start-ver=1.4 cd-journal=joma no-vol=25 cd-vols= no-issue=6 article-no= start-page=1208 end-page=1219 dt-received= dt-revised= dt-accepted= dt-pub-year=2023 dt-pub=20231210 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Nuclear Transformation of the Marine Pennate Diatom Nitzschia sp. Strain NIES-4635 by Multi-Pulse Electroporation en-subtitle= kn-subtitle= en-abstract= kn-abstract=Nitzschia is one of the largest genera of diatoms found in a range of aquatic environments, from freshwater to seawater. This genus contains evolutionarily and ecologically unique species, such as those that have lost photosynthetic capacity or those that live symbiotically in dinoflagellates. Several Nitzschia species have been used as indicators of water pollution. Recently, Nitzschia species have attracted considerable attention in the field of biotechnology. In this study, a transformation method for the marine pennate diatom Nitzschia sp. strain NIES-4635, isolated from the coastal Seto Inland Sea, was established. Plasmids containing the promoter/terminator of the fucoxanthin chlorophyll a/c binding protein gene (fcp, or Lhcf) derived from Nitzschia palea were constructed and introduced into cells by multi-pulse electroporation, resulting in 500 μg/mL nourseothricin-resistant transformants with transformation frequencies of up to 365 colonies per 108 cells. In addition, when transformation was performed using a new plasmid containing a promoter derived from a diatom-infecting virus upstream of the green fluorescent protein gene (gfp), 44% of the nourseothricin-resistant clones exhibited GFP fluorescence. The integration of the genes introduced into the genomes of the transformants was confirmed by Southern blotting. The Nitzschia transformation method established in this study will enable the transformation this species, thus allowing the functional analysis of genes from the genus Nitzschia, which are important species for environmental and biotechnological development. en-copyright= kn-copyright= en-aut-name=OkadaKoki en-aut-sei=Okada en-aut-mei=Koki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=MorimotoYu en-aut-sei=Morimoto en-aut-mei=Yu kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShiraishiYukine en-aut-sei=Shiraishi en-aut-mei=Yukine kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=TamuraTakashi en-aut-sei=Tamura en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=MayamaShigeki en-aut-sei=Mayama en-aut-mei=Shigeki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=KadonoTakashi en-aut-sei=Kadono en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=AdachiMasao en-aut-sei=Adachi en-aut-mei=Masao kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=IfukuKentaro en-aut-sei=Ifuku en-aut-mei=Kentaro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= en-aut-name=NemotoMichiko en-aut-sei=Nemoto en-aut-mei=Michiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=9 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Faculty of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= affil-num=5 en-affil=The Advanced Support Center for Science Teachers, Tokyo Gakugei University kn-affil= affil-num=6 en-affil=Faculty of Agriculture and Marine Science, Kochi University kn-affil= affil-num=7 en-affil=Faculty of Agriculture and Marine Science, Kochi University kn-affil= affil-num=8 en-affil=Graduate School of Agriculture, Kyoto University kn-affil= affil-num=9 en-affil=Faculty of Environmental, Life, Natural Science and Technology, Okayama University kn-affil= en-keyword=Diatom kn-keyword=Diatom en-keyword=Genetic transformation kn-keyword=Genetic transformation en-keyword=Nitzschia kn-keyword=Nitzschia en-keyword=Multi-pulse electroporation kn-keyword=Multi-pulse electroporation END start-ver=1.4 cd-journal=joma no-vol=110 cd-vols= no-issue= article-no= start-page=1 end-page=6 dt-received= dt-revised= dt-accepted= dt-pub-year=2021 dt-pub=20210201 dt-online= en-article= kn-article= en-subject= kn-subject= en-title=A comparative gene analysis reveals a diatom-specific SET domain protein family kn-title=遺伝子比較解析による珪藻類特異的なSET ドメインタンパク質ファミリーの同定 en-subtitle= kn-subtitle= en-abstract= kn-abstract= The silica cell walls of diatoms, which exhibit species-spe-cific micro- and nano- patterned structures are promising candidates for applications in nanotechnology. Previous studies revealed a number of silica cell wall-associated proteins involved in silica formation. However, molecular biological analyses toward understanding of diatom cell wall formation have been mostly limited to model diatom species and general silica formation process in diatoms is still incompletely understood. In this study, to gain a compre-hensive insight into diatom silica biomineralization, tran-scriptome data of three diatom species, Nitzschia palea, Achnanthes kuwaitensis and Pseudoleyanella lunata, were newly developed. The reads obtained from RNA sequencing were assembled into 31,946, 60,767 and 38,314 unique transcripts for N. palea, A. kuwaitensis and P. lunata, respectively. In order to identify the diatom-specific genes, three transcriptome data sets developed in this study and the protein-coding gene sets of five genome-sequenced diatoms were compared. The proteins shared only by eight diatom species that are predicted to possess an endoplasmic reticulum (ER)-targeting signal peptide were selected for further analyses. These include proteins showing homology to silicanin-1, a recently reported diatom-specific protein involved in silica formation, as well as a number of SET domain proteins. The SET domain proteins might be novel diatom-specific family of methyltransferases that may reg-ulate the function of silica formation related proteins or long chain polyamines. The genes encoding the diatom-specific SET domain proteins identified in this study, which were shown to respond to silicon were suggested to be implicated in silica biomineralization. en-copyright= kn-copyright= en-aut-name=NemotoMichiko en-aut-sei=Nemoto en-aut-mei=Michiko kn-aut-name=根本理子 kn-aut-sei=根本 kn-aut-mei=理子 aut-affil-num=1 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil=岡山大学大学院環境生命科学研究科 en-keyword=Biomineralization kn-keyword=Biomineralization en-keyword=Diatom kn-keyword=Diatom en-keyword=Silica kn-keyword=Silica en-keyword=Protein kn-keyword=Protein END start-ver=1.4 cd-journal=joma no-vol= cd-vols= no-issue= article-no= start-page= end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2020 dt-pub=20200603 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Comparative Gene Analysis Focused on Silica Cell Wall Formation: Identification of Diatom-Specific SET Domain Protein Methyltransferases en-subtitle= kn-subtitle= en-abstract= kn-abstract=Silica cell walls of diatoms have attracted attention as a source of nanostructured functional materials and have immense potential for a variety of applications. Previous studies of silica cell wall formation have identified numerous involved proteins, but most of these proteins are species-specific and are not conserved among diatoms. However, because the basic process of diatom cell wall formation is common to all diatom species, ubiquitous proteins and molecules will reveal the mechanisms of cell wall formation. In this study, we assembled de novo transcriptomes of three diatom species, Nitzschia palea, Achnanthes kuwaitensis, and Pseudoleyanella lunata, and compared protein-coding genes of five genome-sequenced diatom species. These analyses revealed a number of diatom-specific genes that encode putative endoplasmic reticulum-targeting proteins. Significant numbers of these proteins showed homology to silicanin-1, which is a conserved diatom protein that reportedly contributes to cell wall formation. These proteins also included a previously unrecognized SET domain protein methyltransferase family that may regulate functions of cell wall formation-related proteins and long-chain polyamines. Proteomic analysis of cell wall-associated proteins in N. palea identified a protein that is also encoded by one of the diatom-specific genes. Expression analysis showed that candidate genes were upregulated in response to silicon, suggesting that these genes play roles in silica cell wall formation. These candidate genes can facilitate further investigations of silica cell wall formation in diatoms. en-copyright= kn-copyright= en-aut-name=NemotoMichiko en-aut-sei=Nemoto en-aut-mei=Michiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=IwakiSayako en-aut-sei=Iwaki en-aut-mei=Sayako kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=MoriyaHisao en-aut-sei=Moriya en-aut-mei=Hisao kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=MondenYuki en-aut-sei=Monden en-aut-mei=Yuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=TamuraTakashi en-aut-sei=Tamura en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=InagakiKenji en-aut-sei=Inagaki en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=MayamaShigeki en-aut-sei=Mayama en-aut-mei=Shigeki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= en-aut-name=ObuseKiori en-aut-sei=Obuse en-aut-mei=Kiori kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=8 ORCID= affil-num=1 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=2 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=3 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=4 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=5 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=6 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= affil-num=7 en-affil=Department of Biology, Tokyo Gakugei University kn-affil= affil-num=8 en-affil=Graduate School of Environmental and Life Science, Okayama University kn-affil= en-keyword=Biomineralization kn-keyword=Biomineralization en-keyword=Diatom kn-keyword=Diatom en-keyword=Silica kn-keyword=Silica en-keyword=Transcriptome kn-keyword=Transcriptome en-keyword=Proteome kn-keyword=Proteome END start-ver=1.4 cd-journal=joma no-vol=6 cd-vols= no-issue= article-no= start-page=19742 end-page= dt-received= dt-revised= dt-accepted= dt-pub-year=2016 dt-pub=20160128 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Molecular evolution of gas cavity in [NiFeSe] hydrogenases resurrected in silico en-subtitle= kn-subtitle= en-abstract= kn-abstract=Oxygen tolerance of selenium-containing [NiFeSe] hydrogenases (Hases) is attributable to the high reducing power of the selenocysteine residue, which sustains the bimetallic Ni–Fe catalytic center in the large subunit. Genes encoding [NiFeSe] Hases are inherited by few sulphate-reducing δ-proteobacteria globally distributed under various anoxic conditions. Ancestral sequences of [NiFeSe] Hases were elucidated and their three-dimensional structures were recreated in silico using homology modelling and molecular dynamic simulation, which suggested that deep gas channels gradually developed in [NiFeSe] Hases under absolute anaerobic conditions, whereas the enzyme remained as a sealed edifice under environmental conditions of a higher oxygen exposure risk. The development of a gas cavity appears to be driven by non-synonymous mutations, which cause subtle conformational changes locally and distantly, even including highly conserved sequence regions. en-copyright= kn-copyright= en-aut-name=TamuraTakashi en-aut-sei=Tamura en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=TsunekawaNaoki en-aut-sei=Tsunekawa en-aut-mei=Naoki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=NemotoMichiko en-aut-sei=Nemoto en-aut-mei=Michiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=InagakiKenji en-aut-sei=Inagaki en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=HiranoToshiyuki en-aut-sei=Hirano en-aut-mei=Toshiyuki kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=SatoFumitoshi en-aut-sei=Sato en-aut-mei=Fumitoshi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= affil-num=1 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=2 en-affil= kn-affil=Institute of Industrial Science, the University of Tokyo affil-num=3 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=4 en-affil= kn-affil=Graduate School of Environmental and Life Science, Okayama University affil-num=5 en-affil= kn-affil=Institute of Industrial Science, the University of Tokyo affil-num=6 en-affil= kn-affil=Institute of Industrial Science, the University of Tokyo END start-ver=1.4 cd-journal=joma no-vol=3 cd-vols= no-issue=4 article-no= start-page=e00715-15 end-page=e00715-15 dt-received= dt-revised= dt-accepted= dt-pub-year=2015 dt-pub=20150709 dt-online= en-article= kn-article= en-subject= kn-subject= en-title= kn-title=Draft Genome Sequence of Streptomyces incarnatus NRRL8089, which Produces the Nucleoside Antibiotic Sinefungin en-subtitle= kn-subtitle= en-abstract= kn-abstract=A draft genome sequence of Streptomyces incarnatus NRRL8089, which produces the nucleoside antibiotic sinefungin, is described here. The genome contains 8,897,465 bp in 76 contigs and 8,266 predicted genes. Interestingly, the genome encodes an open reading frame for selenocysteine-containing formate dehydrogenase-O and the selenoprotein biosynthetic gene cluster selABCD. en-copyright= kn-copyright= en-aut-name=OshimaKenshiro en-aut-sei=Oshima en-aut-mei=Kenshiro kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=1 ORCID= en-aut-name=HattoriMasahira en-aut-sei=Hattori en-aut-mei=Masahira kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=2 ORCID= en-aut-name=ShimizuHitomi en-aut-sei=Shimizu en-aut-mei=Hitomi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=3 ORCID= en-aut-name=FukudaKoji en-aut-sei=Fukuda en-aut-mei=Koji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=4 ORCID= en-aut-name=NemotoMichiko en-aut-sei=Nemoto en-aut-mei=Michiko kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=5 ORCID= en-aut-name=InagakiKenji en-aut-sei=Inagaki en-aut-mei=Kenji kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=6 ORCID= en-aut-name=TamuraTakashi en-aut-sei=Tamura en-aut-mei=Takashi kn-aut-name= kn-aut-sei= kn-aut-mei= aut-affil-num=7 ORCID= affil-num=1 en-affil= kn-affil=The University of Tokyo affil-num=2 en-affil= kn-affil=The University of Tokyo affil-num=3 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Okayama University affil-num=4 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Okayama University affil-num=5 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Okayama University affil-num=6 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Okayama University affil-num=7 en-affil= kn-affil=Graduate School of Life and Environmental Sciences, Okayama University END