scholarly journals Comparison of gene expression patterns of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) under different light wavelengths and CO2 enrichment

2017 ◽  
Author(s):  
Thien Vun Yee ◽  
Kenneth Francis Rodrigues ◽  
Clemente Michael Wong Vui Ling ◽  
Wilson Yong Thau Lym
Keyword(s):  
Gene Expression ◽  
Carbon Fixation ◽  
Kappaphycus Alvarezii ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
Molecular Evidence ◽  
Limited Information ◽  
Metabolic Pattern ◽  
Regulated Gene Expression

AbstractTranscriptomes associated with the process of photosynthesis and carbon fixation have offered insights into the mechanism of gene regulation in terrestrial plants, however limited information is available as far as macroalgae are concerned. Intertidal red alga, Kappaphycus alvarezii is exposed to different wavelengths of light in their lives as light quantity and quality changes at different depths in seawater. This investigation aims to study the underlying mechanisms associated with photosynthesis and carbon fixation under specific light qualities and CO2 enrichment. Light regulation of gene expression has not been previously described for red algae. By using next generation sequencing, transcriptome profiling of K. alvarezii generated 76,871 qualified transcripts with a mean length of 979bp and a N50 length of 1,707bp and 55.83% transcripts were annotated on the basis of function. Blue, green and red light all have demonstrated roles in modulating light responses, such as changes in gene expression. Here we analysed the effects of light regulation on four selected photosynthesis aspects (light-harvesting complex, phycobilisomes, photosystems and photoreceptors). We observed that light-regulated gene expression in this species is not a single light response and different light qualities are transduced to regulate the same metabolic pattern. The carbon fixation pathway was analysed and key genes encoding enzymes involved in the carbon fixation pathway such as ppc, pepc, prk, pgk, ppdk, provided that unequivocal molecular evidence that most of the C3 and C4 pathway genes were actively transcribed in K. alvarezii. In addition to this the CO2 induced transcriptome suggested the possibility of shifting carbon metabolism pathway after acclimation to increased level of CO2. Impact of CO2 enrichment on the cultures has provided new insight into the response to rising CO2.

scholarly journals Redox and light regulation of gene expression in photosynthetic prokaryotes

2003 ◽  
Vol 358 (1429) ◽  
pp. 147-154 ◽  
Author(s):  
Carl Bauer ◽  
Sylvie Elsen ◽  
Lee R. Swem ◽  
Danielle L. Swem ◽  
Shinji Masuda
Keyword(s):  
Gene Expression ◽  
Blue Light ◽  
Carbon Fixation ◽  
Rhodobacter Capsulatus ◽  
Bacterial Species ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
Disulphide Bond ◽  
Control Synthesis ◽  
Cellular Redox

All photosynthetic organisms control expression of photosynthesis genes in response to alterations in light intensity as well as to changes in cellular redox potential. Light regulation in plants involves a well–defined set of red– and blue–light absorbing photoreceptors called phytochrome and cryptochrome. Less understood are the factors that control synthesis of the plant photosystem in response to changes in cellular redox. Among a diverse set of photosynthetic bacteria the best understood regulatory systems are those synthesized by the photosynthetic bacterium Rhodobacter capsulatus . This species uses the global two–component signal transduction cascade, RegB and RegA, to anaerobically de–repress anaerobic gene expression. Under reducing conditions, the phosphate on RegB is transferred to RegA, which then activates genes involved in photosynthesis, nitrogen fixation, carbon fixation, respiration and electron transport. In the presence of oxygen, there is a second regulator known as CrtJ, which is responsible for repressing photosynthesis gene expression. CrtJ responds to redox by forming an intramolecular disulphide bond under oxidizing, but not reducing, growth conditions. The presence of the disulphide bond stimulates DNA binding activity of the repressor. There is also a flavoprotein that functions as a blue–light absorbing anti–repressor of CrtJ in the related bacterial species Rhodobacter sphaeroides called AppA. AppA exhibits a novel long–lived photocycle that is initiated by blue–light absorption by the flavin. Once excited, AppA binds to CrtJ thereby inhibiting the repressor activity of CrtJ. Various mechanistic aspects of this photocycle will be discussed.

scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
High Light ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background: The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression.Results: Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in not-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 µmol quanta m-2 s-1). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment.Conclusion: A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.

scholarly journals Cell-type Specific Expression Quantitative Trait Loci Associated with Alzheimer Disease in Blood and Brain Tissue

2020 ◽  
Author(s):  
Devanshi Patel ◽  
Xiaoling Zhang ◽  
John J. Farrell ◽  
Jaeyoon Chung ◽  
Thor D. Stein ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quantitative Trait ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Cell Types ◽  
Eqtl Analysis ◽  
Cell Type ◽  
Specific Expression ◽  
Cell Type Specific Expression ◽  
Cell Type Specific

ABSTRACTBecause regulation of gene expression is heritable and context-dependent, we investigated AD-related gene expression patterns in cell-types in blood and brain. Cis-expression quantitative trait locus (eQTL) mapping was performed genome-wide in blood from 5,257 Framingham Heart Study (FHS) participants and in brain donated by 475 Religious Orders Study/Memory & Aging Project (ROSMAP) participants. The association of gene expression with genotypes for all cis SNPs within 1Mb of genes was evaluated using linear regression models for unrelated subjects and linear mixed models for related subjects. Cell type-specific eQTL (ct-eQTL) models included an interaction term for expression of “proxy” genes that discriminate particular cell type. Ct-eQTL analysis identified 11,649 and 2,533 additional significant gene-SNP eQTL pairs in brain and blood, respectively, that were not detected in generic eQTL analysis. Of note, 386 unique target eGenes of significant eQTLs shared between blood and brain were enriched in apoptosis and Wnt signaling pathways. Five of these shared genes are established AD loci. The potential importance and relevance to AD of significant results in myeloid cell-types is supported by the observation that a large portion of GWS ct-eQTLs map within 1Mb of established AD loci and 58% (23/40) of the most significant eGenes in these eQTLs have previously been implicated in AD. This study identified cell-type specific expression patterns for established and potentially novel AD genes, found additional evidence for the role of myeloid cells in AD risk, and discovered potential novel blood and brain AD biomarkers that highlight the importance of cell-type specific analysis.

scholarly journals A Large Scale Genetic Analysis of c-Myc-regulated Gene Expression Patterns

2003 ◽  
Vol 278 (14) ◽  
pp. 12563-12573 ◽  
Author(s):  
Brenda C. O'Connell ◽  
Ann F. Cheung ◽  
Carl P. Simkevich ◽  
Wanny Tam ◽  
Xiaojia Ren ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Analysis ◽  
Large Scale ◽  
Expression Patterns ◽  
Gene Expression Patterns ◽  
Regulated Gene Expression

scholarly journals Comparative Genomics and Transcriptomics To Analyze Fruiting Body Development in Filamentous Ascomycetes

Genetics ◽  
2019 ◽  
Vol 213 (4) ◽  
pp. 1545-1563 ◽  
Author(s):  
Ramona Lütkenhaus ◽  
Stefanie Traeger ◽  
Jan Breuer ◽  
Laia Carreté ◽  
Alan Kuo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Fruiting Body ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Comparative Transcriptomics ◽  
Fruiting Bodies ◽  
Body Development ◽  
Fruiting Body Development ◽  
Genes Encoding

Many filamentous ascomycetes develop three-dimensional fruiting bodies for production and dispersal of sexual spores. Fruiting bodies are among the most complex structures differentiated by ascomycetes; however, the molecular mechanisms underlying this process are insufficiently understood. Previous comparative transcriptomics analyses of fruiting body development in different ascomycetes suggested that there might be a core set of genes that are transcriptionally regulated in a similar manner across species. Conserved patterns of gene expression can be indicative of functional relevance, and therefore such a set of genes might constitute promising candidates for functional analyses. In this study, we have sequenced the genome of the Pezizomycete Ascodesmis nigricans, and performed comparative transcriptomics of developing fruiting bodies of this fungus, the Pezizomycete Pyronema confluens, and the Sordariomycete Sordaria macrospora. With only 27 Mb, the A. nigricans genome is the smallest Pezizomycete genome sequenced to date. Comparative transcriptomics indicated that gene expression patterns in developing fruiting bodies of the three species are more similar to each other than to nonsexual hyphae of the same species. An analysis of 83 genes that are upregulated only during fruiting body development in all three species revealed 23 genes encoding proteins with predicted roles in vesicle transport, the endomembrane system, or transport across membranes, and 13 genes encoding proteins with predicted roles in chromatin organization or the regulation of gene expression. Among four genes chosen for functional analysis by deletion in S. macrospora, three were shown to be involved in fruiting body formation, including two predicted chromatin modifier genes.

scholarly journals Global Regulation of Gene Expression and Cell Differentiation in Caulobacter crescentus in Response to Nutrient Availability

2009 ◽  
Vol 192 (3) ◽  
pp. 819-833 ◽  
Author(s):  
Jennifer C. England ◽  
Barrett S. Perchuk ◽  
Michael T. Laub ◽  
James W. Gober
Keyword(s):  
Gene Expression ◽  
Nitrogen Limitation ◽  
Caulobacter Crescentus ◽  
Regulation Of Gene Expression ◽  
Fixed Time ◽  
Natural Environments ◽  
Swarmer Cell ◽  
Regulatory Strategies ◽  
Time Period ◽  
Regulated Gene Expression

ABSTRACT In a developmental strategy designed to efficiently exploit and colonize sparse oligotrophic environments, Caulobacter crescentus cells divide asymmetrically, yielding a motile swarmer cell and a sessile stalked cell. After a relatively fixed time period under typical culture conditions, the swarmer cell differentiates into a replicative stalked cell. Since differentiation into the stalked cell type is irreversible, it is likely that environmental factors such as the availability of essential nutrients would influence the timing of the decision to abandon motility and adopt a sessile lifestyle. We measured two different parameters in nutrient-limited chemostat cultures, biomass concentration and the ratio of nonstalked to stalked cells, over a range of flow rates and found that nitrogen limitation significantly extended the swarmer cell life span. The transcriptional profiling experiments described here generate the first comprehensive picture of the global regulatory strategies used by an oligotroph when confronted with an environment where key macronutrients are sparse. The pattern of regulated gene expression in nitrogen- and carbon-limited cells shares some features in common with most copiotrophic organisms, but critical differences suggest that Caulobacter, and perhaps other oligotrophs, have evolved regulatory strategies to deal distinctly with their natural environments. We hypothesize that nitrogen limitation extends the swarmer cell lifetime by delaying the onset of a sequence of differentiation events, which when initiated by the correct combination of external environmental cues, sets the swarmer cell on a path to differentiate into a stalked cell within a fixed time period.

scholarly journals Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence

2008 ◽  
Vol 389 (3) ◽  
pp. 243-255 ◽  
Author(s):  
Kotb Abdelmohsen ◽  
Yuki Kuwano ◽  
Hyeon Ho Kim ◽  
Myriam Gorospe
Keyword(s):  
Oxidative Stress ◽  
Gene Expression ◽  
Cellular Senescence ◽  
Mammalian Cells ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Oxidant Damage ◽  
Regulated Gene Expression

AbstractTo respond adequately to oxidative stress, mammalian cells elicit rapid and tightly controlled changes in gene expression patterns. Besides alterations in the subsets of transcribed genes, two posttranscriptional processes prominently influence the oxidant-triggered gene expression programs: mRNA turnover and translation. Here, we review recent progress in our knowledge of theturnover andtranslationregulatory (TTR) mRNA-bindingproteins (RBPs) that influence gene expression in response to oxidative damage. Specifically, we identify oxidant damage-regulated mRNAs that are targets of TTR-RBPs, we review the oxidant-triggered signaling pathways that govern TTR-RBP function, and we examine emerging evidence that TTR-RBP activity is altered with senescence and aging. Given the potent influence of TTR-RBPs upon oxidant-regulated gene expression profiles, we propose that the senescence-associated changes in TTR-RBPs directly contribute to the impaired responses to oxidant damage that characterize cellular senescence and advancing age.

scholarly journals Regulation of Gene Expression Patterns in Mosquito Reproduction

PLoS Genetics ◽  
2015 ◽  
Vol 11 (8) ◽  
pp. e1005450 ◽  
Author(s):  
Sourav Roy ◽  
Tusar T. Saha ◽  
Lisa Johnson ◽  
Bo Zhao ◽  
Jisu Ha ◽  
...  
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Gene Expression Patterns

scholarly journals CG gene body DNA methylation changes and evolution of duplicated genes in cassava

2015 ◽  
Vol 112 (44) ◽  
pp. 13729-13734 ◽  
Author(s):  
Haifeng Wang ◽  
Getu Beyene ◽  
Jixian Zhai ◽  
Suhua Feng ◽  
Noah Fahlgren ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Gene Copy ◽  
Gene Body ◽  
Duplicated Genes ◽  
Gene Body Methylation ◽  
Substantial Impact ◽  
Tropical Regions

DNA methylation is important for the regulation of gene expression and the silencing of transposons in plants. Here we present genome-wide methylation patterns at single-base pair resolution for cassava (Manihot esculenta, cultivar TME 7), a crop with a substantial impact in the agriculture of subtropical and tropical regions. On average, DNA methylation levels were higher in all three DNA sequence contexts (CG, CHG, and CHH, where H equals A, T, or C) than those of the most well-studied model plant Arabidopsis thaliana. As in other plants, DNA methylation was found both on transposons and in the transcribed regions (bodies) of many genes. Consistent with these patterns, at least one cassava gene copy of all of the known components of Arabidopsis DNA methylation pathways was identified. Methylation of LTR transposons (GYPSY and COPIA) was found to be unusually high compared with other types of transposons, suggesting that the control of the activity of these two types of transposons may be especially important. Analysis of duplicated gene pairs resulting from whole-genome duplication showed that gene body DNA methylation and gene expression levels have coevolved over short evolutionary time scales, reinforcing the positive relationship between gene body methylation and high levels of gene expression. Duplicated genes with the most divergent gene body methylation and expression patterns were found to have distinct biological functions and may have been under natural or human selection for cassava traits.

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