Abstract:
:We performed a genealogical analysis of the ionotropic glutamate receptor (iGluR) gene family, which includes the animal iGluRs and the newly isolated glutamate receptor-like genes (GLR) of plants discovered in Arabidopsis. Distance measures firmly placed the plant GLR genes within the iGluR clade as opposed to other ion channel clades and indicated that iGluRs may be a primitive signaling mechanism that predated the divergence of animals and plants. Moreover, phylogenetic analyses using both parsimony and neighbor joining indicated that the divergence of animal iGluRs and plant GLR genes predated the divergence of iGluR subtypes (NMDA vs. AMPA/KA) in animals. By estimating the congruence of the various glutamate receptor gene regions, we showed that the different functional domains, including the two ligand-binding domains and the transmembrane regions, have coevolved, suggesting that they assembled together before plants and animals diverged. Based on residue conservation and divergence as well as positions of residues with respect to functional domains of iGluR proteins, we attempted to examine structure-function relationships. This analysis defined M3 as the most highly conserved transmembrane domain and identified potential functionally important conserved residues whose function can be examined in future studies.
journal_name
Mol Biol Evoljournal_title
Molecular biology and evolutionauthors
Chiu J,DeSalle R,Lam HM,Meisel L,Coruzzi Gdoi
10.1093/oxfordjournals.molbev.a026167subject
Has Abstractpub_date
1999-06-01 00:00:00pages
826-38issue
6eissn
0737-4038issn
1537-1719journal_volume
16pub_type
杂志文章abstract::We review all instances in which the nuclear 5S rRNA genes of fungi, protist, nematode, and arthropod species have been reported to be linked to the tandemly repeated units of the rDNA, trans-spliced leader, and histone multigene families. The evolution of these gene arrangements is analyzed by mapping them to indepen...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040223
更新日期:1995-05-01 00:00:00
abstract::Reconstructing phylogenies from intraspecific data (such as human mitochondrial DNA variation) is often a challenging task because of large sample sizes and small genetic distances between individuals. The resulting multitude of plausible trees is best expressed by a network which displays alternative potential evolut...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a026036
更新日期:1999-01-01 00:00:00
abstract::Polyploidization events have occurred during the evolution of many fungi, plant, and animal species and are thought to contribute to speciation and tumorigenesis, however little is known about how ploidy level contributes to adaptation at the molecular level. Here we integrate whole genome sequencing, RNA expression a...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx205
更新日期:2017-10-01 00:00:00
abstract::Signatures of balancing selection can highlight polymorphisms and functions that are important to the long-term fitness of a species. We performed a first genome-wide scan for balancing selection in a bacterial species, Staphylococcus aureus, which is a common cause of serious antimicrobial-resistant infections of hum...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msr286
更新日期:2012-04-01 00:00:00
abstract::Modifications to transcriptional regulators play a major role in adaptation. Here, we compared the effects of multiple beneficial mutations within and between Escherichia coli rpoB, the gene encoding the RNA polymerase β subunit, and rho, which encodes a transcriptional terminator. These two genes have harbored adapti...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx216
更新日期:2017-11-01 00:00:00
abstract::When bacteria evolve resistance against a particular antibiotic, they may simultaneously gain increased sensitivity against a second one. Such collateral sensitivity may be exploited to develop novel, sustainable antibiotic treatment strategies aimed at containing the current, dramatic spread of drug resistance. To da...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msx158
更新日期:2017-09-01 00:00:00
abstract::Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex ch...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa319
更新日期:2020-12-10 00:00:00
abstract::Vertebrate eye lenses mostly contain two abundant types of proteins, the alpha-crystallins and the beta/gamma-crystallins. In addition, certain housekeeping enzymes are highly expressed as crystallins in various taxa. We now observed an unusual approximately 41-kd protein that makes up 16% to 18% of the total protein ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msg116
更新日期:2003-06-01 00:00:00
abstract::Alu is a predominant short interspersed element (SINE) family in the human genome and consists of two monomer units connected by an A-rich linker. At present, dimeric Alu elements are active in humans, but Alu monomers are present as fossilized sequences. A comparative genome analysis of human and chimpanzee genomes r...
journal_title:Molecular biology and evolution
pub_type: 信件
doi:10.1093/molbev/msq218
更新日期:2011-01-01 00:00:00
abstract::Understanding the genetic structure of human populations has important implications for the design and interpretation of disease mapping studies and reconstructing human evolutionary history. To date, inferences of human population structure have primarily been made with common variants. However, recent large-scale re...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msu326
更新日期:2015-03-01 00:00:00
abstract::The transposable element hobo has been introduced into the previously empty Drosophila melanogaster strain Hikone so that its dynamics can be followed and it can be compared with the P element. Five transformed lines were followed over 58 generations. The results were highly dependent on the culture temperature, the s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040251
更新日期:1995-09-01 00:00:00
abstract::The phylogenetic position of the Pedetidae, represented by a single species Pedetes capensis, is controversial, reflecting in part the retention of both Hystricomorphous and Sciurognathous characteristics in this rodent. In an attempt to clarify the species evolutionary relationships, mtDNA gene sequences from 10 rode...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a025698
更新日期:1997-01-01 00:00:00
abstract::Hepcidin is a small bioactive peptide with dual roles as an antimicrobial peptide and as the principal hormonal regulator of iron homeostasis in human and mouse. Hepcidin homologs of very similar structures are found in lower vertebrates, all comprise approximately 20-25 amino acids with 8 highly conserved cysteines f...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msn056
更新日期:2008-06-01 00:00:00
abstract::The relative efficiencies of the maximum parsimony (MP) and distance-matrix methods in obtaining the correct tree (topology) were studied by using computer simulation. The distance-matrix methods examined are the neighbor-joining, distance-Wagner, Tateno et al. modified Farris, Faith, and Li methods. In the computer s...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040497
更新日期:1988-05-01 00:00:00
abstract::Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh198
更新日期:2004-10-01 00:00:00
abstract::During the course of a random sequencing project of the genome of the dimorphic yeast Yarrowia lipolytica, we have identified sequences that were repeated in the genome and that matched the reverse transcriptase (RT) sequence of non-long terminal repeat (non-LTR) retrotransposons. Extension of sequencing on each side ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004125
更新日期:2002-05-01 00:00:00
abstract::Heterotypy is now recognized as a generative force in the formation of new proteins through modification of existing proteins. We report that heterotypy in the N-terminal region of the mature growth/differentiation factor 5 (GDF5) protein occurred during evolution of teleosts. N-terminal length variation of GDF5 was f...
journal_title:Molecular biology and evolution
pub_type: 信件,评审
doi:10.1093/molbev/msn041
更新日期:2008-05-01 00:00:00
abstract::A central goal in biology is to determine the ways in which evolution repeats itself. One of the most remarkable examples in nature of convergent evolutionary novelty is animal venom. Across diverse animal phyla, various specialized organs and anatomical structures have evolved from disparate developmental tissues to ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msaa133
更新日期:2020-10-01 00:00:00
abstract::In chickens, there is a single functional gene (VH1) coding for the heavy chain variable region of immunoglobulins, and immunoglobulin diversity is generated by gene conversion of the VH1 gene by many variable region pseudogenes (psi VH's) that exist on the 5' side of the VH1 gene. To understand the evolution of this ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040194
更新日期:1995-01-01 00:00:00
abstract::Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to det...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp054
更新日期:2009-06-01 00:00:00
abstract::Heterotachy is a general term to describe positions that evolve at different rates in different lineages. Heterotachy also can generally be viewed as multivariate rates-across-sites variation, which can be described as randomly drawing rates (or branch lengths) from a multivariate distribution for each branch at each ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msq346
更新日期:2011-05-01 00:00:00
abstract::Hybridization between different species plays an important role in plant genome evolution, as well as is a widely used approach for crop improvement. McClintock has predicted that plant wide hybridization constitutes a "genomic shock" whereby cryptic transposable elements may be activated. However, direct experimental...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msi082
更新日期:2005-04-01 00:00:00
abstract::Amino acids interact with each other, especially with neighboring amino acids, to generate protein structures. We studied the pattern of association and repulsion of amino acids based on 24,748 protein-coding genes from human, 11,321 from mouse, and 15,028 from Escherichia coli, and documented the pattern of neighbor ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a003982
更新日期:2002-01-01 00:00:00
abstract::To understand the question of whether divergence of eukaryotic genes by gene duplications and domain shufflings proceeded gradually or intermittently during evolution, we have cloned and sequenced Giardia lamblia cDNAs encoding kinesins and kinesin-related proteins and have obtained 13 kinesin-related cDNAs, some of w...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a004215
更新日期:2002-09-01 00:00:00
abstract::Cells react to oxidative stress conditions by launching a defense response through the induction of nuclear gene expression. The advent of microarray technologies allowed monitoring of oxidative stress-dependent changes of transcript levels at a comprehensive and genome-wide scale, resulting in a series of inventories...
journal_title:Molecular biology and evolution
pub_type: 杂志文章,meta分析
doi:10.1093/molbev/msm276
更新日期:2008-03-01 00:00:00
abstract::Taxonomic congruence and total evidence are competing paradigms in phylogenetic inference. Taxonomic congruence focuses on deriving a consensus from the results obtained from separately analyzed data sets, whereas total evidence uses character congruence in the search for the best-fitting hypothesis for all of the ava...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040071
更新日期:1993-11-01 00:00:00
abstract::Several new families of DNA transposons were identified by computer-assisted searches in a wide range of animal species that includes nematodes, flat worms, mosquitoes, sea squirt, zebrafish, and humans. Many of these elements have coding capacity for transposases, which are related to each other and to those encoded ...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msh188
更新日期:2004-09-01 00:00:00
abstract::In Arabidopsis, stem cell homeostasis in the shoot apical meristem (SAM) is controlled by a feedback loop between WUS and CLV functions. We have identified WUS orthologues in maize and rice by a detailed phylogenetic analysis of the WOX gene family and subsequent cloning. A single WUS orthologue is present in the rice...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msl125
更新日期:2006-12-01 00:00:00
abstract::A cDNA that encodes the heart-type lactate dehydrogenase (LDH-B) from the teleost fish Fundulus heteroclitus was cloned and sequenced. The protein encoded by the cDNA was analyzed in relation to 13 LDH proteins from a variety of taxa. One of the deductions from this analysis is that LDH-B proteins have residues in the...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/oxfordjournals.molbev.a040559
更新日期:1989-07-01 00:00:00
abstract::Copy number variants (CNVs) within humans can have both adaptive and deleterious effects. Because of their phenotypic significance, researchers have attempted to find single nucleotide polymorphisms (SNPs) in high linkage disequilibrium (LD) with CNVs to use in genomewide association studies. However, studies have fou...
journal_title:Molecular biology and evolution
pub_type: 杂志文章
doi:10.1093/molbev/msp210
更新日期:2010-01-01 00:00:00