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At least 793 records · Page 44Linked to original sources
PubMed2003

Molecular cloning and characterization of a cDNA encoding cytochrome c oxidase subunit Va from the lesser grain borer, Rhyzopertha dominica (F.) (Coleoptera: Bostrichidae).

A cDNA encoding subunit Va of cytochrome c oxidase (EC 1.9.3.1) was cloned and characterized from a lesser grain borer (Rhyzopertha dominica) cDNA library. The complete cDNA consists of 693-bp and contains an open reading frame of 450-bp that encodes 150 amino acid residues. The sequence includes a 28-bp putative N-terminal and a 122-bp putative mature protein. The estimated molecular weight and pI for the predicted mature protein are 13,962 and 4.60, respectively. The cDNA-deduced amino acid sequence of the mature protein shows 73% identity to that of a corresponding subunit of African malaria mosquito (Anopheles gambiae) and 59% identity to that of the fruit fly (Drosophila melanogaster). In addition, 31% of all amino acid residues are conserved among six different animal species. Evolutionary distance analysis suggests that cytochrome c oxidase subunit Va from R. dominica is most similar to the corresponding subunit from the malaria mosquito. Northern analysis revealed a single 4.9-kb transcript that is much larger than that found in mammalian species.

Amino Acid Sequence↗
PubMed1992

Evolution of the primate lentiviruses: evidence from vpx and vpr.

The genomes of the four primate lentiviral groups are complex and contain several regulatory or accessory genes. Two of these genes, vpr and vpx, are found in various combinations within the four groups and encode proteins whose functions have yet to be elucidated. Comparison of the encoded protein sequences suggests that the vpx gene within the HIV-2 group arose by the duplication of an ancestral vpr gene within this group. Evolutionary distance analysis showed that both genes were well conserved when compared with viral regulatory genes, and indicated that the duplication occurred at approximately the same time as the HIV-2 group and the other primate lentivirus groups diverged from a common ancestor. Furthermore, although the SIVagm vpx proteins are homologous to the HIV-2 group vpx proteins, there are insufficient grounds from sequence analysis for classifying them as vpx proteins. Because of their similarity to the vpr proteins of other groups, we suggest reclassifying the SIVagm vpx gene as a vpr gene. This creates a simpler and more uniform picture of the genomic organization of the primate lentiviruses and allows the genomic organization of their common precursor to be defined; it probably contained five accessory genes: tat, rev, vif, nef and vpr.

Amino Acid Sequence↗
PubMed1993

Phylogeny of the insulin-like growth factors (IGFs) and receptors: a molecular approach.

The IGFs (IGF-I and IGF-II) are essential for normal mammalian growth and development. Their actions are mediated primarily by their interactions with the type I IGF receptor (IGF-I receptor), a transmembrane tyrosine kinase. The ligands and the IGF-I receptor are structurally related to insulin and to the insulin receptor, respectively. Analysis of evolutionary conservation has often provided insights into essential regions of molecules such as hormones and their receptors. The genes for insulin and IGFs have been partially characterized in a number of vertebrate species extending evolutionarily from humans as far back as fish. The sequences of the exons encoding the mature insulin and IGF peptides are highly conserved among vertebrate species, and IGF-I-like molecules are found in species whose origins extend back as much as 550 million years. The insulin receptor is also highly conserved in vertebrate species, and an insulin-receptor-like molecule has been characterized in Drosophila. In contrast, IGF-I receptors have only been characterized in mammalian species and partially studied in Xenopus, in which the tyrosine kinase domain is highly conserved. Studies are presently being undertaken to analyze in more detail the regulation of the genes encoding this important family of growth factors and the structure/function relationships in the gene products themselves.

Amino Acid Sequence↗
PubMed2000

DXS6673E encodes a predominantly nuclear protein, and its mouse ortholog DXHXS6673E is alternatively spliced in a developmental- and tissue-specific manner.

DXS6673E is a candidate gene for nonspecific X-linked mental retardation and encodes a novel Zn-finger protein. The ortholog murine gene DXHXS6673E in XC-D was isolated and characterized. It is ubiquitously expressed in all embryonic stages and adult tissues. Two different transcription start sites exist that result in two major transcripts of 6055 and 5352 nucleotides, each composed of 25 exons. Exon 1A is tissue specific, whereas exon 1B is transcribed constitutively. Both variants are translated into the same 1370-amino-acid protein. Transcripts are subject to alternative splicing at the 5'-end. Some of the isoforms are developmental stage and tissue specific. Among them, one was present only in embryos and adult brain. Sequence analysis demonstrated evolutionary conservation down to the arthropods and defined several conserved protein motifs. Subcellular localization studies with green fluorescent protein as a reporter showed that DXS6673E is predominantly located in the nucleus due to several functional nuclear localization signals. Three distinct protein distribution patterns in COS-7 cells could be identified.

Alternative Splicing↗
PubMed1997

Identification of functional surfaces of the zinc binding domains of intracellular receptors.

Transcriptional regulatory factor complexes assemble on genomic response elements to control gene expression. To gain insights on the surfaces that determine this assembly in the zinc binding domains from intracellular receptors, we systematically analyzed the variations in sequence and function of those domains in the context of their invariant fold. Taking the intracellular receptor superfamily as a whole revealed a hierarchy of amino acid residues along the DNA interface that correlated with response element binding specificity. When only steroid receptors were considered, two additional sites appeared: the known dimer interface, and a novel putative interface suitably located to contact regulatory factors bound to the free face of palindromic response elements commonly used by steroid receptors. Surprisingly, retinoic acid receptors, not known to bind palindromic response elements, contain both of these surfaces, implying that they may dimerize at palindromic elements under some circumstances. This work extends Evolutionary Trace analysis of functional surfaces to protein-DNA interactions, suggests how coordinated exchange of trace residues may predictably switch binding specificity, and demonstrates how to detect functional surfaces that are not apparent from sequence comparison alone.

Amino Acid Sequence↗
PubMed1992

Application of genome sequence information in potyvirus taxonomy: an overview.

The application of protein and nucleic acid sequence analysis in evolutionary and phylogenetic studies is well established. Available sequence information for the 5' untranslated region of potyviruses including the fungus-transmitted barley yellow mosaic virus (BaYMV) RNA-1 suggests that a 12-nucleotide conserved sequence, the "potybox" is unique to this group. Various non-structural proteins of potyviruses share considerable "signature" sequence homology across a broad spectrum of unrelated viruses, which makes their value limited to "supergroup" or "superfamily" identity. However, in potyviruses, the coat-protein N-terminal sequences and 3' noncoding regions are variable among viruses, but similar among strains of the same virus. This suggests that these sequences may be an accurate marker of genetic relatedness. Until complete genome sequences from a large number of potyviruses become available and their value in systematics is tested, coat protein and 3' noncoding regions remain as the choice of taxonomic indicators. The reason being, that cloning and sequencing of the coat-protein gene and 3' noncoding regions are less complicated and time consuming and the sequences show significant differences among the virus species within the family Potyviridae.

Animals↗
PubMed1992

Sequence and diversity of rhesus monkey T-cell receptor beta chain genes.

We have sequenced 23 rearranged T-cell receptor beta chain (Tcrb) cDNA clones derived from peripheral blood lymphocytes (PBL) of a rhesus monkey. All of the clones have a variable-diversity-joining-constant (V-D-J-C) rearrangement similar to that of humans. Two rhesus constant (C) region genes were found, each closely resembling human Cb 1 and 2. All of the rhesus J region sequences align well with ten of the 13 reported human J regions. 17 of the 23 rhesus V region sequences could be assigned to families homologous with eight different human families (Vb 1, 2, 6, 7, 8, 9, 13, and 14). The remaining six V region sequences are more distantly related to human Vb 1 and 13. Thus, the organization and sequences of studied rhesus Tcrb chains resemble human homologs. An evolutionary tree analysis revealed paralogous relationships between specific members of the rhesus and human V region families. Analysis of synonymous and nonsynonymous nucleotide sequence differences indicated that the evolution of the presumed major histocompatibility complex (MHC)-contact regions of the Tcrb chains is less constrained than that of the framework regions.

Amino Acid Sequence↗
PubMed1981

Evolution and longevity-assurance processes.

The role of the development of information fidelity systems in evolution is explored, with evidence that the loss in the ability to maintain the integrity of homeostasis in organisms over time, aging, is correlated with the loss in the ability to maintain integrity at the molecular biological level. Evolutionary-comparative analysis places an upper limit on the number of these systems important to the evolution of longevity in the primates, and suggests the importance of insuring the stability of information bearing macromolecules in evolution and the role of modulators of damage to these moieties in the expression of the senescent state.

Aging↗
PubMed1975

Evolution of 5sRNA.

The evolution of 5sRNA of 17 organisms ranging from human to bacteria has been studied using a sequence homology analysis. The evolutionary rate of 5sRNA genes has been estimated to be 2.2x10(-10) replacement per one nucleotide site per year. This value is about the same as that of cytochrome C or tRNA's (congruent to 2x10(-10)). A phylogenic tree of these organisms including both eukaryotes and prokaryotes has been constructed from the evolutionary distances (the rate of nucleotide substitution per site) data. The time of divergence of prokaryotes and eukaryotes was estimated to be greater than or congruent to 1.75x10(9) years ago and the branching order in eukaryotic kingdoms is consistent with the traditional order. Blue-green algae separated from the bacterial stem greater than or congruent to 1.3x10(9) years ago after eukaryotes had branched.

Animals↗
PubMed1996

Environmental fluctuations and the maintenance of genetic diversity in age or stage-structured populations.

The ability of random fluctuations in selection to maintain genetic diversity is greatly increased when generations overlap. This result has been derived previously using genetic models with very special assumptions about the population age structure. Here we explore its robustness in more realistic population models, with very general age structure or physiological structure. For a range of genetic models (haploid, diploid, single and multi-locus) we find that the condition for maintaining genetic diversity generalizes almost without change. Genetic diversity is maintained by selection if a product of the form (generation overlap) x (selection intensity) x (variability in the selection regime) is sufficiently large, where the generation overlap is measured in units of Fisher's reproductive value. This conclusion is based on a local evolutionary stability analysis, which differs from the standard "protected polymorphism" criterion for the maintenance of genetic diversity. Simulation results match the predictions from the local stability analysis, but not those from the protected polymorphism criterion. The condition obtained here for maintaining genetic diversity requires fitness fluctuations that are substantial but well within the range observed in many studies of natural populations.

Aging↗
PubMed1989

Episodic evolution in the stomach lysozymes of ruminants.

By sequencing lysozymes c from deer and pig stomachs and comparing them to the known amino acid sequences of other lysozymes c, it was possible to examine the rate of sequence change during and after the period in which this enzyme acquired a new function. Evolutionary tree analysis suggests that the rate went up while lysozyme was being recruited to function as a digestive enzyme in the stomach of early ruminants. Later, presumably after lysozyme was well adapted for functioning in the new environment, which contains acid, pepsin, and fermentation products, the rate of amino acid replacement became subnormal.

Adaptation, Physiological↗
PubMed2002

Genetic tools for cyanobacteria.

Cyanobacteria are oxygenic photosynthetic bacteria that have been used increasingly to study diverse biological processes, including photosynthesis and its regulation; cell differentiation and N2 fixation; metabolism of nitrogen, carbon, and hydrogen; resistance to environmental stresses; and molecular evolution. Many vectors and other genetic tools have been developed for unicellular and filamentous strains of cyanobacteria. Transformation, electroporation, and conjugation are used for gene transfer. Diverse methods of mutagenesis allow the isolation of many sought-for kinds of mutants, including site-directed mutants of specific genes. Reporter genes permit measurement of the level of transcription of particular genes, and assays of transcription within individual colonies or within individual cells in a filament. Complete genomic sequences have been obtained for the unicellular cyanobacterium, Synechocystis sp. strain PCC 6803 and the filamentous, heterocyst-forming cyanobacterium, Anabaena sp. strain PCC 7120. Genomic sequence projects are under way for Nostoc punctiforme strain PCC 73102 (ATCC 29133) and strains of the unicellular genera, Synechococcus, Prochlorococcus, and Gloeobacter. Genomic sequence data provide the opportunity for global monitoring of changes in genetic expression at transcriptional and translational levels in response to variations in environmental conditions. The availability of genomic sequences accelerates the identification, study, modification and comparison of cyanobacterial genes, and facilitates analysis of evolutionary relationships, including the relationship of chloroplasts to ancient cyanobacteria. The many available genetic tools enhance the opportunities for possible biotechnological applications of cyanobacteria.

Bacterial Proteins↗
PubMed2026

Chromosome painting in plants: history and future perspectives.

Chromosome painting was developed in mammalian species nearly four decades ago and rapidly became a powerful tool for chromosome identification, comparative cytogenetics, and evolutionary genome analysis. Comparative chromosome painting among diverse mammals generated much of the foundational knowledge of chromosome structure, chromosomal rearrangements, and karyotype evolution before the advent of whole-genome sequencing. Although chromosome painting was first demonstrated in plants in 2001, its applications remained largely restricted to a few plant lineages until the development of oligonucleotide (oligo)-based chromosome painting in 2015. During the last decade, oligo-based chromosome painting has transformed plant cytogenetics, enabling many investigations that were previously impossible. These studies have provided new insights into meiotic chromosome pairing, crossover formation, chromosome fusion, karyotype stability, and chromosome evolution across diverse plant lineages. This review summarizes the history of technological development of chromosome painting in plants, highlights major discoveries enabled by oligo-based chromosome painting, and discusses future opportunities, particularly the integration of chromosome painting with three-dimensional chromosome and genome biology.

Chromosome Painting↗
PubMed2026

T2T and chromosome-level genome assemblies provide insights into the genetic basis of bioactive compound biosynthesis and environmental adaptation in licorice.

Licorice is an important medicinal herb worldwide, including three Chinese Pharmacopoeia species (Glycyrrhiza uralensis, G. inflata, G. glabra), with bioactive compounds crucial for disease treatment and industrial applications. However, the genetic mechanisms underlying the biosynthesis, diversification, and environmental adaptation of bioactive compounds in Glycyrrhiza species have long remained unclear. Herein, we assembled a gapless telomere-to-telomere (T2T) genome of G. uralensis with resolved telomeres and centromeres and three significantly improved high-quality chromosome-level Glycyrrhiza genomes, alongside a variation map of 188 wild accessions. Population analysis revealed evolutionary divergence among species, with selection signals linked to medicinal compound pathways. We identified 4CL5 as a key gene for stress response and compound synthesis. GWAS validation highlighted the GiPHL1-Gi4CL5 module's role in licochalcone A accumulation and enhanced stress adaptation in G. inflata. This study provides the first T2T Glycyrrhiza genome and insights into medicinal compound biosynthesis and environmental adaptation.

Glycyrrhiza↗
PubMed1987

Rapid nucleotide sequence analysis of the small subunit ribosomal RNA of Toxoplasma gondii: evolutionary implications for the Apicomplexa.

A method for obtaining a large proportion of the nucleotide sequence of the small subunit ribosomal RNA (srRNA) was applied to the obligate intracellular protozoon Toxoplasma gondii. The method uses reverse transcription of as little as 8 micrograms of total cellular RNA. This fast, efficient method has numerous advantages over traditional gene cloning methods when nucleotide sequences are required for evolutionary studies. A phylogenetic analysis of the srRNA sequence data showed that T. gondii is not especially closely related to any other organism for which srRNA sequences are available, including another member of the Apicomplexa.

Animals↗
PubMed2004

Avian antimicrobial peptides: the defense role of beta-defensins.

Avian antimicrobial peptides, classified as beta-defensins, have been identified from bloods of chicken, turkey, and ostrich; epithelial cells of chicken and turkey; and king penguin stomach contents. Beta-defensins are a family of antimicrobial peptides characterized by six cysteine residues forming beta-defensin motifs that are also found in bovine, ovine, pig, and human. These peptides are active against a wide range of microorganisms including Gram-positive and Gram-negative bacteria, fungi, and yeast. Analysis of evolutionary relationships of vertebrate beta-defensins showed that there might be a common ancestral gene between avian and other mammalian peptides. This ancient gene may have been passed down and evolved from species older than the oldest living birds, forming a beta-defensin-like precursor molecule. This review describes potential applications of these peptides in health care products.

Animals↗
PubMed2006

Applications of computational algorithm tools to identify functional SNPs in cytokine genes.

Understanding the functions of single nucleotide polymorphisms (SNPs) can greatly help to understand the genetics of the human phenotype variation and especially the genetic basis of human complex diseases. However, how to identify functional SNPs from a pool containing both functional and neutral SNPs is challenging. In this study, we analyzed the genetic variations that can alter the expression and function of a group of cytokine proteins using computational tools. As a result, we extracted 4552 SNPs from 45 cytokine proteins from SNPper database. Of particular interest, 828 SNPs were in the 5'UTR region, 961 SNPs were in the 3' UTR region, and 85 SNPs were non-synonymous SNPs (nsSNPs), which cause amino acid change. Evolutionary conservation analysis using the SIFT tool suggested that 8 nsSNPs may disrupt the protein function. Protein structure analysis using the PolyPhen tool suggested that 5 nsSNPs might alter protein structure. Binding motif analysis using the UTResource tool suggested that 27 SNPs in 5' or 3'UTR might change protein expression levels. Our study demonstrates the presence of naturally occurring genetic variations in the cytokine proteins that may affect their expressions and functions with possible roles in complex human disease, such as immune diseases.

Algorithms↗
PubMed2006

Hominin lower second premolar morphology: evolutionary inferences through geometric morphometric analysis.

Mandibular premolars are increasingly used in taxon-specific diagnostic analyses of hominins. Among the principal difficulties in these evaluations is the absence of discrete, discernible, and comparable anatomical structures for rigorous quantitative assessment. Previous research has addressed either internal crown surface features (such as cusps and fossae) or the morphology of the crown outline. In the present paper, we integrate both types of information in the examination of morphological variation of lower P4s (n = 96) among various fossil hominin species with an emphasis on genus Homo. We use a set of 34 2D landmarks combining coordinate data from four classical dental landmarks on the occlusal surface and 30 sliding semilandmarks of the crown outline. Our results indicate that external shape variation is closely related to the configuration of the occlusal morphological features and influenced by dental size. The external and internal shapes of P4 are polymorphic but still useful in depicting a primitive-derived gradient. The primitive pattern seems to have been an asymmetrical contour with a mesially displaced metaconid, development of a bulging talonid, and a broad occlusal polygon. The trend toward dental reduction during the Pleistocene produced different morphological variants with a reduced occlusal polygon and decreased lingual occlusal surface in later Homo species. Homo heidelbergensis/neanderthalensis have fixed plesiomorphic traits in high percentages, whereas in modern humans a symmetrical outline with a centered metaconid and talonid reduction evolved.

Animals↗