Kazuho Ikeo
Publications
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A new database (GCD) on genome composition for eukaryote and prokaryote genome sequences and their initial analyses.
Genome biology and evolution. 03/2012;
Eukaryote genomes contain many non-coding regions and they are quite complex. To understand these complexities, we constructed a database, GCD (Genome Composition Database), for the whole genome composition statistics for 101 eukaryote genome data, as well as more than 1,000 prokaryote genomes. Freq... [more] Eukaryote genomes contain many non-coding regions and they are quite complex. To understand these complexities, we constructed a database, GCD (Genome Composition Database), for the whole genome composition statistics for 101 eukaryote genome data, as well as more than 1,000 prokaryote genomes. Frequencies of all possible 1-10 oligonucleotides were counted for each genome, and these observed values were compared with expected values computed under observed oligonucleotide frequencies of length 1 to 4. Deviations from expected values were much larger for eukaryotes than prokaryotes, except for fungal genomes. Mammalian genomes showed the largest deviation among animals. The results of comparison are available online at: http://esper.lab.nig.ac.jp/genome-composition-database/
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Evolutionary patterns of recently emerged animal duplogs.
Genome biology and evolution. 08/2011; 3:1119-35.
Duplogs, or intraspecies paralogs, constitute the important portion of eukaryote genomes and serve as a major source of functional innovation. We conducted detailed analyses of recently emerged animal duplogs. Genome data of three vertebrate species (Homo sapiens, Mus musculus, and Danio rerio), Cae... [more] Duplogs, or intraspecies paralogs, constitute the important portion of eukaryote genomes and serve as a major source of functional innovation. We conducted detailed analyses of recently emerged animal duplogs. Genome data of three vertebrate species (Homo sapiens, Mus musculus, and Danio rerio), Caenorhabditis elegans, and two Drosophila species (Drosophila melanogaster and D. pseudoobscura) were used. Duplication events were divided into six age-groups according to the synonymous distance (dS) up to 0.6. Duplogs were classified into four equal-sized classes on physical distances and into three classes on relative orientations. We observed the following shared characteristics among intrachromosomal multiexon duplogs: 1) inverted duplogs account for 20-50%, and about a half of the physically most distant 25%; 2) except for C. elegans, the composition of physical distances, that of relative orientations, and the proportion of inverted duplogs in each physical distance category are more or less uniform; 3) except for C. elegans, the characteristics of the youngest (dS < 0.01) duplogs are similar to the overall characteristics of the entire set. These results suggest that intrachromosomal duplogs with fairly long physical distances were generated at once, rather than resulting from tandem duplications and subsequent genomic rearrangements. This is different from the three well-known modes of gene duplication: tandem duplication, retrotransposition, and genome duplication. We termed this new mode as "drift" duplication. The drift duplication has been producing duplicate copies at paces comparable with tandem duplications since the common ancestor of vertebrates, and it may have already operated in the common ancestor of bilateral animals.
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2.42Impact points
Gene dosage imbalance of human chromosome 21 in mouse embryonic stem cells differentiating to neurons.
Gene. 08/2011; 481(2):93-101.
Gene dosage imbalance is the central working hypothesis in understanding cognitive impairment and learning difficulty in Down syndrome. A mouse embryonic stem cell line containing single human chromosome 21 was used to study genomic and transcriptomic implications of autosomal imbalance during early... [more] Gene dosage imbalance is the central working hypothesis in understanding cognitive impairment and learning difficulty in Down syndrome. A mouse embryonic stem cell line containing single human chromosome 21 was used to study genomic and transcriptomic implications of autosomal imbalance during early neurogenesis. In this study bioinformatic analysis in the differentiating aneuploid neurons showed 53.6% primary dosage, 25% dosage compensation, and 21.4% reverse dosage effects on trisomic genes, revealing locus-specific secondary dosage effects on disomic genes and its specific trans-acting networks for neural attenuation, degeneration and apoptosis. The obtained results supported the significant gene dosage effects of autosomal imbalance on early neural development, suggesting novel molecular regulations for neurodevelopmental abnormalities in Down syndrome.
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3.76Impact points
Evolutionary conserved microRNAs are ubiquitously expressed compared to tick-specific miRNAs in the cattle tick Rhipicephalus (Boophilus) microplus.
BMC genomics. 06/2011; 12:328.
MicroRNAs (miRNAs) are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilu... [more] MicroRNAs (miRNAs) are small non-coding RNAs that act as regulators of gene expression in eukaryotes modulating a large diversity of biological processes. The discovery of miRNAs has provided new opportunities to understand the biology of a number of species. The cattle tick, Rhipicephalus (Boophilus) microplus, causes significant economic losses in cattle production worldwide and this drives us to further understand their biology so that effective control measures can be developed. To be able to provide new insights into the biology of cattle ticks and to expand the repertoire of tick miRNAs we utilized Illumina technology to sequence the small RNA transcriptomes derived from various life stages and selected organs of R. microplus. To discover and profile cattle tick miRNAs we employed two complementary approaches, one aiming to find evolutionary conserved miRNAs and another focused on the discovery of novel cattle-tick specific miRNAs. We found 51 evolutionary conserved R. microplus miRNA loci, with 36 of these previously found in the tick Ixodes scapularis. The majority of the R. microplus miRNAs are perfectly conserved throughout evolution with 11, 5 and 15 of these conserved since the Nephrozoan (640 MYA), Protostomian (620MYA) and Arthropoda (540 MYA) ancestor, respectively. We then employed a de novo computational screening for novel tick miRNAs using the draft genome of I. scapularis and genomic contigs of R. microplus as templates. This identified 36 novel R. microplus miRNA loci of which 12 were conserved in I. scapularis. Overall we found 87 R. microplus miRNA loci, of these 15 showed the expression of both miRNA and miRNA* sequences. R. microplus miRNAs showed a variety of expression profiles, with the evolutionary-conserved miRNAs mainly expressed in all life stages at various levels, while the expression of novel tick-specific miRNAs was mostly limited to particular life stages and/or tick organs. Anciently acquired miRNAs in the R. microplus lineage not only tend to accumulate the least amount of nucleotide substitutions as compared to those recently acquired miRNAs, but also show ubiquitous expression profiles through out tick life stages and organs contrasting with the restricted expression profiles of novel tick-specific miRNAs.
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9.43Impact points
Nematogalectin, a nematocyst protein with GlyXY and galectin domains, demonstrates nematocyte-specific alternative splicing in Hydra.
Proceedings of the National Academy of Sciences of the United States of America. 10/2010; 107(43):18539-44.
Taxonomically restricted genes or lineage-specific genes contribute to morphological diversification in metazoans and provide unique functions for particular taxa in adapting to specific environments. To understand how such genes arise and participate in morphological evolution, we have investigated... [more] Taxonomically restricted genes or lineage-specific genes contribute to morphological diversification in metazoans and provide unique functions for particular taxa in adapting to specific environments. To understand how such genes arise and participate in morphological evolution, we have investigated a gene called nematogalectin in Hydra, which has a structural role in the formation of nematocysts, stinging organelles that are unique to the phylum Cnidaria. Nematogalectin is a 28-kDa protein with an N-terminal GlyXY domain (glycine followed by two hydrophobic amino acids), which can form a collagen triple helix, followed by a galactose-binding lectin domain. Alternative splicing of the nematogalectin transcript allows the gene to encode two proteins, nematogalectin A and nematogalectin B. We demonstrate that expression of nematogalectin A and B is mutually exclusive in different nematocyst types: Desmonemes express nematogalectin B, whereas stenoteles and isorhizas express nematogalectin B early in differentiation, followed by nematogalectin A. Like Hydra, the marine hydrozoan Clytia also has two nematogalectin transcripts, which are expressed in different nematocyte types. By comparison, anthozoans have only one nematogalectin gene. Gene phylogeny indicates that tandem duplication of nematogalectin B exons gave rise to nematogalectin A before the divergence of Anthozoa and Medusozoa and that nematogalectin A was subsequently lost in Anthozoa. The emergence of nematogalectin A may have played a role in the morphological diversification of nematocysts in the medusozoan lineage.
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9.87Impact points
Evolutionary pattern of gene homogenization between primate-specific paralogs after human and macaque speciation using the 4-2-4 method.
Molecular biology and evolution. 09/2010; 27(9):2152-71.
Homogenization of duplicated genes is an important factor for gene family evolution. In the previous study, we developed a method, named 4-2-4 here, to detect partial homogenization with high sensitivity and high specificity using quartets. A quartet is a set of four genes generated by a duplication... [more] Homogenization of duplicated genes is an important factor for gene family evolution. In the previous study, we developed a method, named 4-2-4 here, to detect partial homogenization with high sensitivity and high specificity using quartets. A quartet is a set of four genes generated by a duplication event and the subsequent speciation of two closely related species. We searched the human and macaque genomes and found 430 nonredundant quartets, which correspond to primate-specific paralogs. The prevalence of homogenization in these quartets was 10.0% (43/430), which was ca. one-third of that (29.8% = 206/691) in the rodent-specific nonredundant quartets obtained through comparison of mouse and rat genomes. Part of this difference comes from the fact that primate paralogs tend to be more remotely located to each other than rodent paralogs, and the remainder may be explained by the inherent difference in the neutral evolutionary rate between the primate and rodent lineages. A statistical analysis taking account of the effects of false negatives uncovered negative correlations between sequence divergence and homogenization prevalence both in primates and rodents. Further statistical analyses controlling for false-negative rates and sequence divergences revealed two characteristics shared by the primate and rodent paralogs; 1) significant negative correlations of the homogenization prevalence with physical distances, and 2) no significant correlation between the prevalence and relative transcriptional orientations. Patterns of the homogenization in the genomic alignments of human-macaque quartets indicate that gene conversion, rather than unequal crossing-over, is the major cause of the homogenization.
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34.48Impact points
The dynamic genome of Hydra.
Nature. 03/2010; 464(7288):592-6.
The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successf... [more] The freshwater cnidarian Hydra was first described in 1702 and has been the object of study for 300 years. Experimental studies of Hydra between 1736 and 1744 culminated in the discovery of asexual reproduction of an animal by budding, the first description of regeneration in an animal, and successful transplantation of tissue between animals. Today, Hydra is an important model for studies of axial patterning, stem cell biology and regeneration. Here we report the genome of Hydra magnipapillata and compare it to the genomes of the anthozoan Nematostella vectensis and other animals. The Hydra genome has been shaped by bursts of transposable element expansion, horizontal gene transfer, trans-splicing, and simplification of gene structure and gene content that parallel simplification of the Hydra life cycle. We also report the sequence of the genome of a novel bacterium stably associated with H. magnipapillata. Comparisons of the Hydra genome to the genomes of other animals shed light on the evolution of epithelia, contractile tissues, developmentally regulated transcription factors, the Spemann-Mangold organizer, pluripotency genes and the neuromuscular junction.
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2.02Impact points
Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies.
Advances in experimental medicine and biology. 01/2010; 680:125-35.
The Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) has operated biological databases since 1987 in collaboration with NCBI and EBI. As one of the three major public databases, CIB-DDBJ has run four primary databases DDBJ, CIBEX, DDBJ Trace Archive (DTA), and DDBJ Read Archive (... [more] The Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ) has operated biological databases since 1987 in collaboration with NCBI and EBI. As one of the three major public databases, CIB-DDBJ has run four primary databases DDBJ, CIBEX, DDBJ Trace Archive (DTA), and DDBJ Read Archive (DRA) to collect, archive, and provide various kinds of biological data. As the massively parallel new sequencing platforms are increasingly in use, huge amounts of the raw data have been produced. To archive these raw data, we at CIB-DDBJ began operating a new repository, the DDBJ Read Archive (DRA). To accommodate efficiently the processed data as well, we have developed a new pipeline, the DDBJ Read Annotation Pipeline that deals with both data submission and analysis. For data produced by the next generation platforms, the three archives DRA, DDBJ, and CIBEX, which are interconnected by the pipeline, collect the raw, processed sequence, and quantitative data, respectively. The public biological databases at CIB-DDBJ, EBI, and NCBI will together construct world-wide archives for biological data by data sharing to accelerate research in life sciences in the era of next generation sequencing technologies.
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2.92Impact points
Gene Expression Profile of Fibrovascular Membranes from Patients with Proliferative Diabetic Retinopathy.
The British journal of ophthalmology. 11/2009;
BACKGROUND/AIMS: The purpose of this study was to generate a profile of genes expressed in preretinal fibrovascular membranes (FVMs) from patients with proliferative diabetic retinopathy. METHODS: A polymerase chain reaction (PCR)-amplified cDNA library was constructed using the RNAs isolated from F... [more] BACKGROUND/AIMS: The purpose of this study was to generate a profile of genes expressed in preretinal fibrovascular membranes (FVMs) from patients with proliferative diabetic retinopathy. METHODS: A polymerase chain reaction (PCR)-amplified cDNA library was constructed using the RNAs isolated from FVMs obtained during vitrectomy. The sequence from the 5' end was obtained for randomly selected clones and used to generate expressed sequence tags (ESTs). Functional annotation was retrieved from Ensemble database and analyzed by FatiGo. The web-based VisANT software was used to identify the molecular networks within the FVMs. RESULTS: A total of 2816 ESTs were assembled in 625 nonredundant clusters. Among these, 515 matched the human cDNA database. The 515 clusters were subdivided by functional subsets of genes related to ribosomal activity, oxidative phosphorylation, focal adhesion, cell adhesion, and other functions. Querying against VisANT database yielded 3175 possible physical relationships to other genes/proteins which included an additional 2480 genes that were not detected in the FVM library. CONCLUSIONS: The cDNA library constructed from human FVMs will be a valuable source of information that should facilitate a wide range of studies that can establish the molecular mechanisms underlying the development of FVMs.
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4.38Impact points
Distribution and structural diversity of cilia in tadpole larvae of the ascidian Ciona intestinalis.
Developmental biology. 10/2009;
Accumulating evidence demonstrates that cilia play important roles in a variety of processes in embryogenesis. For functional survey of larval cilia at the cellular level, we exploited the simple cell organization of tadpole larvae in the ascidian Ciona intestinalis. Immunofluorescent microscopy sho... [more] Accumulating evidence demonstrates that cilia play important roles in a variety of processes in embryogenesis. For functional survey of larval cilia at the cellular level, we exploited the simple cell organization of tadpole larvae in the ascidian Ciona intestinalis. Immunofluorescent microscopy showed distribution of cilia not only in previously described tissues but also in a subpopulation of ependymal cells in the sensory vesicle, gut primordium, papillae, apical trunk epidermal neurons, and the endodermal strand. Transmission electron microscopy revealed a variety of axonemal structures, including a 9+0 structure similar to vertebrate primary cilia, a 9+0 structure with electron-dense materials in the center, a 9+2 structure with no dynein arms, and an axoneme with a disorganized structure at the distal end. Extensive description of cilia in the present study gives important insights into the evolution of the ciliary structure and provides a basis for analysis of ciliary functions in establishment of chordate body plan.
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34.28Impact points
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line.
Nature genetics. 05/2009;
Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, w... [more] Using deep sequencing (deepCAGE), the FANTOM4 study measured the genome-wide dynamics of transcription-start-site usage in the human monocytic cell line THP-1 throughout a time course of growth arrest and differentiation. Modeling the expression dynamics in terms of predicted cis-regulatory sites, we identified the key transcription regulators, their time-dependent activities and target genes. Systematic siRNA knockdown of 52 transcription factors confirmed the roles of individual factors in the regulatory network. Our results indicate that cellular states are constrained by complex networks involving both positive and negative regulatory interactions among substantial numbers of transcription factors and that no single transcription factor is both necessary and sufficient to drive the differentiation process.
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3.43Impact points
Optimized ancestral state reconstruction using Sankoff parsimony.
BMC bioinformatics. 03/2009; 10(1):51.
ABSTRACT: BACKGROUND: Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to transitions between character states.... [more] ABSTRACT: BACKGROUND: Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to transitions between character states. Although optimizations exist to reduce the computations in the number of taxa, the original algorithm is quadratic in the number of states 'n', making it impractical for large values of 'n'. RESULTS: In this study we introduce an optimization of Sankoff parsimony for the reconstruction of ancestral states when ultrametric or additive cost matrices are used. We analyzed its performance for randomly generated matrices, Jukes-Cantor and Kimura's two-parameter models of DNA evolution, and in the reconstruction of elongation factor-1 alpha and ancestral metabolic states of a group of eukaryotes, showing that in all cases the execution time is significantly less than with the original implementation. CONCLUSIONS: The algorithms here presented provide a fast computation of Sankoff parsimony for a given phylogeny. Problems where the number of states is large, such as reconstruction of ancestral metabolism, are particularly adequate for this optimization. Since we are reducing the computations required to calculate the parsimony cost of a single tree, our method can be combined with optimizations in the number of taxa that aim at finding the most parsimonious tree.
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2.42Impact points
The evolutionary study of small RNA-directed gene silencing pathways by investigating RNase III enzymes.
Gene. 02/2009;
The RNA-mediated gene silencing pathways are evolutionarily conserved processes. It highlights a fundamental role of short RNAs in eukatyotic gene regulation and antiviral defense. Recently three distinct small RNA-directed silencing pathways are observed, such as the destruction of mRNA via siRNA, ... [more] The RNA-mediated gene silencing pathways are evolutionarily conserved processes. It highlights a fundamental role of short RNAs in eukatyotic gene regulation and antiviral defense. Recently three distinct small RNA-directed silencing pathways are observed, such as the destruction of mRNA via siRNA, inhibition of mRNA translation via miRNA, and epigenetic gene silencing via siRNA. It was also found that in these pathways, the members of ribonuclease III family play important roles in diverse RNA maturation and decay. Here we investigated the evolution of RNase III nucleases, Dicer as representative, to further figure out the evolutionary relationship of these three gene silencing pathways. With the advantage of using genomic sequences as the subject in homolog search, in un-annotated genomic regions, we were able to detect possible candidates for 3 functional domains and genes of dicer and drosha. Moreover, we found that prokaryotes including eubacteria and archaea lack completely the PAZ domain of Dicer. These results show the taxonomic-dependent evolution of the RNA-mediated gene silencing pathways.
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2.42Impact points
An evolutionary origin and selection process of goldfish.
Gene. 12/2008;
Many different physical characteristics of goldfish (Carassius auratus auratus), such as celestial and telescopic eyes, fancy but uncontrollable shapes of tail fin, an unfittingly fat body, and loss of dorsal fins, provide us with a unique opportunity of studying artificial selection on phenotypic c... [more] Many different physical characteristics of goldfish (Carassius auratus auratus), such as celestial and telescopic eyes, fancy but uncontrollable shapes of tail fin, an unfittingly fat body, and loss of dorsal fins, provide us with a unique opportunity of studying artificial selection on phenotypic changes on the basis of molecular evolution. The aim of the present study is to elucidate the evolutionary origin and history of goldfish, taking into account the different characteristics of goldfish and human culture. Collecting 44 samples of a variety of goldfish from Japan and China as well as common and Crucian carps, we determined the nucleotide sequences for a substantial portion of mitochondrial genome including eight gene regions (D-loop, 12SrRNA, 16SrRNA, ND1, ND2, COI, ND5 and Cyt b) of approximately 11,180 bps. We, then, constructed phylogenetic trees for a total of 78 fishes, adding the 19 sequence data available in the international DNA database DDBJ/EMBL/GenBank to our 59 sequence data determined. From the phylogenetic trees obtained, we found that Japanese goldfish are not relative to Japanese Crucian carp (Carassius auratus langsdorfi) and that all the goldfish examined were originated from one of the two groups of the Chinese Crucian carp "Gibelio" (Carassius auratus gibelio). Moreover, we found that the process of artificial selection began from losing the dorsal fin followed by diversification of other characters such as eyes. This is supported by our further observations that the improvement of celestial and telescope eyes took place independently at different times, implying that goldfish was imposed by strong artificial selection only to meet diversified needs of human preferences in a unsystematic way.
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4.34Impact points
Specific expression of Gsta4 in mouse cochlear melanocytes: a novel role for hearing and melanocyte differentiation.
Pigment cell & melanoma research. 11/2008;
Summary Mammalian pigment cells produce melanin as the main pigment. Melanocytes, one of the two types of mammalian pigment cells, differentiate from the neural crest and migrate to a variety of organs during development. Melanocytes exist not only in the skin but also in other sites such as the coc... [more] Summary Mammalian pigment cells produce melanin as the main pigment. Melanocytes, one of the two types of mammalian pigment cells, differentiate from the neural crest and migrate to a variety of organs during development. Melanocytes exist not only in the skin but also in other sites such as the cochlea where they are essential for hearing. Mitf(mi-bw) is one of the known recessive alleles of the mouse microphthalmia-associated transcription factor (Mitf) locus, which is essential for the development of pigment cells. Homozygous Mitf(mi-bw)/Mitf(mi-bw) mice have a completely white coat with black eyes and are deaf due to the lack of melanocytes. By comparing gene expression profiles in cochleae of wild-type and Mitf(mi-bw)/Mitf(mi-bw) mice, we now demonstrate the specific expression of glutathione S-transferase alpha 4 (Gsta4) in the stria vascularis. Gsta4 encodes one of the cytosolic glutathione S-transferases (GSTs) which participate in detoxification processes of many tissues. This gene is specifically expressed in intermediate cells of the stria vascularis, suggesting a novel function for cochlear melanocytes. Moreover, among mammalian pigment cells, expression of Gsta4 was restricted to cochlear melanocytes, suggesting that melanocytes in various tissues differentiate from one another depending on their location.
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7.48Impact points
DDBJ dealing with mass data produced by the second generation sequencer.
Nucleic acids research. 11/2008;
DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period include genome scale data of Bombyx mori, Oryzas latipes, Drosophila and Lotus japonicus. In addition, from... [more] DNA Data Bank of Japan (DDBJ) (http://www.ddbj.nig.ac.jp) collected and released 2 368 110 entries or 1 415 106 598 bases in the period from July 2007 to June 2008. The releases in this period include genome scale data of Bombyx mori, Oryzas latipes, Drosophila and Lotus japonicus. In addition, from this year we collected and released trace archive data in collaboration with National Center for Biotechnology Information (NCBI). The first release contains those of O. latipes and bacterial meta genomes in human gut. To cope with the current progress of sequencing technology, we also accepted and released more than 100 million of short reads of parasitic protozoa and their hosts that were produced by using a Solexa sequencer.
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2.42Impact points
The evolutionary relationship between gene duplication and alternative splicing.
Gene. 10/2008;
Gene duplication and alternative splicing (AS) are the two major evolutionary mechanisms that can bring the functional variation by increasing gene diversification. The purpose of this research is to understand the evolutionary relationship between these two different mechanisms, utilizing available... [more] Gene duplication and alternative splicing (AS) are the two major evolutionary mechanisms that can bring the functional variation by increasing gene diversification. The purpose of this research is to understand the evolutionary relationship between these two different mechanisms, utilizing available data resources. We found the proportion of AS loci and the average number of AS isoforms per locus to be larger in duplicated genes compared to those in singleton genes. However we also found that small gene families have larger proportion of AS loci and larger average number of AS isoforms per locus than large gene families. These results suggest that gene duplication allows for more alternative splicing events to occur on newly duplicated copies than on singletons, probably due to the reduced functional constraint on the duplicates. Smaller average number of AS isoforms in the larger gene families can be explained by the decreased possibility for new useful function to be created via a new alternative splicing event.
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3.29Impact points
Evolutionary origin of the vertebrate blood complement and coagulation systems inferred from liver EST analysis of lamprey.
Developmental and comparative immunology. 09/2008;
The complement and coagulation systems in mammalian blood are composed of multiple components with unique domain structures, and are believed to be established by exon-shufflings and following gene duplications. To elucidate their origin in vertebrates, liver EST and 5'- and 3'-rapid amplifi... [more] The complement and coagulation systems in mammalian blood are composed of multiple components with unique domain structures, and are believed to be established by exon-shufflings and following gene duplications. To elucidate their origin in vertebrates, liver EST and 5'- and 3'-rapid amplification of cDNA ends (RACE) analyses were performed in lamprey, Lethenteron japonicum. For the complement system, the factor I cDNA was cloned for the first time outside of the jawed vertebrates. Evidence for the C3/C4/C5, fB/C2 and MASP-1/MASP-2/C1r/C1s gene duplications was not found, suggesting that these duplications occurred in the jawed vertebrate lineage. In contrast, the coagulation factors VII and X, prothrombin and protein C-like cDNAs were identified, indicating that duplications among them predated the cyclostome-jawed vertebrate divergence. The genes for terminal complement components, coagulation factors XI and XII, or prekallikrein were not found, suggesting that the complement and coagulation systems of an ancestral vertebrate were simpler compared to their mammalian counterparts.
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9.87Impact points
Cilium evolution: identification of a novel protein, nematocilin, in the mechanosensory cilium of Hydra nematocytes.
Molecular biology and evolution. 09/2008; 25(9):2009-17.
The cnidocil at the apical end of Hydra nematocytes is a mechanosensory cilium, which acts as a "trigger" for discharge of the nematocyst capsule. The cnidocil protrudes from the center of the cnidocil apparatus and is composed of singlet and doublet microtubules surrounding an electron-de... [more] The cnidocil at the apical end of Hydra nematocytes is a mechanosensory cilium, which acts as a "trigger" for discharge of the nematocyst capsule. The cnidocil protrudes from the center of the cnidocil apparatus and is composed of singlet and doublet microtubules surrounding an electron-dense central filament. In this paper, we identify a novel protein, nematocilin, which is localized in the central filament. Immunofluorescence staining and immunogold electron microscopy show that nematocilin forms filaments in the central core of the cnidocil. Nematocilin represents a new member of the intermediate filament superfamily. Two paralogous sequences of nematocilin are present in the Hydra genome and appear to be the result of recent gene duplication. Comparison of the exon-intron structure suggests that the nematocilin genes evolved from the nuclear lamin gene by conserving exons encoding the coiled-coil domains and replacing the C-terminal lamin domains. Molecular phylogenetic analyses also support the hypothesis of a common ancestor between lamin and nematocilin. Comparison of cnidocil structures in different cnidarians indicates that a central filament is present in the cnidocils of several hydrozoan and a cubozoan species but is absent in the cnidocils of anthozoans. A nematocilin homolog is absent in the recently completed genome of the anthozoan Nematostella. Thus, the evolution of a novel ciliary structure, which provides mechanical rigidity to the sensory cilium during the process of mechanoreception, is associated with the evolution of a novel protein.
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