scholarly journals Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Rajib Saha ◽  
Deng Liu ◽  
Allison Hoynes-O’Connor ◽  
Michelle Liberton ◽  
Jingjie Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dark Period ◽  
Expression Patterns ◽  
Light Period ◽  
Transcriptional Analysis ◽  
Transcriptional Networks ◽  
Diurnal Changes ◽  
Cellular Processes ◽  
Diurnal Behavior ◽  
Pcc 6803

ABSTRACT Synechocystis sp. strain PCC 6803 is the most widely studied model cyanobacterium, with a well-developed omics level knowledgebase. Like the lifestyles of other cyanobacteria, that of Synechocystis PCC 6803 is tuned to diurnal changes in light intensity. In this study, we analyzed the expression patterns of all of the genes of this cyanobacterium over two consecutive diurnal periods. Using stringent criteria, we determined that the transcript levels of nearly 40% of the genes in Synechocystis PCC 6803 show robust diurnal oscillating behavior, with a majority of the transcripts being upregulated during the early light period. Such transcripts corresponded to a wide array of cellular processes, such as light harvesting, photosynthetic light and dark reactions, and central carbon metabolism. In contrast, transcripts of membrane transporters for transition metals involved in the photosynthetic electron transport chain (e.g., iron, manganese, and copper) were significantly upregulated during the late dark period. Thus, the pattern of global gene expression led to the development of two distinct transcriptional networks of coregulated oscillatory genes. These networks help describe how Synechocystis PCC 6803 regulates its metabolism toward the end of the dark period in anticipation of efficient photosynthesis during the early light period. Furthermore, in silico flux prediction of important cellular processes and experimental measurements of cellular ATP, NADP(H), and glycogen levels showed how this diurnal behavior influences its metabolic characteristics. In particular, NADPH/NADP + showed a strong correlation with the majority of the genes whose expression peaks in the light. We conclude that this ratio is a key endogenous determinant of the diurnal behavior of this cyanobacterium. IMPORTANCE Cyanobacteria are photosynthetic microbes that use energy from sunlight and CO 2 as feedstock. Certain cyanobacterial strains are amenable to facile genetic manipulation, thus enabling synthetic biology and metabolic engineering applications. Such strains are being developed as a chassis for the sustainable production of food, feed, and fuel. To this end, a holistic knowledge of cyanobacterial physiology and its correlation with gene expression patterns under the diurnal cycle is warranted. In this report, a genomewide transcriptional analysis of Synechocystis PCC 6803, the most widely studied model cyanobacterium, sheds light on the global coordination of cellular processes during diurnal periods. Furthermore, we found that, in addition to light, the redox level of NADP(H) is an important endogenous regulator of diurnal entrainment of Synechocystis PCC 6803.

scholarly journals Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Shauna Kehoe ◽  
Katarina Jewgenow ◽  
Paul R. Johnston ◽  
Susan Mbedi ◽  
Beate C. Braun
Keyword(s):  
Gene Expression ◽  
Transforming Growth Factor ◽  
Ovarian Follicle ◽  
Mammalian Species ◽  
Expression Patterns ◽  
Ovarian Follicles ◽  
Domestic Cat ◽  
Transcriptional Analysis ◽  
Ovarian Folliculogenesis

AbstractIn vitro growth (IVG) of dormant primordial ovarian follicles aims to produce mature competent oocytes for assisted reproduction. Success is dependent on optimal in vitro conditions complemented with an understanding of oocyte and ovarian follicle development in vivo. Complete IVG has not been achieved in any other mammalian species besides mice. Furthermore, ovarian folliculogenesis remains sparsely understood overall. Here, gene expression patterns were characterised by RNA-sequencing in primordial (PrF), primary (PF), and secondary (SF) ovarian follicles from Felis catus (domestic cat) ovaries. Two major transitions were investigated: PrF-PF and PF-SF. Transcriptional analysis revealed a higher proportion in gene expression changes during the PrF-PF transition. Key influencing factors during this transition included the interaction between the extracellular matrix (ECM) and matrix metalloproteinase (MMPs) along with nuclear components such as, histone HIST1H1T (H1.6). Conserved signalling factors and expression patterns previously described during mammalian ovarian folliculogenesis were observed. Species-specific features during domestic cat ovarian folliculogenesis were also found. The signalling pathway terms “PI3K-Akt”, “transforming growth factor-β receptor”, “ErbB”, and “HIF-1” from the functional annotation analysis were studied. Some results highlighted mechanistic cues potentially involved in PrF development in the domestic cat. Overall, this study provides an insight into regulatory factors and pathways during preantral ovarian folliculogenesis in domestic cat.

scholarly journals Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803

BMC Genomics ◽  
2008 ◽  
Vol 9 (1) ◽  
pp. 344 ◽  
Author(s):  
Zhigang Zhang ◽  
Ninad D Pendse ◽  
Katherine N Phillips ◽  
James B Cotner ◽  
Arkady Khodursky
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Sulfur Starvation ◽  
Synechocystis Sp ◽  
Pcc 6803

Diurnal Differences in the Innermost Surface of the S2 Layer in Differentiating Tracheids of Cryptomeria japonica Corresponding to a Light-Dark Cycle

Holzforschung ◽  
2003 ◽  
Vol 57 (6) ◽  
pp. 567-573 ◽  
Author(s):  
Y. Hosoo ◽  
M. Yoshida ◽  
T. Imai ◽  
T. Okuyama
Keyword(s):  
Cryptomeria Japonica ◽  
Dark Period ◽  
Amorphous Material ◽  
Light Period ◽  
Cellulose Microfibrils ◽  
Dark Phase ◽  
Diurnal Changes ◽  
Dark Cycle ◽  
Tangential Strain ◽  
S2 Layer

Summary This paper describes the effect of light on the diurnal change in the innermost surface of developing secondary walls. Cryptomeria japonica D. Don saplings were grown in two growth chambers, in which temperature and relative humidity were kept constant and the light-dark phase of the photoperiod varied. One chamber reproduced the natural light-dark phase, while the other reversed it. Samples of differentiating xylem were collected during the dark period when the tangential strain, used as an index of volumetric changes in differentiating cells, was high, and during the light period when the tangential strain was low. The innermost surface of developing secondary walls in differentiating tracheids was observed by field emission scanning electron microscopy. In the specimens collected during the dark period, amorphous material was observed and the cell wall surface was immunogold-labeled with an anti-glucomannan antiserum. In the specimens collected during the light period, cellulose microfibrils were clearly evident, and amorphous material and immunogold labeling were rarely observed. These results demonstrate that the diurnal changes in the innermost surface of developing secondary walls correspond to the light-dark cycle over 24 h.

scholarly journals Global Gene Expression Profiles of the Cyanobacterium Synechocystis sp. Strain PCC 6803 in Response to Irradiation with UV-B and White Light

2002 ◽  
Vol 184 (24) ◽  
pp. 6845-6858 ◽  
Author(s):  
Lixuan Huang ◽  
Michael P. McCluskey ◽  
Hao Ni ◽  
Robert A. LaRossa
Keyword(s):  
Gene Expression ◽  
Heat Shock ◽  
White Light ◽  
Heat Shock Response ◽  
High Intensity ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Stringent Response ◽  
Shock Response ◽  
Pcc 6803

ABSTRACT We developed a transcript profiling methodology to elucidate expression patterns of the cyanobacterium Synechocystis sp. strain PCC 6803 and used the technology to investigate changes in gene expression caused by irradiation with either intermediate-wavelength UV light (UV-B) or high-intensity white light. Several families of transcripts were altered by UV-B treatment, including mRNAs specifying proteins involved in light harvesting, photosynthesis, photoprotection, and the heat shock response. In addition, UV-B light induced the stringent response in Synechocystis, as indicated by the repression of ribosomal protein transcripts and other mRNAs involved in translation. High-intensity white light- and UV-B-mediated expression profiles overlapped in the down-regulation of photosynthesis genes and induction of heat shock response but differed in several other transcriptional processes including those specifying carbon dioxide uptake and fixation, the stringent response, and the induction profile of the high-light-inducible proteins. These two profile comparisons not only corroborated known physiological changes but also suggested coordinated regulation of many pathways, including synchronized induction of D1 protein recycling and a coupling between decreased phycobilisome biosynthesis and increased phycobilisome degradation. Overall, the gene expression profile analysis generated new insights into the integrated network of genes that adapts rapidly to different wavelengths and intensities of light.

scholarly journals Culturing Synechocystis sp. Strain PCC 6803 with N2and CO2in a Diel Regime Reveals Multiphase Glycogen Dynamics with Low Maintenance Costs

2016 ◽  
Vol 82 (14) ◽  
pp. 4180-4189 ◽  
Author(s):  
S. Andreas Angermayr ◽  
Pascal van Alphen ◽  
Dicle Hasdemir ◽  
Gertjan Kramer ◽  
Muzamal Iqbal ◽  
...  
Keyword(s):  
Large Scale ◽  
Dark Period ◽  
Light Regime ◽  
Light Period ◽  
High Light ◽  
Transcript Analysis ◽  
Biotechnological Applications ◽  
Metabolite Analysis ◽  
Content Type ◽  
Pcc 6803

ABSTRACTInvestigating the physiology of cyanobacteria cultured under a diel light regime is relevant for a better understanding of the resulting growth characteristics and for specific biotechnological applications that are foreseen for these photosynthetic organisms. Here, we present the results of a multiomics study of the model cyanobacteriumSynechocystissp. strain PCC 6803, cultured in a lab-scale photobioreactor in physiological conditions relevant for large-scale culturing. The culture was sparged with N2and CO2, leading to an anoxic environment during the dark period. Growth followed the availability of light. Metabolite analysis performed with1H nuclear magnetic resonance analysis showed that amino acids involved in nitrogen and sulfur assimilation showed elevated levels in the light. Most protein levels, analyzed through mass spectrometry, remained rather stable. However, several high-light-response proteins and stress-response proteins showed distinct changes at the onset of the light period. Microarray-based transcript analysis found common patterns of ∼56% of the transcriptome following the diel regime. These oscillating transcripts could be grouped coarsely into genes that were upregulated and downregulated in the dark period. The accumulated glycogen was degraded in the anaerobic environment in the dark. A small part was degraded gradually, reflecting basic maintenance requirements of the cells in darkness. Surprisingly, the largest part was degraded rapidly in a short time span at the end of the dark period. This degradation could allow rapid formation of metabolic intermediates at the end of the dark period, preparing the cells for the resumption of growth at the start of the light period.IMPORTANCEIndustrial-scale biotechnological applications are anticipated for cyanobacteria. We simulated large-scale high-cell-density culturing ofSynechocystissp. PCC 6803 under a diel light regime in a lab-scale photobioreactor. In BG-11 medium,Synechocystisgrew only in the light. Metabolite analysis grouped the collected samples according to the light and dark conditions. Proteome analysis suggested that the majority of enzyme-activity regulation was not hierarchical but rather occurred through enzyme activity regulation. An abrupt light-on condition induced high-light-stress proteins. Transcript analysis showed distinct patterns for the light and dark periods. Glycogen gradually accumulated in the light and was rapidly consumed in the last quarter of the dark period. This suggests that the circadian clock primed the cellular machinery for immediate resumption of growth in the light.

scholarly journals Transcriptome analysis of sevoflurane exposure effects at the different brain regions

2020 ◽  
Author(s):  
Hiroto Yamamoto ◽  
Yutaro Uchida ◽  
Tomoki Chiba ◽  
Ryota Kurimoto ◽  
Takahide Matsushima ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Ontology ◽  
Neural Development ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Transcriptional Analysis ◽  
Rna Seq ◽  
Ontology Term ◽  
Whole Brain ◽  
Differently Expressed Genes

AbstractBackgroundsSevoflurane is a most frequently used volatile anaesthetics, but its molecular mechanisms of action remain unclear. We hypothesized that specific genes play regulatory roles in whole brain exposed to sevoflurane. Thus, we aimed to evaluate the effects of sevoflurane inhalation and identify potential regulatory genes by RNA-seq analysis.MethodsEight-week old mice were exposed to sevoflurane. RNA from four medial prefrontal cortex, striatum, hypothalamus, and hippocampus were analysed using RNA-seq. Differently expressed genes were extracted. Their gene ontology terms and the transcriptome array data of the cerebral cortex of sleeping mice were analysed using Metascape, and the gene expression patterns were compared. Finally, the activities of transcription factors were evaluated using a weighted parametric gene set analysis (wPGSA). JASPAR was used to confirm the existence of binding motifs in the upstream sequences of the differently expressed genes.ResultsThe gene ontology term enrichment analysis result suggests that sevoflurane inhalation upregulated angiogenesis and downregulated neural differentiation in the whole brain. The comparison with the brains of sleeping mice showed that the gene expression changes were specific to anaesthetized mice. Sevoflurane induced Klf4 upregulation in the whole brain. The transcriptional analysis result suggests that KLF4 is a potential transcriptional regulator of angiogenesis and neural development.ConclusionsKlf4 was upregulated by sevoflurane inhalation in whole brain. KLF4 might promote angiogenesis and cause the appearance of undifferentiated neural cells by transcriptional regulation. The roles of KLF4 might be key to elucidating the mechanisms of sevoflurane induced functional modification in the brain.

scholarly journals Raw sequence to target gene prediction: An integrated inference pipeline for ChIP-seq and RNA-seq datasets

2017 ◽  
Author(s):  
Nisar Wani ◽  
Khalid Raza
Keyword(s):  
Gene Expression ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Expression Patterns ◽  
Dna Binding Proteins ◽  
Gene Expression Patterns ◽  
Rna Seq ◽  
Cellular Processes ◽  
Regulatory Effects

AbstractGene expression patterns determine the manner whereby organisms regulate various cellular processes and therefore their organ functions.These patterns do not emerge on their own, but as a result of diverse regulatory factors such as, DNA binding proteins known as transcription factors (TF), chromatin structure and various other environmental factors. TFs play a pivotal role in gene regulation by binding to different locations on the genome and influencing the expression of their target genes. Therefore, predicting target genes and their regulation becomes an important task for understanding mechanisms that control cellular processes governing both healthy and diseased cells.In this paper, we propose an integrated inference pipeline for predicting target genes and their regulatory effects for a specific TF using next-generation data analysis tools.

scholarly journals A genome-wide transcriptional analysis of morphology determination inCandida albicans

2013 ◽  
Vol 24 (3) ◽  
pp. 246-260 ◽  
Author(s):  
Patricia L. Carlisle ◽  
David Kadosh
Keyword(s):  
Gene Expression ◽  
Fungal Infections ◽  
Transcriptional Profiling ◽  
Expression Patterns ◽  
Global Gene Expression ◽  
Transcriptional Analysis ◽  
Specific Gene ◽  
Genome Wide ◽  
A Genome ◽  
Genetically Manipulated

Candida albicans, the most common cause of human fungal infections, undergoes a reversible morphological transition from yeast to pseudohyphal and hyphal filaments, which is required for virulence. For many years, the relationship among global gene expression patterns associated with determination of specific C. albicans morphologies has remained obscure. Using a strain that can be genetically manipulated to sequentially transition from yeast to pseudohyphae to hyphae in the absence of complex environmental cues and upstream signaling pathways, we demonstrate by whole-genome transcriptional profiling that genes associated with pseudohyphae represent a subset of those associated with hyphae and are generally expressed at lower levels. Our results also strongly suggest that in addition to dosage, extended duration of filament-specific gene expression is sufficient to drive the C. albicans yeast-pseudohyphal-hyphal transition. Finally, we describe the first transcriptional profile of the C. albicans reverse hyphal-pseudohyphal-yeast transition and demonstrate that this transition involves not only down-regulation of known hyphal-specific, genes but also differential expression of additional genes that have not previously been associated with the forward transition, including many involved in protein synthesis. These findings provide new insight into genome-wide expression patterns important for determining fungal morphology and suggest that in addition to similarities, there are also fundamental differences in global gene expression as pathogenic filamentous fungi undergo forward and reverse morphological transitions.

scholarly journals A Receptor-type Guanylyl Cyclase Expression Is Regulated under Circadian Clock in Peripheral Tissues of the Silk Moth

2001 ◽  
Vol 276 (50) ◽  
pp. 46765-46769 ◽  
Author(s):  
Shintarou Tanoue ◽  
Takaaki Nishioka
Keyword(s):  
Gene Expression ◽  
Circadian Clock ◽  
Guanylyl Cyclase ◽  
Dark Period ◽  
Light Period ◽  
Receptor Type ◽  
Circadian Regulation ◽  
Peripheral Tissues ◽  
Silk Moth ◽  
Flight Muscles

The mechanisms by which the circadian clock controls behavior through regulating gene expression in peripheral tissues are largely unknown. Here we demonstrate that the expression of a receptor-type guanylyl cyclase (BmGC-I) from the silk mothBombyx moriis regulated in the flight muscles in a circadian fashion.BmGC-ImRNA was expressed from the end of the light period through the middle of the dark period. BmGC-I protein expression and cGMP levels were high around the initiation of eclosion events at the beginning of the photoperiod. The rhythm of theBmGC-Iand cGMP levels free-ran in constant light and synchronized to the environmental photoperiodic cycle. The circadian regulation of BmGC-I expression was also observed in the legs but not in other tissues examined. BmGC-I therefore represents a circadian output gene that regulates eclosion behavior.

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