scholarly journals Comparative transcriptome analysis of differentially expressed genes related to the physiological changes of yellow-green leaf mutant of maize

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10567
Author(s):  
Tingchun Li ◽  
Huaying Yang ◽  
Yan Lu ◽  
Qing Dong ◽  
Guihu Liu ◽  
...  

Chlorophylls, green pigments in chloroplasts, are essential for photosynthesis. Reduction in chlorophyll content may result in retarded growth, dwarfism, and sterility. In this study, a yellow-green leaf mutant of maize, indicative of abnormity in chlorophyll content, was identified. The physiological parameters of this mutant were measured. Next, global gene expression of this mutant was determined using transcriptome analysis and compared to that of wild-type maize plants. The yellow-green leaf mutant of maize was found to contain lower contents of chlorophyll a, chlorophyll b and carotenoid compounds. It contained fewer active PSII centers and displayed lower values of original chlorophyll fluorescence parameters than the wild-type plants. The real-time fluorescence yield, the electron transport rate, and the net photosynthetic rate of the mutant plants showed reduction as well. In contrast, the maximum photochemical quantum yield of PSII of the mutant plants was similar to that of the wild-type plants. Comparative transcriptome analysis of the mutant plants and wild-type plants led to the identification of differentially expressed 1,122 genes, of which 536 genes were up-regulated and 586 genes down-regulated in the mutant. Five genes in the chlorophyll metabolism pathway, nine genes in the tricarboxylic acid cycle and seven genes related to the conversion of sucrose to starch displayed down-regulated expression. In contrast, genes encoding a photosystem II reaction center PsbP family protein and the PGR5-like protein 1A (PGRL1A) exhibited increased transcript abundance.

2020 ◽  
Author(s):  
Tingchun Li ◽  
Huaying Yang ◽  
Yan Lu ◽  
Qing Dong ◽  
Guihu Liu ◽  
...  

Abstract Background Chlorophylls, green pigments in chloroplasts, are essential for photosynthesis. Reduction in chlorophyll contents may result in retarded growth, dwarfism, and sterility. In this study, a yellow-green leaf mutant of maize, indicative of abnormity in chlorophyll contents, was identified. The physiological parameters of this mutant were measured. Next, global gene expression of this mutant was determined using transcriptome analysis and compared to that of wild-type maize plants. Results The yellow-green leaf mutant of maize was found to contain lower contents of chlorophyll a , chlorophyll b and carotenoid compounds. It contained fewer active PSII centers and displayed lower values of original chlorophyll fluorescence parameters than the wild-type plants. The real-time fluorescence yield, the electron transport rate, and the net photosynthetic rate of the mutant plants showed reduction as well. In contrast, the maximum photochemical quantum yield of PSII of the mutant plants was similar to that of the wild-type plants. Comparative transcriptomic analysis of the mutant plants and wild-type plants led to the identification of differentially expressed1122 genes, of which 536 genes were up-regulated and 586 genes down-regulated in the mutant. Five genes in chlorophyll metabolism pathway, nine genes in the tricarboxylic acid cycle and seven genes related to the conversion of sucrose to starch displayed down-regulated expression. In contrast, genes encoding a photosystem II reaction center PsbP family protein and the PGR5-like protein 1A (PGRL1A) exhibited increased transcript abundance. Conclusions The yellow-green leaf mutant of maize contained fewer active PSII centers with lowered net photosynthesis rate, but have the similar value of the maximum photochemical quantum yield of PSII with that of the wild-type plants. Analysis of differentially expressed genes through transcriptome analysis revealed the down-regulated genes which may be responsible for chlorophyll deduction and changes of photosynthetic characteristics. The up-regulated genes would be helpful to maintain the active PSII centers of the yellow-green leaf mutant.


Blood ◽  
2018 ◽  
Vol 132 (Supplement 1) ◽  
pp. 2368-2368
Author(s):  
Sueli Matilde da Silva Costa ◽  
Mirta Tomie Ito ◽  
Bruno Batista Souza ◽  
Pedro Rodrigues Souza Cruz ◽  
Letícia de Carvalho Bapista ◽  
...  

Abstract Retinopathy is one of the major clinical manifestations of sickle cell disease. Its clinical aspects vary depending on the presence or absence of vaso-proliferation, classifying this complication as non-proliferative and proliferative sickle cell retinopathy (PSCR). Endothelial cell activation, injury and dysfunction are importantly involved with pathophysiological mechanisms of sickle cell disease and its complications such as vascular disease. In this study we compared the gene expression profile of endothelial progenitor cells from patients with sickle cell disease and proliferative retinopathy versus without retinopathy. Endothelial Colony-Forming Cells (ECFC) were isolated and cultured from peripheral blood samples of three HbSS patients (Group I) and six HbSC patients (Group II) with proliferative retinopathy as well as from three HbSS patients (Group III) and four HbSC patients (Group IV) without retinopathy. Ophthalmologic evaluation: fundus biomicroscopy, retinal mapping and retinography was performed in all patients. The isolated ECFC were characterized by cobblestone morphology and flow cytometry. RNA was extracted from the cells and transcriptome analysis was performed by next-generation sequencing (RNA-seq). Differentially expressed genes were identified through DESeq2 package. Comparative transcriptome analysis between groups I and III has identified 16 differentially expressed transcripts, 10 negatively regulated and 5 positively regulated. Among these genes, we highlight the most upregulated genes, CDCP1 and NR5A2.The expression of CDCP1 (log2FoldChange = 3,712 and padj value = 0.007) and NR5A2 (log2FoldChange = 3,021 and padj value = 0.019) genes was higher in HbSS patients with PSCR than in patients without retinopathy.On the other side, comparative transcriptome analysis between groups II and IV has identified 34 differentially expressed transcripts, 24 negatively regulated and 10 positively regulated. Among these genes, we highlight the most upregulated genes, ROBO1 and SLC38A5. Importantly, the expression of ROBO1 (log2FoldChange = 4,325 and padj value = 1,35E-11)and SLC38A5 (log2FoldChange = 3,364 and padj value = 1,59E-07)genes was significantly higher in HbSC patients with PSCR than in patients without retinopathy. CDCP1 has been proposed to play a role in regulation of cell differentiation and proliferation through interactions with extracellular matrix.NR5A2 is a constitutively active orphan nuclear receptor. Some of the pathways regulated by nuclear receptors includeangiogenesis, inflammation, and lipid metabolic dysregulation, mechanisms also important in the initiation and development of several retinal diseases.The ROBO1-mediated pathway has been proposed as a target for the treatment of several ocular neovascular diseases. The SLC38A5 gene is the principal mediator of glutamine transport in retinal Müller cells. Since glutamine metabolism is crucial for vessel formation, the blockage of SLC38A5 transporter deserves further attention as an alternative strategy to the inhibition of pathological angiogenesis. Our data suggest that specific pathways can be involved in PSCR of SS and SC hemoglobinopathies. Treatment for PSCR remains palliative, so therapeutic strategies blocking these pathways may contribute to the future development of novel therapies. Disclosures Ozelo: BioMarin: Honoraria, Speakers Bureau; Grifols: Honoraria; Novo Nordisk: Honoraria, Research Funding, Speakers Bureau; Pfizer: Honoraria, Research Funding, Speakers Bureau; Shire: Honoraria, Research Funding, Speakers Bureau; Bioverativ: Honoraria, Research Funding.


2021 ◽  
Vol 12 ◽  
Author(s):  
Xu Qian ◽  
Hui Jin ◽  
Zhuojun Chen ◽  
Qingqing Dai ◽  
Surendra Sarsaiya ◽  
...  

Trichoderma longibrachiatum MD33, a sesquiterpene alkaloid-producing endophyte isolated from Dendrobium nobile, shows potential medical and industrial applications. To understand the molecular mechanisms of sesquiterpene alkaloids production, a comparative transcriptome analysis was performed on strain MD33 and its positive mutant UN32, which was created using Ultraviolet (UV) mutagenesis and nitrogen ion (N+) implantation. The alkaloid production of UN32 was 2.62 times more than that of MD33. One thousand twenty-four differentially expressed genes (DEGs), including 519 up-regulated and 505 down-regulated genes, were identified. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed 139 GO terms and 87 biosynthesis pathways. Dendrobine, arguably the main sesquiterpene alkaloid the strain MD33 produced, might start synthesis through the mevalonate (MVA) pathway. Several MVA pathway enzyme-coding genes (hydroxy-methylglutaryl-CoA synthase, mevalonate kinase, and farnesyl diphosphate synthase) were found to be differentially expressed, suggesting that physical mutagenesis can disrupt genome integrity and gene expression. Some backbone post-modification enzymes and transcript factors were either discovered, suggesting the sesquiterpene alkaloid metabolism in T. longibrachiatum is a complex genetic network. Our findings help to shed light on the underlying molecular regulatory mechanism of sesquiterpene alkaloids production in T. longibrachiatum.


2020 ◽  
Author(s):  
Hongrui Lv ◽  
Jing Xu ◽  
Tao Bo ◽  
Wei Wang

Abstract BackgroundCadmium (Cd) is a nonessential heavy metal with potentially deleterious effects on different organisms. The organisms have evolved sophisticated defense system to alleviate heavy metal toxicity. Hydrogen sulfide (H2S) effectively alleviates heavy metal toxicity in plants. However, the function of H2S for alleviating heavy metal toxicity in aquatic organisms remains less clear. Tetrahymena thermophila is an important model organism to evaluate toxic contaminants in an aquatic environment. In this study, the molecular roles of exogenously H2S application were explored by RNA sequencing under Cd stress in T. thermophila.ResultsThe exposure of 30 µM Cd resulted in T. thermophila growth inhibition, cell nigrescence, and malondialdehyde (MDA) content considerably increase. However, exogenous H2S (70 µM) significantly alleviated the Cd-induced toxicity and improved antioxidant system. Comparative transcriptome analysis showed that the expression levels of 9152 genes changed under Cd stress (4658 upregulated and 4494 downregulated). However, only 1359 genes were differentially expressed with H2S treatment under Cd stress (1087 upregulated and 272 downregulated). The functional categories of the differentially expressed genes (DEGs) by gene ontology (GO) revealed that the transcripts involved in the oxidation–reduction process, oxidoreductase activity, glutathione peroxidase activity, and cell redox homeostasis were the considerable enrichments between Cd stress and H2S treatment under Cd stress. Kyoto Encyclopedia of Genes and Genomes (KEGG) indicated that the carbon metabolism, glutathione metabolism, metabolism of xenobiotics by cytochrome P450, and ABC transporters were significantly differentially expressed components between Cd stress and H2S treatment under Cd stress in T. thermophila. The relative expression levels of six DEGs were further confirmed through quantitative real-time polymerase chain reaction (qRT-PCR).ConclusionH2S alleviated Cd stress mainly through increasing oxidation resistance, enhancing detoxification, and regulation of transport in free-living unicellular T. thermophila. These findings will expand our understanding for H2S functions in the freshwater protozoa.


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