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Results for “evolutionary conservation”

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PubMed1999

Groucho/transducin-like enhancer of split (TLE) family members interact with the yeast transcriptional co-repressor SSN6 and mammalian SSN6-related proteins: implications for evolutionary conservation of transcription repression mechanisms.

The yeast proteins TUP1 and SSN6 form a transcription repressor complex that is recruited to different promoters via pathway-specific DNA-binding proteins and regulates the expression of a variety of genes. TUP1 is functionally related to invertebrate and vertebrate transcriptional repressors of the Groucho/transducin-like Enhancer of split (TLE) family. The aim was to examine whether similar mechanisms underlie the transcription repression functions of TUP1 and Groucho/TLEs by determining whether TLE family members can interact with yeast SSN6 and mammalian SSN6-like proteins. It is shown in the present work that SSN6 binds to TLE1 and mediates transcriptional repression when expressed in mammalian cells. Moreover, TLE1 and TLE2 interact with two mammalian proteins related to SSN6, designated as the products of the ubiquitously transcribed tetratricopeptide-repeat genes on the Y (or X) chromosomes (UTY/X). These findings suggest that mammalian TLE and UTY/X proteins may mediate repression mechanisms similar to those performed by TUP1-SSN6 in yeast.

Basic Helix-Loop-Helix Proteins↗
PubMed2025

Fishing for a reelGene: evaluating gene models with evolution and machine learning.

Assembled genomes and their associated annotations have transformed our study of gene function. However, each new annotated assembly generates new gene models. Inconsistencies between annotations likely arise from biological and technical causes, including pseudogene misclassification, transposon activity, and intron retention from sequencing of unspliced transcripts. To evaluate gene model predictions, we developed reelGene, a pipeline of machine learning models focused on (1) transcription boundaries, (2) mRNA integrity, and (3) protein structure. The first two models leverage sequence characteristics and evolutionary conservation across related taxa to learn the grammar of conserved transcription boundaries and mRNA sequences, while the third uses the conserved evolutionary grammar of protein sequences to predict whether a gene can produce a protein. Evaluating 1.8 million transcript models in Zea mays ssp. mays (maize), reelGene classified 28% as incorrectly annotated or non-functional. We find that reelGene classifies 92.2% of genes in the maize proteome and 99.2% of genes within the maize classical gene list as functional. reelGene also provides a way to further investigate genome biology- for instance, reelGene indicates that 10.3% of dispensable genes in B73 are functional, and within retained duplicate genes, reelGene identifies a 30% bias toward the retention of the M1 subgenome when one copy is functional and the other is non-functional. As an annotation-evaluating tool, reelGene is directly applicable to species of the Andropogoneae tribe, including other important crops like sorghum and miscanthus. As a community resource, reelGene has been integrated onto MaizeGDB both as a browser track and as an individual Shiny App, allowing researchers to evaluate gene model accuracy and further investigate genome biology.

Machine Learning↗
PubMed2005

SVC: structured visualization of evolutionary sequence conservation.

We have developed a web application for the detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes. Given a pair of orthologous genes, the protein-coding sequences are aligned. When these sequences are mapped back onto their encoding exons in the genomes, a scaffold of the conserved gene structure naturally emerges. Sequence similarity between exons and introns is analysed and embedded into the gene structure scaffold. The visualization on the SVC server provides detailed information about evolutionarily conserved features of these genes. It further allows concise representation of complex splice patterns in the context of evolutionary conservation. A particular application of our tool arises from the fact that around mRNA editing sites both exonic and intronic sequences are highly conserved. This aids in delineation of these sites. SVC is available at http://svc.molgen.mpg.de.

Animals↗
PubMed2001

Snake alpha-neurotoxin binding site on the Egyptian cobra (Naja haje) nicotinic acetylcholine receptor Is conserved.

Evolutionary success requires that animal venoms are targeted against phylogenetically conserved molecular structures of fundamental physiological processes. Species producing venoms must be resistant to their action. Venoms of Elapidae snakes (e.g., cobras, kraits) contain alpha-neurotoxins, represented by alpha-bungarotoxin (alpha-BTX) targeted against the nicotinic acetylcholine receptor (nAChR) of the neuromuscular junction. The model which presumes that cobras (Naja spp., Elapidae) have lost their binding site for conspecific alpha-neurotoxins because of the unique amino acid substitutions in their nAChR polypeptide backbone per se is incompatible with the evolutionary theory that (1) the molecular motifs forming the alpha-neurotoxin target site on the nAChR are fundamental for receptor structure and/or function, and (2) the alpha-neurotoxin target site is conserved among Chordata lineages. To test the hypothesis that the alpha-neurotoxin binding site is conserved in Elapidae snakes and to identify the mechanism of resistance against conspecific alpha-neurotoxins, we cloned the ligand binding domain of the Egyptian cobra (Naja haje) nAChR alpha subunit. When expressed as part of a functional Naja/mouse chimeric nAChR in Xenopus oocytes, this domain confers resistance against alpha-BTX but does not alter responses induced by the natural ligand acetylcholine. Further mutational analysis of the Naja/mouse nAChR demonstrated that an N-glycosylation signal in the ligand binding domain that is unique to N. haje is responsible for alpha-BTX resistance. However, when the N-glycosylation signal is eliminated, the nAChR containing the N. haje sequence is inhibited by alpha-BTX with a potency that is comparable to that in mammals. We conclude that the binding site for conspecific alpha-neurotoxin in Elapidae snakes is conserved in the nAChR ligand binding domain polypeptide backbone per se. This conclusion supports the hypothesis that animal toxins are targeted against evolutionarily conserved molecular motifs. Such conservation also calls for a revision of the present model of the alpha-BTX binding site. The approach described here can be used to identify the mechanism of resistance against conspecific venoms in other species and to characterize toxin-receptor coevolution.

Acetylcholine↗
PubMed2006

Determinant factors of spectrum of missense variants in mucopolysaccharidosis IVA gene.

Design of efficient treatment strategies for diseases requires clarification of the nature of each mutation causing the disease. In this study, we have investigated three factors to correctly predict the correlation between genotype and phenotype on N-acetylgalactosamine-6-sulfate sulfatase (GALNS) gene responsible for one of lysosomal storage diseases, known as mucopolysaccharidosis IVA (MPS IVA); (i) evolutionary conservation of amino acid residues among family proteins, (ii) conservativeness of amino acid changes in GALNS, and (iii) structural conservation of amino acid residue. The results showed that (i) the likelihood of a missense variant causing MPS IVA was directly correlated with the level of evolutionary conservation and inversely correlated with conservativeness but not correlated with the structural conservation, (ii) the disease-causative mutations were 9 times more likely to be located on the 'highly conserved' residues than the polymorphisms, (iii) the likelihood of 'non-conservative' amino acid changes in missense mutations was 6.8 times higher than those in the polymorphisms, (iv) the degree of evolutionary conservation was nearly as predictive in phenotype as that of conservativeness of amino acid changes, and (v) the combination of the two factors, evolutionary conservation and conservativeness, provides a better association between missense variants and clinical severity with higher sensitivity (83.5-88.9%) and specificity (71.4-88.3%), than that obtained by either factor alone. These findings suggest that the combination of evolutionary conservation and conservativeness is a useful tool to predict the effect of each mutation on the clinical phenotype and can be applied to the analysis of phenotype/genotype relation in other genetic diseases.

Amino Acid Sequence↗
PubMed2025

Chromosome-level genome assembly of Triplophysa scleroptera.

Triplophysa scleroptera is an endemic fish species in Qinghai Lake and the upper reaches of the Yellow River. However, studies on conservation and evolutionary genetics were seriously impeded by the absence of a reference genome. Here, by using PacBio HiFi sequencing and Hi-C assembly technology, we assembled a chromosome-level genome of T. scleroptera, with a total length of 660.22 Mb and 99.82% of the sequence anchored to 25 chromosomes. The contig N50 and scaffold N50 were 9.09 Mb and 24.38 Mb, respectively. The evaluation using BUSCO indicated the genome assembly to be 96.40% complete. About 33.41% of the genome consists of repeat elements. We predicted 26,168 protein-coding genes in the genome, and 99.02% of them were functionally annotated. This high-quality reference genome would serve as a valuable genomic resource for advancing evolutionary conservation genetics studies in this species.

Animals↗
PubMed1992

A human moderately repeated Y-specific DNA sequence is evolutionarily conserved in the Y chromosome of the great apes.

Evolutionary conservation of the human-derived moderately repeated Y-specific DNA sequence Y-190 (DYZ5) was investigated in the chimpanzee, orangutan, and gorilla. Southern blot analysis showed the presence of the sequence in the Y chromosome of all great apes. Pulsed-field gel electrophoresis and in situ hybridization revealed that the repeat is organized in one major block and confined to a small region of the Y chromosome of the three species. DYZ5 was assigned to the proximal short arm of the Y chromosome of the chimpanzee and orangutan and to the long arm of the Y chromosome of the gorilla. In light of its evolutionary conservation, DYZ5 may have an as yet undetermined structural function in the Y chromosome.

Animals↗
PubMed2004

Conservation and loss of the ERV3 open reading frame in primates.

The human endogenous retrovirus ERV3 possesses an open reading frame for a truncated envelope, which is expressed as mRNA and protein. Here we examine the env sequence in primates for evidence of evolutionary conservation. ERV3 sequences were amplified by PCR from genomic DNA of great ape and Old World primates but not from New World primates or gorilla, suggesting an integration event more than 30 million years ago with a subsequent loss in one species. In the chimpanzee, the protein sequence of Env is 98.18% identical to that of human. In other species the identity falls (93.71% in rhesus macaque) in proportion to the separation from the human lineage. Start and stop codons and domains of functional significance in the envelope protein are conserved. The evolutionary conservation of the ERV3 envelope suggests a beneficial function, though the loss from gorilla shows that it is not essential for survival or reproduction.

Amino Acid Sequence↗
PubMed1997

Nucleotide sequence of a highly conserved region of the canine p53 tumour suppressor gene.

An evolutionary conserved region of the canine tumour suppressor gene, p53, was PCR amplified and its DNA sequence determined. The 1003 bp fragment consisted of exons 5 to 8 and the intervening introns. A high level of sequence homology was demonstrated with human sequences, with the evolutionary conserved domains II, III, IV and V being identical.

Amino Acid Sequence↗
PubMed1988

Antisera probes to an atypical pseudocholinesterase from surgeonfish reveal immunochemical variability and tissue-specific molecular polymorphism.

Polyclonal antisera were raised in rabbits against the purified sialated, presumed-globular tetrameric pseudocholinesterase (pseudo-ChE) from surgeonfish (Leibel: Journal of Experimental Zoology 1988b) and against commercially obtained Electrophorus electroplax AChE. The resulting antisera probes were absolutely specific for their respective antigens and failed to titrate ChE activities heterologously. However, each antisera probe did crossreact with its other respective globular and asymmetric aggregational isozymes. The resultant specific probes were then used to examine interspecific evolutionary conservation of the two ChE activities and, in conjunction with velocity sedimentation analysis and differential paraoxon inhibition, the tissue distribution and molecular polymorphism of these same two enzyme systems in surgeonfish. These experiments suggest the tight evolutionary conservation of AChE in contrast to the apparent high variability of pseudo-ChE amongst the wide range of teleost fishes tested. The native atypical pseudo-ChE was shown to exist, like AChE, as a series of sialated and asialated globular and asymmetric aggregational isozymes whose relative distribution exhibits marked tissue specificity. The extremely high levels of pseudo-ChE characteristic of white skeletal (epaxial) muscle, in particular, was conspicuous, and its occurrence in the sarcolemma is discussed in the context of its possible function and in relation to the apparent lack of evolutionary conservation amongst marine teleosts.

Animals↗
PubMed2006

Using evolutionary and structural information to predict DNA-binding sites on DNA-binding proteins.

Proteins that interact with DNA are involved in a number of fundamental biological activities such as DNA replication, transcription, and repair. A reliable identification of DNA-binding sites in DNA-binding proteins is important for functional annotation, site-directed mutagenesis, and modeling protein-DNA interactions. We apply Support Vector Machine (SVM), a supervised pattern recognition method, to predict DNA-binding sites in DNA-binding proteins using the following features: amino acid sequence, profile of evolutionary conservation of sequence positions, and low-resolution structural information. We use a rigorous statistical approach to study the performance of predictors that utilize different combinations of features and how this performance is affected by structural and sequence properties of proteins. Our results indicate that an SVM predictor based on a properly scaled profile of evolutionary conservation in the form of a position specific scoring matrix (PSSM) significantly outperforms a PSSM-based neural network predictor. The highest accuracy is achieved by SVM predictor that combines the profile of evolutionary conservation with low-resolution structural information. Our results also show that knowledge-based predictors of DNA-binding sites perform significantly better on proteins from mainly-alpha structural class and that the performance of these predictors is significantly correlated with certain structural and sequence properties of proteins. These observations suggest that it may be possible to assign a reliability index to the overall accuracy of the prediction of DNA-binding sites in any given protein using its sequence and structural properties. A web-server implementation of the predictors is freely available online at http://lcg.rit.albany.edu/dp-bind/.

Amino Acid Sequence↗
PubMed2000

RH maps of bovine chromosomes 15 and 29: conservation of human chromosomes 11 and 5.

Comparative mapping data on evolutionary conserved coding sequences and synteny maps between human and cattle are insufficient to define the extent and distribution of conserved segments between these two species, because the order of loci is often rearranged. A 5000-rad cattle whole-genome radiation hybrid (WG-RH) panel was constructed to provide high-resolution comparative maps and also to integrate linkage maps of microsatellites with evolutionary conserved genes and transcripts in a single ordered map. We used the WG-RH panel to construct radiation hybrid maps of bovine Chromosomes (Chrs) 15 and 29 (BTA15 and BTA29), integrating microsatellites from published linkage maps with selected genes. The comprehensive map of BTA15 consists of 24 markers, 13 of which were placed in the framework map. Eleven molecular markers compose the comprehensive map of BTA29, seven of which were placed in the framework map. We identified the homologous regions between bovine Chr 15 (BTA15) and human Chrs 5 and 11 (HSA5 and HSA11), as well as between BTA29 and HSA11. The present study demonstrates that WG-RH mapping is an efficient method for integrating multiple genetic maps into one map and for incorporating monomorphic Type I loci into ordered maps for comparison between species.

Animals↗
PubMed2026

Molting in Pancrustacea Is Characterized by Both Deeply Conserved and Recently Evolved Gene Modules.

Arthropods such as insects and crustaceans, which together form the monophyletic group Pancrustacea, possess a rigid chitinous exoskeleton that must be periodically shed through molting to allow growth and morphological change. Although molting is a deeply conserved developmental process across Arthropoda, our understanding of its molecular mechanisms is still largely derived from insect model species. Lineage-specific innovations and losses of molting-related genes raise fundamental questions about the extent of its conservation outside noninsect arthropods. Here, we investigate the evolutionary conservation of molting gene expression across five representative pancrustacean species using publicly available transcriptomic datasets. Changes in gene expression during molting are characterized by both deeply conserved and lineage-specific gene modules. Temporal gene expression analyses reveal that these lineage-specific signatures are not uniformly distributed across the molting process: the middle transitional phase is more lineage-specific, thereby exhibiting an inverse hourglass pattern. This is likely due to life-history-specific processes, development of the cuticle, and specialized structures of the exoskeleton. Overall, this study provides evidence for both the evolutionary conservation and divergence of this key postembryonic developmental process and highlights the modular architecture of the molting program.

Animals↗
PubMed2006

Inferring protein-protein interacting sites using residue conservation and evolutionary information.

This paper proposes a novel method using protein residue conservation and evolution information, i.e., spatial sequence profile, sequence information entropy and evolution rate, to infer protein binding sites. Some predictors based on support vector machines (SVMs) algorithm are constructed to predict the role of surface residues in protein-protein interface. By combining protein residue characters, the prediction performance can be improved obviously. We then made use of the predicted labels of neighbor residues to improve the performance of the predictors. The efficiency and the effectiveness of our proposed approach are verified by its better prediction performance based on a non-redundant data set of heterodimers.

Amino Acid Sequence↗
PubMed1992

Evolution of the vertebrate Hox homeobox genes.

One of the most remarkable recent findings in developmental biology has been the colinear and homologous relationships shared between the Drosophila HOM-C and vertebrate Hox homeobox gene complexes. These relationships pose the question of the functional significance of colinearity and its molecular basis. While there was much initial resistance to the validity of this comparison, it now appears the Hox/HOM homology reflects a broad degree of evolutionary conservation which has reawakened interest in comparative embryology and evolution. The evolutionary conservation of protein motifs in many gene families (including those for growth factors, secreted and membrane bound signalling factors, adhesion molecules, cytoplasmic receptor kinases, nuclear receptors and transcription factors) has lead to speculation on the extent to which these homology relationships represent common developmental processes and underlying molecular mechanisms. Structural identifies in a protein may indicate the biochemical/molecular function that a protein plays in cellular and developmental processes, without reflecting a conserved role in a cascade of developmental events. However, the analysis of genes encoding transcription factors has provided evidence suggesting that there are gene complexes in arthropods and vertebrates which are true homologues and which may share common roles in the specification of regional identity along embryonic A-P axis. These genes comprise the Hox/HOM-C homeotic complexes. This review will detail some of the evidence for this proposed relationship and will speculate on the functional implications.

Amino Acid Sequence↗
PubMed1991

Selection of DNA sequences from interval 6 of the human Y chromosome with homology to a Y chromosomal fertility gene sequence of Drosophila hydei.

An experimental approach towards the molecular analysis of the male fertility function, located in interval 6 of the human Y chromosome, is presented. This approach is not based on the knowledge of any gene product but on the assumption that the functional DNA structure of male fertility genes, evolutionary conserved with their position on the Y chromosome, may contain an evolutionary conserved frame structure or at least conserved sequence elements. We tested this hypothesis by using dhMiF1, a fertility gene sequence of the Y chromosome of Drosophila hydei, as a screening probe on a pool of cloned human Y-DNA sequences. We were able to select 10 human Y-DNA sequences of which 7 could be mapped to Y interval 6 (the pY6H sequence family). Since the only fertility gene of the human Y chromosome is mapped to the same Y interval, our working hypothesis seems to be strongly supported. Most interesting in this respect is the isolation of the Y-specific repetitive pY6H65 sequence. The pY6H65 locus extends to a length of at least 300 kb in Y interval 6 and has a locus-specific repetitive sequence organization, reminiscent of the functional DNA structure of Y chromosomal fertility genes of Drosophila. We identified the simple sequence family (CA)n as one sequence element conserved between the Drosophila dhMiFi fertility gene sequence and the homologous human Y-DNA sequences.

Animals↗
PubMed2006

Are subspecies useful in evolutionary and conservation biology?

The taxonomic rank of subspecies remains highly contentious, largely because traditional subspecies boundaries have sometimes been contradicted by molecular phylogenetic data. The most complete meta-analysis to date, for instance, found that only 3% of traditional avian subspecies represented distinct phylogenetic lineages. However, the global generality of this phenomenon remains unclear due to this previous study's narrow geographic focus on continental Nearctic and Palearctic subspecies. Here, we present a new global analysis of avian subspecies and show that 36% of avian subspecies are, in fact, phylogenetically distinct. Among biogeographic realms we find significant differences in the proportion of subspecies that are phylogenetically distinct, with Nearctic/Palearctic subspecies showing significantly reduced levels of differentiation. Additionally, there are differences between island and continental subspecies, with continental subspecies significantly less likely to be genetically distinct. These results indicate that the overall level of congruence between taxonomic subspecies and molecular phylogenetic data is greater than previously thought. We suggest that the widespread impression that avian subspecies are not real arises from a predominance of studies focusing on continental subspecies in North America and Eurasia, regions which show unusually low levels of genetic differentiation. The broader picture is that avian subspecies often provide an effective short-cut for estimating patterns of intraspecific genetic diversity, thereby providing a useful tool for the study of evolutionary divergence and conservation.

Animals↗
PubMed2005

Differential accumulation of Lhcb gene products in thylakoid membranes of Zea mays plants grown under contrasting light and temperature conditions.

In higher plants many different genes encode Lhcb proteins that belong to a highly conserved protein family. Evolutionary conservation of this genetic redundancy suggests that individual gene products play different roles in light harvesting and photoprotection depending on environmental conditions. We have tested the hypothesis that expression/accumulation of individual light harvesting complex (Lhc) proteins depends on plant growth conditions. Zea mays plants were grown in different temperature (13 degrees C vs. 24 degrees C) and light (high vs. low) conditions. The thylakoid membranes were isolated and fractionated by sucrose gradient and the protein content of the different bands was analyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Significant differences were found in the accumulation of both the major light harvesting complex of photosystem II (LHCII) complexes and the minor antenna chlorophyll proteins CP29, CP26 and CP24. In particular, temperature seems to play a major role in driving the expression/accumulation of the different proteins: the LHCII/minor antenna ratio increases with decreasing temperature. The pigment composition and the spectroscopic properties of LHCII complexes isolated from low temperature grown plants are significantly different from those of LHCII purified from high temperature grown plants. Two-dimensional maps show that different LHCII proteins are accumulated at different levels depending on growth conditions. Moreover the low temperature/high light grown plants show an increased value of nonphotochemical quenching. These results suggest a specific role of different LHCII complexes in the organization of the potosystem II and photoprotection.

Chemical Fractionation↗