Biomedical subjects

Osamu Gotoh

Publications and source records attributed to Osamu Gotoh.

6 recordsLinked to original sources

PubMed2006

Improvement in accuracy of multiple sequence alignment using novel group-to-group sequence alignment algorithm with piecewise linear gap cost.

BACKGROUND: Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy and speed. In the alignment of a family of protein sequences, global MSA algorithms perform better than local ones in many cases, while local ones perform better than global ones when some sequences have long insertions or deletions (indels) relative to others. Many recent leading MSA algorithms have incorporated pairwise alignment information obtained from a mixture of sources into their scoring system to improve accuracy of alignment containing long indels. RESULTS: We propose a novel group-to-group sequence alignment algorithm that uses a piecewise linear gap cost. We developed a program called PRIME, which employs our proposed algorithm to optimize the well-defined sum-of-pairs score. PRIME stands for Profile-based Randomized Iteration MEthod. We evaluated PRIME and some recent MSA programs using BAliBASE version 3.0 and PREFAB version 4.0 benchmarks. The results of benchmark tests showed that PRIME can construct accurate alignments comparable to the most accurate programs currently available, including L-INS-i of MAFFT, ProbCons, and T-Coffee. CONCLUSION: PRIME enables users to construct accurate alignments without having to employ pairwise alignment information. PRIME is available at http://prime.cbrc.jp/.

Algorithms↗

PubMed2006

Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns.

MOTIVATION: Large-scale detection and classification of alternative splicing and transcriptional initiation (ASTI) is the first step towards detailed studies of the functional implication and mechanisms of these phenomena. RESULTS: We have developed an algorithm that classifies all observed units of ASTI into an extendable set of distinct types (e.g. cassette type) by converting a collection of alignments between a genomic DNA sequence and cDNA sequences into binary description. This description system can uniquely and compactly encode not only typical patterns but also any rare patterns that are usually collectively assigned to 'others.' More than 150 distinct ASTI types were found when this system was applied to genome-wide detection of ASTI units in human and five other eukaryotes. AVAILABILITY: The data detected by this system are available through ASTRA (http://alterna.cbrc.jp/), a database equipped with a Java-based browser that can interactively reorganize the order of displayed splicing patterns on demand.

Algorithms↗

PubMed2005

Genome sequencing and analysis of Aspergillus oryzae.

The genome of Aspergillus oryzae, a fungus important for the production of traditional fermented foods and beverages in Japan, has been sequenced. The ability to secrete large amounts of proteins and the development of a transformation system have facilitated the use of A. oryzae in modern biotechnology. Although both A. oryzae and Aspergillus flavus belong to the section Flavi of the subgenus Circumdati of Aspergillus, A. oryzae, unlike A. flavus, does not produce aflatoxin, and its long history of use in the food industry has proved its safety. Here we show that the 37-megabase (Mb) genome of A. oryzae contains 12,074 genes and is expanded by 7-9 Mb in comparison with the genomes of Aspergillus nidulans and Aspergillus fumigatus. Comparison of the three aspergilli species revealed the presence of syntenic blocks and A. oryzae-specific blocks (lacking synteny with A. nidulans and A. fumigatus) in a mosaic manner throughout the genome of A. oryzae. The blocks of A. oryzae-specific sequence are enriched for genes involved in metabolism, particularly those for the synthesis of secondary metabolites. Specific expansion of genes for secretory hydrolytic enzymes, amino acid metabolism and amino acid/sugar uptake transporters supports the idea that A. oryzae is an ideal microorganism for fermentation.

Aspartic Acid Endopeptidases↗

PubMed2005

Species-specific variation of alternative splicing and transcriptional initiation in six eukaryotes.

The genome-wide detection of alternative splicing and transcriptional initiation (ASTI) was conducted in six eukaryotes (human, mouse, fruit fly, nematode, cress and rice) whose genome sequencing has been completed or nearly completed. Transcriptional isoforms were collected by mapping a batch of full-length cDNA sequences onto the respective cognate genomic sequences. Isoforms mapped on the same gene locus were compared pair-wise, ASTI patterns were segmented into minimal spans, and then the minimal patterns (ASTI units) were classified into unique types, such as the cassette type or the alternative donor site. All these procedures were performed automatically under the same conditions so that the results obtained from different species could be compared directly. The fraction of loci that underwent ASTI of the total mapped loci was the largest for mammals and fruit fly, and the smallest for plants. Exactly the same trend was observed for the number of unique ASTI types found in each species. The observed fractional representations of the ASTI types were similar between evolutionarily close species, such as human and mouse or cress and rice. On the other hand, the relative orders of abundance in individual ASTI type were considerably different between evolutionarily distant species, such as between mammals and plants. In human and mouse, alternative splicing other than the retained introns tended to occur within the protein coding sequence (CDS) regions rather than within the untranslated regions (UTRs), whereas this tendency was obscure in the other four species. In all the species examined, the difference in alternative exon lengths was most likely in multiples of three, and this tendency was most prominent when the alternative exons were embedded within the CDSs. These observations are generally consistent with the idea that higher organisms utilize the ASTI mechanisms more extensively and in a more complicated manner than lower organisms, and that ASTI actively participates in the enhancement of the functional and structural diversity of products generated from a limited number of genes on a genome.

3' Untranslated Regions↗

PubMed2004

A novel induction mechanism of the rat CYP1A2 gene mediated by Ah receptor-Arnt heterodimer.

We have identified an enhancer responsible for induction by 3-methylcholanthrene in the upstream region of the CYP1A2 gene. The enhancer does not contain the invariant core sequence of XREs that are binding sites for the Ah receptor (AhR) and Arnt heterodimer. The enhancer did not show any inducible expression in Hepa-1-derived cell lines, C4 and C12, deficient of Arnt and AhR, respectively. On the other hand, bacterially expressed AhR-Arnt heterodimer could not bind to the enhancer. Mutational analysis of the enhancer revealed that a repeated sequence separated by six nucleotides is important for expression. A factor binding specifically to the enhancer was found by using gel shift assays. Bacterially expressed AhR-Arnt heterodimer interacted with the factor. A dominant negative mutant of the AhR to XRE activated the enhancer. Collectively, these results demonstrate that a novel induction mechanism is present in which the AhR-Arnt heterodimer functions as a coactivator.

Animals↗

PubMed2003

Molecular mechanism of nuclear translocation of an orphan nuclear receptor, SXR.

The steroid and xenobiotic receptor (SXR) is an orphan nuclear receptor that plays a key role in the regulation of xenobiotic response by controlling the expression of drug metabolizing and clearance enzymes. We observed that pregnane X receptor (PXR), the mouse ortholog of SXR, was retained in the cytoplasm of hepatic cells of untreated mice, whereas PXR was translocated to the nucleus after administration of a ligand, pregnenolone 16 alpha-carbonitrile. To understand the molecular mechanisms underlying the xenochemical-dependent nuclear translocation of SXR, we identified the signal sequence of SXR that regulates its nuclear translocation; using an in vitro expression system, we allocated the nuclear localization signal (NLS) to amino acid residues 66 to 92 within the DNA binding domain of SXR. The NLS of SXR is characterized as the bipartite type, and is recognized by the three molecular species of importin alpha: Rch1 (PTAC58), NPI1, and Qip1, in the presence of PTAC97 of importin beta to target the nuclear pore. The nuclear translocation of SXR was observed as an essential regulatory event for transcription of its target genes such as CYP3A4. These results strongly suggest that the molecular mechanism of the nuclear import of SXR was different from that of another xenosensor, the constitutively active receptor, whose translocation into the nucleus is mediated by a leucine-rich xenochemical response signal in its ligand binding domain.

Active Transport, Cell Nucleus↗