Genetic Engineering of Group 2 σ Factor SigE Widely Activates Expressions of Sugar Catabolic Genes in Synechocystis Species PCC 6803

Metabolic engineering of photosynthetic organisms is required for utilization of light energy and for reducing carbon emissions.Control of transcriptional regulators is a powerful approach for changing cellular dynamics, because a set of genes is concomitantly regulated. Here, we show that overexpression of a group 2 σ factor, SigE, enhances the expressions of sugar catabolic genes in the unicellular cyanobacterium, Synechocystis sp. PCC 6803. Transcriptome analysis revealed that genes for the oxidative pentose phosphate pathway and glycogen catabolism are induced by overproduction of SigE. Immunoblotting showed that protein levels of sugar catabolic enzymes, such as glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, glycogen phosphorylase, and isoamylase, are increased. Glycogen levels are reduced in the SigE-overexpressing strain grown under light. Metabolome analysis revealed that metabolite levels of the TCA cycle and acetyl-CoA are significantly altered by SigE overexpression. The SigE-overexpressing strain also exhibited defective growth under mixotrophic or dark conditions. Thus, SigE overexpression changes sugar catabolism at the transcript to phenotype levels, suggesting a σ factor-based engineering method for modifying carbon metabolism in photosynthetic bacteria. Metabolic engineering of photosynthetic organisms is required for utilization of light energy and for reducing carbon emissions.Control of transcriptional regulators is a powerful approach for changing cellular dynamics, because a set of genes is concomitantly regulated. Here, we show that overexpression of a group 2 σ factor, SigE, enhances the expressions of sugar catabolic genes in the unicellular cyanobacterium, Synechocystis sp. PCC 6803. Transcriptome analysis revealed that genes for the oxidative pentose phosphate pathway and glycogen catabolism are induced by overproduction of SigE. Immunoblotting showed that protein levels of sugar catabolic enzymes, such as glucose-6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, glycogen phosphorylase, and isoamylase, are increased. Glycogen levels are reduced in the SigE-overexpressing strain grown under light. Metabolome analysis revealed that metabolite levels of the TCA cycle and acetyl-CoA are significantly altered by SigE overexpression. The SigE-overexpressing strain also exhibited defective growth under mixotrophic or dark conditions. Thus, SigE overexpression changes sugar catabolism at the transcript to phenotype levels, suggesting a σ factor-based engineering method for modifying carbon metabolism in photosynthetic bacteria. IntroductionCarbon metabolism in photosynthetic organisms has received considerable attention because increasing carbon emission is thought to be the cause of global warming. Primary production is governed not only by land plants but also by ocean-dwelling phytoplanktons, including cyanobacteria. Cyanobacteria are widely distributed in diverse ecological niches, and the unicellular cyanobacteria Synechocystis sp. PCC 6803 (hereafter Synechocystis 6803) is one of the most widely used species for the study of photosynthetic bacteria. The genome of Synechocystis 6803 was first determined in 1996 (1Kaneko T. Sato S. Kotani H. Tanaka A. Asamizu E. Nakamura Y. Miyajima N. Hirosawa M. Sugiura M. Sasamoto S. Kimura T. Hosouchi T. Matsuno A. Muraki A. Nakazaki N. Naruo K. Okumura S. Shimpo S. Takeuchi C. Wada T. Watanabe A. Yamada M. Yasuda M. Tabata S. DNA Res. 1996; 3: 185-209Crossref PubMed Scopus (239) Google Scholar), and transcriptome and proteome analyses have been performed. Several genes have been identified whose mutations alter the metabolite levels of primary carbon metabolism (2Takahashi H. Uchimiya H. Hihara Y. J. Exp. Bot. 2008; 59: 3009-3018Crossref PubMed Scopus (90) Google Scholar, 3Laurent S. Jang J. Janicki A. Zhang C.C. Bédu S. Microbiology. 2008; 154: 2161-2167Crossref PubMed Scopus (20) Google Scholar, 4Eisenhut M. Huege J. Schwarz D. Bauwe H. Kopka J. Hagemann M. Plant Physiol. 2008; 148: 2109-2120Crossref PubMed Scopus (67) Google Scholar).The engineering of carbon metabolism leads to modified production of various metabolites; however, the robust control of primary metabolism often obstructs such modification. For example, overexpression of the genes of eight enzymes in yeast cells did not increase ethanol formation or key metabolite levels (5Schaaff I. Heinisch J. Zimmermann F.K. Yeast. 1989; 5: 285-290Crossref PubMed Scopus (241) Google Scholar). Several researchers have modified genes encoding transcriptional regulators instead of metabolic enzymes. Yanagisawa et al. (6Yanagisawa S. Akiyama A. Kisaka H. Uchimiya H. Miwa T. Proc. Natl. Acad. Sci. U.S.A. 2004; 101: 7833-7838Crossref PubMed Scopus (276) Google Scholar) generated transgenic Arabidopsis thaliana plants expressing increased levels of the Dof1 transcription factor, which is an activator of gene expression associated with organic acid metabolism, including phosphoenolpyruvate carboxylase. Overexpression of Dof1 resulted in increased enzymatic activities of phosphoenolpyruvate carboxylase and pyruvate kinase, increased metabolite levels, such as amino acids (asparagine, glutamine, and glutamate), and better growth under low nitrogen conditions (6Yanagisawa S. Akiyama A. Kisaka H. Uchimiya H. Miwa T. Proc. Natl. Acad. Sci. U.S.A. 2004; 101: 7833-7838Crossref PubMed Scopus (276) Google Scholar). These results indicate that modification of transcriptional regulator(s) is practical for metabolic engineering.Primary carbon metabolism is divided into anabolic reactions, such as the Calvin cycle and gluconeogenesis, and catabolic reactions, such as glycolysis and the oxidative pentose phosphate (OPP) 2The abbreviations used are: OPPoxidative pentose phosphateCE/MScapillary electrophoresis/mass spectrometryGlc-6-PDglucose-6-phosphate dehydrogenaseGTglucose-tolerant6PGD6-phosphogluconate dehydrogenaseDIGdigoxigenin. pathway (7Osanai T. Azuma M. Tanaka K. Photochem. Photobiol. Sci. 2007; 6: 508-514Crossref PubMed Scopus (40) Google Scholar). Glycogen, the carbon sink of most cyanobacteria, provides carbon sources and reducing power under heterotrophic conditions. Glycogen degradation is catalyzed by glycogen catabolic enzymes, such as glycogen phosphorylase (encoded by glgP) and isoamylase (encoded by glgX). The genome of Synechocystis 6803 contains two glgP (sll1356 and slr1367) and two glgX (slr0237 and slr1857) genes (8Fu J. Xu X. FEMS Microbiol. Lett. 2006; 260: 201-209Crossref PubMed Scopus (39) Google Scholar). A metabolomic study showed that glucose produced from glycogen is degraded mainly through the OPP pathway under heterotrophic conditions (9Yang C. Hua Q. Shimizu K. Appl. Microbiol. Biotechnol. 2002; 58: 813-822Crossref PubMed Scopus (91) Google Scholar). Glucose-6-phosphate dehydrogenase (Glc-6-PD, encoded by zwf) and 6-phosphogluconate dehydrogenase (6PGD, encoded by gnd) are key enzymes of the OPP pathway, producing NADPH and pentose phosphate for nucleotide biosynthesis. Cyanobacterial Glc-6-PD is up-regulated by OpcA through protein-protein interaction, and opcA is essential for NADPH production during nighttime (10Hagen K.D. Meeks J.C. J. Biol. Chem. 2001; 276: 11477-11486Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar, 11Min H. Golden S.S. J. Bacteriol. 2000; 182: 6214-6221Crossref PubMed Scopus (23) Google Scholar). The transcript levels of genes of the OPP pathway are altered by light-dark transition, circadian cycle, or nitrogen status (12Osanai T. Kanesaki Y. Nakano T. Takahashi H. Asayama M. Shirai M. Kanehisa M. Suzuki I. Murata N. Tanaka K. J. Biol. Chem. 2005; 280: 30653-30659Abstract Full Text Full Text PDF PubMed Scopus (131) Google Scholar, 13Kucho K. Okamoto K. Tsuchiya Y. Nomura S. Nango M. Kanehisa M. Ishiura M. J. Bacteriol. 2005; 187: 2190-2199Crossref PubMed Scopus (119) Google Scholar, 14Osanai T. Imamura S. Asayama M. Shirai M. Suzuki I. Murata N. Tanaka K. DNA Res. 2006; 13: 185-195Crossref PubMed Scopus (105) Google Scholar). Thus, sugar catabolic enzymes, including Glc-6-PD and 6PGD, are regulated at both the transcriptional and post-translational levels in cyanobacteria.σ factors, subunits of the bacterial RNA polymerase, are divided into four groups, and cyanobacteria are characterized by possessing multiple group 2 σ factors, whose promoter recognition is similar to group 1 σ factor (15Tanaka K. Takayanagi Y. Fujita N. Ishihama A. Takahashi H. Proc. Natl. Acad. Sci. U.S.A. 1993; 90: 3511-3515Crossref PubMed Scopus (190) Google Scholar, 16Osanai T. Ikeuchi M. Tanaka K. Physiol. Plant. 2008; 133: 490-506Crossref PubMed Scopus (33) Google Scholar). Transcriptome analysis revealed that the disruption of sigE, one of four group 2 σ factors in Synechocystis, results in decreased transcript levels of three glycolytic genes (pfkA, encoding phosphofructokinase; gap1, encoding glyceraldehyde-3-phosphate dehydrogenase; and pyk, encoding pyruvate kinase), four OPP pathway genes (zwf, opcA, gnd, and tal (encoding transaldolase)), and two glycogen catabolic genes (glgP (sll1356) and glgX (slr0237)) (12Osanai T. Kanesaki Y. Nakano T. Takahashi H. Asayama M. Shirai M. Kanehisa M. Suzuki I. Murata N. Tanaka K. J. Biol. Chem. 2005; 280: 30653-30659Abstract Full Text Full Text PDF PubMed Scopus (131) Google Scholar). SigE protein levels and activities are controlled in response to light signals (17Osanai T. Imashimizu M. Seki A. Sato S. Tabata S. Imamura S. Asayama M. Ikeuchi M. Tanaka K. Proc. Natl. Acad. Sci. U.S.A. 2009; 106: 6860-6865Crossref PubMed Scopus (54) Google Scholar). Phenotypic analysis showed that the disruption of sigE results in decreased level of glycogen and reduced viability under dark conditions (12Osanai T. Kanesaki Y. Nakano T. Takahashi H. Asayama M. Shirai M. Kanehisa M. Suzuki I. Murata N. Tanaka K. J. Biol. Chem. 2005; 280: 30653-30659Abstract Full Text Full Text PDF PubMed Scopus (131) Google Scholar). Thus, transcriptome and phenotypic analyses indicate that SigE is a positive regulator of sugar catabolism, although proteomic and metabolomic analyses have not been performed.In this study, we generated a SigE-overexpressing strain and measured the transcript, protein, and metabolite levels and the phenotypes associated with sugar catabolism. We revealed that SigE overexpression activates the expressions of sugar catabolic enzymes and modifies the amounts of glycogen, acetyl-CoA, and metabolites of the TCA cycle.DISCUSSIONIn this study, we generated a strain overexpressing SigE, and the data showed that sugar catabolism is widely regulated by SigE at the transcript, protein, metabolite, and phenotype levels. The results indicate that RNA polymerase σ factor SigE plays pivotal roles in the transcriptional control of genes involved in primary carbon metabolism in this unicellular cyanobacterium.The transcriptome analysis showed that expressions of genes for four of the OPP pathway enzymes and two glycogen catabolism enzymes were increased by SigE overexpression; however, the expressions of three glycolytic genes (pfkA (sll1196), gap1, and pyk1) did not change (Fig. 8 and supplemental Table S2). These results demonstrate the complex regulation of the expressions of glycolytic genes. Recent studies showed that disruption of a histidine kinase, Hik8, or a response regulator, Rre37, resulted in decreased transcript levels of glycolytic genes (24Singh A.K. Sherman L.A. J. Bacteriol. 2005; 187: 2368-2376Crossref PubMed Scopus (62) Google Scholar, 25Tabei Y. Okada K. Tsuzuki M. Biochem. Biophys. Res. Commun. 2007; 355: 1045-1050Crossref PubMed Scopus (45) Google Scholar, 26Azuma M. Osanai T. Hirai M.Y. Tanaka K. Plant Cell Physiol. 2011; 52: 404-412Crossref PubMed Scopus (55) Google Scholar), indicating that multiple transcriptional regulators control expressions of glycolytic genes. In contrast to enzymes of the OPP pathway and glycogen catabolism, FbaII was reduced by SigE overexpression (supplemental Fig. S3). Considering the metabolic flux, the down-regulation of FbaII may be favorable for activation of sugar catabolism, especially glucose degradation, through the OPP pathway (Fig. 8). It is noteworthy that Rre37 is a positive regulator for the upper half of glycolysis, including FbaII (25Tabei Y. Okada K. Tsuzuki M. Biochem. Biophys. Res. Commun. 2007; 355: 1045-1050Crossref PubMed Scopus (45) Google Scholar, 26Azuma M. Osanai T. Hirai M.Y. Tanaka K. Plant Cell Physiol. 2011; 52: 404-412Crossref PubMed Scopus (55) Google Scholar). Thus, the ratio of glucose degradation through glycolysis or the OPP pathway may be determined by a balance between Rre37 and SigE. Summerfield and Sherman (27Summerfield T.C. Sherman L.A. J. Bacteriol. 2007; 189: 7829-7840Crossref PubMed Scopus (34) Google Scholar) also revealed that other group 2 σ factors, SigB and SigD, regulate the expressions of sugar catabolic genes, including fbaII and gnd, in response to light/dark transition. Further analysis is required to unravel the coordinated regulation of sugar catabolic genes and metabolic flux by various transcriptional regulators.In addition to transcriptional control, post-translational regulation of SigE and enzymes regulated by SigE were controlled by light status. SigE is repressed by ChlH, an H-subunit of magnesium chelatase, by protein-protein interaction under light conditions and is transiently activated under dark conditions (17Osanai T. Imashimizu M. Seki A. Sato S. Tabata S. Imamura S. Asayama M. Ikeuchi M. Tanaka K. Proc. Natl. Acad. Sci. U.S.A. 2009; 106: 6860-6865Crossref PubMed Scopus (54) Google Scholar). Glc-6-PD is up-regulated by OpcA through protein-protein interaction (10Hagen K.D. Meeks J.C. J. Biol. Chem. 2001; 276: 11477-11486Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar), although there have been no reports concerning post-translational control of 6PGD in cyanobacteria. Although the transcript levels of zwf and gnd in the GT strain diminished 1 day after light-to-dark transition, the proteins remained under prolonged dark conditions (Fig. 4), revealing no correlation between the mRNA and protein levels. Our results showing that Glc-6-PD enzymatic activity is increased by light-to-dark transition but that 6PGD activity is not may reflect the difference between their post-translational regulations. OpcA promotes oligomerization of Glc-6-PD (28Sundaram S. Karakaya H. Scanlan D.J. Mann N.H. Microbiology. 1998; 144: 1549-1556Crossref PubMed Scopus (26) Google Scholar); thus, the ratio of the oligomeric form of Glc-6-PD may be increased by light-to-dark conditions or by SigE overexpression. Proteomic studies also revealed that glycogen phosphorylase and FbaII of Synechocystis 6803 are targets of thioredoxin, a small protein involved in disulfide/dithiol reactions (29Perez-Perez M.E. Florencio F.J. Lindahl M. Proteomics. 2006; 1: 186-195Crossref Scopus (50) Google Scholar, 30Pérez-Pérez M.E. Martín-Figueroa E. Florencio F.J. Mol. Plant. 2009; 2: 270-283Abstract Full Text Full Text PDF PubMed Scopus (36) Google Scholar). Disruption of thioredoxin systems in Synechocystis results in defects in adaptation to light and redox changes (30Pérez-Pérez M.E. Martín-Figueroa E. Florencio F.J. Mol. Plant. 2009; 2: 270-283Abstract Full Text Full Text PDF PubMed Scopus (36) Google Scholar). Thus, integrative analysis of transcriptional to post-translational regulation of sugar catabolic enzymes indicates their significance for light adaptation in cyanobacteria. SigE also has some roles under high salt or heat shock conditions, in concert with other group 2 σ factors (31Singh A.K. Summerfield T.C. Li H. Sherman L.A. Arch. Microbiol. 2006; 186: 273-286Crossref PubMed Scopus (71) Google Scholar, 32Pollari M. Gunnelius L. Tuominen I. Ruotsalainen V. Tyystjärvi E. Salminen T. Tyystjärvi T. Plant Physiol. 2008; 147: 1994-2005Crossref PubMed Scopus (36) Google Scholar), suggesting the importance of σ networks to survival during various environmental conditions.CE/MS analysis revealed that metabolite levels upstream of sugar catabolism were not significantly affected, whereas those downstream of sugar catabolism, the TCA cycle and acetyl-CoA, were changed by SigE overexpression (Fig. 6 and supplemental Table S3). These results suggest that metabolites downstream of sugar catabolism have flexibility in their pool sizes, compared with upstream metabolites. Escherichia coli cells show tolerance to drastic changes in metabolic flux and energy production, because of the considerable elasticity in permitted pool sizes for pyruvate and acetyl-CoA (33Causey T.B. Shanmugam K.T. Yomano L.P. Ingram L.O. Proc. Natl. Acad. Sci. U.S.A. 2004; 101: 2235-2240Crossref PubMed Scopus (218) Google Scholar). However, elevated sugar phosphates lead to growth inhibition and loss of viability of E. coli cells (34Kadner R.J. Murphy G.P. Stephens C.M. J. Gen. Microbiol. 1992; 138: 2007-2014Crossref PubMed Scopus (92) Google Scholar). Thus, metabolite levels of sugar phosphates in cyanobacteria might also be robustly controlled because of their toxicity, similarly to enteric bacteria. A glucose-sensitive mutant lacking pmgA (sll1968), a gene named from its defect in survival under photomixotrophic growth conditions and encoding a functionally unknown protein, showed increased levels of isocitrate under both photoautotrophic and photomixotrophic conditions (2Takahashi H. Uchimiya H. Hihara Y. J. Exp. Bot. 2008; 59: 3009-3018Crossref PubMed Scopus (90) Google Scholar). Takahashi et al. (2Takahashi H. Uchimiya H. Hihara Y. J. Exp. Bot. 2008; 59: 3009-3018Crossref PubMed Scopus (90) Google Scholar) also found that levels of malate, succinate, and 2-oxoglutarate were increased by pmgA under photoautotrophic conditions. with results suggest that an TCA cycle might cause the defect in glucose in Synechocystis 6803 suggesting that the of TCA cycle is for mixotrophic growth of unicellular cyanobacteria. In of be for revealing the of of the of cyanobacteria. IntroductionCarbon metabolism in photosynthetic organisms has received considerable attention because increasing carbon emission is thought to be the cause of global warming. Primary production is governed not only by land plants but also by ocean-dwelling phytoplanktons, including cyanobacteria. Cyanobacteria are widely distributed in diverse ecological niches, and the unicellular cyanobacteria Synechocystis sp. PCC 6803 (hereafter Synechocystis 6803) is one of the most widely used species for the study of photosynthetic bacteria. The genome of Synechocystis 6803 was first determined in 1996 (1Kaneko T. Sato S. Kotani H. Tanaka A. Asamizu E. Nakamura Y. Miyajima N. Hirosawa M. Sugiura M. Sasamoto S. Kimura T. Hosouchi T. Matsuno A. Muraki A. Nakazaki N. Naruo K. Okumura S. Shimpo S. Takeuchi C. Wada T. Watanabe A. Yamada M. Yasuda M. Tabata S. DNA Res. 1996; 3: 185-209Crossref PubMed Scopus (239) Google Scholar), and transcriptome and proteome analyses have been performed. Several genes have been identified whose mutations alter the metabolite levels of primary carbon metabolism (2Takahashi H. Uchimiya H. Hihara Y. J. Exp. Bot. 2008; 59: 3009-3018Crossref PubMed Scopus (90) Google Scholar, 3Laurent S. Jang J. Janicki A. Zhang C.C. Bédu S. Microbiology. 2008; 154: 2161-2167Crossref PubMed Scopus (20) Google Scholar, 4Eisenhut M. Huege J. Schwarz D. Bauwe H. Kopka J. Hagemann M. Plant Physiol. 2008; 148: 2109-2120Crossref PubMed Scopus (67) Google Scholar).The engineering of carbon metabolism leads to modified production of various metabolites; however, the robust control of primary metabolism often obstructs such modification. For example, overexpression of the genes of eight enzymes in yeast cells did not increase ethanol formation or key metabolite levels (5Schaaff I. Heinisch J. Zimmermann F.K. Yeast. 1989; 5: 285-290Crossref PubMed Scopus (241) Google Scholar). Several researchers have modified genes encoding transcriptional regulators instead of metabolic enzymes. Yanagisawa et al. (6Yanagisawa S. Akiyama A. Kisaka H. Uchimiya H. Miwa T. Proc. Natl. Acad. Sci. U.S.A. 2004; 101: 7833-7838Crossref PubMed Scopus (276) Google Scholar) generated transgenic Arabidopsis thaliana plants expressing increased levels of the Dof1 transcription factor, which is an activator of gene expression associated with organic acid metabolism, including phosphoenolpyruvate carboxylase. Overexpression of Dof1 resulted in increased enzymatic activities of phosphoenolpyruvate carboxylase and pyruvate kinase, increased metabolite levels, such as amino acids (asparagine, glutamine, and glutamate), and better growth under low nitrogen conditions (6Yanagisawa S. Akiyama A. Kisaka H. Uchimiya H. Miwa T. Proc. Natl. Acad. Sci. U.S.A. 2004; 101: 7833-7838Crossref PubMed Scopus (276) Google Scholar). These results indicate that modification of transcriptional regulator(s) is practical for metabolic engineering.Primary carbon metabolism is divided into anabolic reactions, such as the Calvin cycle and gluconeogenesis, and catabolic reactions, such as glycolysis and the oxidative pentose phosphate (OPP) 2The abbreviations used are: OPPoxidative pentose phosphateCE/MScapillary electrophoresis/mass spectrometryGlc-6-PDglucose-6-phosphate dehydrogenaseGTglucose-tolerant6PGD6-phosphogluconate dehydrogenaseDIGdigoxigenin. pathway (7Osanai T. Azuma M. Tanaka K. Photochem. Photobiol. Sci. 2007; 6: 508-514Crossref PubMed Scopus (40) Google Scholar). Glycogen, the carbon sink of most cyanobacteria, provides carbon sources and reducing power under heterotrophic conditions. Glycogen degradation is catalyzed by glycogen catabolic enzymes, such as glycogen phosphorylase (encoded by glgP) and isoamylase (encoded by glgX). The genome of Synechocystis 6803 contains two glgP (sll1356 and slr1367) and two glgX (slr0237 and slr1857) genes (8Fu J. Xu X. FEMS Microbiol. Lett. 2006; 260: 201-209Crossref PubMed Scopus (39) Google Scholar). A metabolomic study showed that glucose produced from glycogen is degraded mainly through the OPP pathway under heterotrophic conditions (9Yang C. Hua Q. Shimizu K. Appl. Microbiol. Biotechnol. 2002; 58: 813-822Crossref PubMed Scopus (91) Google Scholar). Glucose-6-phosphate dehydrogenase (Glc-6-PD, encoded by zwf) and 6-phosphogluconate dehydrogenase (6PGD, encoded by gnd) are key enzymes of the OPP pathway, producing NADPH and pentose phosphate for nucleotide biosynthesis. Cyanobacterial Glc-6-PD is up-regulated by OpcA through protein-protein interaction, and opcA is essential for NADPH production during nighttime (10Hagen K.D. Meeks J.C. J. Biol. Chem. 2001; 276: 11477-11486Abstract Full Text Full Text PDF PubMed Scopus (42) Google Scholar, 11Min H. Golden S.S. J. Bacteriol. 2000; 182: 6214-6221Crossref PubMed Scopus (23) Google Scholar). The transcript levels of genes of the OPP pathway are altered by light-dark transition, circadian cycle, or nitrogen status (12Osanai T. Kanesaki Y. Nakano T. Takahashi H. Asayama M. Shirai M. Kanehisa M. Suzuki I. Murata N. Tanaka K. J. Biol. Chem. 2005; 280: 30653-30659Abstract Full Text Full Text PDF PubMed Scopus (131) Google Scholar, 13Kucho K. Okamoto K. Tsuchiya Y. Nomura S. Nango M. Kanehisa M. Ishiura M. J. Bacteriol. 2005; 187: 2190-2199Crossref PubMed Scopus (119) Google Scholar, 14Osanai T. Imamura S. Asayama M. Shirai M. Suzuki I. Murata N. Tanaka K. DNA Res. 2006; 13: 185-195Crossref PubMed Scopus (105) Google Scholar). Thus, sugar catabolic enzymes, including Glc-6-PD and 6PGD, are regulated at both the transcriptional and post-translational levels in cyanobacteria.σ factors, subunits of the bacterial RNA polymerase, are divided into four groups, and cyanobacteria are characterized by possessing multiple group 2 σ factors, whose promoter recognition is similar to group 1 σ factor (15Tanaka K. Takayanagi Y. Fujita N. Ishihama A. Takahashi H. Proc. Natl. Acad. Sci. U.S.A. 1993; 90: 3511-3515Crossref PubMed Scopus (190) Google Scholar, 16Osanai T. Ikeuchi M. Tanaka K. Physiol. Plant. 2008; 133: 490-506Crossref PubMed Scopus (33) Google Scholar). Transcriptome analysis revealed that the disruption of sigE, one of four group 2 σ factors in Synechocystis, results in decreased transcript levels of three glycolytic genes (pfkA, encoding phosphofructokinase; gap1, encoding glyceraldehyde-3-phosphate dehydrogenase; and pyk, encoding pyruvate kinase), four OPP pathway genes (zwf, opcA, gnd, and tal (encoding transaldolase)), and two glycogen catabolic genes (glgP (sll1356) and glgX (slr0237)) (12Osanai T. Kanesaki Y. Nakano T. Takahashi H. Asayama M. Shirai M. Kanehisa M. Suzuki I. Murata N. Tanaka K. J. Biol. Chem. 2005; 280: 30653-30659Abstract Full Text Full Text PDF PubMed Scopus (131) Google Scholar). SigE protein levels and activities are controlled in response to light signals (17Osanai T. Imashimizu M. Seki A. Sato S. Tabata S. Imamura S. Asayama M. Ikeuchi M. Tanaka K. Proc. Natl. Acad. Sci. U.S.A. 2009; 106: 6860-6865Crossref PubMed Scopus (54) Google Scholar). Phenotypic analysis showed that the disruption of sigE results in decreased level of glycogen and reduced viability under dark conditions (12Osanai T. Kanesaki Y. Nakano T. Takahashi H. Asayama M. Shirai M. Kanehisa M. Suzuki I. Murata N. Tanaka K. J. Biol. Chem. 2005; 280: 30653-30659Abstract Full Text Full Text PDF PubMed Scopus (131) Google Scholar). Thus, transcriptome and phenotypic analyses indicate that SigE is a positive regulator of sugar catabolism, although proteomic and metabolomic analyses have not been performed.In this study, we generated a SigE-overexpressing strain and measured the transcript, protein, and metabolite levels and the phenotypes associated with sugar catabolism. We revealed that SigE overexpression activates the expressions of sugar catabolic enzymes and modifies the amounts of glycogen, acetyl-CoA, and metabolites of the TCA