Author Report for: Kikuchi HNo contact information in database for Kikuchi H
Morita Y, Sakaguchi T, Matsumoto A, Ida S, Muraki R, Kitajima R, Furuhashi S, Takeda M, Kikuchi H and Takeuchi H <1 more author(s)> Morita Y, Sakaguchi T, Matsumoto A, Ida S, Muraki R, Kitajima R, Furuhashi S, Takeda M, Kikuchi H, Hiramatsu Y, Takeuchi H (- 1) Ref: BMC Surg, 23:344, 2023 : PubMed ESTHER: Morita_2023_BMC.Surg_23_344 PubMedSearch: Morita 2023 BMC.Surg 23 344 PubMedID: 37964345 Abstract BACKGROUND: Pseudoaneurysm (PA) rupture after pancreaticoduodenectomy (PD) is a life-threatening complication. Most PA cases originate from postoperative pancreatic fistulas (POPFs). Although several risk factors for POPF have been identified, specific risk factors for PA formation remain unclear. Therefore, we retrospectively analyzed PD cases with soft pancreas and proposed a novel strategy for early detection of PA formation. METHODS: Overall, 120 patients underwent PD between 2010 and 2020 at our institution; of these, 65 patients with soft pancreas were enrolled. We evaluated the clinicopathological factors influencing PA formation and developed a risk score to predict PA formation. RESULTS: In total, 11 of the 65 patients developed PAs (PA formation group: PAG), and 8 of these 11 PAs ruptured. The median time to PA formation was 15 days, with a minimum of 5 days. The PAG was significantly older than the non-PA formation group, were predominantly men, and had comorbid diabetes mellitus. Pre- and intra-operative findings were similar between the two groups. Importantly, no significant differences were found in postoperative drain amylase levels and total drain amylase content. Cholinesterase and C-reactive protein (CRP) levels on postoperative day (POD) 3 were significantly different between the two groups. Multivariate analysis showed that cholinesterase>=112 U/L and CRP<=16.0 mg/dl on POD 3 were independent predictors of PA formation. CONCLUSIONS: Decreased cholinesterase and elevated CRP on POD 3 (Cho-C score) are useful predictors of PA formation in cases with soft pancreas. In such cases, periodic computed tomography evaluations and strict drain management are necessary to prevent life-threatening hemorrhage. Title: Isolation of a Cyclic Depsipetide, Aspergillicin F, and Synthesis of Aspergillicins with Innate Immune-Modulating Activity Kikuchi H, Hoshikawa T, Fujimura S, Sakata N, Kurata S, Katou Y, Oshima Y Ref: Journal of Natural Products, 78:1949, 2015 : PubMed ESTHER: Kikuchi_2015_J.Nat.Prod_78_1949 PubMedSearch: Kikuchi 2015 J.Nat.Prod 78 1949 PubMedID: 26273902 Gene_locus related to this paper: aspfn-agia Abstract Innate immunity is the front line of self-defense against microbial infection. After searching for natural compounds that regulate innate immunity using an ex vivo Drosophila culture system, we identified a new cyclic depsipeptide, aspergillicin F, from the fungus Aspergillus sp., as an innate immune suppressor. The total synthesis and biological evaluation of the aspergillicin family, including aspergillicin F, were performed, revealing that slight structural differences in the side chains of amino acid residues alter innate immunity-regulating activity. Title: [Pharmacodynamics of pain perception and polymorphism] Kikuchi H Ref: Masui, 58:1084, 2009 : PubMed ESTHER: Kikuchi_2009_Masui_58_1084 PubMedSearch: Kikuchi 2009 Masui 58 1084 PubMedID: 19764429 Abstract The regulation of biotransformation started with the mechanism of mass action between the concentrations of the substrates (product) and enzyme. Thereafter by understanding the protein tertiary structure, allosteric control mechanism appeared. The enzyme induction was brought into a new aspect by the development of genetic analysis. As a cellular economy, energy charge was found to be a new regulatory mechanism for glycolytic pathway. These regulatory systems showed a single concentration-effect curve of pharmacodynamics. By introduction of silent or non sense gene as in atypical cholinesterase, a given function was not operated. As most doctors are aware of the diverse sensitivity to opioids among patients, numbers and species of opioid receptors might be the cause. By extensive gene analysis, polymorphism may explain this phenotype. The polymorphism may also play an important role in the pain mechanism such as incidence of neuropathic pain and in the modulation of pain. You will find several curves of pharmocodynamics. Title: Genome sequencing and analysis of Aspergillus oryzae Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O and Kikuchi H <54 more author(s)> Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y, Abe K, Gomi K, Horiuchi H, Kitamoto K, Kobayashi T, Takeuchi M, Denning DW, Galagan JE, Nierman WC, Yu J, Archer DB, Bennett JW, Bhatnagar D, Cleveland TE, Fedorova ND, Gotoh O, Horikawa H, Hosoyama A, Ichinomiya M, Igarashi R, Iwashita K, Juvvadi PR, Kato M, Kato Y, Kin T, Kokubun A, Maeda H, Maeyama N, Maruyama J, Nagasaki H, Nakajima T, Oda K, Okada K, Paulsen I, Sakamoto K, Sawano T, Takahashi M, Takase K, Terabayashi Y, Wortman JR, Yamada O, Yamagata Y, Anazawa H, Hata Y, Koide Y, Komori T, Koyama Y, Minetoki T, Suharnan S, Tanaka A, Isono K, Kuhara S, Ogasawara N, Kikuchi H (- 54) Ref: Nature, 438:1157, 2005 : PubMed ESTHER: Machida_2005_Nature_438_1157 PubMedSearch: Machida 2005 Nature 438 1157 PubMedID: 16372010 Gene_locus related to this paper: aspor-Q2U722, aspfn-b8mvx2, aspfn-b8mwk1, aspfn-b8n1a4, aspfn-b8n5l3, aspfn-b8n7y0, aspfn-b8n829, aspfn-b8ncj5, aspfn-b8nhj9, aspfn-b8njx6, aspfn-b8nsk2, aspfu-q4wj61, aspor-axe1, aspor-CPI, aspor-cutas, aspor-cuti2, aspor-DPPIV, aspor-faec, aspor-MDLB, aspor-ppme1, aspor-q2tw11, aspor-q2tw16, aspor-q2tw28, aspor-q2twc4, aspor-q2twg0, aspor-q2twj3, aspor-q2twv2, aspor-q2twv4, aspor-q2tx21, aspor-q2txq8, aspor-q2tya1, aspor-q2tyh6, aspor-q2tyn9, aspor-q2typ0, aspor-q2tyq4, aspor-q2tyv8, aspor-q2tz03, aspor-q2tzh3, aspor-q2tzr5, aspor-q2tzv9, aspor-q2u0k7, aspor-q2u0q2, aspor-q2u0r6, aspor-q2u1a5, aspor-q2u1a6, aspor-q2u1k0, aspor-q2u1k8, aspor-q2u1m8, aspor-q2u2a1, aspor-q2u2a4, aspor-q2u3a3, aspor-q2u3a6, aspor-q2u3k5, aspor-q2u3l6, aspor-q2u4a0, aspor-q2u4e0, aspor-q2u4f6, aspor-q2u4g6, aspor-q2u4h9, aspor-q2u4w9, aspor-q2u4y8, aspor-q2u5f5, aspor-q2u5n3, aspor-q2u5y8, aspor-q2u6h7, aspor-q2u6j5, aspor-q2u6m8, aspor-q2u6m9, aspor-q2u6n6, aspor-q2u7i2, aspor-q2u7v0, aspor-q2u8j8, aspor-q2u8r1, aspor-q2u8r4, aspor-q2u8t5, aspor-q2u8z3, aspor-q2u9a1, aspor-q2u9n5, aspor-q2u144, aspor-q2u161, aspor-q2u185, aspor-q2u199, aspor-q2u212, aspor-q2u331, aspor-q2u348, aspor-q2u400, aspor-q2u453, aspor-q2u489, aspor-q2u704, aspor-q2u728, aspor-q2u798, aspor-q2u822, aspor-q2u854, aspor-q2u875, aspor-q2u908, aspor-q2ua10, aspor-q2ua48, aspor-q2uab6, aspor-q2uak9, aspor-q2uaq4, aspor-q2ub32, aspor-q2ub76, aspor-q2uba1, aspor-q2ubd6, aspor-q2ubm2, aspor-q2ubr2, aspor-q2uc28, aspor-q2uc65, aspor-q2uc77, aspor-q2uc98, aspor-q2uck0, aspor-q2ucy7, aspor-q2ud03, aspor-q2ud06, aspor-q2ud08, aspor-q2ud23, aspor-q2udn5, aspor-q2udr0, aspor-q2uec1, aspor-q2uef3, aspor-q2uf10, aspor-q2uf27, aspor-q2uf48, aspor-q2ufd8, aspor-q2ufe5, aspor-q2ufm4, aspor-q2ufr3, aspor-q2ufz8, aspor-q2ug78, aspor-q2ugd6, aspor-q2uge1, aspor-q2ugg7, aspor-q2ugi2, aspor-q2ugl2, aspor-q2ugy9, aspor-q2uh24, aspor-q2uh73, aspor-q2uhe4, aspor-q2uhf0, aspor-q2uhj6, aspor-q2uhn1, aspor-q2uhq0, aspor-q2ui56, aspor-q2uib2, aspor-q2uib5, aspor-q2uie9, aspor-q2uih1, aspor-q2uii1, aspor-q2uik9, aspor-q2uiq0, aspor-q2uiu1, aspor-q2uix9, aspor-q2uiy5, aspor-q2uiz4, aspor-q2uj89, aspor-q2uja2, aspor-q2uju3, aspor-q2uk31, aspor-q2uk42, aspor-q2ukb6, aspor-q2ukq7, aspor-q2ul81, aspor-q2uli9, aspor-q2ulr2, aspor-q2ulv7, aspor-q2umf3, aspor-q2umv2, aspor-q2umx6, aspor-q2unw5, aspor-q2up23, aspor-q2up89, aspor-q2upe6, aspor-q2upi1, aspor-q2upl1, aspor-q2upw4, aspor-q2uq56, aspor-q2uqb4, aspor-q2uqm7, aspor-q2ur58, aspor-q2ur64, aspor-q2ur80, aspor-q2ur83, aspor-q2ure7, aspor-q2urf3, aspor-q2urg5, aspor-q2urq0, aspor-q2urt4, aspor-q2uru5, aspor-q2usi0, aspor-q2usp7, aspor-q2usq8, aspor-q2usv6, aspor-q2uta5, aspor-q2uu89, aspor-q2uub4, aspor-q2uux8, aspor-q2uv29, aspor-TGLA, aspor-q2ue03, aspor-q2uj83, aspno-a0a0l1j1c9 Abstract 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. Title: Complete sequencing and characterization of 21,243 full-length human cDNAs Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H and Sugano S <144 more author(s)> Ota T, Suzuki Y, Nishikawa T, Otsuki T, Sugiyama T, Irie R, Wakamatsu A, Hayashi K, Sato H, Nagai K, Kimura K, Makita H, Sekine M, Obayashi M, Nishi T, Shibahara T, Tanaka T, Ishii S, Yamamoto J, Saito K, Kawai Y, Isono Y, Nakamura Y, Nagahari K, Murakami K, Yasuda T, Iwayanagi T, Wagatsuma M, Shiratori A, Sudo H, Hosoiri T, Kaku Y, Kodaira H, Kondo H, Sugawara M, Takahashi M, Kanda K, Yokoi T, Furuya T, Kikkawa E, Omura Y, Abe K, Kamihara K, Katsuta N, Sato K, Tanikawa M, Yamazaki M, Ninomiya K, Ishibashi T, Yamashita H, Murakawa K, Fujimori K, Tanai H, Kimata M, Watanabe M, Hiraoka S, Chiba Y, Ishida S, Ono Y, Takiguchi S, Watanabe S, Yosida M, Hotuta T, Kusano J, Kanehori K, Takahashi-Fujii A, Hara H, Tanase TO, Nomura Y, Togiya S, Komai F, Hara R, Takeuchi K, Arita M, Imose N, Musashino K, Yuuki H, Oshima A, Sasaki N, Aotsuka S, Yoshikawa Y, Matsunawa H, Ichihara T, Shiohata N, Sano S, Moriya S, Momiyama H, Satoh N, Takami S, Terashima Y, Suzuki O, Nakagawa S, Senoh A, Mizoguchi H, Goto Y, Shimizu F, Wakebe H, Hishigaki H, Watanabe T, Sugiyama A, Takemoto M, Kawakami B, Watanabe K, Kumagai A, Itakura S, Fukuzumi Y, Fujimori Y, Komiyama M, Tashiro H, Tanigami A, Fujiwara T, Ono T, Yamada K, Fujii Y, Ozaki K, Hirao M, Ohmori Y, Kawabata A, Hikiji T, Kobatake N, Inagaki H, Ikema Y, Okamoto S, Okitani R, Kawakami T, Noguchi S, Itoh T, Shigeta K, Senba T, Matsumura K, Nakajima Y, Mizuno T, Morinaga M, Sasaki M, Togashi T, Oyama M, Hata H, Komatsu T, Mizushima-Sugano J, Satoh T, Shirai Y, Takahashi Y, Nakagawa K, Okumura K, Nagase T, Nomura N, Kikuchi H, Masuho Y, Yamashita R, Nakai K, Yada T, Ohara O, Isogai T, Sugano S (- 144) Ref: Nat Genet, 36:40, 2004 : PubMed ESTHER: Ota_2004_Nat.Genet_36_40 PubMedSearch: Ota 2004 Nat.Genet 36 40 PubMedID: 14702039 Gene_locus related to this paper: human-ABHD1, human-ABHD4, human-ABHD12, human-ABHD16A, human-ACOT1, human-LDAH, human-ABHD18, human-CES1, human-CES4A, human-CES5A, human-CPVL, human-DAGLB, human-EPHX2, human-KANSL3, human-LIPA, human-LPL, human-MEST, human-NDRG1, human-NLGN1, human-NLGN4X, human-PRCP, human-PRSS16, human-SERAC1, human-TMEM53 Abstract As a base for human transcriptome and functional genomics, we created the "full-length long Japan" (FLJ) collection of sequenced human cDNAs. We determined the entire sequence of 21,243 selected clones and found that 14,490 cDNAs (10,897 clusters) were unique to the FLJ collection. About half of them (5,416) seemed to be protein-coding. Of those, 1,999 clusters had not been predicted by computational methods. The distribution of GC content of nonpredicted cDNAs had a peak at approximately 58% compared with a peak at approximately 42%for predicted cDNAs. Thus, there seems to be a slight bias against GC-rich transcripts in current gene prediction procedures. The rest of the cDNAs unique to the FLJ collection (5,481) contained no obvious open reading frames (ORFs) and thus are candidate noncoding RNAs. About one-fourth of them (1,378) showed a clear pattern of splicing. The distribution of GC content of noncoding cDNAs was narrow and had a peak at approximately 42%, relatively low compared with that of protein-coding cDNAs. Title: Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S Ref: Nat Biotechnol, 21:526, 2003 : PubMed ESTHER: Ikeda_2003_Nat.Biotechnol_21_526 PubMedSearch: Ikeda 2003 Nat.Biotechnol 21 526 PubMedID: 12692562 Gene_locus related to this paper: strav-cah, strav-GEOB, strav-PCAL, strav-Q93HH8, strav-SAV38, strav-SAV141, strav-SAV154, strav-SAV297, strav-SAV298, strav-SAV433, strav-SAV469, strav-SAV512, strav-SAV519, strav-SAV541, strav-SAV569, strav-SAV620, strav-SAV819, strav-SAV875, strav-SAV888, strav-SAV906, strav-SAV923, strav-SAV974, strav-SAV1231, strav-SAV1256, strav-SAV1457, strav-SAV1549, strav-SAV1585, strav-SAV1746, strav-SAV1898, strav-SAV1906, strav-SAV1959, strav-SAV1968, strav-SAV1973, strav-SAV2099, strav-SAV2105, strav-SAV2113, strav-SAV2604, strav-SAV2722, strav-SAV3039, strav-SAV3080, strav-SAV3081, strav-SAV3092, strav-SAV3099, strav-SAV3144, strav-SAV3359, strav-SAV3461, strav-SAV3624, strav-SAV3810, strav-SAV3854, strav-SAV4041, strav-SAV4252, strav-SAV4410, strav-SAV4434, strav-SAV4531, strav-SAV4564, strav-SAV4596, strav-SAV4674, strav-SAV4779, strav-SAV4863, strav-SAV4922, strav-SAV4968, strav-SAV5173, strav-SAV5300, strav-SAV5344, strav-SAV5668, strav-SAV5711, strav-SAV5844, strav-SAV5965, strav-SAV6079, strav-SAV6138, strav-SAV6422, strav-SAV6559, strav-SAV6609, strav-SAV7067, strav-SAV7089, strav-SAV7110, strav-SAV7198, strav-SAV7423, strav-SAV7455, strav-SAV7475, strav-SLPD, straw-AVEG, straw-pepx, straw-q82bb0, straw-q82en5, straw-q82et1, straw-q93hc9, straw-SAV1543, straw-SAV2023 Abstract Species of the genus Streptomyces are of major pharmaceutical interest because they synthesize a variety of bioactive secondary metabolites. We have determined the complete nucleotide sequence of the linear chromosome of Streptomyces avermitilis. S. avermitilis produces avermectins, a group of antiparasitic agents used in human and veterinary medicine. The genome contains 9,025,608 bases (average GC content, 70.7%) and encodes at least 7,574 potential open reading frames (ORFs). Thirty-five percent of the ORFs (2,664) constitute 721 paralogous families. Thirty gene clusters related to secondary metabolite biosynthesis were identified, corresponding to 6.6% of the genome. Comparison with Streptomyces coelicolor A3(2) revealed that an internal 6.5-Mb region in the S. avermitilis genome was highly conserved with respect to gene order and content, and contained all known essential genes but showed perfectly asymmetric structure at the oriC center. In contrast, the terminal regions were not conserved and preferentially contained nonessential genes. Title: Comparative complete genome sequence analysis of the amino acid replacements responsible for the thermostability of Corynebacterium efficiens Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H and Gojobori T <1 more author(s)> Nishio Y, Nakamura Y, Kawarabayasi Y, Usuda Y, Kimura E, Sugimoto S, Matsui K, Yamagishi A, Kikuchi H, Ikeo K, Gojobori T (- 1) Ref: Genome Res, 13:1572, 2003 : PubMed ESTHER: Nishio_2003_Genome.Res_13_1572 PubMedSearch: Nishio 2003 Genome.Res 13 1572 PubMedID: 12840036 Gene_locus related to this paper: coref-CE0007, coref-CE0093, coref-CE0094, coref-CE0096, coref-CE0103, coref-CE0104, coref-CE0150, coref-CE0293, coref-CE0354, coref-CE0356, coref-CE0596, coref-CE0984, coref-CE1275, coref-CE1488, coref-CE1571, coref-CE1601, coref-CE1609, coref-CE1895, coref-CE2149, coref-CE2296, coref-CE2371, coref-CE2453, coref-CE2486, coref-CE2499, coref-CE2705, coref-CE2710, coref-CE2923, coref-CSPA, coref-METX, coref-q8flv5, coref-q8fm83, coref-q8fmd4, coref-q8fm02 Abstract Corynebacterium efficiens is the closest relative of Corynebacterium glutamicum, a species widely used for the industrial production of amino acids. C. efficiens but not C. glutamicum can grow above 40 degrees C. We sequenced the complete C. efficiens genome to investigate the basis of its thermostability by comparing its genome with that of C. glutamicum. The difference in GC content between the species was reflected in codon usage and nucleotide substitutions. Our comparative genomic study clearly showed that there was tremendous bias in amino acid substitutions in all orthologous ORFs. Analysis of the direction of the amino acid substitutions suggested that three substitutions are important for the stability of the C. efficiens proteins: from lysine to arginine, serine to alanine, and serine to threonine. Our results strongly suggest that the accumulation of these three types of amino acid substitutions correlates with the acquisition of thermostability and is responsible for the greater GC content of C. efficiens. Title: [Assessing liver function by magnetic resonance imaging two-dimensional phase-shift flow measurement of portal venous blood flow after oral intake of glucose] Yagi H, Midorikawa T, Sakamoto M, Masuda E, Saitoh M, Takeyama Y, Haku E, Ishibashi K, Nemoto H and Kumada K <4 more author(s)> Yagi H, Midorikawa T, Sakamoto M, Masuda E, Saitoh M, Takeyama Y, Haku E, Ishibashi K, Nemoto H, Kikuchi H, Sasaya S, Yamaguchi M, Sanada Y, Kumada K (- 4) Ref: Nihon Geka Gakkai Zasshi, 103:441, 2002 : PubMed ESTHER: Yagi_2002_Nihon.Geka.Gakkai.Zasshi_103_441 PubMedSearch: Yagi 2002 Nihon.Geka.Gakkai.Zasshi 103 441 PubMedID: 12048882 Abstract We have already reported that the ratio of portal venous flow 30 min after oral intake of glucose 75 g to that before intake (PVFR30), measured using pulsed-Doppler ultrasonography (US), correlated significantly with other indicators of liver function and that it could be used to estimate hepatic function before surgery, including liver resection. In this study, to assess the disadvantages of pulsed-Doppler ultrasonography, PVFR30 was measured using two-dimensional (2D) phase-shift (PS) magnetic resonance imaging (MRI). PVFR30 was measured in 17 patients and 7 volunteers: 13 with liver cirrhosis (LC) and 11 without LC (non-LC). Portal venous flow could be measured in all patients without any disturbance of intestinal gas or patient fat, or the high degree of technical skill that Doppler US requires. PVFR30 was significantly lower in the LC group than in the non-LC group. In addition, it correlated significantly with other indicators of liver function, including the indocyanine green clearance test, prothrombin time, hepaplastin test, and cholinesterase activity. These results suggest that PVFR30 measured by 2D PS MRI can be used to estimate liver function, and that this MRI method can be performed more easily than pulsed-Doppler US. Title: Complete genome sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7 Kawarabayasi Y, Hino Y, Horikawa H, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H and Kikuchi H <20 more author(s)> Kawarabayasi Y, Hino Y, Horikawa H, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H, Hosoyama A, Fukui S, Nagai Y, Nishijima K, Otsuka R, Nakazawa H, Takamiya M, Kato Y, Yoshizawa T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki K, Masuda S, Yanagii M, Nishimura M, Yamagishi A, Oshima T, Kikuchi H (- 20) Ref: DNA Research, 8:123, 2001 : PubMed ESTHER: Kawarabayasi_2001_DNA.Res_8_123 PubMedSearch: Kawarabayasi 2001 DNA.Res 8 123 PubMedID: 11572479 Gene_locus related to this paper: sulto-ST0002, sulto-ST0071, sulto-ST0672, sulto-ST0779, sulto-ST1414, sulto-ST1737, sulto-ST1745, sulto-ST2026, sulto-ST2099, sulto-ST2511 Abstract The complete genomic sequence of an aerobic thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain7 which optimally grows at 80 degrees C, at low pH, and under aerobic conditions, has been determined by the whole genome shotgun method with slight modifications. The genomic size was 2,694,756 bp long and the G + C content was 32.8%. The following RNA-coding genes were identified: a single 16S-23S rRNA cluster, one 5S rRNA gene and 46 tRNA genes (including 24 intron-containing tRNA genes). The repetitive sequences identified were SR-type repetitive sequences, long dispersed-type repetitive sequences and Tn-like repetitive elements. The genome contained 2826 potential protein-coding regions (open reading frames, ORFs). By similarity search against public databases, 911 (32.2%) ORFs were related to functional assigned genes, 921 (32.6%) were related to conserved ORFs of unknown function, 145 (5.1%) contained some motifs, and remaining 849 (30.0%) did not show any significant similarity to the registered sequences. The ORFs with functional assignments included the candidate genes involved in sulfide metabolism, the TCA cycle and the respiratory chain. Sequence comparison provided evidence suggesting the integration of plasmid, rearrangement of genomic structure, and duplication of genomic regions that may be responsible for the larger genomic size of the S. tokodaii strain7 genome. The genome contained eukaryote-type genes which were not identified in other archaea and lacked the CCA sequence in the tRNA genes. The result suggests that this strain is closer to eukaryotes among the archaea strains so far sequenced. The data presented in this paper are also available on the internet homepage (http:\/\/www.bio.nite.go.jp\/E-home\/genome_list-e.html\/). Title: Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H and Hattori M <4 more author(s)> Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, Kikuchi H, Shiba T, Sakaki Y, Hattori M (- 4) Ref: Proc Natl Acad Sci U S A, 98:12215, 2001 : PubMed ESTHER: Omura_2001_Proc.Natl.Acad.Sci.U.S.A_98_12215 PubMedSearch: Omura 2001 Proc.Natl.Acad.Sci.U.S.A 98 12215 PubMedID: 11572948 Gene_locus related to this paper: strav-cah, strav-GEOB, strav-OLMA7, strav-OLMC, strav-PCAL, strav-PTEA5, strav-PTEH, strav-Q93GY0, strav-Q93GY7, strav-Q93H00, strav-Q93H03, strav-Q93H41, strav-Q93H55, strav-Q93H68, strav-Q93H73, strav-Q93HG2, strav-Q93HH2, strav-Q93HH8, strav-Q93HI2, strav-SAV38, strav-SAV141, strav-SAV154, strav-SAV297, strav-SAV298, strav-SAV299, strav-SAV433, strav-SAV469, strav-SAV512, strav-SAV519, strav-SAV541, strav-SAV569, strav-SAV620, strav-SAV819, strav-SAV875, strav-SAV888, strav-SAV906, strav-SAV923, strav-SAV974, strav-SAV1231, strav-SAV1256, strav-SAV1457, strav-SAV1549, strav-SAV1585, strav-SAV1746, strav-SAV1898, strav-SAV1906, strav-SAV1959, strav-SAV1968, strav-SAV1973, strav-SAV2099, strav-SAV2105, strav-SAV2113, strav-SAV2604, strav-SAV2722, strav-SAV3039, strav-SAV3080, strav-SAV3081, strav-SAV3092, strav-SAV3099, strav-SAV3144, strav-SAV3359, strav-SAV3461, strav-SAV3624, strav-SAV3810, strav-SAV3854, strav-SAV4041, strav-SAV4252, strav-SAV4410, strav-SAV4434, strav-SAV4531, strav-SAV4564, strav-SAV4596, strav-SAV4674, strav-SAV4779, strav-SAV4863, strav-SAV4922, strav-SAV4968, strav-SAV5173, strav-SAV5300, strav-SAV5344, strav-SAV5668, strav-SAV5711, strav-SAV5844, strav-SAV5965, strav-SAV6079, strav-SAV6138, strav-SAV6422, strav-SAV6559, strav-SAV6609, strav-SAV7067, strav-SAV7089, strav-SAV7110, strav-SAV7198, strav-SAV7423, strav-SAV7455, strav-SAV7475, strav-SLPD, straw-AVEG, straw-pepx, straw-q82bb0, straw-q82en5, straw-q82et1, straw-q93hc9, straw-SAV1543, straw-SAV2023, strax-Q93H72 Abstract Streptomyces avermitilis is a soil bacterium that carries out not only a complex morphological differentiation but also the production of secondary metabolites, one of which, avermectin, is commercially important in human and veterinary medicine. The major interest in this genus Streptomyces is the diversity of its production of secondary metabolites as an industrial microorganism. A major factor in its prominence as a producer of the variety of secondary metabolites is its possession of several metabolic pathways for biosynthesis. Here we report sequence analysis of S. avermitilis, covering 99% of its genome. At least 8.7 million base pairs exist in the linear chromosome; this is the largest bacterial genome sequence, and it provides insights into the intrinsic diversity of the production of the secondary metabolites of Streptomyces. Twenty-five kinds of secondary metabolite gene clusters were found in the genome of S. avermitilis. Four of them are concerned with the biosyntheses of melanin pigments, in which two clusters encode tyrosinase and its cofactor, another two encode an ochronotic pigment derived from homogentiginic acid, and another polyketide-derived melanin. The gene clusters for carotenoid and siderophore biosyntheses are composed of seven and five genes, respectively. There are eight kinds of gene clusters for type-I polyketide compound biosyntheses, and two clusters are involved in the biosyntheses of type-II polyketide-derived compounds. Furthermore, a polyketide synthase that resembles phloroglucinol synthase was detected. Eight clusters are involved in the biosyntheses of peptide compounds that are synthesized by nonribosomal peptide synthetases. These secondary metabolite clusters are widely located in the genome but half of them are near both ends of the genome. The total length of these clusters occupies about 6.4% of the genome. Title: A 38 kb segment containing the cdc2 gene from the left arm of fission yeast chromosome II: sequence analysis and characterization of the genomic DNA and cDNAs encoded on the segment Machida M, Yamazaki S, Kunihiro S, Tanaka T, Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S and Yanagida M <9 more author(s)> Machida M, Yamazaki S, Kunihiro S, Tanaka T, Kushida N, Jinnno K, Haikawa Y, Yamazaki J, Yamamoto S, Sekine M, Oguchi A, Nagai Y, Sakai M, Aoki K, Ogura K, Kudoh Y, Kikuchi H, Zhang MQ, Yanagida M (- 9) Ref: Yeast, 16:71, 2000 : PubMed ESTHER: Machida_2000_Yeast_16_71 PubMedSearch: Machida 2000 Yeast 16 71 PubMedID: 10620777 Gene_locus related to this paper: schpo-be46 Abstract A genomic 38 kbp segment on the c1750 cosmid clone containing the cdc2 gene, located in the left arm of chromosome II from Schizosaccharomyces pombe, was sequenced. The segment was found to have five previously known genes, pht1, cdc2, his3, act1 and mei4. Among 11 coding sequences (CDSs) predicted by the gene finding software INTRON.PLOT., four CDSs, pi007, pi010, pi014 and pi016, had considerable similarity to 40S ribosomal protein, glycosyltransferase, cdc2-related protein kinase and alpha-1, 2-mannosyltransferase, respectively. Another unusually huge open reading frame (ORF) (pi011), consisting of 2233 amino acids, existed, having significant homology to alpha-amylase, granule-bound glycogen synthase and the Sz. pombe YS 1110 clone product at the N-terminal, middle and C-terminal regions, respectively. All the predicted 11 CDSs were experimentally analysed by RACE PCR. The sequencing of the RACE products revealed that there were two small overlaps at the 3' untranslated regions (UTRs) between pi004 and pi005 (17 bp) and between pi007 and pi008 (2 bp). The distances between 5' end of the 5'UTR and the putative translation initiation codon varied from 10 to 302 nucleotides (nt) among the nine CDSs successfully analysed by 5'-RACE. The expression level of each CDS on this clone was determined. Among the 16 genes on this clone, the previously determined genes, pht1, cdc2, his3 and act1, were found to be most highly expressed. Finally, cDNAs of all the newly identified genes were detected by RACE, proving the actual expression of these genes. The nucleotide sequence has been submitted to the EMBL database under Accession No. AB004534. Title: Complete genome sequence of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1 Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S and Kikuchi H <20 more author(s)> Kawarabayasi Y, Hino Y, Horikawa H, Yamazaki S, Haikawa Y, Jin-no K, Takahashi M, Sekine M, Baba S, Ankai A, Kosugi H, Hosoyama A, Fukui S, Nagai Y, Nishijima K, Nakazawa H, Takamiya M, Masuda S, Funahashi T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki KI, Kubota K, Nakamura Y, Nomura N, Sako Y, Kikuchi H (- 20) Ref: DNA Research, 6:83, 1999 : PubMed ESTHER: Kawarabayasi_1999_DNA.Res_6_83 PubMedSearch: Kawarabayasi 1999 DNA.Res 6 83 PubMedID: 10382966 Gene_locus related to this paper: aerpe-APE1244, aerpe-APE1547, aerpe-APE1832, aerpe-APE2290, aerpe-APE2361, aerpe-APE2441 Abstract The complete sequence of the genome of an aerobic hyper-thermophilic crenarchaeon, Aeropyrum pernix K1, which optimally grows at 95 degrees C, has been determined by the whole genome shotgun method with some modifications. The entire length of the genome was 1,669,695 bp. The authenticity of the entire sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2,694 open reading frames (ORFs) were assigned. By similarity search against public databases, 633 (23.5%) of the ORFs were related to genes with putative function and 523 (19.4%) to the sequences registered but with unknown function. All the genes in the TCA cycle except for that of alpha-ketoglutarate dehydrogenase were included, and instead of the alpha-ketoglutarate dehydrogenase gene, the genes coding for the two subunits of 2-oxoacid:ferredoxin oxidoreductase were identified. The remaining 1,538 ORFs (57.1%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs suggested that a considerable member of ORFs were generated by sequence duplication. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 47 tRNA genes including 14 genes with intron structures. All the assigned ORFs and RNA coding regions occupied 89.12% of the whole genome. The data presented in this paper are available on the internet homepage (http:\/\/www.mild.nite.go.jp). Title: Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3 Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S, Sekine M, Baba S, Kosugi H and Kikuchi H <15 more author(s)> Kawarabayasi Y, Sawada M, Horikawa H, Haikawa Y, Hino Y, Yamamoto S, Sekine M, Baba S, Kosugi H, Hosoyama A, Nagai Y, Sakai M, Ogura K, Otsuka R, Nakazawa H, Takamiya M, Ohfuku Y, Funahashi T, Tanaka T, Kudoh Y, Yamazaki J, Kushida N, Oguchi A, Aoki K, Kikuchi H (- 15) Ref: DNA Research, 5:55, 1998 : PubMed ESTHER: Kawarabayasi_1998_DNA.Res_5_55 PubMedSearch: Kawarabayasi 1998 DNA.Res 5 55 PubMedID: 9679194 Gene_locus related to this paper: pyrho-PH0594, pyrho-PH0863, pyrho-PH1262 Abstract The complete sequence of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3, has been determined by assembling the sequences of the physical map-based contigs of fosmid clones and of long polymerase chain reaction (PCR) products which were used for gap-filling. The entire length of the genome was 1,738,505 bp. The authenticity of the entire genome sequence was supported by restriction analysis of long PCR products, which were directly amplified from the genomic DNA. As the potential protein-coding regions, a total of 2061 open reading frames (ORFs) were assigned, and by similarity search against public databases, 406 (19.7%) were related to genes with putative function and 453 (22.0%) to the sequences registered but with unknown function. The remaining 1202 ORFs (58.3%) did not show any significant similarity to the sequences in the databases. Sequence comparison among the assigned ORFs in the genome provided evidence that a considerable number of ORFs were generated by sequence duplication. By similarity search, 11 ORFs were assumed to contain the intein elements. The RNA genes identified were a single 16S-23S rRNA operon, two 5S rRNA genes and 46 tRNA genes including two with the intron structure. All the assigned ORFs and RNA coding regions occupied 91.25% of the whole genome. The data presented in this paper are available on the internet at http:@www.nite.go.jp. | |||||||
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