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At least 595 records · Page 33Linked to original sources
PubMed2003

A phylogenetic study of cytochrome b561 proteins.

BACKGROUND: As an antioxidant and cofactor to numerous metabolic enzymes, ascorbate has an essential role in plants and animals. Cytochromes b561 constitute a class of intrinsic membrane proteins involved in ascorbate regeneration. Despite their importance in ascorbate metabolism, no evolutionary analysis has been presented so far on this newly described protein family. RESULTS: Cytochromes b561 have been identified in a large number of phylogenetically distant species, but are absent in fungi and prokaryotes. Most species contain three or four cytochrome b561 paralogous proteins, and the encoding genes usually have four or five exons. At the protein level, sequence similarities are rather low between cytochromes b561 within a single species (34-45% identity), and among phylogenetically distant species (around 30% identity). However, particular structural features characterizing this protein family are well conserved in members from all species investigated. These features comprise six transmembrane helices, four strictly conserved histidine residues, probably coordinating the two heme molecules, and putative ascorbate and monodehydro-ascorbate (MDHA) substrate-binding sites. Analysis of plant cytochromes b561 shows a separation between those from monocotyledonous and dicotyledonous species in a phylogenetic tree. CONCLUSIONS: All cytochromes b561 have probably evolved from a common ancestral protein before the separation of plants and animals. Their phyletic distribution mirrors the use of ascorbate as primary antioxidant, indicating their role in ascorbate homeostasis and antioxidative defense. In plants, the differentiation into four cytochrome b561 isoforms probably occurred before the separation between monocots and dicots.

Animals↗
PubMed2026

Identification of a novel HIV-1 circulating recombinant form (CRF209_cpx) and its descendant unique recombinant form (URF) CRF209_cpx/B among MSM in Guangdong, southern China.

BACKGROUND: The epidemic of human immunodeficiency virus type 1 (HIV-1) continues to pose a significant global health challenge, with increasing genetic diversity. The co-circulation of multiple subtypes among the local population facilitates the emergence of unique or circulating recombinant forms (URFs or CRFs). In China, the predominant strains include CRF07_BC, CRF01_AE, CRF55_01B, and subtype B. This study characterizes a novel CRF209_cpx and its descendant recombinant CRF209_cpx/B among men who have sex with men (MSM) in Guangdong, southern China. METHODS: Individuals infected with URFs with similar genetic characteristics were recruited during routine surveillance of pretreatment drug resistance. Near full-length genomes (NFLGs) were amplified with two overlapping fragments using a serial dilution nested PCR approach after reverse transcription. We used SimPlot and IQ-TREE softwares to conduct recombination analyses and phylogenetic inferences. Time-scaled maximum clade credibility (MCC) phylogenetic trees were reconstructed using BEAST software to estimate evolutionary origins. Genotypic drug resistance mutations were interpreted via the Stanford HIV Database, and coreceptor usage was predicted using geno2pheno coreceptor 2.5 and the HIVcoPRED tool. RESULTS: Four NFLG sequences were obtained and identified as a novel CRF209_cpx, generated by recombination among CRF01_AE, CRF07_BC and subtype B. Phylogenetic analyses revealed that all the parental segments clustered with lineages prevalent among MSM in China. Bayesian evolutionary analysis estimated that the most recent common ancestor (tMRCA) of CRF209_cpx to have evolved between 2011 and 2013. The fifth strain was identified as a URF recombined from nascent CRF209_cpx and B. No transmitted drug resistance mutation was detected in these five sequences. The four CRF209_cpx sequences primarily utilized the CXCR4 coreceptor, while the URF exhibited R5/X4 dual tropism. CONCLUSIONS: The emergence of the complex CRF209_cpx and novel URF of CRF209_cpx/B highlights the active HIV-1 epidemic within the MSM population in Guangdong, underscoring the necessity for enhanced molecular surveillance and precise public health intervention in this key population.

HIV-1↗
PubMed2004

Minireview: structural and functional evolution of the thyrotropin receptor.

TSH receptor (TSHR) is a member of the leucine-rich repeat-containing G protein-coupled receptors. Both TSHR and its ligand TSH have evolved to acquire specificity, minimize cross-reaction to other glycoprotein hormone receptors, and modulate cognate interaction (and thereby thyrotropic activity). TSHR sequences available from two life orders, teleost and mammals, were analyzed. Teleost TSHRs with low affinity are expressed in many nonthyroidal tissues and show a tendency to gene duplication. In some teleosts, TSHR has limited specificity, and in others extremely high constitutive activity, suggesting the possibility of ligand-independent receptor function. Although mammalian TSHR, in contrast to other glycoprotein hormone receptors, maintains relatively high constitutive activity, the thyrotropic activity of TSH appears to decline in hominoids including humans, probably as part of metabolic adaptation to the changing environment. Critical TSHR residues that determine hormone specificity have been identified in the leucine-rich repeats, and others within the cysteine-rich C-flanking region that determines hormonal activation as well as receptor silencing. Transmembrane (TM) helices, particularly the TM5 and TM6, are likely involved in receptor homodimerization and a unique motif in TM7 appears essential to receptor silencing and internalization. Surprisingly, ternary structures in the intracellular domain as opposed to specific sequence motifs are critical for intracellular TSHR trafficking. It is evident that progress in understanding structure-function relationships of TSHR and its ligand can be further stimulated by inclusion of evolutionary analysis of their primary, secondary and tertiary structure. Such an integrated approach should also contribute to the rational design of highly efficacious therapeutics with either agonistic or antagonistic properties.

Amino Acid Sequence↗
PubMed1996

Characterization of the Pal motifs in the upstream glucokinase promoter: binding of a cell type-specific protein complex correlates with transcriptional activation.

The upstream glucokinase (GK) promoter is expressed specifically in several different neural/neuroendocrine (NE) cell types, including the pancreatic beta-cell and pituitary corticotrope. Previously, a mutational and evolutionary analysis of this promoter identified two identical 9-bp motifs (TGGTCACCA) termed Pal-1 and Pal-2 that are essential for high level expression in HIT M2.2.2 cells, an insulinoma cell line. Here we show that these motifs are also necessary for efficient expression in AtT-20 cells, a corticotrope-derived cell line, and that proteins from both NE and non-NE cells bind to the Pal motifs, although the DNA-protein complexes differ by cell type. Complexes formed using nuclear extracts from NE cells contained an extra NE cell-specific band and differed in the relative abundance of two other bands when compared with non-NE cells, UV laser cross-linking experiments further supported the cell-specific binding of two proteins, 110 and 150 kDa in size, to these motifs. The presence or absence of the NE-specific band correlates with transcription of GK promoter fusion gene constructs, suggesting a key role for this protein in determining the cell-specific expression of GK. The Pal motifs themselves do not function as enhancers but seem to be essential components of a larger transcriptional regulatory domain that is active only in certain NE cells. Together, these studies suggest that the NE cell-specific expression of the upstream GK promoter involves the formation of a distinct protein complex on the two Pal motifs.

3T3 Cells↗
PubMed2001

Acne: a biopsychosocial and evolutionary perspective with a focus on shame.

PURPOSE: Hypotheses regarding the psychological factors implicated in the development and maintenance of acne first emerged in the middle of the eighteenth century. However, the psychodermatological literature from this date relating to acne has variously been described as confusing, overly prone to conjecture and, in particular, atheoretical. The current paper has two key objectives; first, to present a biopsychosocial model of acne development and maintenance and, secondly, to understand the psychosocial strain imposed by acne from an evolutionary perspective with a particular emphasis on body shame reactions. METHODS: The psychodermatological literature relating to acne is reviewed with the data analysed for potential biopsychosocial interactions and shame eliciting responses. RESULTS: The review indicates that acne can be reconceptualized as a biopsychosocial phenomena which, in turn, provides the field with innovative hypotheses for empirical inquiry and the potential for expanding and evaluating treatment options. The evolutionary analysis illustrates that acne provides the potential for distressing body shame reactions due to the skin disease's potential for damaging self-other evaluations of attractiveness. CONCLUSIONS: Acne has tended to be viewed as a minor dermatological complaint which imposes minimal psychological distress upon sufferers. The paper concludes that acne has the ability to elicit in some sufferers significant mental health concerns due to a heightened sense of shame relating to appearance.

Journal Article↗
PubMed2006

The many faces of protein-protein interactions: A compendium of interface geometry.

A systematic classification of protein-protein interfaces is a valuable resource for understanding the principles of molecular recognition and for modelling protein complexes. Here, we present a classification of domain interfaces according to their geometry. Our new algorithm uses a hybrid approach of both sequential and structural features. The accuracy is evaluated on a hand-curated dataset of 416 interfaces. Our hybrid procedure achieves 83% precision and 95% recall, which improves the earlier sequence-based method by 5% on both terms. We classify virtually all domain interfaces of known structure, which results in nearly 6,000 distinct types of interfaces. In 40% of the cases, the interacting domain families associate in multiple orientations, suggesting that all the possible binding orientations need to be explored for modelling multidomain proteins and protein complexes. In general, hub proteins are shown to use distinct surface regions (multiple faces) for interactions with different partners. Our classification provides a convenient framework to query genuine gene fusion, which conserves binding orientation in both fused and separate forms. The result suggests that the binding orientations are not conserved in at least one-third of the gene fusion cases detected by a conventional sequence similarity search. We show that any evolutionary analysis on interfaces can be skewed by multiple binding orientations and multiple interaction partners. The taxonomic distribution of interface types suggests that ancient interfaces common to the three major kingdoms of life are enriched by symmetric homodimers. The classification results are online at http://www.scoppi.org.

Amino Acid Sequence↗
PubMed1997

Routes of transmission of hepatitis C virus in an endemic rural area of Japan. Molecular epidemiologic study of hepatitis C virus infection.

We conducted an epidemiological study to investigate the routes of transmission of hepatitis C virus (HCV) infection in an area endemic for HCV. Subjects were the 857 adult inhabitants of K area, Japan. The prevalence of antibody to HCV (anti-HCV) was 26.3%. The HCV genotype 1b was the most prevalent (89.3%) among the anti-HCV positive subjects. Molecular evolutionary analysis, based on the nucleotide sequences of the HCV core region from 23 participants with type 1b, showed that the isolates were distributed into more than 1 group. Multivariate regression analysis demonstrated that an age over 40 years, a history of blood transfusion, the presence of antibody to hepatitis B core antigen (anti-HBc), or a history of surgery were each independently associated with the presence of anti-HCV. No significant differences in the presence of anti-HCV prevalence were observed between the wives of men positive for anti-HCV (33.3%) and age-matched women (36.4%), or between the husbands of women positive for anti-HCV (36.4%) and age-matched men (38.3%), from the same area. Findings suggest that the various strains of HCV type 1b were transmitted via medical procedures, not by the intrafamilial route.

Adult↗
PubMed1993

Lactation: historical patterns and potential for manipulation.

The advent of biotechnology has made data on undomesticated mammals relevant to dairy science. Such data indicate the potential of lactation for modification, reveal genetic material available for use through bioengineering, help distinguish adaptive features from historical artifacts, and clarify limits on lactational diversity that date from early evolution. Evolutionary analysis indicates that a complex degree of lactation preceded divergence of the extant mammalian lineages during the Mesozoic Era. Although aspects of monotreme lactation appear to be ancestral for extant mammals, the marsupials and eutherians exhibit divergent specializations. Evidence is consistent with the idea that protolacteal glands evolved by combining features of skin gland populations into a new functional complex. Secretions of these ancestral glands may have had antimicrobial properties that protected the eggs or hatchlings and organic components that supplemented offspring nutrition. Following development of highly nutritious milks, evolution produced diversity in milk composition and function, milk output, length of lactation, mammary gland anatomy, and contributions of lactation to offspring nutrition. Certain marsupials are specialized in terms of functional independence and temporal plasticity of mammary tissues. Mammalian diversity indicates that artificial selection and physiological manipulation of domestic artiodactyls has only modestly exploited the potential of mammary glands as a nutritional source for humans.

Animals↗
PubMed2004

Silent nucleotide polymorphisms and a phylogeny for Mycobacterium tuberculosis.

Much remains unknown of the phylogeny and evolution of Mycobacterium tuberculosis, an organism that kills 2 million people annually. Using a population-based approach that analyzes multiple loci around the chromosome, we demonstrate that neutral genetic variation in genes associated with antimicrobial drug resistance has sufficient variation to construct a robust phylogenetic tree for M. tuberculosis. The data describe a clonal population with a minimum of four distinct M. tuberculosis lineages, closely related to M. bovis. The lineages are strongly geographically associated. Nucleotide substitutions proven to cause drug resistance are distributed throughout the tree, whereas nonsynonymous base substitutions unrelated to drug resistance have a restricted distribution. The phylogenetic structure is concordant with all the previously described genotypic and phenotypic groupings of M. tuberculosis strains and provides a unifying framework for both epidemiologic and evolutionary analysis of M. tuberculosis populations.

Amidohydrolases↗
PubMed2005

Hybrid Vibrio vulnificus.

The recent emergence of the human-pathogenic Vibrio vulnificus in Israel was investigated by using multilocus genotype data and modern molecular evolutionary analysis tools. We show that this pathogen is a hybrid organism that evolved by the hybridization of the genomes from 2 distinct and independent populations. These findings provide clear evidence of how hybridization between 2 existing and nonpathogenic forms has apparently led to the emergence of an epidemic infectious disease caused by this pathogenic variant. This novel observation shows yet another way in which epidemic organisms arise.

Animals↗
PubMed2001

[HCV genotype as a predictor of response to interferon therapy in patients with chronic hepatitis C].

Hepatitis C virus(HCV) genotype is one of the most important predicting factors of response to interferon(IFN) therapy in patients with chronic hepatitis C. According to the molecular evolutionary analysis, HCV is classified into six major genotypes. The patients infected with genotype 1 show high HCV RNA levels and poor response to IFN therapy compared to those with genotype 2 or 3. No sufficient data are observed on response to IFN in patients with genotype 4 to 6. When PEG-IFN plus ribavirin therapy is introduced, high proportion of patients without genotype 1 must show complete response. In the near future, to predict good response to IFN therapy, it will be necessary to know whether patients have HCV genotype 1 or not.

Forecasting↗
PubMed2001

The impact of whole genome sequence data on drug discovery--a malaria case study.

BACKGROUND: Identification and validation of a drug discovery target is a prominent step in drug development. In the post-genomic era it is possible to reevaluate the association of a gene with a specific biological function to see if a homologous gene can subsume this role. This concept has special relevance to drug discovery in human infectious diseases, like malaria. A trophozoite cysteine protease (falcipain-1) from the papain family, thought to be responsible for the degradation of erythrocyte hemoglobin, has been considered a promising target for drug discovery efforts owing to the antimalarial activity of peptide based covalent cysteine protease inhibitors. This led to the development of non-peptidic non-covalent inhibitors of falcipain-1 and their characterization as antimalarials. It is now clear from sequencing efforts that the malaria genome contains more than one cysteine protease and that falcipain-1 is not the most important contributor to hemoglobin degradation. Rather, falcipain-2 and falcipain-3 appear to account for the majority of cysteine hemoglobinase activity in the plasmodium trophozoite. MATERIALS AND METHODS: We have modeled the falcipain-2 cysteine protease from one of the major human malaria species, Plasmodium falciparum and compared it to our original work on falcipain-1. As with falcipain-1, computa-tional screening of the falcipain-2 active site was conducted using DOCK. Using structural superpositions within the protease family and evolutionary analysis of substrate specificity sites, we focused on the commonalities and the protein specific features to direct our drug discovery effort. RESULTS: Since 1993, the size of the Available Chemicals Directory had increased from 55313 to 195419 unique chemical structures. For falcipain-2, eight inhibitors were identified with IC50's against the enzyme between 1 and 7 microM. Application of three of these inhibitors to infected erythrocytes cured malaria in culture, but parasite death did not correlate with food vacuole abnormalities associated with the activity of mechanistic inhibitors of cysteine proteases like the epoxide E64. CONCLUSIONS: Using plasmodial falcipain proteases, we show how a protein family perspective can influence target discovery and inhibitor design. We suspect that parallel drug discovery programs where a family of targets is considered, rather than serial programs built on a single therapeutic focus, will become the dominant industrial paradigm. Economies of scale in assay development and in compound synthesis are expected owing to the functional and structural features of individual family members. One of the remaining challenges in post-genomic drug discovery is that inhibitors of one target are likely to show some activity against other family members. This lack of specificity may lead to difficulties in functional assignments and target validation as well as a complex side effect profile.

Animals↗
PubMed1999

An Evolutionary Trace Method for Functional Prediction of Genomes.

It is essential for functional genomics to develop an accurate and efficient functional prediction method of genomes. Here, a new method is suggested, that is based on the fact that ortholog-specific motif is an evolutionary trace, in which the functional prediction of genomics is carried out. First, orthologous sets in a family were constructed using evolutionary analysis then functional motifs for each orthologous set were found out and a database consisted of these motifs was built. When this database is completed, unknown genes can be predicted accurately and quickly by searching it. The pilot study on five families proves that our method is feasible.

Journal Article↗
PubMed2003

BLASTing proteomes, yielding phylogenies.

We develop a procedure called RiPE (Retrieval-induced Phylogeny Environment) that automatically performs an evolutionary analysis of a protein (sub)family, (i) by retrieving the relevant sequences via a homology search, (ii) by using the search report to construct the alignment using only homologous subsequences (taking into account their neighborhood with a low chance of homology), (iii) by realigning, and (iv) by generating phylogenetic trees based on the alignment. In a first implementation of our scheme, we start with the available proteome data of model organisms, perform a PSI-BLAST search, use MView to convert hits into a multiple alignment, and perform realignment and tree building. As a test case, we have investigated the human ABC transporters of the subfamily G, starting with the five known human ABCG transporters. Our method retrieved homologous sequences not previously analyzed, generating a tree that is more plausible and better supported than previously published trees. The RiPE 0.1 prototype is available at the RiPE website, http://ifg-izkf.uni-muenster.de/fuellen/RiPE/ripe.html.

ATP Binding Cassette Transporter, Subfamily G, Mem↗
PubMed1992

The Myb DNA-binding domain is highly conserved in Dictyostelium discoideum.

The c-myb proto-oncogene encodes a protein that is highly conserved among birds and mammals. The amino-terminal domain of c-Myb contains three imperfect tandem repeats of approximately 50 amino acids each. This domain is required for DNA binding and has also been conserved to varying degrees in invertebrates, plants and yeast. Given that myb-related genes appear to control cellular differentiation in a variety of eucaryotic systems, the presence of a myb gene in the cellular slime mold Dictyostelium discoideum might provide a tractable system for studying the role of myb in differentiation. Degenerate oligonucleotide primers encoding regions that are highly conserved in the vertebrate and Drosophila Myb DNA-binding domains were used to amplify a related domain from Dictyostelium genomic DNA, which was then used to isolate a genomic clone. The putative DNA-binding domain of Dictyostelium Myb is as closely related to vertebrate c-Myb as is Drosophila Myb (65% identity), whereas the known Myb-related proteins of plants and yeast are more distantly related. The conserved domain of Dictyostelium Myb is capable of binding to the same DNA sequence as the vertebrate and Drosophila Myb proteins. The remainder of the deduced amino acid sequence of Dictyostelium Myb shows no homology to the divergent domains of the known animal, plant and yeast Myb-related proteins. Evolutionary analysis implies that the duplications that generated the repeats of the Myb DNA-binding domain began prior to the divergence of animals, plants, cellular slime molds and yeast.

Amino Acid Sequence↗
PubMed2006

Community heritability measures the evolutionary consequences of indirect genetic effects on community structure.

The evolutionary analysis of community organization is considered a major frontier in biology. Nevertheless, current explanations for community structure exclude the effects of genes and selection at levels above the individual. Here, we demonstrate a genetic basis for community structure, arising from the fitness consequences of genetic interactions among species (i.e., interspecific indirect genetic effects or IIGEs). Using simulated and natural communities of arthropods inhabiting North American cottonwoods (Populus), we show that when species comprising ecological communities are summarized using a multivariate statistical method, nonmetric multidimensional scaling (NMDS), the resulting univariate scores can be analyzed using standard techniques for estimating the heritability of quantitative traits. Our estimates of the broad-sense heritability of arthropod communities on known genotypes of cottonwood trees in common gardens explained 56-63% of the total variation in community phenotype. To justify and help interpret our empirical approach, we modeled synthetic communities in which the number, intensity, and fitness consequences of the genetic interactions among species comprising the community were explicitly known. Results from the model suggest that our empirical estimates of broad-sense community heritability arise from heritable variation in a host tree trait and the fitness consequences of IGEs that extend from tree trait to arthropods. When arthropod traits are heritable, interspecific IGEs cause species interactions to change, and community evolution occurs. Our results have implications for establishing the genetic foundations of communities and ecosystems.

Animals↗
PubMed1995

Y chromosomal DNA variation and the peopling of Japan.

Four loci mapping to the nonrecombining portion of the Y chromosome were genotyped in Japanese populations from Okinawa, the southernmost island of Japan; Shizuoka and Aomori on the main island of Honshu; and a small sample of Taiwanese. The Y Alu polymorphic (YAP) element is present in 42% of the Japanese and absent in the Taiwanese, confirming the irregular distribution of this polymorphism in Asia. Data from the four loci were used to determine genetic distances among populations, construct Y chromosome haplotypes, and estimate the degree of genetic diversity in each population and on different Y chromosome haplotypes. Evolutionary analysis of Y haplotypes suggests that polymorphisms at the YAP (DYS287) and DXYS5Y loci originated a single time, whereas restriction patterns at the DYS1 locus and microsatellite alleles at the DYS19 locus arose more than once. Genetic distance analysis indicated that the Okinawans are differentiated from Japanese living on Honshu. The data support the hypotheses that modern Japanese populations have resulted from distinctive genetic contributions involving the ancient Jomon people and Yayoi immigrants from Korea or mainland China, with Okinawans experiencing the least amount of admixture with the Yayoi. It is suggested that YAP+ chromosomes migrated to Japan with the Jomon people > 10,000 years ago and that a large infusion of YAP- chromosomes entered Japan with the Yayoi migration starting 2,300 years ago. Different degrees of genetic diversity carried by these two ancient chromosomal lineages may be explained by the different life-styles (hunter-gatherer versus agriculturalist). of the migrant groups, the size of the founding populations, and the antiquities of the founding events.

Alleles↗
PubMed1994

Structural characterization of an Ascaris myoglobin.

Globin was purified from the body wall of adults of the parasitic nematode Ascaris suum. Internal peptide fragments were sequenced and cDNAs encoding a polypeptide of 154 amino acids isolated by polymerase chain reaction. The polypeptide lacks a signal sequence, identifying it as a cytosolic myoglobin-like species. The native protein is a dimer. The predicted amino acid sequence shares several unusual substitutions with other nematode globins. Like the abundant pseudocoelomic A. suum hemoglobin it has a Tyr at B10 and a Gln at E7, substitutions thought to be determinants of high affinity. However, the 10-fold lower oxygen affinity of body wall globin suggests that in this molecule Tyr(B10) does not form an additional hydrogen bond with the heme bound oxygen. Evolutionary analysis of the nematode globins suggests that the monodomain myoglobin-like molecules and the two-domain hemoglobin-like molecules diverged about 500 million years ago, well before the divergence of the ascarid genera Ascaris and Pseudoterranova. The absence of introns in the A. suum myoglobin, in contrast to other nematode globin genes, is consistent with the hypothesis that during evolution intron elimination was the predominant event.

Amino Acid Sequence↗