Experts and Doctors on bacterial proteins in Japan


Locale: Japan
Topic: bacterial proteins

Top Publications

  1. Akiyama Y, Kamitani S, Kusukawa N, Ito K. In vitro catalysis of oxidative folding of disulfide-bonded proteins by the Escherichia coli dsbA (ppfA) gene product. J Biol Chem. 1992;267:22440-5 pubmed
    ..We propose that DsbA, which proved to directly catalyze disulfide bond formation, may also have a role in maintaining the bacterial periplasm oxidative. ..
  2. Furuchi T, Kashiwagi K, Kobayashi H, Igarashi K. Characteristics of the gene for a spermidine and putrescine transport system that maps at 15 min on the Escherichia coli chromosome. J Biol Chem. 1991;266:20928-33 pubmed
    ..These results indicate that the spermidine and putrescine transport system can be defined as a bacterial periplasmic transport system...
  3. Takase I, Ishino F, Wachi M, Kamata H, Doi M, Asoh S, et al. Genes encoding two lipoproteins in the leuS-dacA region of the Escherichia coli chromosome. J Bacteriol. 1987;169:5692-9 pubmed
    ..These two lipoproteins may be important in duplication of the cells. ..
  4. Fujiwara T, Morishima S, Takahashi I, Hamada S. Molecular cloning and sequencing of the fimbrilin gene of Porphyromonas gingivalis strains and characterization of recombinant proteins. Biochem Biophys Res Commun. 1993;197:241-7 pubmed publisher
    ..Taken together, these results indicate that four genetical clusters are noted among the fimA gene of P. gingivalis strains...
  5. Ihara K, Watanabe S, Sugimura K, Katagiri I, Mukohata Y. Identification of proteolipid from an extremely halophilic archaeon Halobacterium salinarum as an N,N'-dicyclohexyl-carbodiimide binding subunit of ATP synthase. Arch Biochem Biophys. 1997;341:267-72 pubmed
    ..J. Bult et al. (1996) Science 273, 1058-1073], proteolipids from archaea seem to have diverse characteristics in comparison with those from eubacteria or from eukaryotes. ..
  6. Ujiiye T, Yamamoto I, Satoh T. The dmsR gene encoding a dimethyl sulfoxide-responsive regulator for expression of dmsCBA (dimethyl sulfoxide respiration genes) in Rhodobacter sphaeroides f. sp. denitrificans. Biochim Biophys Acta. 1997;1353:84-92 pubmed
    ..These results indicate that the dmsR gene product acts as a positive regulator for expression of the dmsCBA genes in response to DMSO under anaerobic growth conditions. ..
  7. Wahyudi A, Takeyama H, Matsunaga T. Isolation of Magnetospirillum magneticum AMB-1 mutants defective in bacterial magnetic particle synthesis by transposon mutagenesis. Appl Biochem Biotechnol. 2001;91-93:147-54 pubmed
    ..4% in transconjugants. Further analysis of DNA sequences flanking transposon by inverted polymerase chain reaction allowed isolation of at least 10 genes or DNA sequences involved in BMP synthesis in M. magneticum AMB-1...
  8. Mochizuki S, Hiratsu K, Suwa M, Ishii T, Sugino F, Yamada K, et al. The large linear plasmid pSLA2-L of Streptomyces rochei has an unusually condensed gene organization for secondary metabolism. Mol Microbiol. 2003;48:1501-10 pubmed
  9. Oda M, Kobayashi N, Fujita M, Miyazaki Y, Sadaie Y, Kurusu Y, et al. Analysis of HutP-dependent transcription antitermination in the Bacillus subtilis hut operon: identification of HutP binding sites on hut antiterminator RNA and the involvement of the N-terminus of HutP in binding of HutP to the antiterminator RNA. Mol Microbiol. 2004;51:1155-68 pubmed
    ..A 25-mer peptide consisting of amino acid residues 2-26 of HutP bound to the antiterminator RNA. These results indicated that the N-terminus of HutP is involved in binding of HutP to the antiterminator RNA. ..

More Information

Publications375 found, 100 shown here

  1. Mukaihara T, Tamura N, Murata Y, Iwabuchi M. Genetic screening of Hrp type III-related pathogenicity genes controlled by the HrpB transcriptional activator in Ralstonia solanacearum. Mol Microbiol. 2004;54:863-75 pubmed publisher
    ..We show that a hpaB null mutant still produces Hrp pili on the cell surface although it shows a typical Hrp-defective phenotype on plants...
  2. Verjan N, Hirono I, Aoki T. Genetic loci of major antigenic protein genes of Edwardsiella tarda. Appl Environ Microbiol. 2005;71:5654-8 pubmed
    ..These genes and their products are useful for developing DNA or recombinant subunit vaccines to control edwardsiellosis...
  3. Oshima T, Ishikawa S, Kurokawa K, Aiba H, Ogasawara N. Escherichia coli histone-like protein H-NS preferentially binds to horizontally acquired DNA in association with RNA polymerase. DNA Res. 2006;13:141-53 pubmed
    ..coli genome, sheds light on the mechanism underlying the transcriptional regulation by H-NS, and provides new insight into bacterial genome evolution. ..
  4. Suemori A, Iwakura M. A systematic and comprehensive combinatorial approach to simultaneously improve the activity, reaction specificity, and thermal stability of p-hydroxybenzoate hydroxylase. J Biol Chem. 2007;282:19969-78 pubmed
  5. Yoshida A, Tomita T, Kono H, Fushinobu S, Kuzuyama T, Nishiyama M. Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus. FEBS J. 2009;276:3124-36 pubmed publisher
    ..Comparison of the crystal structures of TtAKbeta and the regulatory subunit of C. glutamicum AK showed that the well-packed hydrophobic core and high Pro content in loops contribute to the high thermostability of TtAKbeta. ..
  6. Ikeda T, Yamamoto M, Arai H, Ohmori D, Ishii M, Igarashi Y. Enzymatic and electron paramagnetic resonance studies of anabolic pyruvate synthesis by pyruvate: ferredoxin oxidoreductase from Hydrogenobacter thermophilus. FEBS J. 2010;277:501-10 pubmed publisher
    ..The reaction mechanism of the reductive carboxylation of acetyl-CoA is also discussed. ..
  7. Miyashita M, Oishi S, Kiso A, Kikuchi Y, Ueda O, Hirai K, et al. Hemoglobin binding activity and hemoglobin-binding protein of Prevotella nigrescens. Eur J Med Res. 2010;15:314-8 pubmed
    ..Molecular weight and isoelectric point of the HbBP were 46 kDa and 6.1, respectively...
  8. Kitamura N, Mori A, Tatsumi H, Nemoto S, Hiroi T, Kaminuma O. Zinc finger protein, multitype 1, suppresses human Th2 development via downregulation of IL-4. Int Arch Allergy Immunol. 2011;155 Suppl 1:53-6 pubmed publisher
    ..ZFPM1 that facilitates human Th1 differentiation via the downregulation of IL-4 is a potential target for the treatment of allergic diseases. ..
  9. Siddiki M, Ueda S, Maeda I. Fluorescent bioassays for toxic metals in milk and yoghurt. BMC Biotechnol. 2012;12:76 pubmed publisher
    ..The feature of regulatory elements is advantageous for establishment of simple and rapid assays of toxic metals in dairy products. ..
  10. Kiyonaka S, Kajimoto T, Sakaguchi R, Shinmi D, Omatsu Kanbe M, Matsuura H, et al. Genetically encoded fluorescent thermosensors visualize subcellular thermoregulation in living cells. Nat Methods. 2013;10:1232-8 pubmed publisher
    ..In HeLa cells, tsGFP targeted to mitochondria reveals heterogeneity in thermogenesis that correlates with the electrochemical gradient. Thus, tsGFPs are powerful tools to noninvasively assess thermogenesis in living cells. ..
  11. Ochi K. Comparative ribosomal protein sequence analyses of a phylogenetically defined genus, Pseudomonas, and its relatives. Int J Syst Bacteriol. 1995;45:268-73 pubmed
    ..Thus, I demonstrated the efficacy of ribosomal protein analysis in bacterial taxonomy. ..
  12. Hiratsu K, Yamamoto K, Makino K. Molecular cloning and functional analysis of an rpoS homologue gene from Vibrio cholerae N86. Genes Genet Syst. 1997;72:115-8 pubmed
    ..coli. In addition, the nlpD-like gene was found in the upstream region of the rpoS gene in the same order as in E. coli. These results suggest that the organization of these genes is highly conserved between E. coli and V. cholerae. ..
  13. Osyczka A, Nagashima K, Sogabe S, Miki K, Yoshida M, Shimada K, et al. Interaction site for soluble cytochromes on the tetraheme cytochrome subunit bound to the bacterial photosynthetic reaction center mapped by site-directed mutagenesis. Biochemistry. 1998;37:11732-44 pubmed
    ..On the basis of these findings, a model is proposed for the hypothetical cytochrome c2-RC transient complex for Blc. viridis...
  14. Hirose I, Sano K, Shioda I, Kumano M, Nakamura K, Yamane K. Proteome analysis of Bacillus subtilis extracellular proteins: a two-dimensional protein electrophoretic study. Microbiology. 2000;146 ( Pt 1):65-75 pubmed
    ..Intracellular proteins Gap, SodA and KatA were identified in the extracellular protein samples. On the basis of these results and computer searches, it was predicted that B. subtilis produces 150 to 180 proteins extracellularly. ..
  15. Komatsuzawa H, Choi G, Fujiwara T, Huang Y, Ohta K, Sugai M, et al. Identification of a fmtA-like gene that has similarity to other PBPs and beta-lactamases in Staphylococcus aureus. FEMS Microbiol Lett. 2000;188:35-9 pubmed
    ..Recombinant FLP protein, however, lacks penicillin binding activity, and the inactivation of flp in two methicillin-resistant S. aureus strains did not cause a reduction in the methicillin resistance...
  16. Kakitani Y, Nagae H, Mizoguchi T, Egawa A, Akiba K, Fujiwara T, et al. Assembly of a mixture of isomeric BChl c from Chlorobium limicola as determined by intermolecular 13C-13C dipolar correlations: coexistence of dimer-based and pseudo-monomer-based stackings. Biochemistry. 2006;45:7574-85 pubmed
  17. Zhang Y, Matsuzaka T, Yano H, Furuta Y, Nakano T, Ishikawa K, et al. Restriction glycosylases: involvement of endonuclease activities in the restriction process. Nucleic Acids Res. 2017;45:1392-1403 pubmed publisher
    ..These results support generalization of the concept of restriction–modification system to the concept of self-recognizing epigenetic system, which combines any epigenetic labeling and any DNA damaging. ..
  18. Yokoseki T, Kutsukake K, Ohnishi K, Iino T. Functional analysis of the flagellar genes in the fliD operon of Salmonella typhimurium. Microbiology. 1995;141 ( Pt 7):1715-22 pubmed
    ..We found that the amount of flagellin excreted was much reduced by the fliS mutation. Based on these results, we conclude that FliS facilitates the export of flagellin through the flagellum-specific export pathway. ..
  19. Kutsukake K, Doi H. Nucleotide sequence of the flgD gene of Salmonella typhimurium which is essential for flagellar hook formation. Biochim Biophys Acta. 1994;1218:443-6 pubmed
    ..However, the N-terminal 86 amino acids of FlgD were found sufficient to complement all the flgD mutations examined. The predicted secondary structure suggested that FlgD has a high content of beta structure. ..
  20. Sano S, Asada K. cDNA cloning of monodehydroascorbate radical reductase from cucumber: a high degree of homology in terms of amino acid sequence between this enzyme and bacterial flavoenzymes. Plant Cell Physiol. 1994;35:425-37 pubmed
    ..MDA reductase has the FAD- and NAD(P)H-binding domains of flavoproteins but shares only limited homology in terms of amino acid sequence with flavoenzymes from eukaryotes...
  21. Iyoda S, Kutsukake K. Molecular dissection of the flagellum-specific anti-sigma factor, FlgM, of Salmonella typhimurium. Mol Gen Genet. 1995;249:417-24 pubmed
    ..These results indicate that the domain essential for export lies in the N-terminal region and that for FliA-binding in the C-terminal region. ..
  22. Sugiyama M, Yuasa K, Bhuiyan M, Iwai Y, Masumi N, Ueda K. IS431mec-mediated integration of a bleomycin-resistance gene into the chromosome of a methicillin-resistant Staphylococcus aureus strain isolated in Japan. Appl Microbiol Biotechnol. 1996;46:61-6 pubmed
    ..The 8-bp duplication sequence, produced by the transposable element, was first found by us. We proposed that bleomycin resistance in MRSA B-26 is attributed to the IS431 mec-mediated integration of pUB110 into the chromosome. ..
  23. Akiyama Y, Ehrmann M, Kihara A, Ito K. Polypeptide binding of Escherichia coli FtsH (HflB). Mol Microbiol. 1998;28:803-12 pubmed
    ..Thus, denatured PhoA binding of FtsH may also occur in vivo...
  24. Yamaguchi S, Yokoe M. A novel protein-deamidating enzyme from Chryseobacterium proteolyticum sp. nov., a newly isolated bacterium from soil. Appl Environ Microbiol. 2000;66:3337-43 pubmed
    ..The levels of DNA-DNA relatedness between the isolate and other related strains were less than 17%. The name Chryseobacterium proteolyticum is proposed for the new species; strain 9670 is the type strain (=FERM P-17664). ..
  25. Terao Y, Kawabata S, Kunitomo E, Nakagawa I, Hamada S. Novel laminin-binding protein of Streptococcus pyogenes, Lbp, is involved in adhesion to epithelial cells. Infect Immun. 2002;70:993-7 pubmed
    ..pyogenes M types. An Lbp-deficient mutant showed a significantly lower efficiency of adhesion to HEp-2 cells than did the wild-type strain. These results indicate that Lbp is one of the important S. pyogenes adhesins...
  26. Horie M, Kajikawa H, Toba T. Identification of Lactobacillus crispatus by polymerase chain reaction targeting S-layer protein gene. Lett Appl Microbiol. 2002;35:57-61 pubmed
    ..crispatus accurately and rapidly. To the authors' knowledge, this is the first paper to provide a PCR method for the specific identification of Lact. crispatus. ..
  27. Okamoto Shibayama K, Sato Y, Yamamoto Y, Ohta K, Kizaki H. Identification of a glucan-binding protein C gene homologue in Streptococcus macacae. Oral Microbiol Immunol. 2006;21:32-41 pubmed publisher
    ..mutans GbpC protein. In addition, Southern hybridization analysis using the S. macacae gbpC homologue as a probe showed a distribution of gbpC homologues throughout the mutans streptococci...
  28. Obata F, Kitami M, Inoue Y, Atsumi S, Yoshizawa Y, Sato R. Analysis of the region for receptor binding and triggering of oligomerization on Bacillus thuringiensis Cry1Aa toxin. FEBS J. 2009;276:5949-59 pubmed publisher
  29. Ogawa Y, Ooka T, Shi F, Ogura Y, Nakayama K, Hayashi T, et al. The genome of Erysipelothrix rhusiopathiae, the causative agent of swine erysipelas, reveals new insights into the evolution of firmicutes and the organism's intracellular adaptations. J Bacteriol. 2011;193:2959-71 pubmed publisher
    ..Thus, the E. rhusiopathiae genome represents evolutionary traits of both Firmicutes and Mollicutes and provides new insights into its evolutionary adaptations for intracellular survival...
  30. Lett M, Sasakawa C, Okada N, Sakai T, Makino S, Yamada M, et al. virG, a plasmid-coded virulence gene of Shigella flexneri: identification of the virG protein and determination of the complete coding sequence. J Bacteriol. 1989;171:353-9 pubmed
    ..The nucleotide sequence of 4,472 bp, which contains the functional virG gene and its own regulatory sequence, was determined, and a large open reading frame encoding 1,102 amino acid residues was identified. ..
  31. Onaka H, Ando N, Nihira T, Yamada Y, Beppu T, Horinouchi S. Cloning and characterization of the A-factor receptor gene from Streptomyces griseus. J Bacteriol. 1995;177:6083-92 pubmed
    ..The presence of ArpA-like proteins among Streptomyces spp., as revealed by PCR, together with the presence of A-factor-like compounds, suggests that a hormonal control similar to the A-factor system exists in many species of this genus...
  32. Honda K, Nakamura K, Nishiguchi M, Yamane K. Cloning and characterization of a Bacillus subtilis gene encoding a homolog of the 54-kilodalton subunit of mammalian signal recognition particle and Escherichia coli Ffh. J Bacteriol. 1993;175:4885-94 pubmed
    ..The depletion of ffh in B. subtilis led to growth arrest and drastic morphological changes. Furthermore, the translocation of beta-lactamase and alpha-amylase under the depleted condition was also defective. ..
  33. Yasuda T, Morimatsu K, Kato R, Usukura J, Takahashi M, Ohmori H. Physical interactions between DinI and RecA nucleoprotein filament for the regulation of SOS mutagenesis. EMBO J. 2001;20:1192-202 pubmed
    ..DinI is thus suited to modulating UmuD processing so as to limit SOS mutagenesis. ..
  34. Nakajima H, Nakagawa E, Kobayashi K, Tagawa S, Aono S. Ligand-switching intermediates for the CO-sensing transcriptional activator CooA measured by pulse radiolysis. J Biol Chem. 2001;276:37895-9 pubmed
    ..9 ms (k = 3.5 x 10(2) x s(-1)) for wild-type CooA. The ligand exchange between Cys75 and His77 took place during the conversion of the second intermediate into the final reduced form. ..
  35. Gunji Y, Yasueda H. Enhancement of L-lysine production in methylotroph Methylophilus methylotrophus by introducing a mutant LysE exporter. J Biotechnol. 2006;127:1-13 pubmed
    ..3 gl(-1) in jar-fermentation) than the parent producer carrying only dapA24 or lysE24. These results show the importance of the factor (lysE24) involved in the excretion of L-lysine on its overproduction in M. methylotrophus...
  36. Kikuchi Y, Date M, Itaya H, Matsui K, Wu L. Functional analysis of the twin-arginine translocation pathway in Corynebacterium glutamicum ATCC 13869. Appl Environ Microbiol. 2006;72:7183-92 pubmed publisher
    ..glutamicum Tat pathway. These observations indicate that IMD is a bona fide Tat substrate and imply great potential of the C. glutamicum Tat system for industrial production of heterologous folded proteins...
  37. Kurosawa N, Hirata T, Suzuki H. Characterization of putative tryptophan monooxygenase from Ralstonia solanacearum [corrected]. J Biochem. 2009;146:23-32 pubmed publisher
    ..These results lead to the conclusion that PTMO and PTMOp belong to proPAO and PAO, respectively. ..
  38. Okahashi N, Nakata M, Terao Y, Isoda R, Sakurai A, Sumitomo T, et al. Pili of oral Streptococcus sanguinis bind to salivary amylase and promote the biofilm formation. Microb Pathog. 2011;50:148-54 pubmed publisher
    ..These results indicate that pilus proteins are members of saliva-binding proteins of oral S. sanguinis, and suggest the involvement of pili in its colonization on saliva-coated tooth surfaces and in the human oral cavity...
  39. Akimaru J, Matsuyama S, Tokuda H, Mizushima S. Reconstitution of a protein translocation system containing purified SecY, SecE, and SecA from Escherichia coli. Proc Natl Acad Sci U S A. 1991;88:6545-9 pubmed
    ..We conclude that SecY, SecE, and SecA are essential components of the protein secretion machinery and that translocation activity can be reconstituted from only these three proteins and phospholipids. ..
  40. Sasakawa C, Adler B, Tobe T, Okada N, Nagai S, Komatsu K, et al. Functional organization and nucleotide sequence of virulence Region-2 on the large virulence plasmid in Shigella flexneri 2a. Mol Microbiol. 1989;3:1191-201 pubmed
    ..The 7663 nucleotides of Region-2 were determined to confirm the five open reading frames encoding 23,655, 17,755, 62,168, 41,077 and 36,660 Dalton proteins, respectively, and their regulatory sequences...
  41. Yoshida K, Sano H, Seki S, Oda M, Fujimura M, Fujita Y. Cloning and sequencing of a 29 kb region of the Bacillus subtilis genome containing the hut and wapA loci. Microbiology. 1995;141 ( Pt 2):337-43 pubmed
    ..Interestingly, the direction of transcription of these hut genes is opposite to that of the movement of the replication fork...
  42. Takayanagi Y, Tanaka K, Takahashi H. Structure of the 5' upstream region and the regulation of the rpoS gene of Escherichia coli. Mol Gen Genet. 1994;243:525-31 pubmed
    ..This strongly suggests that posttranslational regulation is involved in the control of rpoS expression...
  43. Ueguchi C, Kakeda M, Yamada H, Mizuno T. An analogue of the DnaJ molecular chaperone in Escherichia coli. Proc Natl Acad Sci U S A. 1994;91:1054-8 pubmed
    ..These genetic results are interpreted as meaning that the function(s) of CbpA in E. coli is closely related to that of DnaJ. ..
  44. Kashiwagi K, Miyamoto S, Nukui E, Kobayashi H, Igarashi K. Functions of potA and potD proteins in spermidine-preferential uptake system in Escherichia coli. J Biol Chem. 1993;268:19358-63 pubmed
    ..The results taken together indicate that potA and -D proteins are absolutely necessary for spermidine uptake in conjunction with the two channel forming proteins (potB and -C). ..
  45. Akashi A, Ono S, Kuwano K, Arai S. Proteins of 30 and 36 kilodaltons, membrane constituents of the Staphylococcus aureus L form, induce production of tumor necrosis factor alpha and activate the human immunodeficiency virus type 1 long terminal repeat. Infect Immun. 1996;64:3267-72 pubmed
    ..These results indicate that the 30- and 36-kDa proteins, membrane constituents of the S. aureus L form, may play a role in S. aureus infection and/or in human immunodeficiency virus type 1-infected individuals. ..
  46. Ueguchi C, Suzuki T, Yoshida T, Tanaka K, Mizuno T. Systematic mutational analysis revealing the functional domain organization of Escherichia coli nucleoid protein H-NS. J Mol Biol. 1996;263:149-62 pubmed
    ..This finding is also addressed with regard to a unique regulatory mechanism (i.e. silencing) for the bgl operon, which is partly mediated by H-NS. ..
  47. Liu H, Haga K, Yasumoto K, Ohashi Y, Yoshikawa H, Takahashi H. Sequence and analysis of a 31 kb segment of the Bacillus subtilis chromosome in the area of the rrnH and rrnG operons. Microbiology. 1997;143 ( Pt 8):2763-7 pubmed
    ..The gene cluster feuA, B, C reported previously for other strains of B. subtilis was also found in strain 168 and located in this region. ..
  48. Nishino K, Yamaguchi A. Overexpression of the response regulator evgA of the two-component signal transduction system modulates multidrug resistance conferred by multidrug resistance transporters. J Bacteriol. 2001;183:1455-8 pubmed
    ..Since overexpression of the emrKY operon, which is controlled by evgAS, could account only for deoxycholate resistance, the evgAS locus apparently controls expression of at least one other multidrug efflux operon. ..
  49. Yamada S, Ono T, Mizuno A, Nemoto T. A hydrophobic segment within the C-terminal domain is essential for both client-binding and dimer formation of the HSP90-family molecular chaperone. Eur J Biochem. 2003;270:146-54 pubmed
  50. Suzuki M, Mimuro H, Suzuki T, Park M, Yamamoto T, Sasakawa C. Interaction of CagA with Crk plays an important role in Helicobacter pylori-induced loss of gastric epithelial cell adhesion. J Exp Med. 2005;202:1235-47 pubmed
    ..Thus, CagA targeting of Crk plays a central role in inducing the pleiotropic cell responses to H. pylori infection that cause several gastric diseases, including gastric cancer. ..
  51. Sawai J, Hasegawa T, Kamimura T, Okamoto A, Ohmori D, Nosaka N, et al. Growth phase-dependent effect of clindamycin on production of exoproteins by Streptococcus pyogenes. Antimicrob Agents Chemother. 2007;51:461-7 pubmed
    ..Our study indicates that the in vitro effect of clindamycin on the production of exoproteins greatly depends on the growth phase of bacteria and some regulatory factors of Streptococcus pyogenes that are involved in this phenomenon. ..
  52. Isobe K, Fukuda N, Nagasawa S. Analysis of selective production of Nalpha-benzyloxycarbonyl-L-aminoadipate-delta-semialdehyde and Nalpha-benzyloxycarbonyl-L-aminoadipic acid by Rhodococcus sp. AIU Z-35-1. J Biosci Bioeng. 2008;105:152-6 pubmed publisher
    ..The optimum pH of N(alpha)-Z-L-AAA production was affected by the instability of N(alpha)-Z-L-AASA dehydrogenase in the alkaline pH region...
  53. Satsuma K. Complete biodegradation of atrazine by a microbial community isolated from a naturally derived river ecosystem (microcosm). Chemosphere. 2009;77:590-6 pubmed publisher
    ..Another strain, Pedomicrobium sp. strain AN4-9 could mineralize cyanuric acid alone. Therefore, we found that the coexistence of these two community members functionally serves to completely biodegrade atrazine...
  54. Takahashi R, Boussac A, Sugiura M, Noguchi T. Structural coupling of a tyrosine side chain with the non-heme iron center in photosystem II as revealed by light-induced Fourier transform infrared difference spectroscopy. Biochemistry. 2009;48:8994-9001 pubmed publisher
    ..The Tyr residue coupled to the non-heme iron may play a key role in the regulatory function of the iron-bicarbonate center by stabilizing the bicarbonate ligand and forming a rigid hydrogen bond network around the non-heme ion. ..
  55. Nazari B, Saito A, Kobayashi M, Miyashita K, Wang Y, Fujii T. High expression levels of chitinase genes in Streptomyces coelicolor A3(2) grown in soil. FEMS Microbiol Ecol. 2011;77:623-35 pubmed publisher
    ..The disruption of dasR, a transcriptional regulator for the uptake of N-acetylglucosamine, abolished the expression of chiH, demonstrating that DasR is required for the regulation of ChiH expression. ..
  56. Sato Y, Takaya A, Yamamoto T. Meta-analytic approach to the accurate prediction of secreted virulence effectors in gram-negative bacteria. BMC Bioinformatics. 2011;12:442 pubmed publisher
    ..From these findings, a new working hypothesis is proposed regarding mechanisms controlling the translocation of virulence effectors and determining the substrate specificity encoded in the secretion system. ..
  57. Yasuzawa K, Hayashi N, Goshima N, Kohno K, Imamoto F, Kano Y. Histone-like proteins are required for cell growth and constraint of supercoils in DNA. Gene. 1992;122:9-15 pubmed
    ..The bgl operon was expressed in cells depleted of both HU and H-NS as well as in cells depleted of H-NS.(ABSTRACT TRUNCATED AT 250 WORDS) ..
  58. Nakano M, Zuber P. Molecular biology of antibiotic production in Bacillus. Crit Rev Biotechnol. 1990;10:223-40 pubmed
    ..Future experiments involving the molecular dissection of peptide antibiotic biosynthesis genes in Bacillus will be attempted in hopes of further examining the mechanism and regulation of antibiotic production. ..
  59. Fujita M, Yoshikawa H, Ogasawara N. Structure of the dnaA region of Micrococcus luteus: conservation and variations among eubacteria. Gene. 1990;93:73-8 pubmed
    ..These results confirm our hypothesis that the dnaA region is the replication origin of the ancestral bacteria and that the essential feature of the DnaA protein and DnaA-box combination is conserved in eubacteria. ..
  60. Yamamoto J, Shimizu M, Yamane K. Nucleotide sequence of the diaminopimelate-decarboxylase gene from Bacillus subtilis. Nucleic Acids Res. 1989;17:10105 pubmed
  61. Makino S, Uchida I, Terakado N, Sasakawa C, Yoshikawa M. Molecular characterization and protein analysis of the cap region, which is essential for encapsulation in Bacillus anthracis. J Bacteriol. 1989;171:722-30 pubmed
    ..anthracis. Using strains of B. anthracis with or without insertional inactivation of the cap region, we found that the capsule of B. anthracis conferred strong resistance to phagocytosis upon the bacterial host...
  62. Tobe T, Yoshikawa M, Mizuno T, Sasakawa C. Transcriptional control of the invasion regulatory gene virB of Shigella flexneri: activation by virF and repression by H-NS. J Bacteriol. 1993;175:6142-9 pubmed
  63. Baba T, Taura T, Shimoike T, Akiyama Y, Yoshihisa T, Ito K. A cytoplasmic domain is important for the formation of a SecY-SecE translocator complex. Proc Natl Acad Sci U S A. 1994;91:4539-43 pubmed
    ..These results indicate that the secY24 mutation weakens SecY's interaction with SecE. Taken together, we propose that cytoplasmic domain 4 is important for the association between SecY and SecE. ..
  64. Yokoseki T, Iino T, Kutsukake K. Negative regulation by fliD, fliS, and fliT of the export of the flagellum-specific anti-sigma factor, FlgM, in Salmonella typhimurium. J Bacteriol. 1996;178:899-901 pubmed
    ..This indicates that all three genes in the operon are involved in the negative regulation of FlgM export. ..
  65. Tanaka K, Handel K, Loewen P, Takahashi H. Identification and analysis of the rpoS-dependent promoter of katE, encoding catalase HPII in Escherichia coli. Biochim Biophys Acta. 1997;1352:161-6 pubmed
    ..A - 10 sequence similar to that found in other sigma70- and sigma38-dependent E. coli promoters was identified 8 or 7 bp upstream of the start site but a sigma70-dependent -35 sequence was not evident. ..
  66. Tanaka N, Hiyama T, Nakamoto H. Cloning, characterization and functional analysis of groESL operon from thermophilic cyanobacterium Synechococcus vulcanus. Biochim Biophys Acta. 1997;1343:335-48 pubmed
    ..Introduction of the cloned groEL1 gene into a groEL defective mutant of E. coli resulted in the complementation of heat sensitivity, which contrasted with the previous result with groEL2...
  67. Okumura H, Nishiyama S, Sasaki A, Homma M, Kawagishi I. Chemotactic adaptation is altered by changes in the carboxy-terminal sequence conserved among the major methyl-accepting chemoreceptors. J Bacteriol. 1998;180:1862-8 pubmed
    ..These results suggest that the pentapeptide sequence facilitates effective adaptation and methylation by recruiting CheR. ..
  68. Sawada H, Suzuki F, Matsuda I, Saitou N. Phylogenetic analysis of Pseudomonas syringae pathovars suggests the horizontal gene transfer of argK and the evolutionary stability of hrp gene cluster. J Mol Evol. 1999;49:627-44 pubmed
  69. Maehara A, Doi Y, Nishiyama T, Takagi Y, Ueda S, Nakano H, et al. PhaR, a protein of unknown function conserved among short-chain-length polyhydroxyalkanoic acids producing bacteria, is a DNA-binding protein and represses Paracoccus denitrificans phaP expression in vitro. FEMS Microbiol Lett. 2001;200:9-15 pubmed
    ..coli S30 extract, the expression of the phaP gene was repressed by the addition of purified PhaR. These results suggest that PhaR is a DNA-binding protein and may play a role in the regulation of phaP gene expression. ..
  70. Hirakawa H, Nishino K, Yamada J, Hirata T, Yamaguchi A. Beta-lactam resistance modulated by the overexpression of response regulators of two-component signal transduction systems in Escherichia coli. J Antimicrob Chemother. 2003;52:576-82 pubmed
    ..Two-component signal transduction systems contribute to beta-lactam resistance in E. coli. Multidrug exporters play roles in two-component signal transduction system-mediated beta-lactam resistance. ..
  71. Asanuma N, Yoshii T, Hino T. Molecular characterization of CcpA and involvement of this protein in transcriptional regulation of lactate dehydrogenase and pyruvate formate-lyase in the ruminal bacterium Streptococcus bovis. Appl Environ Microbiol. 2004;70:5244-51 pubmed
    ..Thus, CcpA appears to be involved in the global regulation of sugar utilization in S. bovis. ..
  72. Inomata K, Hammam M, Kinoshita H, Murata Y, Khawn H, Noack S, et al. Sterically locked synthetic bilin derivatives and phytochrome Agp1 from Agrobacterium tumefaciens form photoinsensitive Pr- and Pfr-like adducts. J Biol Chem. 2005;280:24491-7 pubmed
    ..In this way, physiological action of Pfr can be studied in vivo and separated from Pr/Pfr cycling and other light effects. ..
  73. Takai N, Ikeuchi S, Manabe K, Kutsuna S. Expression of the circadian clock-related gene pex in cyanobacteria increases in darkness and is required to delay the clock. J Biol Rhythms. 2006;21:235-44 pubmed
    ..5 h (phase delay) compared to control cells. These results suggest that the dark-responsive gene expression of pex delays the circadian clock under daily light-dark cycles. ..
  74. Tanaka Y, Komatsu M, Okamoto S, Tokuyama S, Kaji A, Ikeda H, et al. Antibiotic overproduction by rpsL and rsmG mutants of various actinomycetes. Appl Environ Microbiol. 2009;75:4919-22 pubmed publisher
  75. Mukaihara T, Tamura N, Iwabuchi M. Genome-wide identification of a large repertoire of Ralstonia solanacearum type III effector proteins by a new functional screen. Mol Plant Microbe Interact. 2010;23:251-62 pubmed publisher
    ..We also show that most of the R. solanacearum effector proteins, but not Hrp extracellular components, require an Hrp-associated protein, HpaB, for their effective translocation into plant cells. ..
  76. Wang G, Tanaka Y, Ochi K. The G243D mutation (afsB mutation) in the principal sigma factor sigmaHrdB alters intracellular ppGpp level and antibiotic production in Streptomyces coelicolor A3(2). Microbiology. 2010;156:2384-92 pubmed publisher
  77. Isobe K, Fukuda N, Nagasawa S, Saitou K. Enzymes responsible for the conversion of N alpha-[(Benzyloxy)carbonyl]-D-lysine to N alpha-[(Benzyloxy)carbonyl]-D-aminoadipic acid by Rhodococcus sp. AIU Z-35-1. Chem Biodivers. 2010;7:1549-54 pubmed publisher
    ..The product amount of the D-specific amino acid deaminase reached the maximum at one day of cultivation in the L-lysine medium. The aldehyde dehydrogenase reached the maximum at three days of cultivation. ..
  78. Takeshita R, Ito H, Wachi M. A role of the cspA gene encoding a mycolyltransferase in the growth under alkaline conditions of Corynebacterium glutamicum. Biosci Biotechnol Biochem. 2010;74:1617-23 pubmed
    ..Disruption of cspB had no effect on alkali sensitivity or drug sensitivity. These results indicate that the mycolate layer is important for alkali sensitivity as well as drug susceptibility in this bacterium. ..
  79. Nakai T, Ono K, Kuroda S, Tanizawa K, Okajima T. An unusual subtilisin-like serine protease is essential for biogenesis of quinohemoprotein amine dehydrogenase. J Biol Chem. 2012;287:6530-8 pubmed publisher
    ..These results demonstrate that ORF5 is essential for QHNDH biogenesis, serving as a processing protease to cleave the γ subunit leader peptide nearly in a disposable manner. ..
  80. Ito C, Saito Y, Nozawa T, Fujii S, Sawa T, Inoue H, et al. Endogenous nitrated nucleotide is a key mediator of autophagy and innate defense against bacteria. Mol Cell. 2013;52:794-804 pubmed publisher
    ..These results collectively indicate that 8-nitro-cGMP plays a crucial role in cytoprotection during bacterial infections or inflammations via autophagy upregulation. ..
  81. Taura T, Ueguchi C, Shiba K, Ito K. Insertional disruption of the nusB (ssyB) gene leads to cold-sensitive growth of Escherichia coli and suppression of the secY24 mutation. Mol Gen Genet. 1992;234:429-32 pubmed
    ..5 min rather than 11 min as previously assigned. It is located at the distal end of an operon that contains a gene showing significant homology with a Bacillus subtilis gene involved in riboflavin biosynthesis. ..
  82. Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H. Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. EMBO J. 1991;10:4381-9 pubmed
    ..From these properties of RuvC protein and the phenotypes of the ruvC mutants, we infer that RuvC protein is an endonuclease that resolves Holliday structures in vivo. ..
  83. Yano R, Nagai H, Shiba K, Yura T. A mutation that enhances synthesis of sigma 32 and suppresses temperature-sensitive growth of the rpoH15 mutant of Escherichia coli. J Bacteriol. 1990;172:2124-30 pubmed
    ..coli DNA segment of 1.0 kilobase could complement the cold-sensitive phenotype of the suhB2 mutant. Nucleotide sequence analysis revealed that the segment contained an open reading frame encoding a protein of 29,128 daltons. ..
  84. Matsuyama S, Akimaru J, Mizushima S. SecE-dependent overproduction of SecY in Escherichia coli. Evidence for interaction between two components of the secretory machinery. FEBS Lett. 1990;269:96-100 pubmed
    ..It is suggested that SecY and SecE interact with each other in the cytoplasmic membrane. The numbers of the SecY and SecE molecules per cell were estimated. ..
  85. Amemura M, Makino K, Shinagawa H, Nakata A. Cross talk to the phosphate regulon of Escherichia coli by PhoM protein: PhoM is a histidine protein kinase and catalyzes phosphorylation of PhoB and PhoM-open reading frame 2. J Bacteriol. 1990;172:6300-7 pubmed
    ..Therefore, cross talk by protein phosphorylation appears to occur from PhoM to PhoB but not from PhoR to PhoM-open reading frame 2. ..
  86. Aoyama T, Hirayama T, Tamamoto S, Oka A. Putative start codon TTG for the regulatory protein VirG of the hairy-root-inducing plasmid pRiA4. Gene. 1989;78:173-8 pubmed
    ..The TTG codon preceded by an SD sequence and a T signal is also conserved in the virG sequences from other three tumor-inducing plasmids previously reported. ..
  87. Saiki K, Mogi T, Hori H, Tsubaki M, Anraku Y. Identification of the functional domains in heme O synthase. Site-directed mutagenesis studies on the cyoE gene of the cytochrome bo operon in Escherichia coli. J Biol Chem. 1993;268:26927-34 pubmed
    ..Based on the above observations, we suggest that the conserved amino acid residues present in the cytoplasmic loops II/III and IV/V are part of the catalytic center of heme O synthase. ..
  88. Ide N, Kutsukake K. Identification of a novel Escherichia coli gene whose expression is dependent on the flagellum-specific sigma factor, FliA, but dispensable for motility development. Gene. 1997;199:19-23 pubmed
    ..This mutant was found to be actively motile, suggesting that this gene is unlikely to be involved in the motility phenotype of E. coli. ..
  89. Sugiyama T, Kido N, Kato Y, Koide N, Yoshida T, Yokochi T. Evolutionary relationship among rfb gene clusters synthesizing mannose homopolymer as O-specific polysaccharides in Escherichia coli and Klebsiella. Gene. 1997;198:111-3 pubmed
    ..It was suggested that there was a close evolutionary relationship among rfb gene clusters synthesizing mannose homopolymer as O-specific polysaccharide in E. coli and Klebsiella. ..
  90. Han W, Kawamoto S, Hosoya Y, Fujita M, Sadaie Y, Suzuki K, et al. A novel sporulation-control gene (spo0M) of Bacillus subtilis with a sigmaH-regulated promoter. Gene. 1998;217:31-40 pubmed
  91. Inaoka T, Kasai K, Ochi K. Construction of an in vivo nonsense readthrough assay system and functional analysis of ribosomal proteins S12, S4, and S5 in Bacillus subtilis. J Bacteriol. 2001;183:4958-63 pubmed
    ..subtilis. The efficacy of our in vivo nonsense readthrough assay system was demonstrated in our investigation of the function of ribosomal proteins and translational factors. ..
  92. Chen J, Morita Y, Huda M, Kuroda T, Mizushima T, Tsuchiya T. VmrA, a member of a novel class of Na(+)-coupled multidrug efflux pumps from Vibrio parahaemolyticus. J Bacteriol. 2002;184:572-6 pubmed
    ..VmrA belongs to the DinF branch of MATE family efflux transporters. VmrA catalyzed acriflavine efflux and showed Na(+)/drug transporter activity because the addition of tetraphenylphosphonium to Na(+)-loaded cells caused Na(+) efflux...