Emergent complexity in Myosin V-based organelle inheritance.

Abstract:

:How is adaptability generated in a system composed of interacting cellular machineries, each with a separate and functionally critical job to perform? The machinery for organelle inheritance is precisely one such system, requiring coordination between robust and ancient cellular modules, including the cell cycle, cytoskeleton, and organelle biogenesis/identity. Budding yeasts have emerged as powerful models to study these processes, which are critical for cellular survival, propagation, and differentiation, as organelles must compete for access to myosin V motors that travel along polarized actin cables to vectorially deliver bound cargo to the bud. Under the direction of the cell cycle, myosin V motors are recruited to organelles by specific interactions between their carboxyl-terminal globular tail domains and organelle-specific receptors. We used comparative genomics, phylogenetics, and secondary structure modeling to characterize the evolutionary history of these organelle-specific receptors. We find that while some receptors are retained widely across the animals and fungi, others are limited primarily to the Saccharomycetaceae family of budding yeast, with the emergent pattern of a conserved biogenic and inheritance factor often paired with an evolutionarily novel inheritance adaptor. We propose an evolutionary model whereby the emergence of myosin V-based organelle inheritance has utilized mechanisms of paralogy, mutation, and the appearance of pliable evolutionarily novel adaptor proteins. Our findings suggest an overarching evolutionary mechanism for how diverse cargoes compete for a single myosin V motor in organelle transport and detail one system's solution to obtaining evolutionary adaptability amongst constrained cellular modules.

journal_name

Mol Biol Evol

authors

Mast FD,Rachubinski RA,Dacks JB

doi

10.1093/molbev/msr264

subject

Has Abstract

pub_date

2012-03-01 00:00:00

pages

975-84

issue

3

eissn

0737-4038

issn

1537-1719

pii

msr264

journal_volume

29

pub_type

杂志文章
  • Phenotypic Plasticity Contributes to Maize Adaptation and Heterosis.

    abstract::Plant phenotypic plasticity describes altered phenotypic performance of an individual when grown in different environments. Exploring genetic architecture underlying plant plasticity variation may help mitigate the detrimental effects of a rapidly changing climate on agriculture, but little research has been done in t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa283

    authors: Liu N,Du Y,Warburton ML,Xiao Y,Yan J

    更新日期:2020-11-03 00:00:00

  • Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes.

    abstract::Statistical methods for computing the standard errors of the branching points of an evolutionary tree are developed. These methods are for the unweighted pair-group method-determined (UPGMA) trees reconstructed from molecular data such as amino acid sequences, nucleotide sequences, restriction-sites data, and electrop...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040333

    authors: Nei M,Stephens JC,Saitou N

    更新日期:1985-01-01 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

    doi:10.1093/molbev/msv049

    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

  • Promoter analysis of MADS-box genes in eudicots through phylogenetic footprinting.

    abstract::The MIKC MADS-box gene family has been shaped by extensive gene duplications giving rise to subfamilies of genes with distinct functions and expression patterns. However, within these subfamilies the functional assignment is not that clear-cut, and considerable functional redundancy exists. One way to investigate the ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msk016

    authors: De Bodt S,Theissen G,Van de Peer Y

    更新日期:2006-06-01 00:00:00

  • Distribution of chromosome length variation in natural isolates of Escherichia coli.

    abstract::Large-scale variation in chromosome size was analyzed in 35 natural isolates of Escherichia coli by physical mapping with a restriction enzyme whose sites are restricted to rDNA operons. Although the genetic maps and chromosome lengths of the laboratory strains E. coli K12 and Salmonella enterica sv. Typhimurium LT2 a...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a025847

    authors: Bergthorsson U,Ochman H

    更新日期:1998-01-01 00:00:00

  • Gene duplications and losses within the cyclooxygenase family of teleosts and other chordates.

    abstract::Cyclooxygenase (COX) produces prostaglandins in animals via the oxidation and reduction of arachidonic acid. Different types and numbers of COX genes have been found in corals, sea squirts, fishes, and tetrapods, but no study has used a comparative phylogenetic approach to investigate the evolutionary history of this ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn183

    authors: Havird JC,Miyamoto MM,Choe KP,Evans DH

    更新日期:2008-11-01 00:00:00

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

    abstract::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...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msv206

    authors: Adrion JR,White PS,Montooth KL

    更新日期:2016-01-01 00:00:00

  • Colocality to Cofunctionality: Eukaryotic Gene Neighborhoods as a Resource for Function Discovery.

    abstract::Diverging from the classic paradigm of random gene order in eukaryotes, gene proximity can be leveraged to systematically identify functionally related gene neighborhoods in eukaryotes, utilizing techniques pioneered in bacteria. Current methods of identifying gene neighborhoods typically rely on sequence similarity t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa221

    authors: Foflonker F,Blaby-Haas CE

    更新日期:2021-01-23 00:00:00

  • Phylogenetic Clustering by Linear Integer Programming (PhyCLIP).

    abstract::Subspecies nomenclature systems of pathogens are increasingly based on sequence data. The use of phylogenetics to identify and differentiate between clusters of genetically similar pathogens is particularly prevalent in virology from the nomenclature of human papillomaviruses to highly pathogenic avian influenza (HPAI...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msz053

    authors: Han AX,Parker E,Scholer F,Maurer-Stroh S,Russell CA

    更新日期:2019-07-01 00:00:00

  • Measuring community similarity with phylogenetic networks.

    abstract::Environmental drivers of biodiversity can be identified by relating patterns of community similarity to ecological factors. Community variation has traditionally been assessed by considering changes in species composition and more recently by incorporating phylogenetic information to account for the relative similarit...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/mss200

    authors: Parks DH,Beiko RG

    更新日期:2012-12-01 00:00:00

  • Extensive gene conversion drives the concerted evolution of paralogous copies of the SRY gene in European rabbits.

    abstract::The human Y chromosome consists of ampliconic genes, which are located in palindromes and undergo frequent gene conversion, and single-copy genes including the primary sex-determining locus, SRY. Here, we demonstrate that SRY is duplicated in a large palindrome in the European rabbit (Oryctolagus cuniculus). Furthermo...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq139

    authors: Geraldes A,Rambo T,Wing RA,Ferrand N,Nachman MW

    更新日期:2010-11-01 00:00:00

  • Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo.

    abstract::A common problem in molecular phylogenetics is choosing a model of DNA substitution that does a good job of explaining the DNA sequence alignment without introducing superfluous parameters. A number of methods have been used to choose among a small set of candidate substitution models, such as the likelihood ratio tes...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msh123

    authors: Huelsenbeck JP,Larget B,Alfaro ME

    更新日期:2004-06-01 00:00:00

  • Characterization of the Cadherin-Catenin Complex of the Sea Anemone Nematostella vectensis and Implications for the Evolution of Metazoan Cell-Cell Adhesion.

    abstract::The cadherin-catenin complex (CCC) mediates cell-cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-bind...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msw084

    authors: Clarke DN,Miller PW,Lowe CJ,Weis WI,Nelson WJ

    更新日期:2016-08-01 00:00:00

  • Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1.

    abstract::Human DNA variation is currently a subject of intense research because of its importance for studying human origins, evolution, and demographic history and for association studies of complex diseases. A approximately 10-kb region on chromosome 1, which contains only four small exons (each <155 bp), was sequenced for 6...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a003795

    authors: Yu N,Zhao Z,Fu YX,Sambuughin N,Ramsay M,Jenkins T,Leskinen E,Patthy L,Jorde LB,Kuromori T,Li WH

    更新日期:2001-02-01 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

    doi:10.1093/molbev/msaa257

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

    更新日期:2021-01-23 00:00:00

  • Maximum likelihood outperforms maximum parsimony even when evolutionary rates are heterotachous.

    abstract::Heterotachy occurs when the relative evolutionary rates among sites are not the same across lineages. Sequence alignments are likely to exhibit heterotachy with varying severity because the intensity of purifying selection and adaptive forces at a given amino acid or DNA sequence position is unlikely to be the same in...

    journal_title:Molecular biology and evolution

    pub_type: 信件

    doi:10.1093/molbev/msi212

    authors: Gadagkar SR,Kumar S

    更新日期:2005-11-01 00:00:00

  • ModelTeller: Model Selection for Optimal Phylogenetic Reconstruction Using Machine Learning.

    abstract::Statistical criteria have long been the standard for selecting the best model for phylogenetic reconstruction and downstream statistical inference. Although model selection is regarded as a fundamental step in phylogenetics, existing methods for this task consume computational resources for long processing time, they ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msaa154

    authors: Abadi S,Avram O,Rosset S,Pupko T,Mayrose I

    更新日期:2020-11-01 00:00:00

  • Empirical assessment of RAD sequencing for interspecific phylogeny.

    abstract::Next-generation sequencing opened up new possibilities in phylogenetics; however, choosing an appropriate method of sample preparation remains challenging. Here, we demonstrate that restriction-site-associated DNA sequencing (RAD-seq) generates useful data for phylogenomics. Analysis of our RAD library using current b...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu063

    authors: Cruaud A,Gautier M,Galan M,Foucaud J,Sauné L,Genson G,Dubois E,Nidelet S,Deuve T,Rasplus JY

    更新日期:2014-05-01 00:00:00

  • Statistical potentials for improved structurally constrained evolutionary models.

    abstract::Assessing the influence of three-dimensional protein structure on sequence evolution is a difficult task, mainly because of the assumption of independence between sites required by probabilistic phylogenetic methods. Recently, models that include an explicit treatment of protein structure and site interdependencies ha...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msq047

    authors: Kleinman CL,Rodrigue N,Lartillot N,Philippe H

    更新日期:2010-07-01 00:00:00

  • Estimating selection pressures from limited comparative data.

    abstract::We recently introduced a novel method for estimating selection pressures on proteins, termed "volatility," which requires only a single genome sequence. Some criticisms that have been levied against this approach are valid, but many others are based on misconceptions of volatility, or they apply equally to comparative...

    journal_title:Molecular biology and evolution

    pub_type: 信件

    doi:10.1093/molbev/msl021

    authors: Plotkin JB,Dushoff J,Desai MM,Fraser HB

    更新日期:2006-08-01 00:00:00

  • Observations of amino acid gain and loss during protein evolution are explained by statistical bias.

    abstract::The authors of a recent manuscript in "Nature" claim to have discovered "universal trends" of amino acid gain and loss in protein evolution. Here, we show that this universal trend can be simply explained by a bias that is unavoidable with the 3-taxon trees used in the original analysis. We demonstrate that a rigorous...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msl010

    authors: Goldstein RA,Pollock DD

    更新日期:2006-07-01 00:00:00

  • Population growth of human Y chromosomes: a study of Y chromosome microsatellites.

    abstract::We use variation at a set of eight human Y chromosome microsatellite loci to investigate the demographic history of the Y chromosome. Instead of assuming a population of constant size, as in most of the previous work on the Y chromosome, we consider a model which permits a period of recent population growth. We show t...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a026091

    authors: Pritchard JK,Seielstad MT,Perez-Lezaun A,Feldman MW

    更新日期:1999-12-01 00:00:00

  • Whole chloroplast genome comparison of rice, maize, and wheat: implications for chloroplast gene diversification and phylogeny of cereals.

    abstract::The fully sequenced chloroplast genomes of maize (subfamily Panicoideae), rice (subfamily Bambusoideae), and wheat (subfamily Pooideae) provide the unique opportunity to investigate the evolution of chloroplast genes and genomes in the grass family (Poaceae) by whole-genome comparison. Analyses of nucleotide sequence ...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a004033

    authors: Matsuoka Y,Yamazaki Y,Ogihara Y,Tsunewaki K

    更新日期:2002-12-01 00:00:00

  • Structural molecular components of septate junctions in cnidarians point to the origin of epithelial junctions in eukaryotes.

    abstract::Septate junctions (SJs) insure barrier properties and control paracellular diffusion of solutes across epithelia in invertebrates. However, the origin and evolution of their molecular constituents in Metazoa have not been firmly established. Here, we investigated the genomes of early branching metazoan representatives...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msu265

    authors: Ganot P,Zoccola D,Tambutté E,Voolstra CR,Aranda M,Allemand D,Tambutté S

    更新日期:2015-01-01 00:00:00

  • Proteomics and comparative genomic investigations reveal heterogeneity in evolutionary rate of male reproductive proteins in mice (Mus domesticus).

    abstract::Male reproductive fitness is strongly affected by seminal fluid. In addition to interacting with the female environment, seminal fluid mediates important physiological characteristics of sperm, including capacitation and motility. In mammals, the male reproductive tract shows a striking degree of compartmentalization,...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msp094

    authors: Dean MD,Clark NL,Findlay GD,Karn RC,Yi X,Swanson WJ,MacCoss MJ,Nachman MW

    更新日期:2009-08-01 00:00:00

  • Analysis of Genetic Variation Indicates DNA Shape Involvement in Purifying Selection.

    abstract::Noncoding DNA sequences, which play various roles in gene expression and regulation, are under evolutionary pressure. Gene regulation requires specific protein-DNA binding events, and our previous studies showed that both DNA sequence and shape readout are employed by transcription factors (TFs) to achieve DNA binding...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msy099

    authors: Wang X,Zhou T,Wunderlich Z,Maurano MT,DePace AH,Nuzhdin SV,Rohs R

    更新日期:2018-08-01 00:00:00

  • Recurrent positive selection of the Drosophila hybrid incompatibility gene Hmr.

    abstract::Lethality in hybrids between Drosophila melanogaster and its sibling species Drosophila simulans is caused in part by the interaction of the genes Hybrid male rescue (Hmr) and Lethal hybrid rescue (Lhr). Hmr and Lhr have diverged under positive selection in the hybridizing species. Here we test whether positive select...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msn190

    authors: Maheshwari S,Wang J,Barbash DA

    更新日期:2008-11-01 00:00:00

  • Epidemic Clones, Oceanic Gene Pools, and Eco-LD in the Free Living Marine Pathogen Vibrio parahaemolyticus.

    abstract::We investigated global patterns of variation in 157 whole-genome sequences of Vibrio parahaemolyticus, a free-living and seafood associated marine bacterium. Pandemic clones, responsible for recent outbreaks of gastroenteritis in humans, have spread globally. However, there are oceanic gene pools, one located in the o...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/molbev/msv009

    authors: Cui Y,Yang X,Didelot X,Guo C,Li D,Yan Y,Zhang Y,Yuan Y,Yang H,Wang J,Wang J,Song Y,Zhou D,Falush D,Yang R

    更新日期:2015-06-01 00:00:00

  • Molecular adaptation of a leaf-eating bird: stomach lysozyme of the hoatzin.

    abstract::This report describes a lysozyme expressed at high levels in the stomach of the hoatzin, the only known foregut-fermenting bird. Evolutionary comparison places it among the calcium-binding lysozymes rather than among the conventional types. Conventional lysozymes were recruited as digestive enzymes twice in the evolut...

    journal_title:Molecular biology and evolution

    pub_type: 杂志文章

    doi:10.1093/oxfordjournals.molbev.a040173

    authors: Kornegay JR,Schilling JW,Wilson AC

    更新日期:1994-11-01 00:00:00

  • Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila.

    abstract::To investigate the potential importance of gene duplication in D. melanogaster accessory gland protein (Acp) gene evolution we carried out a computational analysis comparing annotated D. melanogaster Acp genes to the entire D. melanogaster genome. We found that two known Acp genes are actually members of small multige...

    journal_title:Molecular biology and evolution

    pub_type: 信件

    doi:10.1093/molbev/msh195

    authors: Holloway AK,Begun DJ

    更新日期:2004-09-01 00:00:00