Genome-Wide Dynamic Transcriptional Profiling of the Light-to-Dark Transition in<i>Synechocystis</i>sp. Strain PCC 6803

Gill, Ryan T.; Katsoulakis, Eva; Schmitt, William; Taroncher-Oldenburg, Gaspar; Misra, Jatin; Stephanopoulos, Gregory

doi:10.1128/jb.184.13.3671-3681.2002

Cited by 99 publications

(105 citation statements)

References 65 publications

(74 reference statements)

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“…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%

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: Introductionmentioning

confidence: 99%

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

2011

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“…Indeed, when Synechocystis cells that had been preadapted in the dark for 2 d were exposed to Glc with or without light, transcriptional regulation of several glycolytic genes, including glk, pfkA (sll1196), fbaA (sll0018), gpmB (slr1124), and pk, was observed (Tabei et al, 2007). In addition to carbohydrate catabolism-related genes, the genes coding for oxidative phosphorylation components, such as NDH-I, CtaI, and ATP synthase, are also regulated at the transcription level during the light-to-dark transition (Gill et al, 2002;Kucho et al, 2005). The coordinated regulation of carbohydrate catabolism and oxidative phosphorylation would ensure a close connection between the generation of cellular reducing power in the form of NAD(P)H during Glc catabolism and its subsequent utilization via the respiratory electron transport chain for the production of ATP: This has been reported previously for other prokaryotes, including Bacillus subtilis and Escherichia coli (Blencke et al, 2003;Vemuri et al, 2006).…”

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Transcriptional Regulation of the Respiratory Genes in the CyanobacteriumSynechocystissp. PCC 6803 during the Early Response to Glucose Feeding

et al. 2007

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The coordinated expression of the genes involved in respiration in the photosynthetic cyanobacterium Synechocystis sp. PCC 6803 during the early period of glucose (Glc) treatment is poorly understood. When photoautotrophically grown cells were supplemented with 10 mM Glc in the light or after a dark adaptation period of 14 h, significant increases in the respiratory activity, as determined by NAD(P)H turnover, respiratory O 2 uptake rate, and cytosolic alkalization, were observed. At the same time, the transcript levels of 18 genes coding for enzymes associated with respiration increased with differential induction kinetics; these genes were classified into three groups based on their half-rising times. Transcript levels of the four genes gpi, zwf, pdhB, and atpB started to increase along with a net increase in NAD(P)H, while the onset of net NAD(P)H consumption coincided with an increase in those of the genes tktA, ppc, pdhD, icd, ndhD2, ndbA, ctaD1, cydA, and atpE. In contrast, the expression of the atpI/G/D/A/C genes coding for ATP synthase subunits was the slowest among respiratory genes and their expression started to accumulate only after the establishment of cytosolic alkalization. These differential effects of Glc on the transcript levels of respiratory genes were not observed by inactivation of the genes encoding the Glc transporter or glucokinase. In addition, several Glc analogs could not mimic the effects of Glc. Our findings suggest that genes encoding some enzymes involved in central carbon metabolism and oxidative phosphorylation are coordinately regulated at the transcriptional level during the switch of nutritional mode.Respiration releases the energy stored in carbon compounds and also provides many carbon precursors for the biosynthesis of a wide variety of plant biomolecules, including amino acids, lipids, isoprenoids, and porphyrins. D-Glc (hereafter Glc) is an immediate substrate for the four major respiration processes: glycolysis, the oxidative pentose phosphate (OPP) pathway, the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation. In plants, respiration is predominantly controlled by the key metabolites ADP and inorganic phosphate, and the ratio of NADPH to NADP 1 . The cellular concentration of ADP initially controls the rates of electron transfer and ATP synthesis, which in turn affect TCA cycle activity, finally resulting in the regulation of glycolytic reactions.

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“…The major problem related to such microarray platforms is the huge complexity of the system. [68,97,124,152,167,199]. Furthermore, PCR products can be used as probes for the functional gene arrays [31,191].…”

Section: Genome Fragmentsmentioning

confidence: 99%

“…Consequently, targets are derived from mRNA. Initial studies were limited to an organism or tissue of interest and provided insights in particular aspects of the organism s physiology [68,152,167,199]. For these studies, probes representing the genetic profile of organism or tissue of interest were used (e.g.…”

Section: Gene Expression Studiesmentioning

confidence: 99%

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Introduction to Microarray‐Based Detection Methods

Schrenzel

Kostić²,

Bodrossy

et al. 2009

Detection of Highly Dangerous Pathogens

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Microarrays consist of an orderly arrangement of probes (oligonucleotides, DNA fragments, proteins, sugars or lectins) attached to a solid surface. The main advantages of microarray technology are high throughput, parallelism, miniaturization, speed and automation. Despite the fact that microarray analysis is a relatively novel technology, with the publication of the first microarray studies in 1995 [101,152], it is now broadly applied and the milestone of nearly 5000 published microarray papers was recorded in 2004 [80]. The scientific and technological background discussed here will be limited to DNA microarrays, excluding the new evolving fields of protein microarrays and glycomics [140].Analogous to antigen-antibody interactions on immunoarrays, DNA microarrays rely on sequence complementarity of the two strands. They put in practice the fundamentals of complementary base-pairing (hybridization) that were first described by Ed Southern [162]. In general, the strategy of microarray hybridization is reversed to that of a standard dot-blot, leading to recurring confusion in the nomenclature. Therefore, it has been suggested to describe tethered nucleic acid as the probe and free nucleic acid as the target [134].Earlier studies on duplex melting and reformation, carried out on DNA solutions, have provided the basic knowledge about the reaction kinetics. Furthermore, a method for computational determination of the melting point as a function of nucleic acid composition and salt concentration was established [6,148,149]. Much of the pioneering work can be linked to the use of nitrocellulose membranes [69], dot-blots [84] and Southern blots [162]. Development of cDNA or oligonucleotide arrays was possible by combined innovations in micro-engineering, molecular biology [33,120,123,156,163,164] and bioinformatics [59]. The real breakthrough in microarray technology was initiated by two key innovations: the use of non-porous solid supports (such as glass and silicon) and the development of methods for highdensity synthesis of oligonucleotides directly onto the microarray surface [59].

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Genome-Wide Dynamic Transcriptional Profiling of the Light-to-Dark Transition inSynechocystissp. Strain PCC 6803

Cited by 99 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

Transcriptional Regulation of the Respiratory Genes in the CyanobacteriumSynechocystissp. PCC 6803 during the Early Response to Glucose Feeding

Introduction to Microarray‐Based Detection Methods

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