Mitochondrial genome and a nuclear gene indicate a novel phylogenetic position of deep-sea tube-eye fish (Stylephoridae)

The rare, monotypic deep-sea fish family Stylephoridae has long been considered a member of the order Lampridiformes (opahs, velifers, ribbonfishes), and no systematic ichthyologist has questioned its placement within the order for over 80 years. Recently three individuals of Stylephorus chordatus were collected from different oceans, and we sequenced the whole mitochondrial genome and a partial nuclear recombination activating gene 1 (RAG1) gene sequences for each specimen. We aligned these sequences with those available from higher teleosts, including representative lampridiforms, and constructed two separate datasets from the sequences. The resulting trees derived from partitioned Bayesian analyses strongly indicated that S. chordatus is not a lampridiform but is closely related to the order Gadiformes (cod and their relatives). Lampridiformes is diagnosed on the basis of four synapomorphies, three of which are correlated with the rare and possibly unique ability to extend both the maxilla and premaxilla as a unit during feeding. Stylephorus also possesses such unique ability, but lacks two and possibly three of the four synapomorphies, suggesting that further morphological analysis is needed. Considering its unique morphologies with no indication of affinities within Gadiformes (or any other presently recognized order), the present results warrant a recognition of the new order for S. chordatus in fish systematics.     

Diversification and adaptive evolution of putative sweet taste receptors in threespine stickleback

The threespine stickleback Gasterosteus aculeatus is known to include several morphologically and ecologically divergent forms. Its phenotypic traits related to feeding vary among forms, and are considered to be a result of adaptations to various environments to find foods effectively. To examine whether the diversification of feeding modes in the stickleback involves genetic changes of the sense of taste, taste receptor family 1 (T1R) genes in stickleback were analyzed and compared with those in other model fishes. Ten T1R genes and 2 pseudogenes were identified from the stickleback genomic sequences. In particular, putative sweet taste receptors (T1R2s) highly increased in number in stickleback (8 genes and 2 pseudogenes) compared to other fishes (2-3 genes). Maximum likelihood estimations of nonsynonymous-synonymous nucleotide substitution rate have indicated that stickleback T1R2 are under positive selection. Expression analysis by RT-PCR revealed that most stickleback T1R genes were expressed in the taste organs; however, at least two T1R2 genes were not expressed in the taste organs, suggesting that the expression levels of these T1R2 genes may be fluctuated through the life history. In addition, sequencing analysis showed that several T1R2 genes in an anadromous form stickleback individual collected from the western Pacific (Japan) were substantially different from those in genomic data derived from a freshwater form individual collected in North America. This suggested that intra-specific variations of stickleback T1R2 genes were considerably large. Our results imply that, in stickleback, T1R2s have diversified through adaptation to various environments, probably to perceive substances important for its survival and reproduction.     

Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes

Background  

Fishes in the families Cichlidae and Labridae provide good probable examples of vertebrate adaptive radiations. Their spectacular trophic radiations have been widely assumed to be due to structural key innovation in pharyngeal jaw apparatus (PJA), but this idea has never been tested based on a reliable phylogeny. For the first step of evaluating the hypothesis, we investigated the phylogenetic positions of the components of the suborder Labroidei (including Pomacentridae and Embiotocidae in addition to Cichlidae and Labridae) within the Percomorpha, the most diversified (> 15,000 spp) crown clade of teleosts. We examined those based on 78 whole mitochondrial genome sequences (including 12 newly determined sequences) through partitioned Bayesian analyses with concatenated sequences (13,933 bp).     

Remarkable morphological stasis in an extant vertebrate despite tens of millions of years of divergence

The relationship between genotypic and phenotypic divergence over evolutionary time varies widely, and cases of rapid phenotypic differentiation despite genetic similarity have attracted much attention. Here, we report an extreme case of the reverse pattern--morphological stasis in a tropical fish despite massive genetic divergence. We studied the enigmatic African freshwater butterfly fish (Pantodon buchholzi), whose distinctive morphology earns it recognition as a monotypic family. We sequenced the mitochondrial genome of Pantodon from the Congo basin and nine other osteoglossomorph taxa for comparison with previous mitogenomic profiles of Pantodon from the Niger basin and other related taxa. Pantodon populations form a monophyletic group, yet their mitochondrial coding sequences differ by 15.2 per cent between the Niger and Congo basins. The mitogenomic divergence time between these populations is estimated to be greater than 50 Myr, and deep genetic divergence was confirmed by nuclear sequence data. Among six sister-group comparisons of osteoglossomorphs, Pantodon exhibits the slowest rate of morphological divergence despite a level of genetic differentiation comparable to both species-rich (e.g. Mormyridae) and species-poor (e.g. Osteoglossidae) families. Morphological stasis in these two allopatric lineages of Pantodon offers a living vertebrate model for investigating phenotypic stability over millions of generations in the face of profound fluctuations in environmental conditions.     

Distinct roles of protein disulfide isomerase and P5 sulfhydryl oxidoreductases in multiple pathways for oxidation of structurally diverse storage proteins in rice

In the rice (Oryza sativa) endosperm, storage proteins are synthesized on the rough endoplasmic reticulum (ER), in which prolamins are sorted to protein bodies (PBs) called type-I PB (PB-I). Protein disulfide isomerase (PDI) family oxidoreductase PDIL2;3, an ortholog of human P5, contains a conserved structural disulfide in the redox-inactive thioredoxin-like (TRX) domain and was efficiently targeted to the surface of PB-I in a redox active site-dependent manner, whereas PDIL1;1, an ortholog of human PDI, was localized in the ER lumen. Complementation analyses using PDIL1;1 knockout esp2 mutant indicated that the a and a' TRX domains of PDIL1;1 exhibited similar redox activities and that PDIL2;3 was unable to perform the PDIL1;1 functions. PDIL2;3 knockdown inhibited the accumulation of Cys-rich 10-kD prolamin (crP10) in the core of PB-I. Conversely, crP10 knockdown dispersed PDIL2;3 into the ER lumen. Glutathione S-transferase-PDIL2;3 formed a stable tetramer when it was expressed in Escherichia coli, and the recombinant PDIL2;3 tetramer facilitated α-globulin(C79F) mutant protein to form nonnative intermolecular disulfide bonds in vitro. These results indicate that PDIL2;3 and PDIL1;1 are not functionally redundant in sulfhydryl oxidations of structurally diverse storage proteins and play distinct roles in PB development. We discuss PDIL2;3-dependent and PDIL2;3-independent oxidation pathways that sustain disulfide bonds of crP10 in PB-I.     

Newly discovered neutral glycosphingolipids in aureobasidin A-resistant zygomycetes: Identification of a novel family of Gala-series glycolipids with core Gal alpha 1-6Gal beta 1-6Gal beta sequences

We found for the first time that Zygomycetes species showed resistance to Aureobasidin A, an antifungal agent. A novel family of neutral glycosphingolipids (GSLs) was found in these fungi and isolated from Mucor hiemalis, which is a typical Zygomycetes species. Their structures were completely determined by compositional sugar, fatty acid, and sphingoid analyses, methylation analysis, matrix-assisted laser desorption ionization time-of-flight/mass spectrometry, and (1)H NMR spectroscopy. They were as follows: Gal beta 1-6Gal beta 1-1Cer (CDS), Gal alpha 1-6Gal beta 1-6Gal beta 1-1Cer (CTS), Gal alpha 1-6Gal alpha 1-6Gal beta 1-6Gal beta 1-1Cer (CTeS), and Gal alpha 1-6Gal alpha 1-6Gal alpha 1-6Gal beta 1-6Gal beta 1-1Cer (CPS). The ceramide moieties of these GSLs consist of 24:0, 25:0, and 26:0 2-hydroxy acids as major fatty acids and 4-hydroxyoctadecasphinganine (phytosphingosine) as the sole sphingoid. However, the glycosylinositolphosphoceramide families that are the major GSLs components in fungi were not detected in Zygomycetes at all. This seems to be the reason that Aureobasidin A is not effective for Zygomycetes as an antifungal agent. Our results indicate that the biosynthetic pathway for GSLs in Zygomycetes is significantly different from those in other fungi and suggest that any inhibitor of this pathway may be effective for mucormycosis, which is a serious pathogenic disease for humans.     

Single-nucleotide polymorphism g.1548G > A (E469K) in human ICAM-1 gene affects mRNA splicing pattern and TPA-induced apoptosis

The single-nucleotide polymorphism (SNP) g.1548G > A (E469K) in the human intercellular adhesion molecule-1 (ICAM-1) gene has been suggested to have an association with several types of inflammatory diseases. The polymorphism is located at the three-base position upstream of the splice donor site that produces an alternatively spliced short isoform (ICAM-1-S). To clarify its functional relevance, we studied RNA splicing patterns by comparing cells with different genotype (G/G cells and A/A cells). G/G cells expressed a lower amount of ICAM-1-S mRNA than A/A cells. Since ICAM-1-S has no transmembrane or intracellular domain, ICAM-1 signal transduction and cell-cell contact including Fas-FasL interaction may be influenced. In addition, we studied the effect of this change on FLIP-L mRNA and apoptosis. FLIP-L mRNA tended to decrease, while cell death induced by phorbol 12-myristate 13-acetate was increased. These results suggest that the g.1548 polymorphism modifies inflammatory immune responses by changing cell-cell interaction and then regulating apoptosis.     

Embryonic stem cells: hepatic differentiation and regenerative medicine for the treatment of liver disease

Hepatocyte transplantation is considered a potential treatment for liver diseases and a bridge for patients awaiting liver transplantation, but its application has been hampered by a limited supply of hepatocytes. Embryonic stem (ES) cells established from early mouse and human embryos are pluripotent, and proliferate indefinitely in an undifferentiated state in vitro. Since differentiation from ES cells seems to recapitulate early embryonic development, if hepatocytes could be efficiently generated in vitro, ES cells might become a source of transplantable hepatocytes for cell replacement therapy. Hepatocytes have been generated from ES cells in vitro, and the hepatocytes differentiated from ES cells have been found to express many hepatocyte-related genes and perform hepatic functions. However, it remains unclear whether the hepatocytes differentiated from ES cells are derived from definitive endoderm or primitive endoderm. Because visceral endoderm, which expresses many hepatocyte-related genes, is derived from primitive endoderm and is fated to form extraembryonic yolk sac tissues, not to form hepatocytes, ES cells must be directed to a definitive endoderm lineage in vitro. This article discusses the differentiation of ES cells into hepatocytes in vitro in comparison with early embryogenesis, and describes the efficacy of ES cell-derived hepatocyte transplantation.     

A functional model for pMMO (particulate methane monooxygenase): Hydroxylation of alkanes with H2O2 catalyzed by beta-diketiminatocopper(II) complexes

The reaction of copper(II) complexes supported by a series of beta-diketiminate ligands ((R1,R2)L, [(Dipp)N-C(R(2))-C(R(1))-C(R(2))-N(Dipp)](-), Dipp=2,6-diisopropylphenyl; see ) and H(2)O(2) has been examined spectroscopically at a low temperature. The beta-diketiminatocopper(II) complexes with R(2)=H (no substituent on the beta-carbon) provided a copper-oxygen intermediate that exhibited the same spectroscopic features as those of the bis(mu-oxo)dicopper(III) complex generated by the reaction of corresponding beta-diketiminatocopper(I) complex and O(2). On the other hand, the beta-diketiminatocopper(II) complexes with methyl substituent on the beta-carbon (R(2)=Me) did not produce such an intermediate in the same reaction. The beta-diketiminatocopper(II) complexes carrying an electron-withdrawing substituent on the alpha-carbon (R(1)=NO(2) or CN) but no beta-substituent (R(2)=H) exhibited a high catalytic activity in the oxygenation reaction of alkanes with H(2)O(2). Mechanism of the catalytic oxygenation reaction as well as the substituent effects of the ligands on the copper(II)-H(2)O(2) reactivity is discussed.