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Kojima K, Matsumoto U, Keta S, Nakahigashi K, Ikeda K, Takatani N, Omata T, Aichi M. High-Light-Induced Stress Activates Lipid Deacylation at the Sn-2 Position in the Cyanobacterium Synechocystis Sp. PCC 6803. Plant Cell Physiol 2022; 63:82-91. [PMID: 34623441 PMCID: PMC8789269 DOI: 10.1093/pcp/pcab147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 06/01/2023]
Abstract
Cyanobacterial mutants defective in acyl-acyl carrier protein synthetase (Aas) produce free fatty acids (FFAs) because the FFAs generated by deacylation of membrane lipids cannot be recycled. An engineered Aas-deficient mutant of Synechocystis sp. PCC 6803 grew normally under low-light (LL) conditions (50 µmol photons m-2 s-1) but was unable to sustain growth under high-light (HL) conditions (400 µmol photons m-2 s-1), revealing a crucial role of Aas in survival under the HL conditions. Several-times larger amounts of FFAs were produced by HL-exposed cultures than LL-grown cultures. Palmitic acid accounted for ∼85% of total FFAs in HL-exposed cultures, while C18 fatty acids (FAs) constituted ∼80% of the FFAs in LL-grown cultures. Since C16 FAs are esterified to the sn-2 position of lipids in the Synechocystis species, it was deduced that HL irradiation activated deacylation of lipids at the sn-2 position. Heterologous expression of FarB, the FFA exporter protein of Neisseria lactamica, prevented intracellular FFA accumulation and rescued the growth defect of the mutant under HL, indicating that intracellular FFA was the cause of growth inhibition. FarB expression also decreased the 'per-cell' yield of FFA under HL by 90% and decreased the proportion of palmitic acid to ∼15% of total FFA. These results indicated that the HL-induced lipid deacylation is triggered not by strong light per se but by HL-induced damage to the cells. It was deduced that there is a positive feedback loop between HL-induced damage and lipid deacylation, which is lethal unless FFA accumulation is prevented by Aas.
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Affiliation(s)
| | - Ui Matsumoto
- Department of Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, 487-8501 Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Honmachi, Kwaguchi, Saitama 332-0012, Japan
| | - Sumie Keta
- Department of Biological Chemistry, Chubu University, 1200 Matsumoto-cho, Kasugai, 487-8501 Japan
- Japan Science and Technology Agency, CREST, 4-1-8 Honmachi, Kwaguchi, Saitama 332-0012, Japan
| | | | | | - Nobuyuki Takatani
- Japan Science and Technology Agency, CREST, 4-1-8 Honmachi, Kwaguchi, Saitama 332-0012, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
| | - Tatsuo Omata
- Japan Science and Technology Agency, CREST, 4-1-8 Honmachi, Kwaguchi, Saitama 332-0012, Japan
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601 Japan
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Fujishima K, Wang KM, Palmer JA, Abe N, Nakahigashi K, Endy D, Rothschild LJ. Reconstruction of cysteine biosynthesis using engineered cysteine-free enzymes. Sci Rep 2018; 8:1776. [PMID: 29379050 PMCID: PMC5788988 DOI: 10.1038/s41598-018-19920-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 01/03/2018] [Indexed: 12/28/2022] Open
Abstract
Amino acid biosynthesis pathways observed in nature typically require enzymes that are made with the amino acids they produce. For example, Escherichia coli produces cysteine from serine via two enzymes that contain cysteine: serine acetyltransferase (CysE) and O-acetylserine sulfhydrylase (CysK/CysM). To solve this chicken-and-egg problem, we substituted alternate amino acids in CysE, CysK and CysM for cysteine and methionine, which are the only two sulfur-containing proteinogenic amino acids. Using a cysteine-dependent auxotrophic E. coli strain, CysE function was rescued by cysteine-free and methionine-deficient enzymes, and CysM function was rescued by cysteine-free enzymes. CysK function, however, was not rescued in either case. Enzymatic assays showed that the enzymes responsible for rescuing the function in CysE and CysM also retained their activities in vitro. Additionally, substitution of the two highly conserved methionines in CysM decreased but did not eliminate overall activity. Engineering amino acid biosynthetic enzymes to lack the so-produced amino acids can provide insights into, and perhaps eventually fully recapitulate via a synthetic approach, the biogenesis of biotic amino acids.
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Affiliation(s)
- Kosuke Fujishima
- Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, 1528550, Japan.,Universities Space Research Association, NASA Ames Research Center, Moffett Field, California, 94035, USA.,Institute for Advanced Biosciences, Keio University, Tsuruoka, 9970035, Japan
| | - Kendrick M Wang
- Stanford University Department of Bioengineering, Stanford, California, 94305, USA
| | - Jesse A Palmer
- Universities Space Research Association, NASA Ames Research Center, Moffett Field, California, 94035, USA
| | - Nozomi Abe
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 9970035, Japan
| | - Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, 9970035, Japan.,Spiber Inc. 234-1 Mizukami, Kakuganji, Tsuruoka, 9970052, Japan
| | - Drew Endy
- Stanford University Department of Bioengineering, Stanford, California, 94305, USA
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Noro E, Mori M, Makino G, Takai Y, Ohnuma S, Sato A, Tomita M, Nakahigashi K, Kanai A. Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. RNA Biol 2016; 14:206-218. [PMID: 27981881 PMCID: PMC5324740 DOI: 10.1080/15476286.2016.1270001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A new screening system for artificial small RNAs (sRNAs) that inhibit the growth of Escherichia coli was constructed. In this system, we used a plasmid library to express RNAs of ∼120 nucleotides, each with a random 30-nucleotide sequence that can recognize its target mRNA(s). After approximately 60,000 independent colonies were screened, several plasmids that inhibited bacterial growth were isolated. To understand the inhibitory mechanism, we focused on one sRNA, S-20, that exerted a strong inhibitory effect. A time-course analysis of the proteome of S-20-expressing E. coli and a bioinformatic analysis were used to identify potential S-20 target mRNAs, and suggested that S-20 binds the translation initiation sites of several mRNAs encoding enzymes such as peroxiredoxin (osmC), glycyl-tRNA synthetase α subunit (glyQ), uncharacterized protein ygiM, and tryptophan synthase β chain (trpB). An in vitro translation analysis of chimeric luciferase-encoding mRNAs, each containing a potential S-20 target sequence, indicated that the translation of these mRNAs was inhibited in the presence of S-20. A gel shift analysis combined with the analysis of a series of S-20 mutants suggested that S-20 targets multiple mRNAs that are responsible for inhibiting E. coli growth. These data also suggest that S-20 acts like an endogenous sRNA and that E. coli can utilize artificial sRNAs.
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Affiliation(s)
- Emiko Noro
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Masaru Mori
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan
| | - Gakuto Makino
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,c Faculty of Environment and Information Studies, Keio University , Fujisawa , Japan
| | - Yuki Takai
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Sumiko Ohnuma
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Asako Sato
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan
| | - Masaru Tomita
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan.,c Faculty of Environment and Information Studies, Keio University , Fujisawa , Japan
| | - Kenji Nakahigashi
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan
| | - Akio Kanai
- a Institute for Advanced Biosciences, Keio University , Tsuruoka , Japan.,b Systems Biology Program, Graduate School of Media and Governance, Keio University , Fujisawa , Japan.,c Faculty of Environment and Information Studies, Keio University , Fujisawa , Japan
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Nakahigashi K, Takai Y, Kimura M, Abe N, Nakayashiki T, Shiwa Y, Yoshikawa H, Wanner BL, Ishihama Y, Mori H. Comprehensive identification of translation start sites by tetracycline-inhibited ribosome profiling. DNA Res 2016; 23:193-201. [PMID: 27013550 PMCID: PMC4909307 DOI: 10.1093/dnares/dsw008] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 02/06/2016] [Indexed: 01/12/2023] Open
Abstract
Tetracycline-inhibited ribosome profiling (TetRP) provides a powerful new experimental tool for comprehensive genome-wide identification of translation initiation sites in bacteria. We validated TetRP by confirming the translation start sites of protein-coding genes in accordance with the 2006 version of Escherichia coli K-12 annotation record (GenBank U00096.2) and found ∼150 new start sites within 60 nucleotides of the annotated site. This analysis revealed 72 per cent of the genes whose initiation site annotations were changed from the 2006 GenBank record to the newer 2014 annotation record (GenBank U00096.3), indicating a high sensitivity. Also, results from reporter fusion and proteomics of N-terminally enriched peptides showed high specificity of the TetRP results. In addition, we discovered over 300 translation start sites within non-coding, intergenic regions of the genome, using a threshold that retains ∼2,000 known coding genes. While some appear to correspond to pseudogenes, others may encode small peptides or have previously unforeseen roles. In summary, we showed that ribosome profiling upon translation inhibition by tetracycline offers a simple, reliable and comprehensive experimental tool for precise annotation of translation start sites of expressed genes in bacteria.
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Affiliation(s)
- Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Yuki Takai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Michiko Kimura
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Nozomi Abe
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Toru Nakayashiki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Yuh Shiwa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Hirofumi Yoshikawa
- Genome Research Center, NODAI Research Institute, Tokyo University of Agriculture, Tokyo 156-8502, Japan Department of Bioscience, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Barry L Wanner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yasushi Ishihama
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
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Munakata H, Nakada T, Nakahigashi K, Nozaki H, Tomita M. Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis
(Volvocales, Chlorophyceae), among Unicellular Algae. J Eukaryot Microbiol 2015; 63:340-8. [DOI: 10.1111/jeu.12283] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 11/10/2015] [Accepted: 11/13/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Hidehito Munakata
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Takashi Nakada
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Kenji Nakahigashi
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
| | - Hisayoshi Nozaki
- Department of Biological Sciences; Graduate School of Science; University of Tokyo; 7-3-1 Hongo, Bunkyo Tokyo 113-0033 Japan
| | - Masaru Tomita
- Systems Biology Program; Graduate School of Media and Governance; Keio University; Fujisawa 252-0882 Japan
- Institute for Advanced Biosciences; Keio University; Kakuganji Tsuruoka 997-0052 Japan
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Kato A, Takatani N, Use K, Uesaka K, Ikeda K, Chang Y, Kojima K, Aichi M, Ihara K, Nakahigashi K, Maeda SI, Omata T. Identification of a Cyanobacterial RND-Type Efflux System Involved in Export of Free Fatty Acids. Plant Cell Physiol 2015; 56:2467-77. [PMID: 26468506 DOI: 10.1093/pcp/pcv150] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/07/2015] [Indexed: 05/28/2023]
Abstract
An RND (resistance-nodulation-division)-type transporter having the capacity to export free fatty acids (FFAs) was identified in the cyanobacterium Synechococcus elongatus strain PCC 7942 during characterization of a mutant strain engineered to produce FFAs. The basic strategy for construction of the FFA-producing mutant was a commonly used one, involving inactivation of the endogenous acyl-acyl carrier protein synthetase gene (aas) and introduction of a foreign thioesterase gene ('tesA), but a nitrate transport mutant NA3 was used as the parental strain to achieve slow, nitrate-limited growth in batch cultures. Also, a nitrogen-regulated promoter PnirA was used to drive 'tesA to maximize thioesterase expression during the nitrate-limited growth. The resulting mutant (dAS2T) was, however, incapable of growth under the conditions of nitrate limitation, presumably due to toxicity associated with FFA overproduction. Incubation of the mutant culture under the non-permissive conditions allowed for isolation of a pseudorevertant (dAS2T-pr1) capable of growth on nitrate. Genome sequence and gene expression analyses of this strain suggested that expression of an RND-type efflux system had rescued growth on nitrate. Targeted inactivation of the RND-type transporter genes in the wild-type strain resulted in loss of tolerance to exogenously added FFAs including capric, lauric, myristic, oleic and linolenic acids. Overexpression of the genes in dAS2T, on the other hand, enhanced FFA excretion and cell growth in nitrate-containing medium, verifying that the genes encode an efflux pump for FFAs. These results demonstrate the importance of the efflux system in efficient FFA production using genetically engineered cyanobacteria.
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Affiliation(s)
- Akihiro Kato
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Nobuyuki Takatani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan Japan Science and Technology Agency, CREST
| | - Kazuhide Use
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Kazuma Uesaka
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan Japan Science and Technology Agency, CREST
| | - Kazutaka Ikeda
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0052 Japan Japan Science and Technology Agency, CREST Present address: Laboratory for Metabolomics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045 Japan
| | - Yajun Chang
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan Japan Science and Technology Agency, CREST Present address: Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, Jiangsu, PR China
| | - Kouji Kojima
- Department of Biological Chemistry, Chubu University, Kasugai, 487-8501 Japan Japan Science and Technology Agency, CREST Present address: Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan
| | - Makiko Aichi
- Department of Biological Chemistry, Chubu University, Kasugai, 487-8501 Japan Japan Science and Technology Agency, CREST
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Nagoya, 464-8602 Japan Japan Science and Technology Agency, CREST
| | - Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0052 Japan Japan Science and Technology Agency, CREST
| | - Shin-Ichi Maeda
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan Japan Science and Technology Agency, CREST
| | - Tatsuo Omata
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan Japan Science and Technology Agency, CREST
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Nakahigashi K, Takai Y, Shiwa Y, Wada M, Honma M, Yoshikawa H, Tomita M, Kanai A, Mori H. Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo. BMC Genomics 2014; 15:1115. [PMID: 25512115 PMCID: PMC4378010 DOI: 10.1186/1471-2164-15-1115] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/09/2014] [Indexed: 11/10/2022] Open
Abstract
Background There is a significant difference between synonymous codon usage in many organisms, and it is known that codons used more frequently generally showed efficient decoding rate. At the gene level, however, there are conflicting reports on the existence of a correlation between codon adaptation and translation efficiency, even in the same organism. Results To resolve this issue, we cultured Escherichia coli under conditions designed to maintain constant levels of mRNA and protein and subjected the cells to ribosome profiling (RP) and mRNA-seq analyses. We showed that the RP results correlated more closely with protein levels generated under similar culture conditions than with the mRNA abundance from the mRNA-seq. Our result indicated that RP/mRNA ratio could be used as a measure of translation efficiency at gene level. On the other hand, the RP data showed that codon-specific ribosome density at the decoding site negatively correlated with codon usage, consistent with the hypothesis that preferred codons display lower ribosome densities due to their faster decoding rate. However, highly codon-adapted genes showed higher ribosome densities at the gene level, indicating that the efficiency of translation initiation, rather than higher elongation efficiency of preferred codons, exerted a greater effect on ribosome density and thus translation efficiency. Conclusions These findings indicate that evolutionary pressure on highly expressed genes influenced both codon bias and translation initiation efficiency and therefore explains contradictory findings that codon usage bias correlates with translation efficiency of native genes, but not with the artificially created gene pool, which was not subjected to evolution pressure. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1115) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan.
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Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K, Yamamoto N, Dose H, Nakahigashi K, Tanishima S, Suharnan S, Nomura W, Nakayashiki T, Aref WG, Bochner BR, Conway T, Gribskov M, Kihara D, Rudd KE, Tohsato Y, Wanner BL, Mori H. GenoBase: comprehensive resource database of Escherichia coli K-12. Nucleic Acids Res 2014; 43:D606-17. [PMID: 25399415 PMCID: PMC4383962 DOI: 10.1093/nar/gku1164] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources.
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Affiliation(s)
- Yuta Otsuka
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Ai Muto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Rikiya Takeuchi
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Chihiro Okada
- Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
| | - Motokazu Ishikawa
- Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
| | - Koichiro Nakamura
- Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
| | - Natsuko Yamamoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Hitomi Dose
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Kenji Nakahigashi
- Institute of Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
| | - Shigeki Tanishima
- Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
| | - Sivasundaram Suharnan
- Axiohelix, Okinawa Sangyo Shien Center, 502,1831-1, Oroku, Naha-shi, Okinawa 901-0152, Japan
| | - Wataru Nomura
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Toru Nakayashiki
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Walid G Aref
- Department of Computer Science, Purdue University, 305 N. University Street, West Lafayette, IN 47907-2107, USA
| | | | - Tyrrell Conway
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019-0245, USA
| | - Michael Gribskov
- Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, 305 N. University Street, West Lafayette, IN 47907-2107, USA Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA
| | - Kenneth E Rudd
- Department Biochemistry and Molecular Biology, University of Miami, P.O. Box 016129, Miami, FL 33101-6129, USA
| | - Yukako Tohsato
- Department of Bioinformatics, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Barry L Wanner
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
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Martínez P, Gálvez S, Ohtsuka N, Budinich M, Cortés MP, Serpell C, Nakahigashi K, Hirayama A, Tomita M, Soga T, Martínez S, Maass A, Parada P. Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay. Metabolomics 2013; 9:247-257. [PMID: 23335869 PMCID: PMC3548112 DOI: 10.1007/s11306-012-0443-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2011] [Accepted: 06/29/2012] [Indexed: 12/20/2022]
Abstract
In this study, we present the first metabolic profiles for two bioleaching bacteria using capillary electrophoresis coupled with mass spectrometry. The bacteria, Acidithiobacillus ferrooxidans strain Wenelen (DSM 16786) and Acidithiobacillus thiooxidans strain Licanantay (DSM 17318), were sampled at different growth phases and on different substrates: the former was grown with iron and sulfur, and the latter with sulfur and chalcopyrite. Metabolic profiles were scored from planktonic and sessile states. Spermidine was detected in intra- and extracellular samples for both strains, suggesting it has an important role in biofilm formation in the presence of solid substrate. The canonical pathway for spermidine synthesis seems absent as its upstream precursor, putrescine, was not present in samples. Glutathione, a catalytic activator of elemental sulfur, was identified as one of the most abundant metabolites in the intracellular space in A. thiooxidans strain Licanantay, confirming its participation in the sulfur oxidation pathway. Amino acid profiles varied according to the growth conditions and bioleaching species. Glutamic and aspartic acid were highly abundant in intra- and extracellular extracts. Both are constituents of the extracellular matrix, and have a probable role in cell detoxification. This novel metabolomic information validates previous knowledge from in silico metabolic reconstructions based on genomic sequences, and reveals important biomining functions such as biofilm formation, energy management and stress responses. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11306-012-0443-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Marko Budinich
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - María Paz Cortés
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Cristián Serpell
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Akiyoshi Hirayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata Japan
| | - Servet Martínez
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
- Department of Mathematical Engineering and Center for Mathematical Modeling (UMI 2807, CNRS), Faculty of Mathematical and Physical Sciences, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Alejandro Maass
- Laboratory of Bioinformatics and Mathematics of the Genome, Center for Mathematical Modeling (UMI 2807, CNRS) and Center for Genome Regulation, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
- Department of Mathematical Engineering and Center for Mathematical Modeling (UMI 2807, CNRS), Faculty of Mathematical and Physical Sciences, University of Chile, Avda. Blanco Encalada 2120, 7th Floor, Santiago, Chile
| | - Pilar Parada
- BioSigma S.A., Loteo Los Libertadores, Lote 106, Colina, Chile
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10
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Toya Y, Nakahigashi K, Tomita M, Shimizu K. Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. Mol Biosyst 2013; 8:2593-604. [PMID: 22790675 DOI: 10.1039/c2mb25069a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It is of practical interest to investigate the effect of nitrates on bacterial metabolic regulation of both fermentation and energy generation, as compared to aerobic and anaerobic growth without nitrates. Although gene level regulation has previously been studied for nitrate assimilation, it is important to understand this metabolic regulation in terms of global regulators. In the present study, therefore, we measured gene expression using DNA microarrays, intracellular metabolite concentrations using CE-TOFMS, and metabolic fluxes using the (13)C-labeling technique for wild-type E. coli and the ΔarcA (a global regulatory gene for anoxic response control, ArcA) mutant to compare the metabolic state under nitrate conditions to that under aerobic and anaerobic conditions without nitrates in continuous culture conditions at a dilution rate of 0.2 h(-1). In wild-type, although the measured metabolite concentrations changed very little among the three culture conditions, the TCA cycle and the pentose phosphate pathway fluxes were significantly different under each condition. These results suggested that the ATP production rate was 29% higher under nitrate conditions than that under anaerobic conditions, whereas the ATP production rate was 10% lower than that under aerobic conditions. The flux changes in the TCA cycle were caused by changes in control at the gene expression level. In ΔarcA mutant, the TCA cycle flux was significantly increased (4.4 times higher than that of the wild type) under nitrate conditions. Similarly, the intracellular ATP/ADP ratio increased approximately two-fold compared to that of the wild-type strain.
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Affiliation(s)
- Yoshihiro Toya
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
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11
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Itaya M, Kawata Y, Sato M, Tomita M, Nakahigashi K. A simple method to provide a shuttling plasmid for delivery to other host ascertained by prolonged stability of extracellular plasmid DNA released from Escherichia coli K12 endA mutant, deficient in major endonuclease. J Biochem 2012; 152:501-4. [PMID: 23055537 DOI: 10.1093/jb/mvs111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Escherichia coli lyses by lambda phage propagation. Circular plasmid DNA was present during E. coli lysis as an extracellular plasmid DNA (excpDNA) that was stable enough to transform coexisting competent Bacillus subtilis cells. Detailed investigations unveiled that excpDNA is transient in both quality and quantity, with stability lasting no more than several hours. A survey using E. coli lambda lysogens with various genetic backgrounds demonstrated that the loss of Endonuclease I (ΔendA::kan) conferred extraordinary stability upon excpDNA for as long as 48 h. Studies on endA mutants suggested that excpDNA remained localized in cell debris, in contrast to E. coli genome DNA, which diffused into medium at an early point in lysis. Lambda lysogens constructed on endA recA mutants are presented for potential pipelines in delivery to other competent proficient microbes.
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Affiliation(s)
- Mitsuhiro Itaya
- Institute for Advanced Biosciences, Keio University, Nipponkoku, Tsuruoka, Yamagata 997-0017, Japan.
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12
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Yamamotoya T, Dose H, Tian Z, Fauré A, Toya Y, Honma M, Igarashi K, Nakahigashi K, Soga T, Mori H, Matsuno H. Glycogen is the primary source of glucose during the lag phase of E. coli proliferation. Biochim Biophys Acta 2012; 1824:1442-8. [PMID: 22750467 DOI: 10.1016/j.bbapap.2012.06.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/31/2012] [Accepted: 06/18/2012] [Indexed: 10/28/2022]
Abstract
In the studies of Escherichia coli (E. coli), metabolomics analyses have mainly been performed using steady state culture. However, to analyze the dynamic changes in cellular metabolism, we performed a profiling of concentration of metabolites by using batch culture. As a first step, we focused on glucose uptake and the behavior of the first metabolite, G6P (glucose-6-phosphate). A computational formula was derived to express the glucose uptake rate by a single cell from two kinds of experimental data, extracellular glucose concentration and cell growth, being simulated by Cell Illustrator. In addition, average concentration of G6P has been measured by CE-MS. The existence of another carbon source was suggested from the computational result. After careful comparison between cell growth, G6P concentration, and the computationally obtained curve of glucose uptake rate, we predicted the consumption of glycogen in lag phase and its accumulation as an energy source in an E. coli cell for the next proliferation. We confirmed our prediction experimentally. This behavior indicates the importance of glycogen participation in the lag phase for the growth of E. coli. This article is part of a Special Issue entitled: Computational Methods for Protein Interaction and Structural Prediction.
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Affiliation(s)
- Tomoaki Yamamotoya
- Graduate School of Science and Engineering, Yamaguchi University, 1677-1 Yoshida, Yamaguchi-shi, Yamaguchi 753-8512, Japan
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13
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Shinhara A, Matsui M, Hiraoka K, Nomura W, Hirano R, Nakahigashi K, Tomita M, Mori H, Kanai A. Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics 2011; 12:428. [PMID: 21864382 PMCID: PMC3175480 DOI: 10.1186/1471-2164-12-428] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2011] [Accepted: 08/24/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND 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 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. RESULTS 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. CONCLUSIONS 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.
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Affiliation(s)
- Atsuko Shinhara
- Institute for Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
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14
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Yao R, Hirose Y, Sarkar D, Nakahigashi K, Ye Q, Shimizu K. Catabolic regulation analysis of Escherichia coli and its crp, mlc, mgsA, pgi and ptsG mutants. Microb Cell Fact 2011; 10:67. [PMID: 21831320 PMCID: PMC3169459 DOI: 10.1186/1475-2859-10-67] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Accepted: 08/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Most bacteria can use various compounds as carbon sources. These carbon sources can be either co-metabolized or sequentially metabolized, where the latter phenomenon typically occurs as catabolite repression. From the practical application point of view of utilizing lignocellulose for the production of biofuels etc., it is strongly desirable to ferment all sugars obtained by hydrolysis from lignocellulosic materials, where simultaneous consumption of sugars would benefit the formation of bioproducts. However, most organisms consume glucose prior to consumption of other carbon sources, and exhibit diauxic growth. It has been shown by fermentation experiments that simultaneous consumption of sugars can be attained by ptsG, mgsA mutants etc., but its mechanism has not been well understood. It is strongly desirable to understand the mechanism of metabolic regulation for catabolite regulation to improve the performance of fermentation. RESULTS In order to make clear the catabolic regulation mechanism, several continuous cultures were conducted at different dilution rates of 0.2, 0.4, 0.6 and 0.7 h⁻¹ using wild type Escherichia coli. The result indicates that the transcript levels of global regulators such as crp, cra, mlc and rpoS decreased, while those of fadR, iclR, soxR/S increased as the dilution rate increased. These affected the metabolic pathway genes, which in turn affected fermentation result where the specific glucose uptake rate, the specific acetate formation rate, and the specific CO₂ evolution rate (CER) were increased as the dilution rate was increased. This was confirmed by the ¹³C-flux analysis. In order to make clear the catabolite regulation, the effect of crp gene knockout (Δcrp) and crp enhancement (crp⁺) as well as mlc, mgsA, pgi and ptsG gene knockout on the metabolism was then investigated by the continuous culture at the dilution rate of 0.2 h⁻¹ and by some batch cultures. In the case of Δcrp (and also Δmlc) mutant, TCA cycle and glyoxylate were repressed, which caused acetate accumulation. In the case of crp⁺ mutant, glycolysis, TCA cycle, and gluconeogenesis were activated, and simultaneous consumption of multiple carbon sources can be attained, but the glucose consumption rate became less due to repression of ptsG and ptsH by the activation of Mlc. Simultaneous consumption of multiple carbon sources could be attained by mgsA, pgi, and ptsG mutants due to increase in crp as well as cyaA, while glucose consumption rate became lower. CONCLUSIONS The transcriptional catabolite regulation mechanism was made clear for the wild type E. coli, and its crp, mlc, ptsG, pgi, and mgsA gene knockout mutants. The results indicate that catabolite repression can be relaxed and crp as well as cyaA can be increased by crp⁺, mgsA, pgi, and ptsG mutants, and thus simultaneous consumption of multiple carbon sources including glucose can be made, whereas the glucose uptake rate became lower as compared to wild type due to inactivation of ptsG in all the mutants considered.
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Affiliation(s)
- Ruilian Yao
- Department of Bioscience and Bioinformatics, Kyushu Institute of Technology, Iizuka, Fukuoka 820-8502, Japan
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15
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Toya Y, Ishii N, Nakahigashi K, Hirasawa T, Soga T, Tomita M, Shimizu K. 13C-metabolic flux analysis for batch culture of Escherichia coli and its Pyk and Pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites. Biotechnol Prog 2010; 26:975-92. [PMID: 20730757 DOI: 10.1002/btpr.420] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Since most bio-production processes are conducted in a batch or fed-batch manner, the evaluation of metabolism with respect to time is highly desirable. Toward this aim, we applied (13)C-metabolic flux analysis to nonstationary conditions by measuring the mass isotopomer distribution of intracellular metabolites. We performed our analysis on batch cultures of wild-type Escherichia coli, as well as on Pyk and Pgi mutants, obtained the fluxes and metabolite concentrations as a function of time. Our results for the wild-type indicated that the TCA cycle flux tended to increase during growth on glucose. Following glucose exhaustion, cells controlled the branch ratio between the glyoxylate pathway and the TCA cycle, depending on the availability of acetate. In the Pyk mutant, the concentrations of glycolytic intermediates changed drastically over time due to the dumping and feedback inhibition caused by PEP accumulation. Nevertheless, the flux distribution and free amino acid concentrations changed little. The growth rate and the fluxes remained constant in the Pgi mutant and the glucose-6-phosphate dehydrogenase reaction was the rate-limiting step. The measured fluxes were compared with those predicted by flux balance analysis using maximization of biomass yield or ATP production. Our findings indicate that the objective function of biosynthesis became less important as time proceeds on glucose in the wild-type, while it remained highly important in the Pyk mutant. Furthermore, ATP production was the primary objective function in the Pgi mutant. This study demonstrates how cells adjust their metabolism in response to environmental changes and/or genetic perturbations in the batch cultivation.
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Affiliation(s)
- Yoshihiro Toya
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
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16
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Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H. Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol 2009; 5:335. [PMID: 20029369 PMCID: PMC2824493 DOI: 10.1038/msb.2009.92] [Citation(s) in RCA: 187] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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17
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Nakahigashi K, Toya Y, Ishii N, Soga T, Hasegawa M, Watanabe H, Takai Y, Honma M, Mori H, Tomita M. Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol 2009; 5:306. [PMID: 19756045 PMCID: PMC2758719 DOI: 10.1038/msb.2009.65] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 08/05/2009] [Indexed: 11/09/2022] Open
Abstract
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, 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.
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Affiliation(s)
- Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yoshihiro Toya
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nobuyoshi Ishii
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Miki Hasegawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Hisami Watanabe
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yuki Takai
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masayuki Honma
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Hirotada Mori
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
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18
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Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 2007; 316:593-7. [PMID: 17379776 DOI: 10.1126/science.1132067] [Citation(s) in RCA: 484] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Analysis of cellular components at multiple levels of biological information can provide valuable functional insights. We performed multiple high-throughput measurements to study the response of Escherichia coli cells to genetic and environmental perturbations. Analysis of metabolic enzyme gene disruptants revealed unexpectedly small changes in messenger RNA and proteins for most disruptants. Overall, metabolite levels were also stable, reflecting the rerouting of fluxes in the metabolic network. In contrast, E. coli actively regulated enzyme levels to maintain a stable metabolic state in response to changes in growth rate. E. coli thus seems to use complementary strategies that result in a metabolic network robust against perturbations.
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Affiliation(s)
- Nobuyoshi Ishii
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
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19
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Sung S, He Y, Eshoo TW, Tamada Y, Johnson L, Nakahigashi K, Goto K, Jacobsen SE, Amasino RM. Epigenetic maintenance of the vernalized state in Arabidopsis thaliana requires LIKE HETEROCHROMATIN PROTEIN 1. Nat Genet 2006; 38:706-10. [PMID: 16682972 DOI: 10.1038/ng1795] [Citation(s) in RCA: 216] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2005] [Accepted: 04/05/2006] [Indexed: 01/14/2023]
Abstract
Vernalization is the process by which sensing a prolonged exposure to winter cold leads to competence to flower in the spring. In winter annual Arabidopsis thaliana accessions, flowering is suppressed in the fall by expression of the potent floral repressor FLOWERING LOCUS C (FLC). Vernalization promotes flowering via epigenetic repression of FLC. Repression is accompanied by a series of histone modifications of FLC chromatin that include dimethylation of histone H3 at Lys9 (H3K9) and Lys27 (H3K27). Here, we report that A. thaliana LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) is necessary to maintain the epigenetically repressed state of FLC upon return to warm conditions typical of spring. LHP1 is enriched at FLC chromatin after prolonged exposure to cold, and LHP1 activity is needed to maintain the increased levels of H3K9 dimethylation at FLC chromatin that are characteristic of the vernalized state.
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Affiliation(s)
- Sibum Sung
- Department of Biochemistry, University of Wisconsin at Madison, Madison, Wisconsin, USA
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20
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Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H. Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 2006; 16:686-91. [PMID: 16606699 PMCID: PMC1457052 DOI: 10.1101/gr.4527806] [Citation(s) in RCA: 333] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Protein-protein interactions play key roles in protein function and the structural organization of a cell. A thorough description of these interactions should facilitate elucidation of cellular activities, targeted-drug design, and whole cell engineering. A large-scale comprehensive pull-down assay was performed using a His-tagged Escherichia coli ORF clone library. Of 4339 bait proteins tested, partners were found for 2667, including 779 of unknown function. Proteins copurifying with hexahistidine-tagged baits on a Ni2+-NTA column were identified by MALDI-TOF MS (matrix-assisted laser desorption ionization time of flight mass spectrometry). An extended analysis of these interacting networks by bioinformatics and experimentation should provide new insights and novel strategies for E. coli systems biology.
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Affiliation(s)
- Mohammad Arifuzzaman
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- Kyowa Hakko Branch, Japan Bioindustry Association in Tokyo Research Laboratories, Kyowa Hakko Kogyo, Machida-shi, Tokyo 194-8533, Japan
| | - Maki Maeda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- CREST, JST (Japan Science and Technology), Kawaguchi, Saitama 332-0012, Japan
| | - Aya Itoh
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Kensaku Nishikata
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Chiharu Takita
- CREST, JST (Japan Science and Technology), Kawaguchi, Saitama 332-0012, Japan
| | - Rintaro Saito
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Takeshi Ara
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Kenji Nakahigashi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Hsuan-Cheng Huang
- Institute of Bioinformatics, National Yang-Ming University, Taipei 112, Taiwan, China
| | - Aki Hirai
- CREST, JST (Japan Science and Technology), Kawaguchi, Saitama 332-0012, Japan
| | - Kohei Tsuzuki
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Seira Nakamura
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Mohammad Altaf-Ul-Amin
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Taku Oshima
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Tomoya Baba
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Natsuko Yamamoto
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- Kyowa Hakko Branch, Japan Bioindustry Association in Tokyo Research Laboratories, Kyowa Hakko Kogyo, Machida-shi, Tokyo 194-8533, Japan
| | - Tomoyo Kawamura
- CREST, JST (Japan Science and Technology), Kawaguchi, Saitama 332-0012, Japan
| | | | - Masanari Kitagawa
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
| | - Shigehiko Kanaya
- Graduate School of Information Science, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Chieko Wada
- Institute for Virus Research, Kyoto University, Sakyo, Kyoto 606-8507, Japan
- Corresponding authors.E-mail ; fax. +81-743-72-5669.E-mail ; fax +81-75-753-7905
| | - Hirotada Mori
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0035, Japan
- Corresponding authors.E-mail ; fax. +81-743-72-5669.E-mail ; fax +81-75-753-7905
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Nakahigashi K, Jasencakova Z, Schubert I, Goto K. The Arabidopsis heterochromatin protein1 homolog (TERMINAL FLOWER2) silences genes within the euchromatic region but not genes positioned in heterochromatin. Plant Cell Physiol 2005; 46:1747-56. [PMID: 16131496 DOI: 10.1093/pcp/pci195] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
TERMINAL FLOWER2 (TFL2) is the only homolog of heterochromatin protein1 (HP1) in the Arabidopsis genome. Because proteins of the HP1 family in fission yeast and animals act as key components of gene silencing in heterochromatin by binding to histone H3 methylated on lysine 9 (K9), here we examined whether TFL2 has a similar role in Arabidopsis. Unexpectedly, genes positioned in heterochromatin were not activated in tfl2 mutants. Moreover, the TFL2 protein localized preferentially to euchromatic regions and not to heterochromatic chromocenters, where K9-methylated histone H3 is clustered. Instead, TFL2 acts as a repressor of genes related to plant development, i.e. flowering, floral organ identity, meiosis and seed maturation. Up-regulation of the floral homeotic genes PISTILLATA, APETALA3, AGAMOUS and SEPALLATA3 in tfl2 mutants was independent of LEAFY or APETALA3, known activators of the above genes. In addition, transduced APETALA3 promoter fragments as short as 500 bp were sufficient for TFL2-mediated gene repression. Taken together, TFL2 silences specific genes within euchromatin but not genes positioned in heterochromatin of Arabidopsis.
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22
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Kotake T, Takada S, Nakahigashi K, Ohto M, Goto K. Arabidopsis TERMINAL FLOWER 2 gene encodes a heterochromatin protein 1 homolog and represses both FLOWERING LOCUS T to regulate flowering time and several floral homeotic genes. Plant Cell Physiol 2003; 44:555-64. [PMID: 12826620 DOI: 10.1093/pcp/pcg091] [Citation(s) in RCA: 191] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Floral transition should be strictly regulated because it is one of the most critical developmental processes in plants. Arabidopsis terminal flower 2 (tfl2) mutants show an early-flowering phenotype that is relatively insensitive to photoperiod, as well as several other pleiotropic phenotypes. We found that the early flowering of tfl2 is caused mainly by ectopic expression of the FLOWERING LOCUS T (FT) gene, a floral pathway integrator. Molecular cloning of TFL2 showed that it encodes a protein with homology to heterochromatin protein 1 (HP1) of animals and Swi6 of fission yeast. TFL2 protein localizes in subnuclear foci and expression of the TFL2 gene complemented yeast swi6(-) mutants. These results suggested that TFL2 might function as an HP1 in Arabidopsis: Gene expression analyses using DNA microarrays, however, did not show an increase in the expression of heterochromatin genes in tfl2 mutants but instead showed the upregulation of the floral homeotic genes APETALA3, PISTILLATA, AGAMOUS and SEPALLATA3. The pleiotropic phenotype of the tfl2 mutant could reflect the fact that TFL2 represses the expression of multiple genes. Our results demonstrate that despite its homology to HP1, TFL2 is involved in the repression of specific euchromatin genes and not heterochromatin genes in Arabidopsis.
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Affiliation(s)
- Toshihisa Kotake
- Research Institute for Biological Sciences, Okayama, 716-1241 Japan
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Mohri Y, Goto S, Nakahigashi K, Inokuchi H. tRNA2Thr complements temperature sensitivity caused by null mutations in the htrB gene in Escherichia coli. J Bacteriol 2003; 185:1726-9. [PMID: 12591892 PMCID: PMC148054 DOI: 10.1128/jb.185.5.1726-1729.2003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
According to the wobble rule, tRNA2Thr is nonessential for protein synthesis, because the codon (ACG) that is recognized by tRNA2Thr is also recognized by tRNA4Thr. In order to investigate the reason that this nonessential tRNA nevertheless exists in Escherichia coli, we attempted to isolate tRNA2Thr-requiring mutants. Using strain JM101F(-), which lacks the gene for tRNA2Thr, we succeeded in isolating two temperature-sensitive mutants whose temperature sensitivity was complemented by introduction of the gene for tRNA2Thr. These mutants had a mutation in the htrB gene, whose product is an enzyme involved in lipid A biosynthesis. Although it is known that some null mutations in the htrB gene give a temperature-sensitive phenotype, our mutants exhibited tighter temperature sensitivity. We discuss a possible mechanism for the requirement for tRNA2Thr.
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Affiliation(s)
- Yoshio Mohri
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan
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Kusaba A, Ansai T, Akifusa S, Nakahigashi K, Inokuchi H, Takehara T. Cloning and sequencing a HemK-family gene in Porphyromonas gingivalis. DNA Seq 2003; 14:71-4. [PMID: 12751333 DOI: 10.1080/1042517021000050561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
HemK, a universally conserved protein of unknown function, has high amino acid similarity with DNA-(adenine-N6) methyltransferases (MTases). In the present study, we sequenced a 5026 bp DNA fragment just downstream of the PgPepO gene reported previously. The DNA sequence analysis revealed three ORFs. The ORF2 gene encoded a protein of 294 amino acids with a calculated molecular weight of 32,160 Da. The deduced amino acid sequence of the ORF2 gene exhibited a significant similarity to sequence of HemK from E. coli (35% identical residues). The ORF2 gene complemented an E. coli hemK mutant. Thus, ORF2 was named PgHemK. From the point of veiw of our recent finding, that E. coli HemK catalyses the methylation of polypeptide chain release factors such as RF1 and RF2, we postulated that PgHemK might function as a protein MTase containing the DNA MTase motif.
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Affiliation(s)
- Akito Kusaba
- Department of Preventive Dentistry, Kyushu Dental College, Kokurakita-ku, Kitakyushu 803-8580, Japan
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Kusaba A, Ansai T, Akifusa S, Nakahigashi K, Taketani S, Inokuchi H, Takehara T. Cloning and expression of a Porphyromonas gingivalis gene for protoporphyrinogen oxidase by complementation of a hemG mutant of Escherichia coli. Oral Microbiol Immunol 2002; 17:290-5. [PMID: 12354210 DOI: 10.1034/j.1399-302x.2002.170505.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Porphyromonas gingivalis, a bacterium implicated in periodontal pathogenesis, has a growth requirement for iron protoporphyrin IX. By complementation with a P. gingivalis 381 chromosomal DNA library, we were able to isolate a clone that enhanced the poor growth of a hemG mutant of Escherichia coli. The DNA sequence analysis of this clone revealed three open reading frames (ORFs). ORF3 encoded a protein of 466 amino acids with a calculated molecular weight of 51 695 Da. The deduced amino acid sequence of the ORF3 gene had significant similarity to sequences of protoporphyrinogen oxidase (PPO) from Myxococcus xanthus (30% identical residues). When the ORF3 gene was overexpressed in E. coli, the extract had much higher PPO activity than a control extract, and this activity was inhibited by acifluorfen, a specific inhibitor of PPO. Thus, ORF3 was named PgHemG. Furthermore, several porphyrin-related genes, including hemD, hemN and hemH, were identified in the data bases on the websites available on-line. We postulated that a porphyrin biosynthetic pathway to heme from preuroporphyrin may be conserved in P. gingivalis.
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Affiliation(s)
- A Kusaba
- Department of Preventive Dentistry, Kyushu Dental College, Kokurakita-ku, Kitakyushu 803-8580, Japan
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Rosen R, Büttner K, Becher D, Nakahigashi K, Yura T, Hecker M, Ron EZ. Heat shock proteome of Agrobacterium tumefaciens: evidence for new control systems. J Bacteriol 2002; 184:1772-8. [PMID: 11872730 PMCID: PMC134891 DOI: 10.1128/jb.184.6.1772-1778.2002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The regulation of Agrobacterium tumefaciens heat shock genes involves a transcriptional activator (RpoH) and repressor elements (HrcA-CIRCE). Using proteome analysis and mutants in these control elements, we show that the heat shock induction of 32 (out of 56) heat shock proteins is independent of RpoH and HrcA. These results indicate the existence of additional regulatory factors in the A. tumefaciens heat shock response.
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Affiliation(s)
- Ran Rosen
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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27
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Nakahigashi K, Kubo N, Narita SI, Shimaoka T, Goto S, Oshima T, Mori H, Maeda M, Wada C, Inokuchi H. HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and hemK knockout induces defects in translational termination. Proc Natl Acad Sci U S A 2002; 99:1473-8. [PMID: 11805295 PMCID: PMC122215 DOI: 10.1073/pnas.032488499] [Citation(s) in RCA: 92] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
HemK, a universally conserved protein of unknown function, has high amino acid similarity with DNA-(adenine-N6) methyl transferases (MTases). A certain mutation in hemK gene rescues the photosensitive phenotype of a ferrochelatase-deficient (hemH) mutant in Escherichia coli. A hemK knockout strain of E. coli not only suffered severe growth defects, but also showed a global shift in gene expression to anaerobic respiration, as determined by microarray analysis, and this shift may lead to the abrogation of photosensitivity by reducing the oxidative stress. Suppressor mutations that abrogated the growth defects of the hemK knockout strain were isolated and shown to be caused by a threonine to alanine change at codon 246 of polypeptide chain release factor (RF) 2, indicating that hemK plays a role in translational termination. Consistent with such a role, the hemK knockout strain showed an enhanced rate of read-through of nonsense codons and induction of transfer-mRNA-mediated tagging of proteins within the cell. By analysis of the methylation of RF1 and RF2 in vivo and in vitro, we showed that HemK methylates RF1 and RF2 in vitro within the tryptic fragment containing the conserved GGQ motif, and that hemK is required for the methylation within the same fragment of, at least, RF1 in vivo. This is an example of a protein MTase containing the DNA MTase motif and also a protein-(glutamine-N5) MTase.
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Affiliation(s)
- Kenji Nakahigashi
- Department of Biophysics, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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Kanjo N, Nakahigashi K, Oeda K, Inokuchi H. Isolation and characterization of a cDNA from soybean and its homolog from Escherichia coli, which both complement the light sensitivity of Escherichia coli hemH mutant strain VS101. Genes Genet Syst 2001; 76:327-34. [PMID: 11817648 DOI: 10.1266/ggs.76.327] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Using Escherichia coli strain VS101, whose hemH gene encoding the ferrochelatase is partially defective, we isolated and analyzed a clone (designated XWH-1) from a X phage library of soybean (Glycine max) cDNA, which exhibited weak complementation activity against the light sensitivity of VS101. In VS101 bacteria lysogenized with lambdaWH-1, a significant decrease in accumulation of protoporphyrin IX (PROTO IX) was detected as compared with that in non-lysogenic bacteria. On the other hand, in the wild-type E. coli strains lysogenized with lambdaWH-1, significant accumulation of delta-aminolevulinic acid (ALA) was observed, although accumulation of other intermediates such as uroporphyrinogen III (UROGEN III) and coproporphyrinogen III (COPROGEN III), was not observed. The growth of the wild-type bacteria in which the insert cDNA from deltaWH-1 had been introduced via a plasmid vector was markedly inhibited. By constructing, testing and sequencing a series of deletion clones of the insert, it was found that the insert encodes two proteins, a trancated LepA and a hypothetical protein ORF296, and that only ORF296 possesses the ability to block the heme biosynthetic pathway. ORF296 showed about 30% identity with the E. coli hypothetical protein YicL. By cloning and examining the gene for YicL in E. coli, we found that YicL shows the same effect as that of the soybean cDNA. From these findings, we concluded that the clone from soybean and yicL from E. coli block a step in an early stage of the heme biosynthetic pathway (probably the step catalyzed by HemB). Consequently, we postulate that the VS101 bacteria harboring these genes became light resistant as a result of a decrease in accumulated PROTO IX, and that the growth of the bacteria harboring these genes was inhibited because of the inhibition of heme biosynthesis at the step catalyzed by HemB.
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Affiliation(s)
- N Kanjo
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
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29
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Abstract
We investigated the viability of Escherichia coli cells during long-term cultivation in Brain Heart Infusion (BHI) medium and observed that the number of viable cells increased, then decreased, and increased again, in this medium, and finally the cells died out within about 10 days. This cell death may result from an increase in the pH of the medium. After repeated cultivation in BHI, bacterial cells that did not die out even under conditions of further cultivation were obtainable from cultures showing a stabilized viable count. We propose that long-term cultivation in BHI medium is a good system for studying growth phase-specific events in E. coli cells, because the total life-cycle of a population of E. coli, including exponential growth, stationary phase, and extinction, can be seen during a period of only about 10 days. Also, this system clearly allows detection of a phenotype that may not be detectable in other commonly used media. Moreover, in this report, we show that mutants displaying the GASP (growth advantage in stationary phase) phenotype appear at high frequency under long-term cultivation conditions.
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Affiliation(s)
- T Fukuda
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
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Nakahigashi K, Yanagi H, Yura T. DnaK chaperone-mediated control of activity of a sigma(32) homolog (RpoH) plays a major role in the heat shock response of Agrobacterium tumefaciens. J Bacteriol 2001; 183:5302-10. [PMID: 11514513 PMCID: PMC95412 DOI: 10.1128/jb.183.18.5302-5310.2001] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
RpoH (Escherichia coli sigma(32) and its homologs) is the central regulator of the heat shock response in gram-negative proteobacteria. Here we studied salient regulatory features of RpoH in Agrobacterium tumefaciens by examining its synthesis, stability, and activity while increasing the temperature from 25 to 37 degrees C. Heat induction of RpoH synthesis occurred at the level of transcription from an RpoH-dependent promoter, coordinately with that of DnaK, and followed by an increase in the RpoH level. Essentially normal induction of heat shock proteins was observed even with a strain that was unable to increase the RpoH level upon heat shock. Moreover, heat-induced accumulation of dnaK mRNA occurred without protein synthesis, showing that preexisting RpoH was sufficient for induction of the heat shock response. These results suggested that controlling the activity, rather than the amount, of RpoH plays a major role in regulation of the heat shock response. In addition, increasing or decreasing the DnaK-DnaJ chaperones specifically reduced or enhanced the RpoH activity, respectively. On the other hand, the RpoH protein was normally stable and remained stable during the induction phase but was destabilized transiently during the adaptation phase. We propose that the DnaK-mediated control of RpoH activity plays a primary role in the induction of heat shock response in A. tumefaciens, in contrast to what has been found in E. coli.
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Affiliation(s)
- K Nakahigashi
- HSP Research Institute, Kyoto Research Park, Kyoto 600-8813, Japan
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Nakahigashi K, Ron EZ, Yanagi H, Yura T. Differential and independent roles of a sigma(32) homolog (RpoH) and an HrcA repressor in the heat shock response of Agrobacterium tumefaciens. J Bacteriol 1999; 181:7509-15. [PMID: 10601208 PMCID: PMC94208 DOI: 10.1128/jb.181.24.7509-7515.1999] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The heat shock response in alpha proteobacteria is unique in that a combination of two regulators is involved: a positive regulator, RpoH (sigma(32) homolog), found in the alpha, beta, and gamma proteobacteria, and a negative regulator, HrcA, widely distributed in eubacteria but not in the gamma proteobacteria. To assess the differential roles of the two regulators in these bacteria, we cloned the hrcA-grpE operon of Agrobacterium tumefaciens, analyzed its transcription, and constructed deletion mutants lacking RpoH and/or HrcA. The DeltarpoH mutant and DeltarpoH DeltahrcA double mutant were unable to grow above 30 degrees C. Whereas the synthesis of heat shock proteins (e.g., DnaK, GroEL, and ClpB) was transiently induced upon temperature upshift from 25 to 37 degrees C in the wild type, such induction was not observed in the DeltarpoH mutant, except that GroEL synthesis was still partially induced. By contrast, the DeltahrcA mutant grew normally and exhibited essentially normal heat induction except for a higher level of GroEL expression, especially before heat shock. The DeltarpoH DeltahrcA double mutant showed the combined phenotypes of each of the single mutants. The amounts of dnaK and groE transcripts before and after heat shock, as determined by primer extension, were consistent with those of the proteins synthesized. The cellular level of RpoH but not HrcA increased significantly upon heat shock. We conclude that RpoH plays a major and global role in the induction of most heat shock proteins, whereas HrcA plays a restricted role in repressing groE expression under nonstress conditions.
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Affiliation(s)
- K Nakahigashi
- HSP Research Institute, Kyoto Research Park, Shimogyo-ku, Kyoto 600-8813, Japan
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32
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Abstract
Current models of both heat induction and the chaperone-mediated feedback control of the sigma32 regulon in Escherichia coli have been further substantiated, and the extent of conservation among Gram-negative bacteria has been assessed. Analyses of the 'CIRCE' and other regulons or operons in Gram-positive and Gram-negative bacteria have provided new insights into their significance and regulatory mechanisms.
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Affiliation(s)
- T Yura
- HSP Research Institute, Kyoto Research Park, Shimogyo-ku, Kyoto, 600-8813, Japan.
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Nakahigashi K, Yanagi H, Yura T. Regulatory conservation and divergence of sigma32 homologs from gram-negative bacteria: Serratia marcescens, Proteus mirabilis, Pseudomonas aeruginosa, and Agrobacterium tumefaciens. J Bacteriol 1998; 180:2402-8. [PMID: 9573192 PMCID: PMC107182 DOI: 10.1128/jb.180.9.2402-2408.1998] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The heat shock response in Escherichia coli is mediated primarily by the rpoH gene, encoding sigma32, which is specifically required for transcription of heat shock genes. A number of sigma32 homologs have recently been cloned from gram-negative bacteria that belong to the gamma or alpha subdivisions of the proteobacteria. We report here some of the regulatory features of several such homologs (RpoH) expressed in E. coli as well as in respective cognate bacteria. When expressed in an E. coli delta rpoH strain lacking its own sigma32, these homologs activated the transcription of heat shock genes (groE and dnaK) from the start sites normally used in E. coli. The level of RpoH in Serratia marcescens and Pseudomonas aeruginosa cells was very low at 30 degrees C but was elevated markedly upon a shift to 42 degrees C, as found previously with E. coli. The increased RpoH levels upon heat shock resulted from both increased synthesis and stabilization of the normally unstable RpoH protein. In contrast, the RpoH level in Proteus mirabilis was relatively high at 30 degrees C and increased less markedly upon heat shock, mostly by increased synthesis; this sigma32 homolog was already stable at 30 degrees C, and little further stabilization occurred upon the shift to 42 degrees C. The increased synthesis of RpoH homologs in all these gamma proteobacteria was observed even in the presence of rifampin, suggesting that the induction occurred at the level of translation. Thus, the basic regulatory strategy of the heat shock response by enhancing the RpoH level is well conserved in the gamma proteobacteria, but some divergence in the actual mechanisms used occurred during evolution.
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Ishibashi H, Tamura J, Nakahigashi K. Electron-density distribution in γ-CuBr by the maximum entropy method. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396085583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Sekii Y, Ishibashi H, Nakahigashi K. Electron-density distribution of superconductor Sr 2RuO 4by the maximum entropy method. Acta Crystallogr A 1996. [DOI: 10.1107/s0108767396085595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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36
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McCarty JS, Rüdiger S, Schönfeld HJ, Schneider-Mergener J, Nakahigashi K, Yura T, Bukau B. Regulatory region C of the E. coli heat shock transcription factor, sigma32, constitutes a DnaK binding site and is conserved among eubacteria. J Mol Biol 1996; 256:829-37. [PMID: 8601834 DOI: 10.1006/jmbi.1996.0129] [Citation(s) in RCA: 96] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The E. coli heat shock response is regulated at the transcriptional level through stress-dependent controls of the heat shock promoter-specific sigma32 subunit of RNA polymerase. A key aspect of this regulation, the sensing of stress and transmission of this information to sigma32, involves the chaperone system formed by the DnaK, DnaJ and GrpE heat shock proteins. This system mediates stress- dependent controls of levels and activity of sigma32 which rely, at least in part, on direct association of DnaK and DnaJ with sigma32. We identified DnaK binding sites within the sigma32 sequence by probing a cellulose-bound peptide library scanning sigma32. Two sites with high affinity for DnaK, containing the motifs RKLFFNLR and LRNWRIVK, were located centrally and peripherally, respectively, to the region C of sigma32, previously implicated genetically in chaperone-dependent control of sigma32 levels. Cloning and sequencing of rpoH homologs from five Gram-negative proteobacteria revealed that region C, including the DnaK binding motif central to it, is highly conserved among sigma32 homologs but missing in the other sigma factors. We propose that binding of DnaK to region C is central to a conserved regulatory mechanism allowing the sensing of stress by the heat shock gene transcription machinery.
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Affiliation(s)
- J S McCarty
- Zentrum fur Molekulare Biologie Heidelberg Universitat Heidelberg, FRG
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Abstract
In procaryotes such as Escherichia coli, transcriptional activation of heat shock genes in response to elevated temperature is caused primarily by transient increase in the amount of sigma 32 (rpoH gene product) specifically required for transcription from the heat shock promoters. The increase in sigma 32 level results from increased translation of rpoH mRNA and from stabilization of sigma 32 which is ordinarily very unstable. Some of the factors and cis-acting elements that constitute the complex regulatory circuits have been identified and characterized, but detailed mechanisms as well as nature of sensors and signals remain to be elucidated. Whereas this "classical" heat shock regulon (sigma 32 regulon) provides major protective functions against thermal stress, a second heat shock regulon mediated by sigma E (sigma 24) encodes functions apparently required under more extreme conditions, and is activated by responding to extracytoplasmic signals. These regulons mediated by minor sigma factors (sigma 32 in particular) appear to be conserved in most gram-negative bacteria, but not in gram-positive bacteria.
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Affiliation(s)
- T Yura
- HSP Research Institute, Kyoto Research Park, Japan
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38
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Nakahigashi K, Yanagi H, Yura T. Isolation and sequence analysis of rpoH genes encoding sigma 32 homologs from gram negative bacteria: conserved mRNA and protein segments for heat shock regulation. Nucleic Acids Res 1995; 23:4383-90. [PMID: 7501460 PMCID: PMC307394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The rpoH genes encoding homologs of Escherichia coli sigma 32 (heat shock sigma factor) were isolated and sequenced from five gram negative proteobacteria (gamma or alpha subgroup): Enterobacter cloacae (gamma), Serratia marcescens (gamma), Proteus mirabilis (gamma), Agrobacterium tumefaciens (alpha) and Zymomonas mobilis (alpha). Comparison of these and three known genes from E.coli (gamma), Citrobacter freundii (gamma) and Pseudomonas aeruginosa (gamma) revealed marked similarities that should reflect conserved function and regulation of sigma 32 in the heat shock response. Both the sequence complementary to part of 16S rRNA (the 'downstream box') and a predicted mRNA secondary structure similar to those involved in translational control of sigma 32 in E.coli were found for the rpoH genes from the gamma, but not the alpha, subgroup, despite considerable divergence in nucleotide sequence. Moreover, a stretch of nine amino acid residues Q(R/K)(K/R)LFFNLR, designated the 'RpoH box', was absolutely conserved among all sigma 32 homologs, but absent in other sigma factors; this sequence overlapped with the segment of polypeptide thought to be involved in DnaK/DnaJ chaperone-mediated negative control of synthesis and stability of sigma 32. In addition, a putative sigma E (sigma 24)-specific promoter was found in front of all rpoH genes from the gamma, but not alpha, subgroup. These results suggest that the regulatory mechanisms, as well as the function, of the heat shock response known in E.coli are very well conserved among the gamma subgroup and partially conserved among the alpha proteobacteria.
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Ishibashi E, Higashimine K, Minamigawa S, Nakahigashi K. Electron distribution in germanium by maximum entropy method. Acta Crystallogr A 1993. [DOI: 10.1107/s0108767378098955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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40
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Nakahigashi K, Miyamoto K, Nishimura K, Inokuchi H. Isolation and characterization of a light-sensitive mutant of Escherichia coli K-12 with a mutation in a gene that is required for the biosynthesis of ubiquinone. J Bacteriol 1992; 174:7352-9. [PMID: 1339425 PMCID: PMC207431 DOI: 10.1128/jb.174.22.7352-7359.1992] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Cells with a novel mutation that is lethal when the cells are exposed to visible light were isolated from Escherichia coli K-12. The mutation was mapped at 63 min on the linkage map of the E. coli chromosome, and the gene, designated visB, was cloned and sequenced. From its map position and the evidence that the gene product VisB exhibits homology with flavin monooxygenase of Pseudomonas fluorescens, the visB gene was deduced to be identical to the ubiH gene, which is a gene required for the biosynthesis of ubiquinone and is thought to be similar to the gene for flavin monooxygenase. The photosensitive phenotype appears to be due to the accumulation of the substrate for the reaction catalyzed by the visB (ubiH) gene product because other mutations that block earlier steps in the biosynthesis of ubiquinone can reverse the photosensitivity. The accumulated intermediates may produce active species of oxygen in the mutant bacteria upon illumination by visible light, and these active oxygen species may cause the death of the cells by a mechanism similar to that associated with mutations in visA (hemH).
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Affiliation(s)
- K Nakahigashi
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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41
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Affiliation(s)
- K Nishimura
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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42
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Kogachi M, Minamigawa S, Nakahigashi K. Determination of long range order and vacancy content in the NiAl β′-phase alloys by x-ray diffractometry. ACTA ACUST UNITED AC 1992. [DOI: 10.1016/0956-7151(92)90410-g] [Citation(s) in RCA: 57] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Nakahigashi K, Nishimura K, Miyamoto K, Inokuchi H. Photosensitivity of a protoporphyrin-accumulating, light-sensitive mutant (visA) of Escherichia coli K-12. Proc Natl Acad Sci U S A 1991; 88:10520-4. [PMID: 1835790 PMCID: PMC52960 DOI: 10.1073/pnas.88.23.10520] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Mutations in the visA gene of Escherichia coli cause the mutant bacteria to die upon illumination with visible light. We confirmed genetically that the visA gene is a structural gene for ferrochelatase (protoheme ferro-lyase, EC 4.99.1.1). Since other mutations in the genes involved in the biosynthesis of heme can cure the photosensitivity, the light-induced cell death appears to be brought about by the accumulation of protoporphyrin IX, one of the substrates of ferrochelatase. When cells are illuminated with visible light, protoporphyrin IX seems to produce an active species of oxygen (probably 1O2) that is harmful to the cells. This defect is the same as that associated with the human disease protoporphyria.
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Affiliation(s)
- K Nakahigashi
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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Abstract
Six mutants of Escherichia coli K12 that are sensitive to visible light have been isolated. Five of them, including an amber mutant, are defective in a gene that maps near 11 minutes on the linkage map of the chromosome, and this gene has been designated visA. The sixth mutant, which was isolated from bacteria that carried the visA+/visA+ diploid allele, is defective in a gene that maps near 63 minutes on the linkage map, which has been designated visB. These mutant strains of bacteria are killed by illumination with visible light. The effective wavelength of the light is around 460 nm. The nucleotide sequence of the visA gene was determined. As a result of a search for homologous products, we found that visA may be identical to hemH, the structural gene for ferrochelatase which catalyzes a final step in the biosynthesis of heme. A possible mechanism for the killing of the visA mutant bacteria is discussed.
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Affiliation(s)
- K Miyamoto
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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Affiliation(s)
- K Nakahigashi
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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Abstract
It has been discovered that expression of promoter activity can be inhibited by visible light when specific fragments of E. coli DNA are inserted in a vector system designed to assay for promoter activity. These fragments have been located on regions of the E. coli chromosome to which no gene has been assigned to date. The effective wavelength of light that produces this phenomenon has been determined.
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Affiliation(s)
- K Nakahigashi
- Department of Biophysics, Faculty of Science, Kyoto University
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Affiliation(s)
- K Nakahigashi
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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Nakahigashi K, Inokuchi H, Ozeki H. Functional expression of the mutants of the chloroplast tRNA(Lys) gene from the liverwort, Marchantia polymorpha, in Escherichia coli. FEBS Lett 1990; 265:59-62. [PMID: 2194832 DOI: 10.1016/0014-5793(90)80883-k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The anticodon of the tRNA(Lys) gene (trnK) in the liverwort, Marchantia polymorpha, was artificially converted to an amber anticodon. This mutant tRNA(Lys) (CTA) gene carrying either the intron of the C27-C43 mismatch at the anticodon-stem is not functional in Escherichia coli, but without both of them, it does work as a tRNA(Lys) amber suppressor.
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Affiliation(s)
- K Nakahigashi
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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Kohchi T, Umesono K, Ogura Y, Komine Y, Nakahigashi K, Komano T, Yamada Y, Ozeki H, Ohyama K. A nicked group II intron and trans-splicing in liverwort, Marchantia polymorpha, chloroplasts. Nucleic Acids Res 1988; 16:10025-36. [PMID: 3194192 PMCID: PMC338834 DOI: 10.1093/nar/16.21.10025] [Citation(s) in RCA: 33] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The chloroplast gene rps12 for ribosomal protein S12 in a liverwort, Marchantia polymorpha, is split into three exons by two introns, one of which (intron 1) is discontinuous. Exon 1 of rps12 for the N-terminal portion of the S12 protein is far from exons 2 and 3 for the C-terminal portion on the opposite DNA strand. S1-nuclease protection analysis and Northern hybridization with RNA isolated from the liverwort chloroplasts showed that: (i) the exons 1 and 2-3 of the rps12 gene with the neighboring genes were transcribed separately, (ii) the trans-splicing of intron 1 occurred after the processing of two primary transcripts to two pre-mRNAs, and (iii) there was no particular order for the splicing of intron 1 (trans) and intron 2 (cis) in the rps12 gene. We propose a bimolecular interaction model for trans-splicing by assuming that intermolecular base pairings between two pre-mRNAs result in the formation of the structure typical of group II introns except for disruption in the loop III region. This structure could be constructed in intron 1 of tobacco rps12 gene.
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Affiliation(s)
- T Kohchi
- Research Center for Cell and Tissue Culture, Kyoto University, Japan
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Ozeki H, Ohyama K, Inokuchi H, Fukuzawa H, Kohchi T, Sano T, Nakahigashi K, Umesono K. Genetic system of chloroplasts. Cold Spring Harb Symp Quant Biol 1987; 52:791-804. [PMID: 3502722 DOI: 10.1101/sqb.1987.052.01.088] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- H Ozeki
- Department of Biophysics, Faculty of Science, Kyoto University, Japan
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