scholarly journals Gene co-expression reveals the modularity and integration of C4 and CAM in Portulaca

2021 ◽  
Author(s):  
Ian S Gilman ◽  
Jose J Moreno-Villena ◽  
Zachary R Lewis ◽  
Eric W Goolsby ◽  
Erika J Edwards
Keyword(s):  
Gene Networks ◽  
Carbon Fixation ◽  
Water Status ◽  
Photosynthetic System ◽  
Regulatory Motifs ◽  
Network Analyses ◽  
Gene Modules ◽  
Low Levels ◽  
Angiosperm Species ◽  
Expression Module

C4 and Crassulacean acid metabolism (CAM) have been considered as largely independent photosynthetic adaptations in spite of sharing key biochemical modules. Portulaca is a geographically widespread clade of over 100 annual and perennial angiosperm species that primarily use C4 photosynthesis, but facultatively exhibit CAM when drought stressed, a photosynthetic system known as C4+CAM. It has been hypothesized that C4+CAM is rare because of pleiotropic constraints, but these have not been deeply explored. We generated a chromosome-level genome assembly of P. amilis and sampled mRNA from P. amilis and P. oleracea during CAM induction. Gene co-expression network analyses identified C4 and CAM gene modules shared and unique to both Portulaca species. A conserved CAM module linked phosphoenolpyruvate carboxylase (PEPC) to starch turnover during the day-night transition and was enriched in circadian clock regulatory motifs in the P. amilis genome. Preservation of this co-expression module regardless of water status suggests that Portulaca constitutively operate a weak CAM cycle that is transcriptionally and post-transcriptionally upregulated during drought. C4 and CAM mostly used mutually exclusive paralogs for primary carbon fixation and, although it is likely that nocturnal CAM malate stores are shuttled into diurnal C4 decarboxylation pathways, we find some evidence that metabolite cycling may occur at low levels. C4 likely evolved in Portulaca through co-option of redundant paralogs and integration of the diurnal portion of CAM. Thus, the ancestral CAM system did not strongly constrain C4 evolution because photosynthetic gene networks are not co-regulated for both daytime and nighttime functions.

scholarly journals Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1744
Author(s):  
Stefania Pilati ◽  
Giulia Malacarne ◽  
David Navarro-Payá ◽  
Gabriele Tomè ◽  
Laura Riscica ◽  
...  
Keyword(s):  
Gene Networks ◽  
Functional Characterization ◽  
Gene Families ◽  
Stilbene Synthase ◽  
Breeding Programs ◽  
Transcriptomic Data ◽  
Network Analyses ◽  
Manual Curation ◽  
Inference Methods

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.

Effects of frozen storage duration and soil temperature on the stomatal conductance and net photosynthesis of Piceaglauca seedlings

1993 ◽  
Vol 23 (12) ◽  
pp. 2459-2466 ◽  
Author(s):  
George J. Harper ◽  
Edith L. Camm
Keyword(s):  
Stomatal Conductance ◽  
Soil Temperature ◽  
Carbon Fixation ◽  
Frozen Storage ◽  
Net Photosynthesis ◽  
Storage Duration ◽  
Growing Period ◽  
Soil Temperatures ◽  
Low Levels ◽  
And Storage

Nursery grown seedlings of Piceaglauca (Moench) Voss were stored frozen in the dark from approximately 10–31 weeks, thawed and grown for 28 days in a growth chamber at three soil temperatures (3, 7, and 11 °C). During the growing period gas exchange measurements were made every three days. Seedling net photosynthesis (pn) and stomatal conductance (gs) showed significant interactions between soil temperature and storage duration treatments. Soil temperature did not affect seedling gs or pn, though the degree and extent of storage duration effects were dependent on soil temperature. Recovery of gs occurred over a 4–7 day period from low levels after planting. Seedlings stored longer than 22 weeks showed lower rates of pn, than those stored for shorter durations. The lower pn in long-stored seedlings did not result from stomatal limitations to carbon fixation, as gs increased in seedlings stored >22 weeks.

scholarly journals Photosynthesis by Thin Leaf Slices in Solution II. Osmotic Stress and Its Effects on Photosynthesis

1973 ◽  
Vol 26 (1) ◽  
pp. 25 ◽  
Author(s):  
HG Jones
Keyword(s):  
Sodium Chloride ◽  
Osmotic Stress ◽  
Ethylene Glycol ◽  
Carbon Fixation ◽  
Water Status ◽  
Cotton Leaf ◽  
Relative Importance ◽  
Tissue Water

The effects of osmotic stresses on photosynthetic 14C02 fixation by cotton leaf slices were investigated. Using mannitol and sodium chloride as examples of osmotica which entered leaf cells fairly slowly, and ethylene glycol as a rapidly permeating osmoticum, the relative importance of different components of tissue water status in inhibiting carbon fixation was studied.

Cortical Intracellular Electrical Potential in Roots of Unstressed and Stressed Sunflower Seedlings. I. Dependence on Water Status

1997 ◽  
Vol 24 (5) ◽  
pp. 643 ◽  
Author(s):  
P. M. Cortes
Keyword(s):  
Water Stress ◽  
Helianthus Annuus ◽  
Nutrient Solution ◽  
Lateral Root ◽  
Water Status ◽  
Electrical Potential ◽  
Cortical Cells ◽  
Seedling Roots ◽  
Low Levels ◽  
Intact Roots

The intracellular electrical potential (Ec) was measured with a microelectrode in cortical cells of intact roots of sunflower (Helianthus annuus) seedlings subjected to differing levels of water stress and illumination. Water stress was rapidly imposed and relieved by lowering and raising the level of nutrient solution in a tank which contained all the seedling roots except the lateral root in which Ec was measured. The base value of Ec for unstressed, illuminated seedlings was –120 mV. When placed in the dark, a small reversible depolarisation of approximately 10 mV could be measured in roots of seedlings grown under low levels of radiation but was not evident in seedlings grown under high levels of radiation. The imposition of and relief from extreme water stress (leaves and apex severely wilted) resulted in a reversible depolarisation of approximately 50 mV. The effect of water stress was greatly reduced by the presence of sucrose and glucose in the nutrient solution perfusing the 30 mm portion of the lateral root in which Ec was measured. It appears likely that the variation in potential was mediated by a reduction in the supply of photosynthate to the roots.

Macromolecular dynamics of the photosynthetic system over a seasonal developmental progression in Spartina alterniflora

2007 ◽  
Vol 85 (5) ◽  
pp. 476-483 ◽  
Author(s):  
Andrea J. Morash ◽  
Douglas A. Campbell ◽  
Robert J. Ireland
Keyword(s):  
Spartina Alterniflora ◽  
Cross Sections ◽  
Metabolic Flux ◽  
Carbon Fixation ◽  
Ribulose Bisphosphate Carboxylase ◽  
Bisphosphate Carboxylase ◽  
Photosynthetic System ◽  
Antenna Performance ◽  
Developmental Progression ◽  
Ribulose Bisphosphate Carboxylase Oxygenase

Spartina alterniflora Loisel. is a dominant primary producer in salt marsh intertidal zones along the Bay of Fundy of New Brunswick and Nova Scotia, Canada, where it has a 5-month growing season from May to September. We quantified key subunits of the S. alterniflora photosynthetic system (chlorophyll, PsbA, PsaC, AtpB, RbcL) over a seasonal developmental progression to determine resource allocations and estimate capacities for key subprocesses of photosynthesis catalyzed by light-harvesting antennae, photosystems I and II (PSI and PSII, respectively), ATP (adenosine triphosphate) synthase, and RuBisCO (ribulose bisphosphate carboxylase–oxygenase). Early in the season, all of the macromolecules peaked in concentration around day 159, but then declined as leaves elongated. Later in the season, just after flowering, chlorophyll b, PsbA, PsaC, and AtpB peaked again before declining at the end of the season. RbcL, however, did not exhibit a second late-season peak, but continually declined from the early-season peak. Estimates of metabolic flux per PSII and per RuBisCO were closely parallel until late in the season, indicating coordinated regulation of catalytic turnover per complex. Early in the season, carbon fixation per RuBisCO peaked near the expected turnover rate (kcat) for a C4 plant, but then declined. The effective absorbance cross sections of PSII varied seasonally, reflecting significant regulation of antenna performance across the season.

scholarly journals Identification and Functional Annotation of Genes Related to Horses’ Performance: From GWAS to Post-GWAS

Animals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 1173
Author(s):  
Thayssa O. Littiere ◽  
Gustavo H. F. Castro ◽  
Maria del Pilar R. Rodriguez ◽  
Cristina M. Bonafé ◽  
Ana F. B. Magalhães ◽  
...  
Keyword(s):  
Systematic Review ◽  
Transcription Factors ◽  
Candidate Genes ◽  
Gene Networks ◽  
Actin Polymerization ◽  
Biological Processes ◽  
Network Analyses ◽  
Arterial Blood ◽  
Gene Network Analysis ◽  
Genetic Mechanisms

Integration of genomic data with gene network analysis can be a relevant strategy for unraveling genetic mechanisms. It can be used to explore shared biological processes between genes, as well as highlighting transcription factors (TFs) related to phenotypes of interest. Unlike other species, gene–TF network analyses have not yet been well applied to horse traits. We aimed to (1) identify candidate genes associated with horse performance via systematic review, and (2) build biological processes and gene–TF networks from the identified genes aiming to highlight the most candidate genes for horse performance. Our systematic review considered peer-reviewed articles using 20 combinations of keywords. Nine articles were selected and placed into groups for functional analysis via gene networks. A total of 669 candidate genes were identified. From that, gene networks of biological processes from each group were constructed, highlighting processes associated with horse performance (e.g., regulation of systemic arterial blood pressure by vasopressin and regulation of actin polymerization and depolymerization). Transcription factors associated with candidate genes were also identified. Based on their biological processes and evidence from the literature, we identified the main TFs related to horse performance traits, which allowed us to construct a gene–TF network highlighting TFs and the most candidate genes for horse performance.

scholarly journals Genome-wide expression of the residual lung reacting to experimental Pneumonectomy

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Valerio Napolioni ◽  
Fortunato Bianconi ◽  
Rossella Potenza ◽  
Francesco M. Carpi ◽  
Vienna Ludovini ◽  
...  
Keyword(s):  
Gene Networks ◽  
Expression Patterns ◽  
Specific Gene ◽  
Swine Model ◽  
Rna Seq ◽  
Network Analyses ◽  
Genome Wide ◽  
Significant Enrichment ◽  
Transcriptome Expression ◽  
Left Pneumonectomy

Abstract Background Acute or chronic irreversible respiratory failure may occur in patients undergoing pneumonectomy. Aim of this study was to determine transcriptome expression changes after experimental pneumonectomy in swine model. Experimental left pneumonectomy was performed in five pigs under general anaesthesia. Both the resected and the remaining lung, after 60 post-operative completely uneventful days, underwent genome-wide bulk RNA-Sequencing (RNA-Seq). Results Histological analysis showed dilation of air spaces and rupture of interalveolar septa. In addition, mild inflammation, no fibrosis, radial stretch of the bronchus, strong enlargement of airspaces and thinning of the blood supply were observed. Bioinformatic analyses of bulk RNA-Seq data identified 553 Differentially Expressed Genes (DEGs) at adjusted P-value below 0.001, between pre- and post-pneumonectomy. The top 10 up-regulated DEGs were Edn1, Areg, Havcr2, Gadd45g, Depp1, Cldn4, Atf3, Myc, Gadd45b, Socs3; the top 10 down-regulated DEGs were Obscn, Cdkn2b, ENSSSCG00000015738, Prrt2, Amer1, Flrt3, Efnb2, Tox3, Znf793, Znf365. Leveraging digital cytometry tools, no difference in cellular abundance was found between the two experimental groups, while the analysis of cell type-specific gene expression patterns highlighted a striking predominance of macrophage-specific genes among the DEGs. DAVID-based gene ontology analysis showed a significant enrichment of “Extrinsic apoptotic signaling pathway” (FDR q = 7.60 × 10− 3) and “Response to insulin” (FDR q = 7.60 × 10− 3) genes, along with an enrichment of genes involved as “Negative regulators of DDX58/IFIH1 signaling” (FDR q = 7.50 × 10− 4) found by querying the REACTOME pathway database. Gene network analyses indicated a general dysregulation of gene inter-connections. Conclusion This translational genomics study highlighted the existence both of individual genes, mostly dysregulated in certain cellular populations (e.g., macrophages), and gene-networks involved in pulmonary reaction after left pneumonectomy. Their involvement in lung homeostasis is largely supported by previous studies, carried out both in humans and in other animal models (under homeostatic or disease-related conditions), that adopted candidate-gene approaches. Overall, the present findings represent a preliminary assessment for future, more focused, studies on compensatory lung adaptation, pulmonary regeneration and functional reload.

scholarly journals Exploring Biomarkers Related to Autophagy in Alzheimer's Disease Based on Pathway Crosstalk Analysis

2021 ◽  
Author(s):  
Fang Qian ◽  
Wei Kong ◽  
Shuaiqun Wang
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Single Gene ◽  
Therapeutic Targets ◽  
Clinical Information ◽  
Analysis Method ◽  
Pathway Crosstalk ◽  
Pathological Mechanism ◽  
Gene Modules ◽  
Expression Module

Abstract The pathological mechanism of Alzheimer's disease (AD) involves multiple pathways, and the crosstalk between autophagy and other pathways plays an increasingly prominent role in AD. However, current methods are primarily based on single-gene analysis or a single signal pathway to find therapeutic targets for AD, which are somewhat limited. The aim of our study is to identify autophagy-related biomarkers in AD based on the crosstalk between autophagy and other pathways. The pathway analysis method (PAGI) was applied to find the feature mRNAs involved in the crosstalk between autophagy and many other AD-related pathways. Then, the weighted gene co-expression network analysis (WGCNA) was used to construct a co-expression module of feature mRNAs and differential lncRNAs. Finally, clinical information was used to screen the biomarkers related to the prognosis of AD in the co-expressed gene modules. The experiment finally identified 8 mRNAs and 2 lncRNAs (TLN1, ARRB1, FZD4, AKT1, JMJD7-PLA2G4B, STAT5A, SMAD7, ZNF274; AC113349.1, AC015878.2) as biomarkers of AD, and they all interact directly or indirectly with autophagy. In summary, we provide an effective method for extracting autophagy-related biomarkers based on pathway crosstalk in AD. This method enriches the therapeutic targets of AD and provides new insights into the molecular mechanism of autophagy in AD.

scholarly journals PhytoNet: Comparative co-expression network analyses across phytoplankton and land plants

2018 ◽  
Author(s):  
Camilla Ferrari ◽  
Sebastian Proost ◽  
Colin Ruprecht ◽  
Marek Mutwil
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Gene Networks ◽  
Photosynthetic Activity ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Land Plants ◽  
Expression Data ◽  
Network Analyses ◽  
Crucial Component

ABSTRACTPhytoplankton consists of autotrophic, photosynthesizing microorganisms that are a crucial component of freshwater and ocean ecosystems. However, despite being the major primary producers of organic compounds, accounting for half of the photosynthetic activity worldwide and serving as the entry point to the food chain, functions of most of the genes of the model phytoplankton organisms remain unknown. To remedy this, we have gathered publicly available expression data for one chlorophyte, one rhodophyte, one haptophyte, two heterokonts and four cyanobacteria and integrated it into our PlaNet (Plant Networks) database, which now allows mining gene expression profiles and identification of co-expressed genes of 19 species. We exemplify how the co-expressed gene networks can be used to reveal functionally related genes and how the comparative features of PhytoNet allow detection of conserved transcriptional programs between cyanobacteria, green algae, and land plants. Additionally, we illustrate how the database allows detection of duplicated transcriptional programs within an organism, as exemplified by two DNA repair programs within Chlamydomonas reinhardtii. PhytoNet is available from www.gene2function.de.

scholarly journals Co-expression network analysis of the genes associated with pistillody-stamen development in wheat

2020 ◽  
Author(s):  
Mingli Liao ◽  
Zhenyong Chen ◽  
Zaijun Yang ◽  
Weiying Chen ◽  
Shuhong Wei ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Network Analysis ◽  
Male Sterility ◽  
Gene Networks ◽  
Theoretical Research ◽  
Ovary Development ◽  
Mads Box ◽  
Stamen Development ◽  
Network Analyses ◽  
Wheat Tissues

Abstract Background: Crop male sterility has great values in both theoretical research and breeding application. Wheat pistillody-stamen is an important male sterility phenomenon, and HTS-1 is an important pistillody-stamen material. However the molecular mechanism of HTS-1 stamens transformed into pistils or pistil-like structures remains a mystery. Weighted gene co-expression network analysis (WGCNA) are widely used to explore hub genes and gene interaction networks from high throughput data in various plants. Results: In the present study, for exploring gene networks associated with wheat pistillody-stamen development, WGCNA was employed to analyze 11 RNA-sequencing (RNA-seq) data of wheat tissues, including stamens of CSTP, pistils and pistillody-stamen of HTS-1. 19 out of 25 merged modules were highly associated with specific wheat tissues, and the MEdarkseagreen1 module was highly related to wheat pistillody-stamen (correlation with weight r =0.7, correlation p-value p =0.02). Then 180 genes about wheat flower development were identified from the MEdarkseagreen1 module by GO term analysis. Among 180 genes, the hub gene number associated with anther, filament, style, and ovary development were 12, 3, 3, and 10, respectively. We compared the published pistillody related proteins with proteins of HTS-1 by BLAST. A total of 58 pistillody-stamen development associated proteins were validated by BLAST. MADS-box and YABBY transcription factor about pistillody-stamen development were also analyzed in wheat flower. There were 47 of MADS-box and 17 of YABBY transcription factors were identified. BLAST program was used to align the published pistillody associated MADS-box and YABBY transcription factors with transcription factors identified in wheat flower. Totally, 36 of 47 MADS-box and 14 of 17 YABBY transcription factors were considered to regulate the development of pistillody-stamen, which had never been reported yet. Conclusion: These results have systematically identified the key candidate genes about the development of HTS-1 substructures flower. The tissue-specific correlation network analyses provide important insights into the molecular interactions underlying psitillody-stamen development.

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