Hirotada Mori

Publications of Hirotada Mori

• Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.

  Authors: Atsuko Shinhara, Motomu Matsui, Kiriko Hiraoka, Wataru Nomura, Reiko Hirano, Kenji Nakahigashi, Masaru Tomita, Hirotada Mori, Akio Kanai

  BMC genomics. 08/2011; 12:428.

  In Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview ofIn Escherichia coli, approximately 100 regulatory small RNAs (sRNAs) have been identified experimentally and many more have been predicted by various methods. To provide a comprehensive overview of sRNAs, we analysed the low-molecular-weight RNAs (< 200 nt) of E. coli with deep sequencing, because the regulatory RNAs in bacteria are usually 50-200 nt in length. We discovered 229 novel candidate sRNAs (≥ 50 nt) with computational or experimental evidence of transcription initiation. Among them, the expression of seven intergenic sRNAs and three cis-antisense sRNAs was detected by northern blot analysis. Interestingly, five novel sRNAs are expressed from prophage regions and we note that these sRNAs have several specific characteristics. Furthermore, we conducted an evolutionary conservation analysis of the candidate sRNAs and summarised the data among closely related bacterial strains. This comprehensive screen for E. coli sRNAs using a deep sequencing approach has shown that many as-yet-undiscovered sRNAs are potentially encoded in the E. coli genome. We constructed the Escherichia coli Small RNA Browser (ECSBrowser; http://rna.iab.keio.ac.jp/), which integrates the data for previously identified sRNAs and the novel sRNAs found in this study.

• Environmental dependency of gene knockouts on phenotype microarray analysis in Escherichia coli.

  Authors: Yukako Tohsato, Tomoya Baba, Yusaku Mazaki, Masahiro Ito, Barry L Wanner, Hirotada Mori

  Journal of bioinformatics and computational biology. 12/2010; 8 Suppl 1:83-99.

  Systematic studies have revealed that single gene deletions often display little phenotypic effects under laboratory conditions and that in many cases gene dispensability depends on the experimentalSystematic studies have revealed that single gene deletions often display little phenotypic effects under laboratory conditions and that in many cases gene dispensability depends on the experimental conditions. To elucidate the environmental dependency of genes, we analyzed the effects of gene deletions by Phenotype MicroArray™ (PM), a system for quantitative screening of thousands of phenotypes in a high-throughput manner. Here, we proposed a new statistical approach to minimize error inherent in measurements of low respiration rates and find which mutants showed significant phenotypic changes in comparison to the wild-type. We show analyzing results from comprehensive PM assays of 298 single-gene knockout mutants in the Keio collection and two additional mutants under 1,920 different conditions. We focused on isozymes of these genes as simple duplications and analyzed correlations between phenotype changes and protein expression levels. Our results revealed divergence of the environmental dependency of the gene among the knockout genes and have also given some insights into possibilities of alternative pathways and availabilities of information on protein synthesis patterns to classify or predict functions of target genes from systematic phenotype screening.

• Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments.

  Authors: Eiji Aono, Tomoya Baba, Takeshi Ara, Tatsunari Nishi, Tomoko Nakamichi, Eiji Inamoto, Hiromi Toyonaga, Miki Hasegawa, Yuki Takai, Yoshiko Okumura, Miki Baba, Masaru Tomita, Chiaki Kato, Taku Oshima, Kaoru Nakasone, Hirotada Mori

  Molecular bioSystems. 07/2010; 6(7):1216-26.

  Remineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilicRemineralization of organic matter in deep-sea sediments is important in oceanic biogeochemical cycles, and bacteria play a major role in this process. Shewanella violacea DSS12 is a psychrophilic and piezophilic gamma-proteobacterium that was isolated from the surface layer of deep sea sediment at a depth of 5110 m. Here, we report the complete genome sequence of S. violacea and comparative analysis with the genome of S. oneidensis MR-1, isolated from sediments of a freshwater lake. Unlike S. oneidensis, this deep-sea Shewanella possesses very few terminal reductases for anaerobic respiration and no c-type cytochromes or outer membrane proteins involved in respiratory Fe(iii) reduction, which is characteristic of most Shewanella species. Instead, the S. violacea genome contains more terminal oxidases for aerobic respiration and a much greater number of putative secreted proteases and polysaccharases, in particular, for hydrolysis of collagen, cellulose and chitin, than are encoded in S. oneidensis. Transporters and assimilatory reductases for nitrate and nitrite, and nitric oxide-detoxifying mechanisms (flavohemoglobin and flavorubredoxin) are found in S. violacea. Comparative analysis of the S. violacea genome revealed the respiratory adaptation of this bacterium to aerobiosis, leading to predominantly aerobic oxidation of organic matter in surface sediments, as well as its ability to efficiently use diverse organic matter and to assimilate inorganic nitrogen as a survival strategy in the nutrient-poor deep-sea floor.

• The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology.

  Authors: Seesandra V Rajagopala, Natsuko Yamamoto, Adrienne E Zweifel, Tomoko Nakamichi, Hsi-Kuang Huang, Jorge David Mendez-Rios, Jonathan Franca-Koh, Meher Preethi Boorgula, Kazutoshi Fujita, Ken-ichirou Suzuki, James C Hu, Barry L Wanner, Hirotada Mori, Peter Uetz

  BMC genomics. 01/2010; 11:470.

  Systems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allowSystems biology and functional genomics require genome-wide datasets and resources. Complete sets of cloned open reading frames (ORFs) have been made for about a dozen bacterial species and allow researchers to express and study complete proteomes in a high-throughput fashion. We have constructed an open reading frame (ORFeome) collection of 3974 or 94% of the known Escherichia coli K-12 ORFs in Gateway entry vector pENTR/Zeo. The collection has been used for protein expression and protein interaction studies. For example, we have compared interactions among YgjD, YjeE and YeaZ proteins in E. coli, Streptococcus pneumoniae, and Staphylococcus aureus. We also compare this ORFeome with other Gateway-compatible bacterial ORFeomes and show its utility for comparative functional genomics. The E. coli ORFeome provides a useful resource for functional genomics and other areas of protein research in a highly flexible format. Our comparison with other ORFeomes makes comparative analyses straighforward and facilitates direct comparisons of many proteins across many genomes.

• Glutathione production by efficient ATP-regenerating Escherichia coli mutants.

  Authors: Kiyotaka Y Hara, Natsuka Shimodate, Yasutaka Hirokawa, Mikito Ito, Tomoya Baba, Hirotada Mori, Hideo Mori

  FEMS microbiology letters. 07/2009;

  There is an ongoing demand to improve the ATP-regenerating system for industrial ATP-driven bioprocesses because of the low efficiency of ATP regeneration. To address this issue, we investigated theThere is an ongoing demand to improve the ATP-regenerating system for industrial ATP-driven bioprocesses because of the low efficiency of ATP regeneration. To address this issue, we investigated the efficiency of ATP regeneration in Escherichia coli using the Permeable Cell Assay. This assay identified 40 single-gene deletion strains that had over 150% higher total cellular ATP synthetic activity relative to the parental strain. Most of them also showed higher ATP-driven glutathione synthesis. The deleted genes of the identified strains that showed increased efficiency of ATP regeneration for glutathione production could be divided into the following four groups: (1) glycolytic pathway-related genes, (2) genes related to degradation of ATP or adenosine, (3) global regulatory genes, and (4) genes whose contribution to the ATP regeneration is unknown. Furthermore, the high glutathione productivity of DeltanlpD, the highest glutathione-producing mutant strain, was due to its reduced sensitivity to the externally added ATP for ATP regeneration. This study showed that the Permeable Cell Assay was useful for improving the ATP-regenerating activity of E. coli for practical applications in various ATP-driven bioprocesses, much as that of glutathione production.

• Predicting essential genes based on network and sequence analysis.

  Authors: Yih-Chii Hwang, Chen-Ching Lin, Jen-Yun Chang, Hirotada Mori, Hsueh-Fen Juan, Hsuan-Cheng Huang

  Molecular bioSystems. 06/2009;

  Essential genes are indispensable to the viability of an organism. Identification and analysis of essential genes is key to understanding the systems level organization of living cells. On the otherEssential genes are indispensable to the viability of an organism. Identification and analysis of essential genes is key to understanding the systems level organization of living cells. On the other hand, the ability to predict these genes in pathogens is of great importance for directed drug development. Global analysis of protein interaction networks provides an effective way to elucidate the relationships between genes. It has been found that essential genes tend to be highly connected and generally have more interactions than nonessential ones. With recent large-scale identifications of essential genes and protein-protein interactions in Saccharomyces cerevisiae and Escherichia coli, we have systematically investigated the topological properties of essential and nonessential genes in the protein-protein interaction networks. Essential genes tend to play topologically more important roles in protein interaction networks. Many topological features were found to be statistically discriminative between essential and nonessential genes. In addition, we have also examined sequence properties such as open reading frame length, strand, and phyletic retention for their association with the gene essentiality. Employing the topological features in the protein interaction network and the sequence properties, we have built a machine learning classifier capable of predicting essential genes. Computational prediction of essential genes circumvents expensive and difficult experimental screens and will help antimicrobial drug development.

• Essential core of protein-protein interaction network in Escherichia coli.

  Authors: Chen-Ching Lin, Hsueh-Fen Juan, Jen-Tsung Hsiang, Yih-Chii Hwang, Hirotada Mori, Hsuan-Cheng Huang

  Journal of proteome research. 03/2009;

  Essential genes are responsible for the viability of an organism. Global protein interaction network analysis provides an effective way to understand the relationships between protein products ofEssential genes are responsible for the viability of an organism. Global protein interaction network analysis provides an effective way to understand the relationships between protein products of genes. By means of large-scale identification of essential genes and protein-protein interactions, we investigated the substructure of the protein interaction network in Escherichia coli and identified all the cliques in the network. Our analysis showed that larger cliques tend to have larger fractions of proteins encoded by essential genes. By merging the maximum clique with overlapping neighboring cliques, we observed a dense core of the protein interaction network in Escherichia coli with significantly higher ratio of essential genes. The protein network of Saccharomyces cerevisiae also shows strong correlation between clique and essentiality, and there exist similar dense clusters with high essentiality. Our results indicated that the observed structure of essential cores might exist in higher organisms and play important roles in their respective protein networks.

• Update on the Keio collection of Escherichia coli single-gene deletion mutants.

  Authors: Natsuko Yamamoto, Kenji Nakahigashi, Tomoko Nakamichi, Mihoko Yoshino, Yuki Takai, Yae Touda, Akemi Furubayashi, Satoko Kinjyo, Hitomi Dose, Miki Hasegawa, Kirill A Datsenko, Toru Nakayashiki, Masaru Tomita, Barry L Wanner, Hirotada Mori

  Molecular systems biology. 01/2009; 5:335.

• Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.

  Authors: Kenji Nakahigashi, Yoshihiro Toya, Nobuyoshi Ishii, Tomoyoshi Soga, Miki Hasegawa, Hisami Watanabe, Yuki Takai, Masayuki Honma, Hirotada Mori, Masaru Tomita

  Molecular systems biology. 01/2009; 5:306.

  Central carbon metabolism is a basic and exhaustively analyzed pathway. However, the intrinsic robustness of the pathway might still conceal uncharacterized reactions. To test this hypothesis, weCentral carbon metabolism is a basic and exhaustively analyzed pathway. However, the intrinsic robustness of the pathway might still conceal uncharacterized reactions. To test this hypothesis, we constructed systematic multiple-knockout mutants involved in central carbon catabolism in Escherichia coli and tested their growth under 12 different nutrient conditions. Differences between in silico predictions and experimental growth indicated that unreported reactions existed within this extensively analyzed metabolic network. These putative reactions were then confirmed by metabolome analysis and in vitro enzymatic assays. Novel reactions regarding the breakdown of sedoheptulose-7-phosphate to erythrose-4-phosphate and dihydroxyacetone phosphate were observed in transaldolase-deficient mutants, without any noticeable changes in gene expression. These reactions, triggered by an accumulation of sedoheptulose-7-phosphate, were catalyzed by the universally conserved glycolytic enzymes ATP-dependent phosphofructokinase and aldolase. The emergence of an alternative pathway not requiring any changes in gene expression, but rather relying on the accumulation of an intermediate metabolite may be a novel mechanism mediating the robustness of these metabolic networks.

• High-throughput, quantitative analyses of genetic interactions in E. coli.

  Authors: Athanasios Typas, Robert J Nichols, Deborah A Siegele, Michael Shales, Sean R Collins, Bentley Lim, Hannes Braberg, Natsuko Yamamoto, Rikiya Takeuchi, Barry L Wanner, Hirotada Mori, Jonathan S Weissman, Nevan J Krogan, Carol A Gross

  Nature methods. 10/2008; 5(9):781-7.

  Large-scale genetic interaction studies provide the basis for defining gene function and pathway architecture. Recent advances in the ability to generate double mutants en masse in SaccharomycesLarge-scale genetic interaction studies provide the basis for defining gene function and pathway architecture. Recent advances in the ability to generate double mutants en masse in Saccharomyces cerevisiae have dramatically accelerated the acquisition of genetic interaction information and the biological inferences that follow. Here we describe a method based on F factor-driven conjugation, which allows for high-throughput generation of double mutants in Escherichia coli. This method, termed genetic interaction analysis technology for E. coli (GIANT-coli), permits us to systematically generate and array double-mutant cells on solid media in high-density arrays. We show that colony size provides a robust and quantitative output of cellular fitness and that GIANT-coli can recapitulate known synthetic interactions and identify previously unidentified negative (synthetic sickness or lethality) and positive (suppressive or epistatic) relationships. Finally, we describe a complementary strategy for genome-wide suppressor-mutant identification. Together, these methods permit rapid, large-scale genetic interaction studies in E. coli.

• The outer membrane TolC is involved in cysteine tolerance and overproduction in Escherichia coli.

  Authors: Natthawut Wiriyathanawudhiwong, Iwao Ohtsu, Zhao-Di Li, Hirotada Mori, Hiroshi Takagi

  Applied microbiology and biotechnology. 10/2008;

  L: -Cysteine is an important amino acid in terms of its industrial applications. We previously found marked production of L: -cysteine directly from glucose in recombinant Escherichia coli cells byL: -Cysteine is an important amino acid in terms of its industrial applications. We previously found marked production of L: -cysteine directly from glucose in recombinant Escherichia coli cells by the combination of enhancing biosynthetic activity and weakening the degradation pathway. Further improvements in L: -cysteine production are expected to use the amino acid efflux system. Here, we identified a novel gene involved in L: -cysteine export using a systematic and comprehensive collection of gene-disrupted E. coli K-12 mutants (the Keio collection). Among the 3,985 nonessential gene mutants, tolC-disrupted cells showed hypersensitivity to L: -cysteine relative to wild-type cells. Gene expression analysis revealed that the tolC gene encoding the outer membrane channel is essential for L: -cysteine tolerance in E. coli cells. However, L: -cysteine tolerance is not mediated by TolC-dependent drug efflux systems such as AcrA and AcrB. It also appears that other outer membrane porins including OmpA and OmpF do not participate in TolC-dependent L: -cysteine tolerance. When a low-copy-number plasmid carrying the tolC gene was introduced into E. coli cells with enhanced biosynthesis, weakened degradation, and improved export of L: -cysteine, the transformants exhibited more L: -cysteine tolerance and production than cells carrying the vector only. We concluded that TolC plays an important role in L: -cysteine tolerance probably due to its export ability and that TolC overexpression is effective for L: -cysteine production in E. coli.

• eSGA: E. coli synthetic genetic array analysis.

  Authors: Gareth Butland, Mohan Babu, J Javier Díaz-Mejía, Fedyshyn Bohdana, Sadhna Phanse, Barbara Gold, Wenhong Yang, Joyce Li, Alla G Gagarinova, Oxana Pogoutse [......] Sarah Joe, Kirill A Datsenko, Natsuko Yamamoto, Brenda J Andrews, Charles Boone, Huiming Ding, Bilal Sheikh, Gabriel Moreno-Hagelseib, Jack F Greenblatt, Andrew Emili

  Nature methods. 09/2008;

  Physical and functional interactions define the molecular organization of the cell. Genetic interactions, or epistasis, tend to occur between gene products involved in parallel pathways orPhysical and functional interactions define the molecular organization of the cell. Genetic interactions, or epistasis, tend to occur between gene products involved in parallel pathways or interlinked biological processes. High-throughput experimental systems to examine genetic interactions on a genome-wide scale have been devised for Saccharomyces cerevisiae, Schizosaccharomyces pombe, Caenorhabditis elegans and Drosophila melanogaster, but have not been reported previously for prokaryotes. Here we describe the development of a quantitative screening procedure for monitoring bacterial genetic interactions based on conjugation of Escherichia coli deletion or hypomorphic strains to create double mutants on a genome-wide scale. The patterns of synthetic sickness and synthetic lethality (aggravating genetic interactions) we observed for certain double mutant combinations provided information about functional relationships and redundancy between pathways and enabled us to group bacterial gene products into functional modules.

• Systematic genome-wide scanning for genes involved in ATP generation in Escherichia coli.

  Authors: Kiyotaka Y Hara, Natsuka Shimodate, Mikito Ito, Tomoya Baba, Hirotada Mori, Hideo Mori

  Metabolic engineering. 08/2008;

  Adenosine 5'-triphosphate (ATP) generation is an essential biological reaction for all living cells. Recently, we developed a Permeable Cell Assay for high-throughput measurement of cellular ATPAdenosine 5'-triphosphate (ATP) generation is an essential biological reaction for all living cells. Recently, we developed a Permeable Cell Assay for high-throughput measurement of cellular ATP synthetic activity, mainly resulting from glycolysis [Hara, K.Y., Mori, H., 2006. An efficient method for quantitative determination of cellular ATP synthetic activity. J. Biomol. Screen. 11, 310-317]. By using this method, we determined the cellular ATP synthetic activity in the stationary phase of a complete set of single-gene deletion strains of Escherichia coli. Their activities ranged from a minimum of 2% to a maximum of 445%, relative to parental strains. Deletions of metabolism-related genes frequently caused an increase in the rate of ATP synthetic activity, while activity was reduced by deletions of a variety of functional genes, including many poorly characterized genes. We also demonstrated that the deletion of the ptsG gene doubled ATP-driven glutathione synthesis and increased cellular ATP synthetic activity. Our study also indicated that it should be easy to obtain active strains for ATP synthesis from deletion strains. Overall, the data set of this study may be useful to improve E. coli strains for ATP-dependent industrial processes and, therefore, may be important for the design of so-called cell factories.

• Genome Structure of the Legume, Lotus japonicus.

  Authors: Shusei Sato, Yasukazu Nakamura, Takakazu Kaneko, Erika Asamizu, Tomohiko Kato, Mitsuteru Nakao, Shigemi Sasamoto, Akiko Watanabe, Akiko Ono, Kumiko Kawashima [......] Chika Takahashi, Tsuyuko Wada, Manabu Yamada, Nobuko Ohmido, Makoto Hayashi, Kiichi Fukui, Tomoya Baba, Tomoko Nakamichi, Hirotada Mori, Satoshi Tabata

  DNA research : an international journal for rapid publication of reports on genes and genomes. 06/2008;

  The legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structuralThe legume Lotus japonicus has been widely used as a model system to investigate the genetic background of legume-specific phenomena such as symbiotic nitrogen fixation. Here, we report structural features of the L. japonicus genome. The 315.1-Mb sequences determined in this and previous studies correspond to 67% of the genome (472 Mb), and are likely to cover 91.3% of the gene space. Linkage mapping anchored 130-Mb sequences onto the six linkage groups. A total of 10 951 complete and 19 848 partial structures of protein-encoding genes were assigned to the genome. Comparative analysis of these genes revealed the expansion of several functional domains and gene families that are characteristic of L. japonicus. Synteny analysis detected traces of whole-genome duplication and the presence of synteny blocks with other plant genomes to various degrees. This study provides the first opportunity to look into the complex and unique genetic system of legumes.

• The construction of systematic in-frame, single-gene knockout mutant collection in Escherichia coli K-12.

  Authors: Tomoya Baba, Hirotada Mori

  Methods in molecular biology (Clifton, N.J.). 02/2008; 416:171-81.

  Here we describe the systematic construction of well-defined, in-frame, single-gene deletions of all nonessential genes in Escherichia coli K-12. The principal strategy is based on the method forHere we describe the systematic construction of well-defined, in-frame, single-gene deletions of all nonessential genes in Escherichia coli K-12. The principal strategy is based on the method for one-step inactivation of chromosomal genes in E. coli K-12 established by Datsenko and Wanner (1), namely, the replacement of a target gene with a selectable antibiotic-resistant marker generated by polymerase chain reaction (PCR) using oligonucleotide DNA primers homologous to the gene flanking regions. The advantages of this method include complete deletion of an entire open reading frame and precise design eliminating polar effects for the downstream genes on E. coli chromosome.

• The applications of systematic in-frame, single-gene knockout mutant collection of Escherichia coli K-12.

  Authors: Tomoya Baba, Hsuan-Cheng Huan, Kirill Datsenko, Barry L Wanner, Hirotada Mori

  Methods in molecular biology (Clifton, N.J.). 02/2008; 416:183-94.

  The increasing genome sequence data of microorganisms has provided the basis for comprehensive understanding of organisms at the molecular level. Besides sequence data, a large number of experimentalThe increasing genome sequence data of microorganisms has provided the basis for comprehensive understanding of organisms at the molecular level. Besides sequence data, a large number of experimental and computational resources are required for genome-scale analyses. Escherichia coli K-12 has been one of the best characterized organisms in molecular biology. Recently, the whole-genome sequences of two closely related E. coli K-12 strains, MG1655 (1) and W3110 (2), were compared and confirmed by resequencing selected regions from both strains (2). The availability of highly accurate E. coli K-12 genomes provided an impetus for the cooperative reannotation of both MG1655 and W3110 (3). A set of precisely defined, single-gene knockout mutants of all nonessential genes in E. coli K-12 was constructed based on the recent accurate genome sequence data ([4] and Chapter 11). These mutants were designed to create in-frame (nonpolar) deletions upon elimination of the resistance cassette. These mutants have provided new key information on E. coli biology. First, the vast majority of the 3985 genes that were independently disrupted at least twice are probably nonessential, at least under the conditions of selection. Second, the 303 genes that we repeatedly failed to disrupt are candidates for E. coli essential genes. Lastly, phenotypic effects of all these mutations in the uniform genetic background of E. coli BW25113 were assessed by profiling mutants' growth yields on rich and minimal media (4). These mutants should provide not only a basic resource for systematic functional genomics but also an experimental data source for systems biology applications. The mutants can serve as fundamental tools for a number of reverse genetics approaches, permitting analysis of the consequences of the complete loss of gene function, in contrast with forward genetics approaches in which mutant phenotypes are associated with a corresponding gene or genes.

• Phenotype profiling of single gene deletion mutants of E. coli using Biolog technology.

  Authors: Yukako Tohsato, Hirotada Mori

  Genome informatics. International Conference on Genome Informatics. 02/2008; 21:42-52.

  Phenotype MicroArray (PM) technology is high-throughput phenotyping system and is directly applicable to assay the effects of genetic changes in cells. In this study, we performed comprehensive PMPhenotype MicroArray (PM) technology is high-throughput phenotyping system and is directly applicable to assay the effects of genetic changes in cells. In this study, we performed comprehensive PM analysis using single gene deletion mutants of central metabolic pathway and related genes. To elucidate the structure of central metabolic networks in Escherichia coli K-12, we focused 288 different PM conditions of carbon and nitrogen sources and performed bioinformatic analysis. For data processing, we employed noise reduction procedures. The distance between each of the mutants was defined by Manhattan distance and agglomerative Ward's hierarchical method was applied for clustering analysis. As a result, five clusters were revealed which represented to activate or repress cellular respiratory activities. Furthermore, the results might suggest that Glyceraldehyde-3P plays a key role as a molecular switch of central metabolic network.

• A genome-wide approach to identify the genes involved in biofilm formation in E. coli.

  Authors: Emma Tabe Eko Niba, Yoshiaki Naka, Megumi Nagase, Hirotada Mori, Madoka Kitakawa

  DNA research : an international journal for rapid publication of reports on genes and genomes. 01/2008; 14(6):237-46.

  Biofilm forming cells are distinctive from the well-investigated planktonic cells and exhibit a different type of gene expression. Several new Escherichia coli genes related to biofilm formation haveBiofilm forming cells are distinctive from the well-investigated planktonic cells and exhibit a different type of gene expression. Several new Escherichia coli genes related to biofilm formation have recently been identified through genomic approaches such as DNA microarray analysis. However, many others involved in this process might have escaped detection due to poor expression, regulatory mechanism, or genetic backgrounds. Here, we screened a collection of single-gene deletion mutants of E. coli named 'Keio collection' to identify genes required for biofilm formation. Of the 3985 mutants of non-essential genes in the collection thus examined, 110 showed a reduction in biofilm formation nine of which have not been well characterized yet. Systematic and quantitative analysis revealed the involvement of genes of various functions and reinforced the importance in biofilm formation of the genes for cell surface structures and cell membrane. Characterization of the nine mutants of function-unknown genes indicated that some of them, such as yfgA that genetically interacts with a periplasmic chaperone gene surA together with yciB and yciM, might be required for the integrity of outer membrane.

• B1500, a small membrane protein, connects the two-component systems EvgS/EvgA and PhoQ/PhoP in Escherichia coli.

  Authors: Yoko Eguchi, Junji Itou, Masatake Yamane, Ryo Demizu, Fumiyuki Yamato, Ario Okada, Hirotada Mori, Akinori Kato, Ryutaro Utsumi

  Proceedings of the National Academy of Sciences of the United States of America. 12/2007; 104(47):18712-7.

  Two-component signal-transduction systems (TCSs) of bacteria are considered to form an intricate signal network to cope with various environmental stresses. One example of such a network inTwo-component signal-transduction systems (TCSs) of bacteria are considered to form an intricate signal network to cope with various environmental stresses. One example of such a network in Escherichia coli is the signal transduction cascade from the EvgS/EvgA system to the PhoQ/PhoP system, where activation of the EvgS/EvgA system promotes expression of PhoP-activated genes. As a factor connecting this signal transduction cascade, we have identified a small inner membrane protein (65 aa), B1500. Expression of the b1500 gene is directly regulated by the EvgS/EvgA system, and b1500 expression from a heterologous promoter simultaneously activated the expression of mgtA and other PhoP regulon genes. This activation was PhoQ/PhoP-dependent and EvgS/EvgA-independent. Furthermore, deletion of b1500 from an EvgS-activated strain suppressed mgtA expression. B1500 is localized in the inner membrane, and bacterial two-hybrid data showed that B1500 formed a complex with the sensor PhoQ. These results indicate that the small membrane protein, B1500, connected the signal transduction between EvgS/EvgA and PhoQ/PhoP systems by directly interacting with PhoQ, thus activating the PhoQ/PhoP system.

• P-BOSS: a new filtering method for treasure hunting in metabolomics.

  Authors: Mineo Morohashi, Kaori Shimizu, Yoshiaki Ohashi, Junji Abe, Hirotada Mori, Masaru Tomita, Tomoyoshi Soga

  Journal of chromatography. A. 08/2007; 1159(1-2):142-8.

  Metabolomics is expected to boost data driven research. In biomarker discovery, powerful filtering methods to remove noise and outliers are essential for screening significant candidates from theMetabolomics is expected to boost data driven research. In biomarker discovery, powerful filtering methods to remove noise and outliers are essential for screening significant candidates from the huge volume of omic data. Here we propose a post-measurement peak filtering method (named P-BOSS) for CE electrospray ionization-time-of-flight MS (CE-TOFMS) data. Combining outlier detection method functions in parallel, we applied P-BOSS to the data using Escherichia coli knockout mutants of the tryptophan and purine biosynthesis pathways. As the result, P-BOSS showed remarkably superior performance, reducing 65% of all peaks, while leaving significant peaks.