Alterations in Global Patterns of Gene Expression in Synechocystis sp. PCC 6803 in Response to Inorganic Carbon Limitation and the Inactivation of ndhR, a LysR Family Regulator

Wang, Hongliang; Postier, Bradley L.; Burnap, Robert L.

doi:10.1074/jbc.m311336200

Cited by 244 publications

(399 citation statements)

References 65 publications

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“…These genes included sll0797 and sll0798 that encode a two-component system with multiple regulatory roles responding to Ni 2+ , cellular redox and inorganic carbon availability (Li & Sherman, 2000;Ló pez-Maury et al, 2002;Wang et al, 2004a). The gene slr1285 that encodes Hik34 was also downregulated in the wild-type.…”

Section: The Absence Of Hik31 Alters Transcriptional Response To Low mentioning

confidence: 99%

“…Decreased mRNA levels of these genes were observed in conditions associated with decreased growth; e.g. during the linear growth phase, after the transition from light to dark, under sulfur deprivation and during acclimation to decreased inorganic carbon (Foster et al, 2007;Summerfield & Sherman, 2007;Wang et al, 2004a;Zhang et al, 2008). Response to low-oxygen conditions involved the upregulation of genes that encoded proteins involved in sensing and responding to environmental change and maintaining cellular homeostasis, including some stress-responsive proteins, regulatory proteins and transport and binding proteins.…”

Section: Differential Transcript Abundance In the Wild-type Followingmentioning

confidence: 99%

“…Transcriptional responses to numerous stimuli have been well characterized in the freshwater cyanobacterium Synechocystis sp. PCC 6803 (hereafter Synechocystis); stimuli included changes in light conditions, pH, nutrient availability, salt stress and temperature stress (Gill et al, 2002;Hihara et al, 2001;Huang et al, 2002;Singh et al, 2003Singh et al, , 2006Wang et al, 2004a, b). In addition, we have examined the response to low-oxygen conditions in Synechocystis .…”

Section: Introductionmentioning

confidence: 99%

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Gene expression under low-oxygen conditions in the cyanobacterium Synechocystis sp. PCC 6803 demonstrates Hik31-dependent and -independent responses

2011

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We have investigated the response of the cyanobacterium Synechocystis sp. PCC 6803 during growth at very low O 2 concentration (bubbled with 99.9 % N 2 /0.1 % CO 2 ). Significant transcriptional changes upon low-O 2 incubation included upregulation of a cluster of genes that contained psbA1 and an operon that includes a gene encoding the two-component regulatory histidine kinase, Hik31. This regulatory cluster is of particular interest, since there are virtually identical copies on both the chromosome and plasmid pSYSX. We used a knockout mutant lacking the chromosomal copy of hik31 and studied differential transcription during the aerobiclow-O 2 transition in this DHik31 strain and the wild-type. We observed two distinct responses to this transition, one Hik31 dependent, the other Hik31 independent. The Hik31-independent responses included the psbA1 induction and genes involved in chlorophyll biosynthesis. In addition, there were changes in a number of genes that may be involved in assembling or stabilizing photosystem (PS)II, and the hox operon and the LexA-like protein (Sll1626) were upregulated during low-O 2 growth. This family of responses mostly focused on PSII and overall redox control. There was also a large set of genes that responded differently in the absence of the chromosomal Hik31. In the vast majority of these cases, Hik31 functioned as a repressor and transcription was enhanced when Hik31 was deleted. Genes in this category encoded both core and peripheral proteins for PSI and PSII, the main phycobilisome proteins, chaperones, the ATP synthase cluster and virtually all of the ribosomal proteins. These findings, coupled with the fact that DHik31 grew better than the wild-type under low-O 2 conditions, suggested that Hik31 helps to regulate growth and overall cellular homeostasis. We detected changes in the transcription of other regulatory genes that may compensate for the loss of Hik31. We conclude that Hik31 regulates an important series of genes that relate to energy production and growth and that help to determine how Synechocystis responds to changes in O 2 conditions.

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Section: The Absence Of Hik31 Alters Transcriptional Response To Low mentioning

confidence: 99%

Section: Differential Transcript Abundance In the Wild-type Followingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Gene expression under low-oxygen conditions in the cyanobacterium Synechocystis sp. PCC 6803 demonstrates Hik31-dependent and -independent responses

2011

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“…At least three transcriptional factors, CmpR, NdhR, and AbrB-like proteins, were found to be involved in the up-regulation of functionally defined gene groups (e.g. C i transporters, NDH1 complexes, and photosynthetic complexes; Omata et al, 2001;Wang et al, 2004;Lieman-Hurwitz et al, 2009). Moreover, the affinity of the transcription factor CmpR for the cmp promoter was stimulated by the binding of 2-phosphoglycolate (2PG; Nishimura et al, 2008), the first metabolite of the photorespiratory 2PG metabolism (Eisenhut et al, 2008b).…”

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confidence: 97%

Metabolic and Transcriptomic Phenotyping of Inorganic Carbon Acclimation in the Cyanobacterium Synechococcus elongatus PCC 7942

et al. 2011

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The amount of inorganic carbon is one of the main limiting environmental factors for photosynthetic organisms such as cyanobacteria. Using Synechococcus elongatus PCC 7942, we characterized metabolic and transcriptomic changes in cells that had been shifted from high to low CO 2 levels. Metabolic phenotyping indicated an activation of glycolysis, the oxidative pentose phosphate cycle, and glycolate metabolism at lowered CO 2 levels. The metabolic changes coincided with a general reprogramming of gene expression, which included not only increased transcription of inorganic carbon transporter genes but also genes for enzymes involved in glycolytic and photorespiratory metabolism. In contrast, the mRNA content for genes from nitrogen assimilatory pathways decreased. These observations indicated that cyanobacteria control the homeostasis of the carbon-nitrogen ratio. Therefore, results obtained from the wild type were compared with the MP2 mutant of Synechococcus 7942, which is defective for the carbon-nitrogen ratio-regulating PII protein. Metabolites and genes linked to nitrogen assimilation were differentially regulated, whereas the changes in metabolite concentrations and gene expression for processes related to central carbon metabolism were mostly similar in mutant and wild-type cells after shifts to low-CO 2 conditions. The PII signaling appears to down-regulate the nitrogen metabolism at lowered CO 2 , whereas the specific shortage of inorganic carbon is recognized by different mechanisms.

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“…PCC 6803 in conditions where the oxygen concentration is constant. A smaller induction under the same conditions was previously recorded in a microarray study [18] but never verified by other methods of investigation until now. Further, we explored the possibility that oxygen does not play any role at all in the induction of psbA gene given the fact that the previously employed methods for obtaining microaerobic conditions [6] were depleting not only oxygen but also other atmospheric gases including CO 2 and the induction of psbA1 gene might result from the cumulative effect of O 2 and CO 2 depletion.…”

Section: Discussionmentioning

confidence: 82%

Expression of psbA1 gene in Synechocystis sp. PCC 6803 is influenced by CO2

et al. 2017

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Abstract:In almost all cyanobacteria a small gene family encodes the photosystem II reaction center D1 proteins that play vital roles in the cell. Recently, several types of this protein were functionally characterised and the conditions for their transcript regulation were identified. One of the D1-encoding genes previously believed to be silent is induced by microaerobic conditions. This gene was first described in Synechocystis sp. PCC 6803 as psbA1 encoding the D1' isoform. When Synechocystis cells are shifted from high to ambient level CO 2 we recorded an increase in gene expression, similar, but to a lesser extent, to microaerobic conditions. When synthetic air is used to remove the ambient CO 2 , the induction of the gene is absent. We documented for the first time that expression of a psbA gene is regulated by the inorganic carbon status of the cell. Our conclusion is that both CO 2 and microaerobic conditions are independently influencing the expression of psbA1 gene in Synechocystis sp. PCC 6803. Hence, it is crucial to understand the mechanisms of regulation and function of D1 proteins as it could be used for future bio-technological applications as a virtual tool-box for modulating the function of PSII.

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Alterations in Global Patterns of Gene Expression in Synechocystis sp. PCC 6803 in Response to Inorganic Carbon Limitation and the Inactivation of ndhR, a LysR Family Regulator

Cited by 244 publications

References 65 publications

Gene expression under low-oxygen conditions in the cyanobacterium Synechocystis sp. PCC 6803 demonstrates Hik31-dependent and -independent responses

Gene expression under low-oxygen conditions in the cyanobacterium Synechocystis sp. PCC 6803 demonstrates Hik31-dependent and -independent responses

Metabolic and Transcriptomic Phenotyping of Inorganic Carbon Acclimation in the Cyanobacterium Synechococcus elongatus PCC 7942

Expression of psbA1 gene in Synechocystis sp. PCC 6803 is influenced by CO2

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