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Akihiko Koga

Publications and source records attributed to Akihiko Koga.

15 recordsLinked to original sources
PubMed2024

Questioning inbreeding: Could outbreeding affect productivity in the North African catfish in Thailand?

The North African catfish (Clarias gariepinus) is a significant species in aquaculture, which is crucial for ensuring food and nutrition security. Their high adaptability to diverse environments has led to an increase in the number of farms that are available for their production. However, long-term closed breeding adversely affects their reproductive performance, leading to a decrease in production efficiency. This is possibly caused by inbreeding depression. To investigate the root cause of this issue, the genetic diversity of captive North African catfish populations was assessed in this study. Microsatellite genotyping and mitochondrial DNA D-loop sequencing were applied to 136 catfish specimens, collected from three populations captured for breeding in Thailand. Interestingly, extremely low inbreeding coefficients were obtained within each population, and distinct genetic diversity was observed among the three populations, indicating that their genetic origins are markedly different. This suggests that outbreeding depression by genetic admixture among currently captured populations of different origins may account for the low productivity of the North African catfish in Thailand. Genetic improvement of the North African catfish populations is required by introducing new populations whose origins are clearly known. This strategy should be systematically integrated into breeding programs to establish an ideal founder stock for selective breeding.

Animals↗
PubMed2006

Vertebrate DNA transposon as a natural mutator: the medaka fish Tol2 element contributes to genetic variation without recognizable traces.

DNA-based transposable elements, or DNA transposons, transpose in a cut-and-paste fashion, involving excision from the chromosome. If this process affects the function of a host gene and the excision rate is high, any gene associated with such an element would clearly be in a genetically "unstable" state, and there are many examples of unstable genes in various organisms. However, none have hitherto been reported in vertebrates. We here document the finding of an unstable mutant gene in the medaka fish, Oryzias latipes, a useful model animal for vertebrate genetics and evolutionary studies. In an inbred strain, excision of the Tol2 element inserted in a pigmentation gene occurs spontaneously, giving rise to different heritable phenotypes and new mutant genes that carry different excision footprint sequences. The phenotypic mutation rate is as high as 2% per gamete, representing a 1000-fold increase from spontaneous mutation rates so far determined with the same organism. With mutations caused by insertion, and then excision, of transposons, one can no longer recognize participation of transposons in their generation. Thus, the impact of DNA transposons on vertebrate genomes may be, and may have been, larger than commonly supposed.

Alleles↗
PubMed2006

Targeted reduction of the DNA methylation level with 5-azacytidine promotes excision of the medaka fish Tol2 transposable element.

The Tol2 element of the medaka fish Oryzias latipes is a member of the hAT (hobo/Activator/Tam3) transposable element family. There is evidence for rapid expansion in the genome and throughout the species in the past but a high spontaneous transposition rate is not observed with current fish materials, suggesting that the Tol2 element and its host species have already acquired an interactive mechanism to control the transposition frequency. DNA methylation is a possible contributing factor, given its involvement with many other transposable elements. We therefore soaked embryos in 5-azacytidine, a reagent that causes reduction in the DNA methylation level, and examined amounts of PCR products reflecting the somatic excision frequency, obtaining direct evidence that exposure promotes Tol2 excision. Our results thus suggest that methylation of the genome DNA is a factor included in the putative mechanisms of control of transposition of the Tol2 element.

Animals↗
PubMed2006

Color reversion of the albino medaka fish associated with spontaneous somatic excision of the Tol-1 transposable element from the tyrosinase gene.

The medaka fish albino mutant, i(1) is one of the Tomita collection of medaka pigmentation mutants which exhibits a complete albino phenotype, because of inactivation of the tyrosinase gene due to insertion of a transposable element, Tol-1. Recently, mosaic black-pigmented i(1) medaka fish have arisen in one of our laboratory breeding populations. Their pigmented cells have been observed in all of the tissues, including the eye and skin, in which melanin is detectable in the wild type. In this study, we analyzed the tyrosinase gene of revertants and showed Tol-1 to have been precisely excised from the gene, suggesting a causal relationship. Mosaic patterns of pigmentation indicate spontaneous somatic excision of the element from the tyrosinase gene. To our knowledge, this is the first transposable element with somatic excision activity demonstrated phenotypically in vertebrates. The pattern of pigmentation in mosaic revertants indicates frequencies of melanin pigments to be consistent with the numbers of melanophores per unit area of body sites, such as the eyes, head and dorsal trunk.

Albinism↗
PubMed2005

Reversion mutation of ib oculocutaneous albinism to wild-type pigmentation in medaka fish.

We have previously identified three naturally occurring mutations in the medaka fish tyrosinase gene caused by transposable element insertions. Tyr-i(b) is one of these, containing the Tol2 element in the promoter region. Its homozygous carriers exhibit a weak oculocutaneous albino phenotype. We report here spontaneous reversion of the albino phenotype to the wild-type pigmentation, associated with excision of the Tol2 element. The newly arising mutant gene is inherited in the Mendelian fashion. Thus, oculocutaneous albinism is not strictly irreversible, at least in this organism and the results also indicate that the insertion of the Tol2 element is the main, and possibly the only, cause of the i(b) albinism. Importantly our data also suggest that medaka fish possess an active transposase.

Albinism, Oculocutaneous↗
PubMed2004

The tyrosinase gene of the i(b) albino mutant of the medaka fish carries a transposable element insertion in the promoter region.

The i locus of the medaka fish contains the tyrosinase gene whose product is the key enzyme required for melanin biosynthesis. The i(b) allele at this locus, also denoted as i( 5), causes oculocutaneous albinism in homozygous carriers. Its albino phenotype is very weak, characterized mainly by small and varying sized melanophores in juveniles. Cloning and sequencing analyses of the tyrosinase gene for the i (b) allele revealed the presence of a 4.7-kb extra DNA fragment in the 5' untranslated region, this being Tol2, a DNA-based transposable element of the hobo Activator Tam3 (hAT) family which had previously been identified as a cause of another mutant allele i(4). Its insertion point was 85 bp upstream of the main transcription initiation site and 50 bp downstream of the CATGTG motif that has been suggested to be essential for the promoter function of the tyrosinase gene. The transcription level of the tyrosinase gene was decreased in i(b)/i(b) fish, compared with wild-type fish. The insertion is thus a likely cause of the weak albino phenotype. The Tol2 element transposes in a cut-and-paste fashion, and its excision is mostly imprecise, leaving some nucleotides and/or removing excess nucleotides. The i (b) mutant strain can thus be expected to serve as a source from which various other mutations in the promoter region can be derived.

Albinism↗
PubMed2004

Low transposition frequency of the medaka fish Tol2 element may be due to extranuclear localization of its transposase.

Transposase proteins of some highly active DNA-based transposable elements, such as the maize Activator element, are known to possess nuclear localization signals (NLSs). We examined if this is also the case for the transposase of the medaka fish Tol2 element, a member of the hAT (hobo/Activator/Tam3) transposable element family, using human and mouse culture cells. Unexpectedly, the transposase-lacZ fusion protein, in which the lacZ is a location marker, was found to be present in the cytoplasm rather than in the nucleus, suggesting that the Tol2 transposase contains a signal for extranuclear localization. The same staining pattern was also observed with a fusion protein containing a 33-amino-acid region at about the center of the primary structure of the transposase. The Tol2 element might have a mechanism to control its transposition frequency that includes extranuclear localization of its transposase.

Animals↗
PubMed2004

Transposition mechanisms and biothechnology applications of the medaka fish tol2 transposable element.

The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision footprints being heterogeneous. In more than half of excision events, however, breakage and rejoining of DNA molecules occur within the 8-bp target site duplication region, removing the entire Tol2 sequence and retaining parts of the target site duplications. In the reminder of the excision events, either the left or the right terminal region is left and the other end is lost together with its flanking region. Thus, there might be two different mechanisms of excision. Insertion of Tol2 occurs without detectable preference for target sequences and creates a target site duplication of exactly 8 bp. In addition to the medaka fish and related fish species, Tol2 transposes in mammalian cells in culture, including human and mouse examples. Autonomy is also retained in these cases. A gene transfer vector using Tol2 has already been established in fish. Foreign DNA fragements inserted in Tol2 can be efficiently delivered to the chromosomes by transposition. The latest version of the vector contains, between the Tol2 terminal regions, a bacterial drug-resistance gene and a plasmid replication origin. This allows simple recovery of insertion regions, as plasmid DNA, from genomic DNA of transformants. Modification of this system for other vertebrates, especially for mammals, are now in progress.

Journal Article↗
PubMed2004

Transposition mechanisms and biotechnology applications of the medaka fish Tol2 transposable element.

The Tol2 element of the medaka fish is a member of the hAT (hobo/Activator/ Tam3) transposable element family. About 20 copies are present in the medaka fish genome and, unlike many other hAT family elements, virtually all the copies are autonomous or potentially autonomous, containing an intact transposase gene. Excision of Tol2 is not precise at the nucleotide sequence level, excision foot-prints being heterogeneous. In more than half of excision events, however, breakage and rejoining of DNA molecules occur within the 8-bp target site duplication region, removing the entire Tol2 sequence and retaining parts of the target site duplications. In the reminder of the excision events, either the left or the right terminal region is left and the other end is lost together with its flanking region. Thus, there might be two different mechanisms of excision. Insertion of Tol2 occurs without detectable preference for target sequences and creates a target site duplication of exactly 8 bp. In addition to the medaka fish and related fish species, Tol2 transposes in mammalian cells in culture, including human and mouse examples. Autonomy is also retained in these cases. A gene transfer vector using Tol2 has already been established in fish. Foreign DNA fragements inserted in Tol2 can be efficiently delivered to the chromosomes by transposition. The latest version of the vector contains, between the Tol2 terminal regions, a bacterial drug-resistance gene and a plasmid replication origin. This allows simple recovery of insertion regions, as plasmid DNA, from genomic DNA of transformants. Modification of this system for other vertebrates, especially for mammals, are now in progress.

Amino Acid Sequence↗
PubMed2003

The medaka fish Tol2 transposable element can undergo excision in human and mouse cells.

Tol2 is an active DNA-based transposable element identified in the medaka fish, Oryzias latipes. Originating from a vertebrate and belonging to the hAT ( hobo/ Activator/ Tam3) transposable element family, featuring a wide distribution among organisms, Tol2 would be expected to be active if introduced into mammals. We, therefore, examined if excision, one part of the transposition reaction, can occur in human and mouse culture cells. A Tol2 clone was introduced into cells and, after incubation, recovered. PCR and sequencing analysis provided evidence for precise and near precise excision in these cells. Tol2 can thus be expected to serve as a material for developing a gene transfer vector and other genetic tools applicable to mammals. It was also suggested that an intact Tol2 element could retain autonomy as a transposable element in mammalian cells.

3T3 Cells↗
PubMed2003

Long and short mRnas transcribed from the medaka fish transposon Tol2 respectively exert positive and negative effects on excision.

The medaka fish transposable element, Tol2, is a member of the hAT family of transposons. It has been directly demonstrated to be active and two mRNAs, differing in length, have been isolated. They cover exons 1-4 and exons 2-4 and the longer form has already been proven to catalyse transposition reactions. However, the function of the shorter mRNA in medaka cells has hitherto remained unclear. In the present study, first we constructed a quantitative system to detect Tol2 excision using an indicator plasmid carrying a non-autonomous Tol2 within its lacZ gene; second we injected mRNAs with the plasmid into medaka eggs. Excision of Tol2 was detected as E. coli blue colonies caused by the recovery of lacZ activity. Addition of the longer mRNA increased excision, but the shorter did not. Moreover, co-injection of both mRNAs greatly lowered the frequency compared with the case of treatment with the longer mRNA alone. These results indicate that the shorter mRNA has an inhibitory effect on the excision reaction, and that the N-terminal region of the transposase encoded by exon 1, including a BED zinc finger, presumably plays an important role in excision. Here, we suggest a regulatory mechanism of Tol2 transposition involving the expression of these mRNAs.

Animals↗
PubMed2002

Gene transfer and cloning of flanking chromosomal regions using the medaka fish Tol2 transposable element.

For the ultimate purpose of developing genetic tools using the medaka fish Tol2 transposable element, we examined whether it can transfer a marker gene into the fish genome and also be applied for cloning of chromosomal regions adjacent to insertion points. An internal region of Tol2 was removed and replaced with the green fluorescent protein (GFP) gene and a bacterial plasmid replication origin. This modified Tol2 clone was microinjected into fertilized eggs together with messenger RNA for the Tol2 transposase. The GFP gene was found to be integrated into chromosomes and transmitted to subsequent generations. Restriction enzyme digestion of genomic DNA of a transformant fish, followed by ligation and introduction into bacteria, produced a plasmid containing the entire element and flanking chromosomal regions. Sequencing analysis of this clone demonstrated transposition of the element in the germline of the first generation. Thus, the basic requirements for a gene transfer vector and gene tagging system were fulfilled.

Journal Article↗
PubMed2002

Transposable elements in medaka fish.

DNA-based transposable elements appear to have been nearly or completely inactivated in vertebrates. Therefore the elements of the medaka fish Oryzias latipes that still have transposition activity provide precious materials for studying transposition mechanisms, as well as the evolution, of transposable elements in vertebrates. Fortunately, the medaka fish has a strong background for genetic and evolutionary studies. The advantages of this host species and their elements, together with results so far obtained, are here described.

Animals↗