記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Oxford University Press (OUP)  

Abstract

Changes in the epigenome can affect the phenotype without the presence of changes in the genomic sequence. Given the high identity of the human and chimpanzee genome sequences, a substantial portion of their phenotypic divergence likely arises from epigenomic differences between the two species. In this study, the transcriptome and epigenome were determined for induced pluripotent stem cells (iPSCs) generated from human and chimpanzee individuals. The transcriptome and epigenomes for trimethylated histone H3 at lysine-4 (H3K4me3) and at lysine-27 (H3K27me3) showed high levels of similarity between the two species. However, there were some differences in histone modifications. Although such regions, in general, did not show significant enrichment of interspecies nucleotide variations, gains in binding motifs for pluripotency-related transcription factors, especially POU5F1 and SOX2, were frequently found in species-specific H3K4me3 regions. We also revealed that species-specific insertions of retrotransposons, including the LTR5_Hs subfamily in human and a newly identified LTR5_Pt subfamily in chimpanzee, created species-specific H3K4me3 regions associated with increased expression of nearby genes. Human iPSCs have more species-specific H3K27me3 regions, resulting in more abundant bivalent domains. Only a limited number of these species-specific H3K4me3 and H3K27me3 regions overlap with species-biased enhancers in cranial neural crest cells, suggesting that differences in the epigenetic state of developmental enhancers appear late in development. Therefore, iPSCs serve as a suitable starting material for studying evolutionary changes in epigenome dynamics during development.

DOI： 10.1093/molbev/msac208

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その他リンク： https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msac208/46548545/msac208.pdf

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

DOI： 10.1007/s10265-021-01329-w

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その他リンク： https://link.springer.com/article/10.1007/s10265-021-01329-w/fulltext.html

記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Japanese Society of Veterinary Science  

Here, we performed next-generation sequencing (NGS) on six large flying foxes (Pteropus vampyrus) collected in Indonesia. Seventy-five virus species in the liver tissue of each specimen were listed. Viral homologous sequences in the bat genome were identified from the listed viruses. This finding provides collateral evidence of viral endogenization into the host genome. We found that two of the six specimens bore partial sequences that were homologous to the plant pathogens Geminiviridae and Luteoviridae. These sequences were absent in the P. vampyrus chromosomal sequences. Hence, plant viral homologous sequences were localized to the hepatocytes as extrachromosomal DNA fragments. Therefore, this suggests that the bat is a potential carrier or vector of plant viruses. The present investigation on wild animals offered novel perspectives on viral invasion, variation, and host interaction.

DOI： 10.1292/jvms.21-0115

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PubMed

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Oxford University Press (OUP)  

Abstract

More than one million copies of short interspersed elements (SINEs), a class of retrotransposons, are present in the mammalian genomes, particularly within gene-rich genomic regions. Evidence has accumulated that ancient SINE sequences have acquired new binding sites for transcription factors (TFs) through multiple mutations following retrotransposition, and as a result have rewired the host regulatory network during the course of evolution. However, it remains unclear whether currently active SINEs contribute to the expansion of TF binding sites. To study the mobility, expression, and function of SINE copies, we first identified about 2,000 insertional polymorphisms of SINE B1 and B2 families within Mus musculus. Using a novel RNA sequencing method designated as melRNA-seq, we detected the expression of SINEs in male germ cells at both the subfamily and genomic copy levels: the vast majority of B1 RNAs originated from evolutionarily young subfamilies, whereas B2 RNAs originated from both young and old subfamilies. DNA methylation and chromatin immunoprecipitation-sequencing (ChIP-seq) analyses in liver revealed that polymorphic B2 insertions served as a boundary element inhibiting the expansion of DNA hypomethylated and histone hyperacetylated regions, and decreased the expression of neighboring genes. Moreover, genomic B2 copies were enriched at the boundary of various histone modifications, and chromatin insulator protein, CCCTC-binding factor, a well-known chromatin boundary protein, bound to >100 polymorphic and >10,000 non-polymorphic B2 insertions. These results suggest that the currently active B2 copies are mobile boundary elements that can modulate chromatin modifications and gene expression, and are likely involved in epigenomic and phenotypic diversification of the mouse species.

DOI： 10.1093/molbev/msab033

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Wiley  

DOI： 10.1111/tpj.12705

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Portland Press Ltd.  

NDH (NADH-quinone oxidoreductase)-1 complexes in cyanobacteria have specific functions in respiration and cyclic electron flow as well as in active CO2 uptake. In order to isolate NDH-1 complexes and to study complex–complex interactions, several strains of Thermosynechococcus elongatus were constructed by adding a His-tag (histidine tag) to different subunits of NDH-1. Two strains with His-tag on CupA and NdhL were successfully used to isolate NDH-1 complexes by one-step Ni2+ column chromatography. BN (blue-native)/SDS/PAGE analysis of the proteins eluted from the Ni2+ column revealed the presence of three complexes with molecular masses of about 450, 300 and 190 kDa, which were identified by MS to be NDH-1L, NDH-1M and NDH-1S respectively, previously found in Synechocystis sp. PCC 6803. A larger complex of about 490 kDa was also isolated from the NdhL-His strain. This complex, designated ‘NDH-1MS’, was composed of NDH-1M and NDH-1S. NDH-1L complex was recovered from WT (wild-type) cells of T. elongatus by Ni2+ column chromatography. NdhF1 subunit present only in NDH-1L has a sequence of -HHDHHSHH- internally, which appears to have an affinity for the Ni2+ column. NDH-1S or NDH-1M was not recovered from WT cells by chromatography of this kind. The BN/SDS/PAGE analysis of membranes solubilized by a low concentration of detergent indicated the presence of abundant NDH-1MS, but not NDH-1M or NDH-1S. These results clearly demonstrated that NDH-1S is associated with NDH-1M in vivo.

DOI： 10.1042/bj20050390

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1074/jbc.m407268200

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1074/jbc.m204175200

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Elsevier BV  

DOI： 10.1074/jbc.m112468200

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：CSIRO Publishing  

The cyanobacterium Synechocystis sp. strain PCC6803possesses two CO2 uptake systems; one constitutive,dependent on NdhD3/NdhF3/CupA (Sll1734), and one low-CO2 inducible,dependent on NdhD4/NdhF4/CupB (Slr1302). Homologues of these genes arepresent in pairs in most cyanobacterial strains.Synechocystis PCC6803 also possesses two types ofHCO3– transporters; anATP-binding cassette (ABC)-type transporter encoded by thecmp operon, and a novel sodium-dependent transporterencoded byslr1512(sbtA) that playsa central role in HCO3–uptake. Mutants impaired for one of these four inorganic-carbon acquisitionsystems did not show mutant phenotype. Mutants inactivated for bothCO2 uptake systems were unable to grow at pH 7.0 in air,although they grew normally at pH 9.0 in air. Additional inactivation of theSbtA-type HCO3– transporter abolished growth at pH 9.0 in air. Afragment containing the promoter region of ndhF3 fusedto the coding region of luxAB was inserted into a neutralsite of the ΔndhD4 mutant to constructapF3-lux/ ΔndhD4 strain. The luminescenceintensity of this strain was low in high-CO2 growncells, and was increased about 100 times after acclimation to air.Inactivation of the pF3-lux/ ΔndhD4 strainwith a transposon-tagging library enabled us to isolate mutants incapable ofacclimation to low CO2.

DOI： 10.1071/pp01188

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担当区分：筆頭著者   記述言語：英語   出版者・発行元：The Japanese Society of Sericultural Science  

The sorbitol dehydrogenase (SDH) gene of Bombyx mori begins to be expressed in diapause eggs after 5°C-chilling for 40-50 days. Because three elements similar to consensus sequences bound by members of the steroid hormone receptor superfamily such as Seven-up (SVP)/COUP-TF, were found in the 5′-upstream region of the SDH gene, we tried to isolate cDNAs for SVP from Bombyx eggs, as a step to understand the mechanism of how 5°C controls the SDH gene expression. Two cDNAs for SVP were cloned and named Bm svp-α and β, respectively. From the deduced amino-acid sequences, Bm svp-α protein was shown to have partial A/B region and C, D, E and F regions, whereas Bm svp-β protein lacked E (corresponding to the ligand-binding domain) and F regions. In non-diapause eggs, the temporal profile in the amount of Bm svp-α mRNA showed a peak in the middle of embryogenesis, while mRNA amounts of svp-β were much lower than those of svp-α. On the other hand, in diapause eggs, 5°C-chilling for 40-60 days enhanced levels of mRNA and protein for Bm svp-α, suggesting that Bm svp-α protein is a strong candidate of transcription factors that control the SDH gene expression induced by the cold.

DOI： 10.11416/jibs2001.71.17

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Oxford University Press (OUP)  

DOI： 10.1093/pcp/pce106

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Society for Microbiology  

ABSTRACT

Genes encoding polypeptides of an ATP binding cassette (ABC)-type ferric iron transporter that plays a major role in iron acquisition in Synechocystis sp. strain PCC 6803 were identified. These genes are slr1295, slr0513, slr0327 , and recently reported sll1878 (Katoh et al., J. Bacteriol. 182:6523–6524, 2000) and were designated futA1, futA2, futB , and futC , respectively, for their involvement in ferric iron uptake. Inactivation of these genes individually or futA1 and futA2 together greatly reduced the activity of ferric iron uptake in cells grown in complete medium or iron-deprived medium. All the fut genes are expressed in cells grown in complete medium, and expression was enhanced by iron starvation. The futA1 and futA2 genes appear to encode periplasmic proteins that play a redundant role in iron binding. The deduced products of futB and futC genes contain nucleotide-binding motifs and belong to the ABC transporter family of inner-membrane-bound and membrane-associated proteins, respectively. These results and sequence similarities among the four genes suggest that the Fut system is related to the Sfu/Fbp family of iron transporters. Inactivation of slr1392 , a homologue of feoB in Escherichia coli , greatly reduced the activity of ferrous iron transport. This system is induced by intracellular low iron concentrations that are achieved in cells exposed to iron-free medium or in the fut -less mutants grown in complete medium.

DOI： 10.1128/jb.183.9.2779-2784.2001

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担当区分：筆頭著者   記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Society for Microbiology  

ABSTRACT

A mutant of Synechocystis sp. strain PCC 6803 disrupted for sll1878 exhibited greatly reduced Fe ³⁺ transport activity. The K _m value of sll1878 -dependent Fe ³⁺ transport in cells grown in iron-replete medium was 0.5 μM. Both the maximal rate and K _m value were increased in iron-starved cells.

DOI： 10.1128/jb.182.22.6523-6524.2000

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Society for Microbiology  

ABSTRACT

The product of pxcA (formerly known as cotA ) is involved in light-induced Na ⁺ -dependent proton extrusion. In the presence of 2,5-dimethyl- p -benzoquinone, net proton extrusion by Synechocystis sp. strain PCC6803 ceased after 1 min of illumination and a postillumination influx of protons was observed, suggesting that the PxcA-dependent, light-dependent proton extrusion equilibrates with a light-independent influx of protons. A photosystem I (PS I) deletion mutant extruded a large number of protons in the light. Thus, PS II-dependent electron transfer and proton translocation are major factors in light-driven proton extrusion, presumably mediated by ATP synthesis. Inhibition of CO ₂ fixation by glyceraldehyde in a cytochrome c oxidase (COX) deletion mutant strongly inhibited the proton extrusion. Leakage of PS II-generated electrons to oxygen via COX appears to be required for proton extrusion when CO ₂ fixation is inhibited. At pH 8.0, NO ₃⁻ uptake activity was very low in the pxcA mutant at low [Na ⁺ ] (∼100 μM). At pH 6.5, the pxcA strain did not take up CO ₂ or NO ₃⁻ at low [Na ⁺ ] and showed very low CO ₂ uptake activity even at 15 mM Na ⁺ . A possible role of PxcA-dependent proton exchange in charge and pH homeostasis during uptake of CO ₂ , HCO ₃⁻ , and NO ₃⁻ is discussed.

DOI： 10.1128/jb.180.15.3799-3803.1998

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Canadian Science Publishing  

Mutants of cyanobacteria defective in parts of the CO₂-concentrating mechanism are classified into three types. (i) Mutants defective in inorganic carbon transporters. One of these mutants was constructed by inactivating cmpA encoding 42 kDa protein in the cytoplasmic membrane. (ii) Mutants defective in NAD(P)H dehydrogenase(s). There are five ndhD genes in Synechocystis PCC6803, two of them expressed constitutively and three inducible by low CO₂. Two kinds of NAD(P)H dehydrogenase appear to be involved in energizing and inducing the high affinity inorganic carbon transport system. (iii) Mutants defective in carboxysome with impaired ccm or icfA genes. New type of mutants with impaired cotA (renamed as pxcA) have also been isolated. These mutants did not show light-induced proton extrusion and were unable to grow at acidic pHs. A mutant constructed by inactivating cotA (pxcA) in the wild-type Synechocystis was unable to transport CO₂ at pH 6.5. We concluded that cotA (pxcA) has a role in light-induced proton extrusion that is essential at acidic pHs to extrude protons produced during CO₂ transport.Key words: CO₂-concentrating mechanism (CCM), CO₂ transport, NAD(P)H dehydrogenase, proton extrusion, carboxysome, mutant.

DOI： 10.1139/b98-076

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Society for Microbiology  

cotA of Synechocystis sp. strain PCC6803 is a gene involved in light-induced proton extrusion (A. Katoh, M. Sonoda, H. Katoh, and T. Ogawa, J. Bacteriol. 178:5452-5455, 1996). There are two possible initiation codons in cotA, and either long (L-) or short (S-) cotA encoding a protein of 440 or 247 amino acids could be postulated. To determine the gene size, we inserted L-cotA and S-cotA into the genome of a cotA-less mutant (M29) to construct M29(L-cotA) and M29(S-cotA), respectively. M29(L-cotA) showed essentially the same net proton movement profile as the wild type, whereas no light-induced proton extrusion was observed with M29(S-cotA). Two kinds of antibodies were raised against partial gene products of the N- and C-terminal regions of L-cotA, respectively, fused to glutathione S-transferase expressed in Escherichia coli. Both antibodies cross-reacted with a band at 52 kDa in both cytoplasmic and thylakoid membrane fractions of the wild-type cells. The same cross-reacting band was present in the membranes of M29(L-cotA) but not in M29 or M29(S-cotA). These antibodies cross-reacted more strongly with the cytoplasmic membrane fraction than with the thylakoid membrane fraction. The antibody against NrtA, a nitrate transporter protein present only in the cytoplasmic membrane, also cross-reacted with the thylakoid membrane fraction strongly. Based on these results we concluded that CotA of 440 amino acids (51 kDa) is located in the cytoplasmic membrane. Whether CotA is absent in the thylakoid membrane remains to be solved.

DOI： 10.1128/jb.179.12.3845-3850.1997

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：Springer Science and Business Media LLC  

DOI： 10.1023/a:1005830303453

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記述言語：英語   掲載種別：研究論文（学術雑誌）   出版者・発行元：American Society for Microbiology  

cotA of Synechocystis sp. strain PCC6803 was isolated as a gene that complemented a mutant defective in CO2 transport and is homologous to cemA that encodes a chloroplast envelope membrane protein (A. Katoh, K.S. Lee, H. Fukuzawa, K. Ohyama, and T. Ogawa, Proc. Natl. Acad. Sci. USA 93:4006-4010, 1996). A mutant (M29) constructed by replacing cotA in the wild-type (WT) Synechocystis strain with the omega fragment was unable to grow in BG11 medium (approximately 17 mM Na+) at pH 6.4 or at any pH in a low-sodium medium (100 microM Na+) under aeration with 3% (vol/vol) CO2 in air. The WT cells grew well in the pH range between 6.4 and 8.5 in BG11 medium but only at alkaline pH in the low-sodium medium. Illumination of the WT cells resulted in an extrusion followed by an uptake of protons. In contrast, only proton uptake was observed for the M29 mutant in the light without proton extrusion. There was no difference in sodium uptake activity between the WT and mutant. The mutant still possessed 51% of the WT CO2 transport activity in the presence of 15 mM NaCl. On the basis of these results we concluded that cotA has a role in light-induced proton extrusion and that the inhibition of CO2 transport in the M29 mutant is a secondary effect of the inhibition of proton extrusion.

DOI： 10.1128/jb.178.18.5452-5455.1996

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出版者・発行元：日本植物生理学会  

イネ無胚乳変異体enl1は劣性一遺伝子座の変異で、その種子は胚乳を形成できない。一方、その胚は肥大化し休眠性を喪失しているが発芽能をもつ。我々はenl1のマッピングを行い、第4染色体長腕上テロメア近くに存在する推定遺伝子領域のエキソン内に欠失変異を見つけた。さらにこの遺伝子領域を含む野生型ゲノム断片を用いた形質転換によりenl1変異の表現型が完全に相補されたことから、本遺伝子がenl1変異の原因遺伝子であると結論した。ENL1遺伝子はSNF2ファミリーATPaseドメインとHELICcドメインを持つSNF2様ヘリカーゼをコードし、植物のみならず広く真核生物にそのオルソログが存在する。ヒトのENL1オルソログであるPICHタンパク質は細胞分裂時の染色体凝集や染色体腕部のアーキテクチャー維持、あるいは姉妹染色分体の解離に必要であることが報告されている。PI染色法を用いて初期胚乳形成過程の核・染色体の様子を共焦点レーザー顕微鏡観察したところ、野生型では細胞化に先立つ遊離核の一様な分布が見られたのに対し、enl1変異体では染色体の分離異常の結果と考えられる巨大化した核が観察された。これらの結果は、多核期胚乳における染色体サイクルの異常が、enl1変異体における無胚乳表現型の原因であることを示している。

DOI： 10.14841/jspp.2011.0.0060.0

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記述言語：日本語  

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