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PubMed1985

Nucleotide sequence analysis of DNA replication origins of the small Bacillus bacteriophages: evolutionary relationships.

The ends of the small Bacillus phage genomes serve as origins and termini of their DNA replication. We have determined nucleotide sequences at the termini of four different phage DNAs and compared them with those of phi 29 DNA which has been described previously. A high degree of homology was found at the extreme ends of DNAs from phi 29, phi 15 (group A), M2Y and Nf (group B). 17 bp at the far left of the DNAs are identical. A highly conserved dodecanucleotide sequence, CCATTTCCCCAT, was also found in the righthand terminus of all these phage DNAs, at positions 27-38 from the end. Nucleotide sequences of phage GA-1 are not very similar to those of the other phages. Examination of the 5'-terminal and 3'-terminal sequences of all the phages suggests that stable 'panhandle' structures are unlikely to be formed via base pairing of both ends. However, thermodynamically more stable panhandle structures might be formed by displaced single-stranded DNA, although this requires rather large loops.

Bacillus subtilis↗
PubMed2004

Identification of 24 genes and two pseudogenes coding for olfactory receptors in Japanese loach, classified into four subfamilies: a putative evolutionary process for fish olfactory receptor genes by comprehensive phylogenetic analysis.

Twenty-four olfactory receptor (OR) genes and two pseudogenes have been identified in the genome of Japanese loach (Misgurnus anguillicaudatus). The genes were classified into four subfamilies according to the similarity of the amino acid sequences. In each subfamily, members showed high sequence similarity not only to each other but also to orthologues of other fish species. The number of members in each OR subfamily was roughly estimated to be from 3 to 10 by genomic Southern blot analysis. The genes of all four OR subfamilies were shown to express on olfactory neurons of the olfactory epithelium by in situ hybridization analysis. Two major features of fish OR genes were found by comprehensive and comparative analyses on OR genes of Japanese loach and other fish species including catfish, zebrafish and pufferfish. First, the phylogenetic tree comprising of representative subfamily members suggests the existence of several prototype genes common to the genomes of many fish species. Second, when all members of orthologous subfamilies identified in each clade of the tree are integrated, the members of a single species comprise a monophyletic group. This means that 'intraspecies' sequence homology, that is, homology among paralogous genes of the same subfamily in a species, is higher than 'interspecies' homology, that is, homology between orthologous genes of different species. This suggests that the subfamily members of a species have evolved recently. Taken together, fish OR genes have evolved from a limited number of prototype genes common to most fish species, and several genes in a subfamily have diversely evolved in each species from each prototype.

Amino Acid Sequence↗
PubMed2004

The evolutionary origin of long-crowing chicken: its evolutionary relationship with fighting cocks disclosed by the mtDNA sequence analysis.

Chickens with exceptionally long crow are often favored all over the world, and connoisseur breeders have bred certain types of chicken exclusively for this trait. In Japan, three chicken varieties have been specifically bred to develop an exceptionally long crow of over 15 s. Although these three long-crowing chickens, Naganakidori, are honored as heritage varieties of Japan, the domestication process and genealogical origin of long-crowing chickens remain unclear. The purpose of this study is to clarify these issues using nucleotide sequences of the mitochondrial DNA D-loop region. Blood samples from a total of nine long-crowing chickens and 74 chickens from 11 Japanese native varieties were collected. DNA sequence data of two Junglefowl species were also collected from the International DNA database (DDBJ /EMBL/GenBank) for use as the outgroup. A phylogenetic tree was then constructed revealing that all three Naganakidori varieties were monophyletic and originated from a fighting cock, a Shamo, for cockfighting. These results suggest that these three long-crowing chickens share a common origin in spite of their conspicuously different characters, and that human cultures favoring long-crowing chickens might have been preceded by a tradition of cockfighting. Moreover, these long-crowing varieties first separated from the fighting cocks of Okinawa, which is geographically closer to Southern China and Indochina than Mainland Japan (Honshu/Kyushu). This implies that Japanese long-crowing chickens were first brought to Mainland Japan as fighting cocks from the surrounding regions of Southern China or Indochina and through Okinawa.

Aggression↗
PubMed2005

A genomic perspective on the chromodomain-containing retrotransposons: Chromoviruses.

Chromoviruses, chromodomain-containing retrotransposons, are the only Metaviridae (Ty3/gypsy group of retrotransposons) clade with a Eukaryota-wide distribution. They have a common evolutionary origin and are the most prolific and diverse Metaviridae clade. The fusion of a retrotransposon and a chromodomain, was most probably responsible for their extreme evolutionary success in Eukaryota. Analysis of the massive amount of genome sequence data for different eukaryotic lineages has provided an in depth insight into the diversity, evolution, neofunctionalization, high rate of genomic turnover and origin of chromoviruses in Eukaryota. This review attempts to summarise the unique aspects of chromoviruses from a genomic perspective.

Amino Acid Sequence↗
PubMed2005

Comparative analyses of sheep and human TRG joining regions: evolution of J genes in Bovidae is driven by sequence conservation in their promoters for germline transcription.

The availability of genomic clones representative of the T cell receptor gamma (TRG1@ and TRG2@) ovine loci enabled us to compare the germline genomic organization and nucleotide diversity of joining (J) segments and reconstruct their evolutionary history by phylogenetic analysis of cattle, sheep and human expressed sequences. Expression profiling (RT-PCR data) in fetus and adult indicated that only the ovine J genes in which two or more of the key sequence features, such as recombination signal sequences (RSS), 3' splice sites, and core sequences, are missing or severely altered fail to be transcribed. Comparative genomic examination of the two human with the six sheep germline transcription promoters located at 5' of the relevant constant (C)-distal J segments showed a strong conservation of the redundant STAT consensus motifs, indicating that TRG1@ and TRG2@ loci are under the influence of IL-7 and STAT signalling. These findings support the phylogenetic analysis of human and Bovidae (cattle and sheep) that revealed a different grouping pattern of C-distal compared to C-proximal J segments. Likewise, the phylogenetic behaviour of either C-distal and C-proximal J segments is in accordance with the Bovidae TRG clusters evolution. Comparison of sheep and human structures of recombination signal sequences (RSS) has highlighted a greater conservation in sheep 12 RSS rather than 23 RSS thus suggesting that the initial recruitment of recombination activating genes (RAG) products requires at least one relatively high-affinity RSS per recombination event.

Animals↗
PubMed2025

Dissemination of antimicrobial resistance in Klebsiella spp. from urban aquatic environments: a multi-country genomic perspective.

INTRODUCTION: Antibiotic resistance, particularly carbapenem-resistant Klebsiella pneumoniae (CRKP), poses significant clinical and environmental threats, especially in urban aquatic ecosystems and hospital wastewaters. OBJECTIVES: This study aims to analyze the epidemiological and genomic features of CRKP isolates in urban aquatic environments and evaluate their public health and environmental impacts. METHODS AND RESULTS: Water samples were collected from 113 rivers and 3 hospitals in China, Sri Lanka, and Nepal to isolate carbapenem-resistant Klebsiella spp. isolates. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatics analyses were performed to characterize resistance phenotypes, antibiotic resistance genes (ARGs), and evolutionary trends. Big data analysis further elucidated the genomic characteristics of CRKP in global water sources, and Galleria mellonella larvae were used to assess virulence. Statistical analysis validated the findings. A total of 192 carbapenem-resistant Klebsiella spp. isolates were identified from urban aquatic ecosystems in China (n = 60) and Nepal (n = 132), with CRKP (n = 161) being the predominant species. All CRKP isolates exhibited a multidrug-resistant phenotype, yet significant differences in resistance profiles and associated ARGs were observed between isolates from the two countries. Nine carbapenem resistance genes (CRGs) were detected, with blaNDM-1 being the most prevalent (57.8 %). Correlation analysis revealed a strong association between these CRGs and multiple Inc-type plasmids. Global genomic analysis of CRKP from water sources across eight countries identified ten distinct CRGs across 45 serotypes, with KL64 being the most predominant. Notably, carbapenem-resistant hypervirulent Klebsiella pneumoniae was detected in water samples from Nepal. CONCLUSION: Our findings highlight significant regional disparities in CRKP prevalence and ARG dissemination across urban aquatic environments, with Nepal showing the highest prevalence, particularly in untreated rivers. China exhibited lower prevalence but distinct resistance gene profiles, while no CRKP was detected in Sri Lanka, underscoring the impact of environmental management and healthcare infrastructure on ARG spread.

Humans↗
PubMed2006

Functionality of unspliced XBP1 is required to explain evolution of overlapping reading frames.

Eukaryotic genes with overlapping reading frames exemplify some of the most striking biological phenomena. Transcript of one such gene, the gene encoding X-box protein (XBP1), has evolved a mechanism for "on-demand" switching of translation between two overlapping reading frames. Despite the existence of this elaborate system, only one reading frame was believed to be functional. Here, we show that XBP1 evolves in a fashion that is only consistent with functionality of both reading frames. Our study provides a novel evolutionary framework for the analysis of loci with overlapping reading frames, which can be used for identification and analyses of novel dual-coding genes.

Animals↗
PubMed2006

Evolutionary flexibility of pair-rule patterning revealed by functional analysis of secondary pair-rule genes, paired and sloppy-paired in the short-germ insect, Tribolium castaneum.

In the Drosophila segmentation hierarchy, periodic expression of pair-rule genes translates gradients of regional information from maternal and gap genes into the segmental expression of segment polarity genes. In Tribolium, homologs of almost all the eight canonical Drosophila pair-rule genes are expressed in pair-rule domains, but only five have pair-rule functions. even-skipped, runt and odd-skipped act as primary pair-rule genes, while the functions of paired (prd) and sloppy-paired (slp) are secondary. Since secondary pair-rule genes directly regulate segment polarity genes in Drosophila, we analyzed Tc-prd and Tc-slp to determine the extent to which this paradigm is conserved in Tribolium. We found that the role of prd is conserved between Drosophila and Tribolium; it is required in both insects to activate engrailed in odd-numbered parasegments and wingless (wg) in even-numbered parasegments. Similarly, slp is required to activate wg in alternate parasegments and to maintain the remaining wg stripes in both insects. However, the parasegmental register for Tc-slp is opposite that of Drosophila slp1. Thus, while prd is functionally conserved, the fact that the register of slp function has evolved differently in the lineages leading to Drosophila and Tribolium reveals an unprecedented flexibility in pair-rule patterning.

Amino Acid Sequence↗
PubMed1998

Yeast RNase H(35) is the counterpart of the mammalian RNase HI, and is evolutionarily related to prokaryotic RNase HII.

We cloned the Saccharomyces cerevisiae homologue of mammalian RNase HI, which itself is related to the prokaryotic RNase HII, an enzyme of unknown function and previously described as having minor activity in Escherichia coli. Expression of the corresponding yeast 35 kDa protein (named by us RNase H(35)) in E. coli and immunological analysis proves a close evolutionary relationship to mammalian RNase HI. Deletion of the gene (called RNH35) from the yeast genome leads to an about 75% decrease of RNase H activity in preparations from the mutated, still viable cells. Sequence comparison discriminates this new yeast RNase H from earlier described yeast enzymes, RNase H(70) and RNase HI.

Amino Acid Sequence↗
PubMed1995

Post traumatic stress disorder: an evolving concept.

This inductive inquiry used Rodgers' evolutionary view of concept analysis to define the concept post-traumatic stress disorder (PTSD). Medline, a computerized database, was used to generate the literature sample. Based on the analysis, PTSD was defined as a complex varying psychological and biological response to an acute stressor experienced directly or indirectly, or to chronic stress. PTSD is detrimental to normal functioning of individuals. People who had prolonged exposure to a stressor, who felt guilt for their own actions, and who had a less adequate support system had more severe symptoms. Future research is needed to find ways to prevent or minimize development of PTSD.

Humans↗
PubMed2002

Eph family functions from an evolutionary perspective.

Eph receptor tyrosine kinases and ephrins have been identified in organisms ranging from sponges to flies and worms to chick, mice and humans, thus allowing their function to be approached also from an evolutionary perspective. The structural analysis of Eph/ephrin crystals is providing hints for the existence of Eph and ephrin folds in plants and suggests a mechanism for triggering bi-directional signalling.

Animals↗
PubMed2002

Phylogenetics of Australian Acacia thrips: the evolution of behaviour and ecology.

The species of thrips found on Acacia constitute a major component of the Australian thrips fauna, with at least 235 species in more than 30 genera, many of these being in the process of description as new. These thrips exhibit social behaviours, ranging from solitary and colonial species to a variety of more complex social organisations. Furthermore, the domiciliary habits of these species include domicile construction, gall induction, and opportunistic use of abandoned galls and domiciles. This suite of thrips also includes a variety of inquiline and kleptoparasitic taxa. To understand how these various traits have evolved and interact in this diverse group, we have reconstructed a phylogeny for 42 species of thrips associated with Acacia around Australia. We obtained DNA sequence data from two nuclear genes (Elongation Factor-1alpha and wingless) and one mitochondrial gene (cytochrome oxidase I) and analysed these using maximum parsimony and maximum likelihood methods. A phylogeny resulting from such analysis allows inference of evolutionary transitions in domiciliary habits, social organisations, and parasitic behaviours. Gall induction and parasitic behaviour are postulated to each have a single origin, with no losses of either trait. Once parasitism evolved a remarkable radiation followed that allowed exploitation of very diverse hosts. Our data do not allow hypotheses of single versus multiple origins of domicile building to be resolved while opportunistic gall use appears to have arisen several times.

Animals↗
PubMed2003

Evolution of dietary antioxidants.

Oxygen is vital for most organisms but, paradoxically, damages key biological sites. Oxygenic threat is met by antioxidants that evolved in parallel with our oxygenic atmosphere. Plants employ antioxidants to defend their structures against reactive oxygen species (ROS; oxidants) produced during photosynthesis. The human body is exposed to these same oxidants, and we have also evolved an effective antioxidant system. However, this is not infallible. ROS breach defences, oxidative damage ensues, accumulates with age, and causes a variety of pathological changes. Plant-based, antioxidant-rich foods traditionally formed the major part of the human diet, and plant-based dietary antioxidants are hypothesized to have an important role in maintaining human health. This hypothesis is logical in evolutionary terms, especially when we consider the relatively hypoxic environment in which humans may have evolved. In this paper, the human diet is discussed briefly in terms of its evolutionary development, different strategies of antioxidant defence are outlined, and evolution of dietary antioxidants is discussed from the perspectives of plant need and our current dietary requirements. Finally, possibilities in regard to dietary antioxidants, evolution, and human health are presented, and an evolutionary cost-benefit analysis is presented in relation to why we lost the ability to make ascorbic acid (vitamin C) although we retained an absolute requirement for it.

Animals↗
PubMed2000

Analysis of birth intervals in a non-contracepting Indian population: an evolutionary ecological approach.

Reproductive strategies are related to ecological constraints. This paper examines data on early birth spacing in a scheduled caste, Bengali-speaking, non-contracepting population of the Karimganj district of southern Assam, India, taking an evolutionary ecological perspective. It is found that on average birth intervals closed by boy-boy are longer than those closed by girl-girl. Birth spacing tends to be longer among upper-income and Craftsman sub-caste mothers. The presence of a 'grandmother' in the household shortens spacing. These findings are compatible with an evolutionary-based reproductive decision-making process.

Analysis of Variance↗
PubMed1997

Endosymbiotic interactions in anaerobic protozoa.

Several aspects of the endosymbiosis of methanogenic archaea with anaerobic protozoa are reviewed. Special attention is played to the role of hydrogenosomes and plastid-like organelles that seem to provide the substrates for the methanogenic endosymbionts. Evidence is presented that hydrogenosomes evolved several times in the various protoctistan taxa. Hydrogenosomes are seemingly different, and their common denominator is the production of hydrogen. The absence of nucleic acids and a protein-synthesizing machinery hampers the analysis of their divergent evolutionary history, and molecular genetic data argue not only for different but even a chimeric origin of the hydrogenosomes.

Anaerobiosis↗
PubMed2006

Molecular dissection of arginyltransferases guided by similarity to bacterial peptidoglycan synthases.

Post-translational protein arginylation is essential for cardiovascular development and angiogenesis in mice and is mediated by arginyl-transfer RNA-protein transferases Ate1-a functionally conserved but poorly understood class of enzymes. Here, we used sequence analysis to detect the evolutionary relationship between the Ate1 family and bacterial FemABX family of aminoacyl-tRNA-peptide transferases, and to predict the functionally important residues in arginyltransferases, which were then used to construct a panel of mutants for further molecular dissection of mouse Ate1. Point mutations of the residues in the predicted regions of functional importance resulted in changes in enzymatic activity, including complete inactivation of mouse Ate1; other mutations altered its substrate specificity. Our results provide the first insights into the mechanisms of Ate1-mediated arginyl transfer reaction and substrate recognition, and define a new protein superfamily called Dupli-GNAT to reflect its origin by the duplication of the GNAT acetyltransferase domain.

Amino Acid Sequence↗
PubMed2002

Psoriasis of early and late onset: a clinical and epidemiologic study from Spain.

BACKGROUND: The existence of 2 distinct forms of psoriasis related to age at onset has been postulated. However, precise data regarding the clinical and epidemiologic characteristics of psoriasis depending on the age at onset are still lacking. OBJECTIVE: The purpose of this study was to define the clinical and epidemiologic features of this disease in Spain and to compare patients with psoriasis of early and late onset. METHODS: An observational, analytic, cross-sectional, multicenter study was carried out. From January 1999 to November 1999, 179 participating dermatologists completed a questionnaire detailing the clinical and epidemiologic features of the first 10 consecutive patients with psoriasis seen in their clinical practice. The sample distribution was proportional to the Spanish population. Both statistical and descriptive analyses were performed. RESULTS: Available data were obtained from 1774 patients. The onset of the disease before 30 years of age was significantly associated with a higher incidence of family history of psoriasis, a more severe and extensive cutaneous involvement, and greater psychosocial impact. Guttate psoriasis, nail involvement, evidence of precipitating factors, and a recurrent clinical course were more frequent in this group of patients. Patients with psoriasis of late onset had a less severe clinical course and a more continuous evolution. Palmoplantar pustulosis was more frequent in this group of patients. No significant relationship was detected between the age at onset and development of joint involvement. CONCLUSION: Patients with early and late onset psoriasis often show different clinical and evolutionary features. From the analysis of our data, it seems that 2 different groups of patients with psoriasis related to age at onset can be defined.

Adolescent↗
PubMed2004

The 4-coumarate:CoA ligase gene family in Arabidopsis thaliana comprises one rare, sinapate-activating and three commonly occurring isoenzymes.

4-Coumarate:CoA ligase (4CL; EC 6.2.1.12) has a pivotal role in the biosynthesis of plant secondary compounds at the divergence point from general phenylpropanoid metabolism to several major branch pathways. In Arabidopsis thaliana, we have identified a previously undetected, fourth and final member of the At4CL gene family. The encoded enzyme, At4CL4, exhibits the rare property of efficiently activating sinapate, besides the usual 4CL substrates (4-coumarate, caffeate, and ferulate), indicating a distinct metabolic function. Phylogenetic analysis suggests an early evolutionary and functional divergence of three of the four gene family members, At4CL2-4, whereas At4CL1 appears to have originated much later by duplication of its structurally and functionally closest relative, At4CL2. Various characteristics shared by all known plant 4CL genes, as well as by the encoded proteins, define and delimit the At4CL gene family and distinguish it from the closely related family of "At4CL-like" genes.

Arabidopsis↗