Yucasin Sigma

Yucasin Sigma

 School of Science 
Department of Biological Sciences 
Laboratories
Molecular Neuroscience 
Developmental Biology
Cellular Genetics
Molecular Genetics
Plant Development and Physiology
Cellular Biochemistry
Neurobiology
Evolutionary Genetics
Plant Environmental Responses
Environmental Microbiology
Animal Ecology
Plant Ecology
Systematic Zoology
Systematic Botany
Photosynthetic Microbial Consortia
'How many genes are essential for the simplest cellular organism to live?' 'What are the functions of the genes included in the minimum gene set?' We are trying to answer these questions using the bacteria, Escherichia coli, which is well understood and can be investigated in detail at the molecular level.
ProfJun-ichi Katoe-mail
Asc ProfShigeki Ehirae-mail
 To identify the minimum set of genetic information which is essential for cell proliferation, several types of long chromosomal deletions were systematically constructed. Using these long chromosomal deletions, we identified all of the essential genetic information including small essential genes and essential chromosome regions encoding no proteins or no RNA. The deletion mutations we have constructed cover more than 90% of the whole genome, and during construction of these deletions, we identified novel essential genes. We also succeeded in constructing an E. coli strain that lacks about 30% of the parental chromosome; there are no organisms which have such significantly reduced genome. Our final goal is to construct 'minimum E. coli' which has the minimum gene set. 
 = 100) document.getElementById('caption11').style.width = document.img11.width'> Systematic Construction of E. coli deletion mutants 
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Functional analysis of non-characterized essential genes
 We are trying not only to identify all of the essential genes but also to clarify their cellular functions. Our first approach to understanding the functions of the non-characterized essential genes is genetic analysis. Isolation of their mutants (temperature-sensitive mutants) and analyses of their phenotypes at the non-permissive temperature sometimes provide clues, and further isolation of suppressor mutants may enable identification of functionally relevant genes and yield hints. On the basis of these genetic analyses, biochemical studies at the molecular level are necessary to understand in detail the activity of the gene products. We are especially interested in the mechanism of chromosome replication, partition and cell division. We have identified many important essential factors, topoisomerase IV, Hda protein and so on. Recently, we have also investigated the regulatory mechanism of gene expression and RNA degradation. 
 = 100) document.getElementById('caption21').style.width = document.img21.width'> Identification of essential DNA topoisomerase, topo IV 
Regulatory network of cellular differentiation in cyanobacteria
 Cyanobacteria are a large and morphologically diverse group of phototrophic prokaryotes with wide ecological tolerance that they occur in almost every habitat on earth. Some cyanobacteria can use not only CO2 as a carbon source by photosynthesis, but also N2 as a nitrogen source by nitrogen fixation. Filamentous cyanobacteria, such as Anabaena sp. strain PCC 7120, form differentiated cells called heterocysts, which are specialized cells for nitrogen fixation. Upon limitation of combined nitrogen in the medium, particular vegetative cells within linear multicellular filaments differentiate into heterocysts with a regular spacing of 10-15 cells. Heterocyst differentiation takes about 24 h to complete, when approximately 10% of chromosomal genes are upregulated with spatiotemporal regulation. We are analysing the molecular mechanisms of cellular differentiation and pattern formation using cyanobacteria. 
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PEC (Profiling of E. coli chromosome)
Shimmori, Y., Kanesaki, Y., Nozawa, M., Yoshikawa, H., Ehira, S. (2018) Transcriptional activation of glycogen catabolism and the oxidative pentose phosphate pathway by NrrA facilitates cell survival under nitrogen starvation in the cyanobacterium Synechococcus sp. strain PCC 7002. Plant Cell Physiol. in press. doi:10.1093/pcp/pcy059 
Ehira, S., Takeuchi, T, Higo, A. (2018) Spatial separation of photosynthesis and ethanol production by cell type-specific metabolic engineering of filamentous cyanobacteria. Appl. Microbiol. Biotechnol. 102:1523-1531. 
Higo, A., Isu, A., Fukaya, Y., Ehira, S., Hisabori, T. (2018) Application of CRISPR interference for metabolic engineering of the heterocyst-forming multicellular cyanobacterium Anabaena sp. PCC 7120. Plant Cell Physiol. 59:119-127. 
Iwadate, Y. and Kato, J. (2017) Involvement of the ytfK gene from the PhoB regulon in stationary-phase H2O2 stress tolerance in Escherichia coli. Microbiology. 163: 1912-1923. 
Iwadate, Y., Funabasama, N. and Kato, J. (2017) Involvement of formate dehydrogenases in stationary phase oxidative stress tolerance in Escherichia coli. FEMS Microbiology Letter. 364(20). doi: 10.1093/femsle/fnx193. 
Ehira, S., Shimmori, Y., Watanabe, S., Kato, H., Yoshikawa, H., Ohmori, M. (2017) The nitrogen-regulated response regulator NrrA is a conserved regulator of glycogen catabolism in ƒÀ-cyanobacteria. Microbiology 163:1711-1719. 
Fujisawa, T., Narikawa, R., Maeda, SI., Watanabe, S., Kanesaki, Y., Kobayashi, K., Nomata, J., Hanaoka, M., Watanabe, M., Ehira, S., Suzuki, E., Awai, K., Nakamura, Y. (2017) CyanoBase: A large-scale update on its 20th anniversary. Nucleic Acids Res. 45:D551-D554. 
Watanabe, K., Tominaga, K., Kitamura, M., and Kato, J. (2016) Systematic identification of synthetic lethal mutations with reduced-genome Escherichia coli: synthetic genetic interactions among yoaA, xthA and holC related to survival from MMS exposure. Genes Genet. Syst. 91: 183-188. 
Ohbayashi, R., Watanabe, S., Ehira, S., Kanesaki, Y., Chibazakura, T., Yoshikawa, H. (2016) Diversification of DnaA dependency for DNA replication in cyanobacterial evolution. ISME J. 10:1113-1121. 
Kurata, T., Nakanishi, S., Hashimoto, M., Taoka, M., Yamazaki, Y., Isobe, T., and Kato, J. (2015) Novel essential gene involved in 16S rRNA processing in Escherichia coli. J Mol. Biol. 427: 955-965. 
Ehira, S., Miyazaki, S. (2015) Regulation of genes involved in heterocyst differentiation in the cyanobacterium Anabaena sp. strain PCC 7120 by a group 2 sigma factor SigC. Life 5:587-603. 
Nishimura, T., Hayashi, K., Suzuki, H., Gyohda, A., Takaoka, C., Sakaguchi, Y., Matsumoto, S., Kasahara, H., Sakai, T., Kato, J., Kamiya, Y., and Koshiba, T. (2014) Yucasin is a potent inhibitor of YUCCA, a key enzyme in auxin biosynthesis. The Plant Journal. 77: 352-366. 
Ehira, S., Kimura, S., Miyazaki, S., Ohmori, M. (2014) Sucrose synthesis in the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120 is controlled by the two-component response regulator OrrA. Appl. Environ. Microbiol. 80:5672-5679. 
Halimatul, H.S.M., Ehira, S., Awai, K. (2014) Fatty alcohols can complement functions of heterocyst specific glycolipids in Anabaena sp. PCC 7120. Biochem. Biophys. Res. Commun. 450:178-183. 
Ehira, S. and Ohmori, M. (2014) NrrA directly regulates expression of the fraF gene and antisense RNAs for fraE in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. Microbiology 160:844-850. 
Watanabe, M., Semchonok, D.A., Webber-Birungi, M.T., Ehira, S., Kondo, K., Narikawa, R., Ohmori, M., Boekema, E.J. and Ikeuchi, M. (2014) Attachment of phycobilisomes in an antenna-photosystem I supercomplex of cyanobacteria. Proc. Natl. Acad. Sci. USA 111:2512-2517. 
Hashimoto, C., Hashimoto, M., Honda, H., and Kato, J. (2013) Effects on IS1 transposition frequency of a mutation in the ygjD gene involved in an essential tRNA Modification in Escherichia coli. FEMS Microbiology Letter. 347: 140-148. 
Ehira, S. (2013) Transcriptional regulation of heterocyst differentiation in Anabaena sp. strain PCC 7120. Russ. J. Plant Physiol. 60:443-452. 
Kushige, H., H. Kugenuma, M. Matsuoka, S. Ehira, M. Ohmori, and H. Iwasaki. (2013) Genome-wide and heterocyst-specific circadian gene expression in the filamentous cyanobacterium, Anabaena sp. PCC 7120. J. Bacteriol. 195:1276-1284. 
Iwamoto, A., Osawa, A., Kawai, M., Honda, H., Yoshida, S., Furuya, N., and Kato, J. (2012) Mutations in the essential Escherichia coli gene, yqgF, and their effects on transcription. J. Mol. Microbiol. Biotechnol. 22: 17-23. 
Ehira, S., and M. Ohmori. (2012) The redox-sensing transcriptional regulator RexT controls expression of thioredoxin A2 in the cyanobacterium Anabaena sp. strain PCC 7120. J. Biol. Chem. 287:40433-40440. 
Ehira, S., and M. Ohmori. (2012) The pknH gene restrictively expressed in heterocysts is required for diazotrophic growth in the cyanobacterium Anabaena sp. strain PCC 7120. Microbiology 158:1437-1443. 
Tanaka, Y., S. Ehira, H. Teramoto, M. Inui, and H. Yukawa. (2012) Coordinated regulation of gnd encoding 6-phosphogluconate dehydrogenase by two transcriptional regulators GntR1 and RamA in Corynebacterium glutamicum. J. Bacteriol. 194: 6527-6536. 
Hashimoto, C., Sakaguchi, K., Taniguchi, Y., Honda, H., Oshima, T., Ogasawara, N., and Kato, J. (2011) Effects on transcription of mutations in ygjD, yeaZ, and yjeE genes involved in a universal tRNA modification in Escherichia coli. J. Bacteriol. 193: 6075-6079. 
Iwadate, Y., Honda, H., Sato, H., Hashimoto, M. and Kato, J. (2011) Oxidative stress sensitivity of engineered Escherichia coli cells with a reduced genome. FEMS Microbiology Letter. 322: 25-33. 
Tachikawa, T., and Kato, J. (2011) Suppression of the temperature-sensitive mutation of the bamD gene required for the assembly of outer membrane proteins by multicopy of the yiaD gene in Escherichia coli. Biosci. Biotechnol. Biochem. 75: 162-164. 
Ehira, S., and M. Ohmori. (2011) NrrA, a nitrogen-regulated response regulator protein, controls glycogen catabolism in the nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. J. Biol. Chem. 286:38109-38114. 
Ehira, S., H. Teramoto, M. Inui, and H. Yukawa. (2010) A novel redox-sensing transcriptional regulator CyeR controls expression of an old yellow enzyme family protein in Corynebacterium glutamicum. Microbiology 156:1335-1341. 
Yoshimura, H., Y. Kaneko, S. Ehira, S. Yoshihara, M. Ikeuchi, and M. Ohmori. (2010) CccS and CccP are involved in construction of cell surface components in the cyanobacterium Synechocystis sp. strain PCC 6803. Plant Cell Physiol. 51:1163-1172. 
Fujisawa, T., R. Narikawa, S. Okamoto, S. Ehira, H. Yoshimura, I. Suzuki, T. Masuda, M. Mochimaru, S. Takaichi, K. Awai, M. Sekine, H. Horikawa, I. Yashiro, S. Omata, H. Takarada, Y. Katano, H. Kosugi, S. Tanikawa, K. Ohmori, N. Sato, M. Ikeuchi, N. Fujita, and M. Ohmori. (2010) Genomic structure of an economically important cyanobacterium, Arthrospira (Spirulina) platensis NIES-39. DNA Res. 17:85-103. 
Toyoshima, M., N. Sasaki, M. Fujiwara, S. Ehira, M. Ohmori, and N. Sato. (2010) Early candidacy for differentiation into heterocysts in the filamentous cyanobacterium Anabaena sp. PCC 7120. Arch. Microbiol. 192:23-31. 
Ehira, S., H. Ogino, H. Teramoto, M. Inui, and H. Yukawa. (2009) Regulation of quinone oxidoreductase by a redox-sensing transcriptional regulator QorR in Corynebacterium glutamicum. J. Biol. Chem. 284:16736-16742. 
Ehira, S., H. Teramoto, M. Inui, and H. Yukawa. (2009) Regulation of Corynebacterium glutamicum heat shock response by the extracytoplasmic-function sigma factor SigH and transcriptional regulators HspR and HrcA. J. Bacteriol. 191:2964-2972. 
Asai, H., S. Iwamori, K. Kawai, S. Ehira, J. Ishihara, K. Aihara, S. Shoji, and H. Iwasaki. (2009) Cyanobacterial cell lineage analysis of the spatiotemporal hetR expression profile during heterocyst pattern formation in Anabaena sp. PCC 7120. PLoS ONE 4:e7371. 
Ohmori, K., S. Ehira, S. Kimura, and M. Ohmori. (2009) Changes in the amount of cellular trehalose, the activity of maltooligosyl trehalose hydrolase, and the expression of its gene in response to salt stress in the cyanobacterium Spirulina platensis. Microbes Environ. 24:52-56. 
Inoue, A., Murata, Y., Takahashi, H., Tsuji, N., Fujisaki, S., and Kato, J. (2008) Involvement of an essential gene, mviN, in murein synthesis in Escherichia coli. J. Bacteriol. 190: 7298-7301. 
Mizoguchi, H., Sawano, Y., Kato, J., and Mori, H. (2008) Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome. DNA Research 15: 277-284. 
Kato, J. and Hashimoto, M. (2008) Construction of long chromosomal deletion mutants of Escherichia coli and minimization of the genome. Methods in Molecular Biology (Microbial Gene Essentiality - Protocols and Bioinformatics) 416: 279-293. (Osterman, A. L. and Gerdes, S. Y. (ed.), Humana Press, Totowa, New Jersey) 
Ehira, S., T. Shirai, H. Teramoto, M. Inui, and H. Yukawa. (2008) Group 2 sigma factor SigB of Corynebacterium glutamicum positively regulates glucose metabolism under conditions of oxygen deprivation. Appl. Environ. Microbiol. 74:5146-5152. 
Kato, J. and Hashimoto, M. (2007) Construction of consecutive deletions of the Escherichia coli chromosome, Mol. Syst. Biol. 3: Article number 132 
Ikeuchi, Y., Shigi, N., Kato, J., Nishimura, A., and Suzuki, T. (2006) Mechanistic insights into sulfur-relay by multiple sulfur mediators involved in thiouridine biosynthesis at tRNA wobble positions. Mol Cell 21: 97-108. 
Ote, T., Hashimoto, M., Ikeuchi, Y., Su'etsugu, M., Suzuki, T., Katayama, T., and Kato, J. (2006) Involvement of the Escherichia coli folate-binding protein YgfZ in RNA modification and regulation of chromosomal replication initiation . Mol. Microbiol. 59: 265-275. 
Ehira, S., and M. Ohmori. (2006) NrrA directly regulates expression of hetR during heterocyst differentiation in the cyanobacterium Anabaena sp. strain PCC 7120. J. Bacteriol. 188:8520-8525. 
Ehira, S., and M. Ohmori. (2006) NrrA, a nitrogen-responsive response regulator facilitates heterocyst development in the cyanobacterium Anabaena sp. strain PCC 7120. Mol. Microbiol. 59:1692-1703. 
Kato, J. (2005) Regulatory network of the initiation of chromosomal replication in Escherichia coli. Crit. Rev. Biochem. Mol. Biol. (Critical Reviews in Biochemistry and Molecular Biology) 40: 331-342. 
Ikeuchi, Y., Soma, A., Ote, T., Kato, J., Sekine, Y., and Suzuki, T. (2005) Molecular mechanism of lysidine synthesis that determines tRNA identity and codon recognition. Mol. Cell 19: 235-246. 
Hashimoto, M., Ichimura, T., Mizoguchi, H., Tanaka, K., Fujimitsu, K., Keyamura, K., Ote, T., Yamakawa, T., Yamazaki, Y., Mori, H., Katayama, T. and Kato, J. (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol. Microbiol. 55: 137-149. 
Soma, A., Ikeuchi, Y., Kanemasa, S., Kobayashi, K., Ogasawara, N., Ote, T., Kato, J., Watanabe, K., Sekine, Y., and Suzuki, T. (2003) An RNA-modifying enzyme that governs both the codon and amino acid specificities of isoleucine tRNA. Mol. Cell 12:689-698. 
Hashimoto M, Kato J. (2003) Indispensabilityof the Escherichia coli carbonic anhydrases YadF and CynT in cell proliferation at a low CO2 partial pressure. Biosci Biotech Biochem. 67: 919-922. 
Ehira, S., M. Ohmori, and N. Sato. (2003) Genome-wide expression analysis of the responses to nitrogen deprivation in the heterocyst-forming cyanobacterium Anabaena sp. strain PCC 7120. DNA Res. 10:97-113. 
Kato, J. and Katayama, T. (2001) Hda, a novel DnaA-related protein, regulates the replication cycle in Escherichia coli. EMBO Journal 20: 4253-4262. 
Kato, J., Fujisaki, S., Nakajima, K., Nishimura, Y., Sato, M., and Nakano, A. (1999) The E. coli homologue of yeast Rer2, a key enzyme of dolichol synthesis, is essential for carrier lipid formation in bacterial cell wall synthesis. J. Bacteriol. 181: 2733-2738. 
Tsukamoto, Y., Kato, J., and Ikeda, H. (1997) Silencing factors participate in DNA repair and recombination in Saccharomyces cerevisiae. Nature 388: 900-903. 
Shimizu, H., Yamaguchi, H., Ashizawa, Y., Kohno, Y., Asami, M., Kato, J., and Ikeda, H. (1997) Short-homology-independent illegitimate recombination in Escherichia coli: distinct mechanism from short-homology-dependent illegitimate recombination. J. Mol. Biol. 266: 297-305. 
Yokochi, T., Kato, J., and Ikeda, H. (1996) DNA nicking by Escherichia coli topoisomerase IV with a substitution mutation from tyrosine to histidine at the active site. Genes to Cells 1: 1069-1075. 
Kato, J., Suzuki, H., and Ikeda, H. (1992). Purification and characterization of DNA topoisomerase IV in Escherichia coli. J. Biol. Chem. 267: 25676-25684. 
Kato, J., Nishimura, Y., Imamura, R., Niki, H., Hiraga, S., and Suzuki, H. (1990). New topoisomerase essential for chromosome segregation in E. coli. Cell 63: 393-404. 
 ©2015 Department of Biological Sciences, Tokyo Metropolitan University 
What is Six Sigma?Six Sigma is a methodology used to improve business processes by utilizing statistical analysis rather than guesswork. Processes are improved by controlling variation and understanding the intricacies within them. This results in more predictable and profitable business processes. Six Sigma is more than 'training'; it is an approach based on data and geared toward projects with quantifiable business outcomes. This proven approach has been implemented within a wide range of industries to achieve both hard and soft money savings, while increasing customer satisfaction. For instance, in 1999 GE Capital was able to save $2 Billion with Six Sigma.
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Six Sigma Champions Are:
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Masters of Six Sigma Methodologies with proven track records.
Individuals with an advanced understanding of the Statistical Tools used within Six Sigma.
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Individuals who obtain instruction concerning the road map of Six Sigma.
Receive four weeks of instruction that focus on the Six Sigma road map. This training will include an extensive look at statistical methodologies.
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Six Sigma Green Belts:

Receive two weeks of class time which will cover the important aspects of the statistical methods needed to complete Six Sigma projects while learning the Six Sigma road map.
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The project should be a process or problem that is not functioning properly without a clear reason. On average, Black Belts will work on projects with at least $100,000 in potential savings, while Green Belts choose projects around $50,000. This will vary based on company size. Using the Six Sigma road map and the DMAIC method as a guide, this 4 to 6-month project should result in improved organizational knowledge and financial savings. The finance or accounting department should sign off on any Six Sigma project savings.
Learn More About Our Six Sigma Training Courses:
Available Courses: (To learn more please visit ourCourse Schedule)
Yucasin Sigma LogoSix Sigma Champion Implementation – Consists of 2 days of onsite training.
Six Sigma Process Green Belt – Consists of 2 weeks of training either offsite or onsite.
Slots free bonus. Six Sigma Process Black Belt – Consists of 2 weeks of Green Belt & 2 weeks of Black Belt after Green Belt either offsite or onsite.
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Design for Six Sigma or DFSS – Consists of 5 days or 10 days of training which is offered at your location or online only.
Introduction to Minitab for Six Sigma Belts – Consists of ½ day of training offered at your location only.

The Six Sigma methodology is defined by five DMAIC steps and a preceding 'step zero' known as Six Sigma Leadership.
DMAIC is the acronym for:
Define – What is important?
Measure – How are we doing?
Analyze – What is wrong?
Improve – What needs to be done?
Control – How do we guarantee performance?
The People Roles In Six Sigma:
Six Sigma Champions Are:
Those who implement and back the introduction of Six Sigma within the firm.
Company executives who lead Six Sigma by backing projects.
Leaders responsible for choosing employees to be 'Belts' and mentoring project leaders.
Individuals who receive instruction regarding the basic principles of Six Sigma and its methodology.
Six Sigma Master Black Belts Are:
Masters of Six Sigma Methodologies with proven track records.
Individuals with an advanced understanding of the Statistical Tools used within Six Sigma.
Aligned with a Champion to offer support and provide Project Descriptions.
Experts who will advise and instruct Green Belts and Black Belts.
Professionals with widespread project management knowledge.
Prospective leaders of a corporation.
Six Sigma Black Belts:
Individuals who obtain instruction concerning the road map of Six Sigma.
Receive four weeks of instruction that focus on the Six Sigma road map. This training will include an extensive look at statistical methodologies.
Successful Black Belts are project leaders whose job requires at least 75% of their time dedicated to completing four to six month Six Sigma Projects.
Individuals who successfully complete all required training, exams, and a live project.
Learn More About Six Sigma Black Belt
Six Sigma Green Belts:
Receive two weeks of class time which will cover the important aspects of the statistical methods needed to complete Six Sigma projects while learning the Six Sigma road map.
Green Belts spend up to 50% of their time working on Six Sigma projects that last for four to six months each.
Individuals who successfully complete all required training, exams, and a live project.
Learn More About Six Sigma Green Belt
Six Sigma Projects – Nonprofit Example Project
The project should be a process or problem that is not functioning properly without a clear reason. On average, Black Belts will work on projects with at least $100,000 in potential savings, while Green Belts choose projects around $50,000. This will vary based on company size. Using the Six Sigma road map and the DMAIC method as a guide, this 4 to 6-month project should result in improved organizational knowledge and financial savings. The finance or accounting department should sign off on any Six Sigma project savings.
Learn More About Our Six Sigma Training Courses:
Available Courses: (To learn more please visit ourCourse Schedule)
Yucasin Sigma LogoSix Sigma Champion Implementation – Consists of 2 days of onsite training.
Six Sigma Process Green Belt – Consists of 2 weeks of training either offsite or onsite.
Slots free bonus. Six Sigma Process Black Belt – Consists of 2 weeks of Green Belt & 2 weeks of Black Belt after Green Belt either offsite or onsite.
Yucasin Sigma EpsilonSix Sigma Transactional Green Belt – Consists of 2 weeks of training either offsite or onsite.
Six Sigma Transactional Process Black Belt – Consists of 2 weeks of Green Belt & 2 weeks of Black Belt after Green Belt either offsite or onsite.
Six Sigma Master Black Belt – Consists of 2 weeks of training either offsite or onsite.
Design for Six Sigma or DFSS – Consists of 5 days or 10 days of training which is offered at your location or online only.
Introduction to Minitab for Six Sigma Belts – Consists of ½ day of training offered at your location only.
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Statistical Thinking for Leaders – 2 days
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Test Methods – 2 days
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