antigen (HLA), resulting in improved HIV-1 control. However, the actual mechanism of the observed heterozygote ad...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Arora J,Pierini F,McLaren PJ,Carrington M,Fellay J,Lenz TL

    更新日期:2020-03-01 00:00:00

  • Sexual dimorphism and the evolution of sex-biased gene expression in the brown alga ectocarpus.

    abstract::Males and females often have marked phenotypic differences, and the expression of these dissimilarities invariably involves sex differences in gene expression. Sex-biased gene expression has been well characterized in animal species, where a high proportion of the genome may be differentially regulated in males and fe...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Lipinska A,Cormier A,Luthringer R,Peters AF,Corre E,Gachon CM,Cock JM,Coelho SM

    更新日期:2015-06-01 00:00:00

  • Widespread recombination throughout Wolbachia genomes.

    abstract::Evidence is growing that homologous recombination is a powerful source of genetic variability among closely related free-living bacteria. Here we investigate the extent of recombination among housekeeping genes of the endosymbiotic bacteria Wolbachia. Four housekeeping genes, gltA, dnaA, ftsZ, and groEL, were sequence...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Baldo L,Bordenstein S,Wernegreen JJ,Werren JH

    更新日期:2006-02-01 00:00:00

  • A genomewide comparison of population structure at STRPs and nearby SNPs in humans.

    abstract::Patterns of population structure provide insights into evolutionary processes and help identify groups of individuals for genotype-phenotype association studies. With increasing availability of polymorphic molecular markers across genomes, the examination of population structure using large numbers of unlinked loci ha...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Payseur BA,Jing P

    更新日期:2009-06-01 00:00:00

  • DNA sequence variation in the mitochondrial control region of red-backed voles (Clethrionomys).

    abstract::The complete mitochondrial DNA (mtDNA) control region was sequenced for 71 individuals from five species of the rodent genus Clethrionomys both to understand patterns of variation and to explore the existence of previously described domains and other elements. Among species, the control region ranged from 942 to 971 b...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Matson CW,Baker RJ

    更新日期:2001-08-01 00:00:00

  • The elevated GC content at exonic third sites is not evidence against neutralist models of isochore evolution.

    abstract::The human genome is divided into isochores, large stretches (>300 kb) of genomic DNA with more or less consistent GC content. Mutational/neutralist and selectionist models have been put forward to explain their existence. A major criticism of the mutational models is that they cannot account for the higher GC content ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Duret L,Hurst LD

    更新日期:2001-05-01 00:00:00

  • Automated structural comparisons clarify the phylogeny of the right-hand-shaped polymerases.

    abstract::Polymerases are essential for life, being responsible for replication, transcription, and the repair of nucleic acid molecules. Those that share a right-hand-shaped fold and catalytic site structurally similar to the DNA polymerase I of Escherichia coli may catalyze RNA- or DNA-dependent RNA polymerization, reverse tr...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Mönttinen HA,Ravantti JJ,Stuart DI,Poranen MM

    更新日期:2014-10-01 00:00:00

  • ERAD-derived preprotein transport across the second outermost plastid membrane of diatoms.

    abstract::The diatom Phaeodactylum tricornutum harbors a plastid that is surrounded by four membranes and evolved by way of secondary endosymbiosis. Like land plants, most of its plastid proteins are encoded as preproteins on the nuclear genome of the host cell and are resultantly redirected into the organelle. Because two more...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hempel F,Bullmann L,Lau J,Zauner S,Maier UG

    更新日期:2009-08-01 00:00:00

  • Asymmetric Context-Dependent Mutation Patterns Revealed through Mutation-Accumulation Experiments.

    abstract::Despite the general assumption that site-specific mutation rates are independent of the local sequence context, a growing body of evidence suggests otherwise. To further examine context-dependent patterns of mutation, we amassed 5,645 spontaneous mutations in wild- type (WT) and mismatch-repair deficient (MMR(-)) muta...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Sung W,Ackerman MS,Gout JF,Miller SF,Williams E,Foster PL,Lynch M

    更新日期:2015-07-01 00:00:00

  • Phylogenomic analysis supports the monophyly of cryptophytes and haptophytes and the association of rhizaria with chromalveolates.

    abstract::Here we use phylogenomics with expressed sequence tag (EST) data from the ecologically important coccolithophore-forming alga Emiliania huxleyi and the plastid-lacking cryptophyte Goniomonas cf. pacifica to establish their phylogenetic positions in the eukaryotic tree. Haptophytes and cryptophytes are members of the p...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Hackett JD,Yoon HS,Li S,Reyes-Prieto A,Rümmele SE,Bhattacharya D

    更新日期:2007-08-01 00:00:00

  • In Planta Recapitulation of Isoprene Synthase Evolution from Ocimene Synthases.

    abstract::Isoprene is the most abundant biogenic volatile hydrocarbon compound naturally emitted by plants and plays a major role in atmospheric chemistry. It has been proposed that isoprene synthases (IspS) may readily evolve from other terpene synthases, but this hypothesis has not been experimentally investigated. We isolate...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Li M,Xu J,Algarra Alarcon A,Carlin S,Barbaro E,Cappellin L,Velikova V,Vrhovsek U,Loreto F,Varotto C

    更新日期:2017-10-01 00:00:00

  • Complete mtDNA sequence of the North American freshwater mussel, Lampsilis ornata (Unionidae): an examination of the evolution and phylogenetic utility of mitochondrial genome organization in Bivalvia (Mollusca).

    abstract::Molluscs in general, and bivalves in particular, exhibit an extraordinary degree of mitochondrial gene order variation when compared with other metazoans. Two factors inhibiting our understanding the evolution of gene rearrangement in bivalves are inadequate taxonomic sampling and failure to examine gene order in a ph...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Serb JM,Lydeard C

    更新日期:2003-11-01 00:00:00

  • Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia.

    abstract::The genotypic signature of spatially varying selection is ubiquitous across the Drosophila melanogaster genome. Spatially structured adaptive phenotypic differences are also commonly found, particularly along New World and Australian latitudinal gradients. However, investigation of gene expression variation in one or ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Levine MT,Eckert ML,Begun DJ

    更新日期:2011-01-01 00:00:00

  • Novel rearrangements of arthropod mitochondrial DNA detected with long-PCR: applications to arthropod phylogeny and evolution.

    abstract::Rearrangements of mitochondrial DNA gene order have been suggested as a tool for defining the pattern of evolutionary divergence in arthropod taxa. We have employed a combination of highly conserved insect-based polymerase chain reaction (PCR) primers with long-PCR to survey 14 noninsect arthropods for mitochondrial g...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Roehrdanz RL,Degrugillier ME,Black WC 4th

    更新日期:2002-06-01 00:00:00

  • Molecular Biology and Evolution of Cancer: From Discovery to Action.

    abstract::Cancer progression is an evolutionary process. During this process, evolving cancer cell populations encounter restrictive ecological niches within the body, such as the primary tumor, circulatory system, and diverse metastatic sites. Efforts to prevent or delay cancer evolution-and progression-require a deep understa...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Somarelli JA,Gardner H,Cannataro VL,Gunady EF,Boddy AM,Johnson NA,Fisk JN,Gaffney SG,Chuang JH,Li S,Ciccarelli FD,Panchenko AR,Megquier K,Kumar S,Dornburg A,DeGregori J,Townsend JP

    更新日期:2020-02-01 00:00:00

  • Estimation of phylogenetic inconsistencies in the three domains of life.

    abstract::Discrepancies in phylogenetic trees of bacteria and archaea are often explained as lateral gene transfer events. However, such discrepancies may also be due to phylogenetic artifacts or orthology assignment problems. A first step that may help to resolve this dilemma is to estimate the extent of phylogenetic inconsist...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Soria-Carrasco V,Castresana J

    更新日期:2008-11-01 00:00:00

  • Loss of Heterozygosity Drives Adaptation in Hybrid Yeast.

    abstract::Hybridization is often considered maladaptive, but sometimes hybrids can invade new ecological niches and adapt to novel or stressful environments better than their parents. The genomic changes that occur following hybridization that facilitate genome resolution and/or adaptation are not well understood. Here, we exam...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Smukowski Heil CS,DeSevo CG,Pai DA,Tucker CM,Hoang ML,Dunham MJ

    更新日期:2017-07-01 00:00:00

  • Model-based verification of hypotheses on the origin of modern Japanese revisited by Bayesian inference based on genome-wide SNP data.

    abstract::Various hypotheses for the peopling of the Japanese archipelago have been proposed, which can be classified into three models: transformation, replacement, and hybridization. In recent years, one of the hybridization models ("dual-structure model") has been widely accepted. According to this model, Neolithic hunter-ga...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章


    authors: Nakagome S,Sato T,Ishida H,Hanihara T,Yamaguchi T,Kimura R,Mano S,Oota H,Asian DNA Repository Consortium.

    更新日期:2015-06-01 00:00:00