scholarly journals The Coordinated Upregulated Expression of Genes Involved in MEP, Chlorophyll, Carotenoid and Tocopherol Pathways, Mirrored the Corresponding Metabolite Contents in Rice Leaves during De-Etiolation

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1456
Author(s):  
Xin Jin ◽  
Can Baysal ◽  
Margit Drapal ◽  
Yanmin Sheng ◽  
Xin Huang ◽  
...  
Keyword(s):  
Higher Plants ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Isoprenoid Biosynthesis ◽  
Promoter Regions ◽  
Expression Of Genes ◽  
Coordinated Expression ◽  
Rice Leaves ◽  
Mechanistic Basis ◽  
Phosphate Synthase

Light is an essential regulator of many developmental processes in higher plants. We investigated the effect of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1/2 genes (OsHDR1/2) and isopentenyl diphosphate isomerase 1/2 genes (OsIPPI1/2) on the biosynthesis of chlorophylls, carotenoids, and phytosterols in 14-day-old etiolated rice (Oyza sativa L.) leaves during de-etiolation. However, little is known about the effect of isoprenoid biosynthesis genes on the corresponding metabolites during the de-etiolation of etiolated rice leaves. The results showed that the levels of α-tocopherol were significantly increased in de-etiolated rice leaves. Similar to 1-deoxy-D-xylulose-5-phosphate synthase 3 gene (OsDXS3), both OsDXS1 and OsDXS2 genes encode functional 1-deoxy-D-xylulose-5-phosphate synthase (DXS) activities. Their expression patterns and the synthesis of chlorophyll, carotenoid, and tocopherol metabolites suggested that OsDXS1 is responsible for the biosynthesis of plastidial isoprenoids in de-etiolated rice leaves. The expression analysis of isoprenoid biosynthesis genes revealed that the coordinated expression of the MEP (2-C-methyl-D-erythritol 4-phosphate) pathway, chlorophyll, carotenoid, and tocopherol pathway genes mirrored the changes in the levels of the corresponding metabolites during de-etiolation. The underpinning mechanistic basis of coordinated light-upregulated gene expression was elucidated during the de-etiolation process, specifically the role of light-responsive cis-regulatory motifs in the promoter region of these genes. In silico promoter analysis showed that the light-responsive cis-regulatory elements presented in all the promoter regions of each light-upregulated gene, providing an important link between observed phenotype during de-etiolation and the molecular machinery controlling expression of these genes.

scholarly journals Genome-Wide Identification of Sultr Genes in Malus domestica and Low Sulfur-Induced MhSultr3;1a to Increase Cysteine-Improving Growth

2021 ◽  
Vol 12 ◽  
Author(s):  
Mi Xun ◽  
Jianfei Song ◽  
Junyuan Shi ◽  
Jiaqi Li ◽  
Yujia Shi ◽  
...  
Keyword(s):  
Malus Domestica ◽  
Higher Plants ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Specific Expression ◽  
Essential Nutrient ◽  
Function Characterization ◽  
Gene Structures ◽  
Low Sulfur

Sulfur is an essential nutrient for plant growth and development. Sulfate transporters (Sultrs) are critical for sulfate (SO42-) uptake from the soil by the roots in higher plants. However, knowledge about Sultrs in apples (Malus domestica) is scarce. Here, nine putative MdSultrs were identified and classified into two groups according to the their phylogenetic relationships, gene structures, and conserved motifs. Various cis-regulatory elements related to abiotic stress and plant hormone responsiveness were found in the promoter regions of MdSultrs. These MdSultrs exhibited tissue-specific expression patterns and responded to low sulfur (S), abscisic acid (ABA), indole-3-acetic acid (IAA), and methyl jasmonate (MeJA), wherein MdSultr3;1a was especially expressed in the roots and induced by low S. The uptake of SO42- in cultivated apples depends on the roots of its rootstock, and MhSultr3;1a was isolated from Malus hupehensis roots used as a rootstock. MhSultr3;1a shared 99.85% homology with MdSultr3;1a and localized on the plasma membrane and nucleus membrane. Further function characterization revealed that MhSultr3;1a complemented an SO42- transport-deficient yeast mutant and improved the growth of yeast and apple calli under low S conditions. The MhSultr3;1a-overexpressing apple calli had a higher fresh weight compared with the wild type (WT) under a low-S treatment because of the increased SO42- and cysteine (Cys) content. These results demonstrate that MhSultr3;1a may increase the content of SO42- and Cys to meet the demands of S-containing compounds and improve their growth under S-limiting conditions.

scholarly journals Genome-Wide Analysis of the Fatty Acid Desaturase Gene Family Reveals the Key Role of PfFAD3 in α-Linolenic Acid Biosynthesis in Perilla Seeds

2021 ◽  
Vol 12 ◽  
Author(s):  
Wu Duan ◽  
Yang Shi-Mei ◽  
Shang Zhi-Wei ◽  
Xu Jing ◽  
Zhao De-Gang ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Gene Family ◽  
Linolenic Acid ◽  
Seed Development ◽  
Expression Patterns ◽  
Fatty Acid Desaturase ◽  
Regulatory Elements ◽  
Oilseed Crop ◽  
Promoter Regions ◽  
Evolutionary Features

Perilla (Perilla frutescens), a traditional medicinal and oilseed crop in Asia, contains extremely high levels of polyunsaturated α-linolenic acid (ALA) (up to 60.9%) in its seeds. ALA biosynthesis is a multistep process catalyzed by fatty acid desaturases (FADs), but the FAD gene family in perilla has not been systematically characterized. Here, we identified 42 PfFADs in the perilla genome and classified them into five subfamilies. Subfamily members of PfFADs had similar exon/intron structures, conserved domain sequences, subcellular localizations, and cis-regulatory elements in their promoter regions. PfFADs also possessed various expression patterns. PfFAD3.1 was highly expressed in the middle stage of seed development, whereas PfFAD7/8.3 and PfFAD7/8.5 were highly expressed in leaf and later stages of seed development, respectively. Phylogenetic analysis revealed that the evolutionary features coincided with the functionalization of different subfamilies of PUFA desaturase. Heterologous overexpression of PfFAD3.1 in Arabidopsis thaliana seeds increased ALA content by 17.68%–37.03%. These findings provided insights into the characteristics and functions of PfFAD genes in perilla.

scholarly journals Characterization and functional analysis of two novel 3-hydroxy-3-methylglutaryl-coenzyme A reductase genes (GbHMGR2 and GbHMGR3) from Ginkgo biloba

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Shen Rao ◽  
Xiangxiang Meng ◽  
Yongling Liao ◽  
Tian Yu ◽  
Jie Cao ◽  
...  
Keyword(s):  
Ginkgo Biloba ◽  
High Performance ◽  
Coenzyme A ◽  
Expression Patterns ◽  
Mevalonic Acid ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Mva Pathway ◽  
Cdna Sequences ◽  
Coenzyme A Reductase

Abstract Terpene trilactones (TTLs) are the main secondary metabolites of Ginkgo biloba. As one of the rate-limiting enzymes in the mevalonic acid (MVA) pathway of TTL biosynthesis, 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) catalyzes the 3-hydroxy-3-methylglutaryl coenzyme A to form MVA. In this study, two cDNA sequences of HMGR genes, namely, GbHMGR2 and GbHMGR3, were cloned from G. biloba. The protein sequences of GbHMGR2 and GbHMGR3, which contain several functional domains, were analyzed. Regulatory elements related to light, hormone, and stress response were detected in the promoter regions of GbHMGR2 and GbHMGR3. The catalytic activity of these genes was verified by a functional complement experiment in yeast. Quantitative real-time PCR (qRT-PCR) showed the distinct expression patterns of the two genes in different organs. The TTL contents in the organs were detected by high-performance liquid chromatography– evaporative light scattering detector. GbHMGR2 and GbHMGR3 were responded to cold, dark, methyl jasmonate (MJ), abscisic acid (ABA), salicylic acid (SA), and ethephon (Eth) treatments. The TTL contents were also regulated by cold, dark, MJ, ABA, SA, and Eth treatment. In conclusion, GbHMGR2 and GbHMGR3 may participate in the MVA pathway of TTL biosynthesis.

scholarly journals In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression

2014 ◽  
Vol 12 (02) ◽  
pp. 1441009 ◽  
Author(s):  
Elizaveta A. Zagrijchuk ◽  
Marat A. Sabirov ◽  
David M. Holloway ◽  
Alexander V. Spirov
Keyword(s):  
Expression Patterns ◽  
Regulatory Region ◽  
Fruit Fly ◽  
Regulatory Sequences ◽  
Developmental Genes ◽  
Expression Of Genes ◽  
Open Questions ◽  
Coordinated Expression ◽  
Spatial Domains ◽  
Partial Redundancy

Biological development depends on the coordinated expression of genes in time and space. Developmental genes have extensive cis-regulatory regions which control their expression. These regions are organized in a modular manner, with different modules controlling expression at different times and locations. Both how modularity evolved and what function it serves are open questions. We present a computational model for the cis-regulation of the hunchback (hb) gene in the fruit fly (Drosophila). We simulate evolution (using an evolutionary computation approach from computer science) to find the optimal cis-regulatory arrangements for fitting experimental hb expression patterns. We find that the cis-regulatory region tends to readily evolve modularity. These cis-regulatory modules (CRMs) do not tend to control single spatial domains, but show a multi-CRM/multi-domain correspondence. We find that the CRM-domain correspondence seen in Drosophila evolves with a high probability in our model, supporting the biological relevance of the approach. The partial redundancy resulting from multi-CRM control may confer some biological robustness against corruption of regulatory sequences. The technique developed on hb could readily be applied to other multi-CRM developmental genes.

Expression analysis of seed-specific genes in four angiosperm species with an emphasis on the unconserved expression patterns of homologous genes

2013 ◽  
Vol 23 (4) ◽  
pp. 223-231 ◽  
Author(s):  
Lichao Ma ◽  
Yanrong Wang ◽  
Wenxian Liu ◽  
Zhipeng Liu
Keyword(s):  
Gene Expression ◽  
Expression Patterns ◽  
Homologous Gene ◽  
Promoter Regions ◽  
Specific Expression ◽  
Seed Formation ◽  
Control Seed ◽  
Homologous Genes ◽  
Expression Of Genes ◽  
Angiosperm Species

AbstractMedicago truncatula, soybean (Glycine max), Arabidopsis thaliana and rice (Oryza sativa) all belong to the core angiosperm group of plants. Seed-specific genes are important for seed formation and development in these angiosperms. The identification of genes specifically expressed in angiosperm seeds and the comparison of the expression patterns of homologous genes among different angiosperm species can provide novel insights into the functions of genes that control seed development and the evolution of angiosperms. We downloaded the sequences and expression data from the relevant databases, and the seed-specific expression of genes was identified with cut-offs of a gene expression level ratio ≥ 5 and a Z-score ≥ 6. The genes were analysed using local BLAST software with an E-value ≤ 1.0E − 505. A total of 605, 581, 778 and 722 genes showed specific expression in the seeds of Medicago, soybean, Arabidopsis and rice, respectively. Additionally, we compared the expression patterns of seed-specific genes from each species with their homologues in the other three species, and found that the degree of variation in the expression patterns of homologous genes was low among closely related species but higher among more distantly related ones. The discrepancy between the homologous gene expression patterns may be caused by the different characteristics of the cis-elements in the promoter regions of the homologous genes.

Abiotic and oxidative stress-dependent regulation of expression of the thioredoxin h multigenic family in grape Vitis vinifera

Biologia ◽  
2014 ◽  
Vol 69 (2) ◽  
Author(s):  
Raheem Haddad ◽  
Reza Heidari Japelaghi
Keyword(s):  
Higher Plants ◽  
Expression Patterns ◽  
In Silico Analysis ◽  
Regulatory Elements ◽  
Stress Conditions ◽  
Exchange Reactions ◽  
Regulation Of Expression ◽  
Environmental Signals ◽  
Multigenic Family ◽  
Stress Dependent

AbstractThioredoxins (Trxs) are small ubiquitous oxidoreductases that participate in dithiol-disulphide exchange reactions. They are present in all organisms from prokaryotes to higher eukaryotes and involved in a variety of cellular processes in higher plants. The expression pattern of the multigenic family of grape Trxsh was analysed in different tissues by semiquantitative RT-PCR. The grape Trxh genes were approximately expressed in all tissues, but with different expression patterns than each other. The in silico analysis of the promoter regions of grape Trxs h demonstrated the presence of a number of potential cis-acting elements to respond to environmental signals, suggesting that Trxsh may respond to a variety of environmental signals, including dehydration, salinity, heat, cold, heavy metals, light, pathogens, and plant hormones. The grape Trx h genes were also found to be differentially induced under abiotic stress conditions due to the presence of different putative regulatory elements in their promoters. Collectively, the distinct expression patterns and different responses to environmental stress conditions suggest that each isoform of the multigenic family of VvTrxh may have a specific and non-redundant function in grape.

scholarly journals Evolutionary insights into PtdIns3P signaling through FYVE and PHOX effector proteins from the moss Physcomitrella patens

2019 ◽  
Author(s):  
Patricia Agudelo-Romero ◽  
Ana Margarida Fortes ◽  
Trinidad Suárez ◽  
Hernán Ramiro Lascano ◽  
Laura Saavedra
Keyword(s):  
Stress Responses ◽  
Growth And Development ◽  
Physcomitrella Patens ◽  
Higher Plants ◽  
Regulatory Elements ◽  
Plant Evolution ◽  
Effector Proteins ◽  
Promoter Regions ◽  
Photosynthetic Organisms ◽  
Binding Domains

ABSTRACTPhosphatidylinositol 3-phosphate (PtdIns3P) is one of the five different phosphoinositides (PPIs) species in plant cells, which regulate several aspects of plant growth and development, as well as responses to biotic and abiotic stresses. The mechanistic insights underlying PtdIns3P mode of action, specifically through PtdIns3P-binding effectors such as FYVE and PHOX proteins have been partially explored in plants with main focus on Arabidopsis thaliana. Additionally, they have been underexplored in other plant organisms such as bryophytes, the earliest diverging group of terrestrial flora.In this study, we searched for genes coding for FYVE and PHOX domains containing sequences from different photosynthetic organisms in order to gather evolutionary insights on these PPI binding domains, followed by an in silico characterization of the FYVE and PHOX gene family in the moss Physcomitrella patens. Phylogenetic analysis showed that PpFYVE proteins can be grouped in 7 subclasses, with an additional subclass whose FYVE domain was lost during evolution to higher plants. On the other hand, PpPHOX proteins are classified into 5 subclasses. Expression analyses based on RNAseq data together with the analysis of cis-acting regulatory elements and transcription factor binding sites in promoter regions suggest the importance of these proteins in regulating stress responses but mainly developmental processes in P. patens. The results provide valuable information and robust candidate genes for future functional analysis aiming to further explore the role of this signaling pathway mainly during growth and development of tip growing cells and during the transition from 2D to 3D growth, which could provide ancestral regulatory players undertaken during plant evolution.

scholarly journals Lineage specific conservation of cis-regulatory elements in Cytokinin Response Factors

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rachel V. Powell ◽  
Courtney R. Willett ◽  
Leslie R. Goertzen ◽  
Aaron M. Rashotte
Keyword(s):  
Expression Patterns ◽  
Regulatory Elements ◽  
Promoter Regions ◽  
Response Factors ◽  
Functional Roles ◽  
Promoter Sequences ◽  
Significant Patterns ◽  
In Cis ◽  
Cytokinin Response ◽  
Specific Conservation

Abstract Expression patterns of genes are controlled by short regions of DNA in promoter regions known as cis-regulatory elements. How expression patterns change due to alterations in cis-regulatory elements in the context of gene duplication are not well studied in plants. Over 300 promoter sequences from a small, well-conserved family of plant transcription factors known as Cytokinin Response Factors (CRFs) were examined for conserved motifs across several known clades present in Angiosperms. General CRF and lineage specific motifs were identified. Once identified, significantly enriched motifs were then compared to known transcription factor binding sites to elucidate potential functional roles. Additionally, presence of similar motifs shows that levels of conservation exist between different CRFs across land plants, likely occurring through processes of neo- or sub-functionalization. Furthermore, significant patterns of motif conservation are seen within and between CRF clades suggesting cis-regulatory regions have been conserved throughout CRF evolution.

scholarly journals Comprehensive analysis of multiprotein bridging factor 1 family genes and SlMBF1c negatively regulate the resistance to Botrytis cinerea in tomato

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Xu Zhang ◽  
Zhixuan Xu ◽  
Lichen Chen ◽  
Zhonghai Ren
Keyword(s):  
Botrytis Cinerea ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Evolutionary Relationship ◽  
Regulatory Elements ◽  
Comprehensive Analysis ◽  
Promoter Regions ◽  
Functional Studies ◽  
Different Tissues

Abstract Background Multiprotein bridging factor 1 s (MBF1s) are members of the transcriptional co-activator family that have involved in plant growth, development and stress responses. However, little is known about the Solanum lycopersicum MBF1 (SlMBF1) gene family. Results In total, five SlMBF1 genes were identified based on the tomato reference genome, and these genes were mapped to five chromosomes. All of the SlMBF1 proteins were highly conserved, with a typical MBF1 domain and helix-turn-helix_3 domain. In addition, the promoter regions of the SlMBF1 genes have various stress and hormone responsive cis-regulatory elements. Encouragingly, the SlMBF1 genes were expressed with different expression profiles in different tissues and responded to various stress and hormone treatments. The biological function of SlMBF1c was further identified through its overexpression in tomato, and the transgenic tomato lines showed increased susceptibility to Botrytis cinerea (B. cinerea). Additionally, the expression patterns of salicylic acid (SA)-, jasmonic acid (JA)- and ethylene (ET)- mediated defense related genes were altered in the transgenic plants. Conclusions Our comprehensive analysis provides valuable information for clarifying the evolutionary relationship of the SlMBF1 members and their expression patterns in different tissues and under different stresses. The overexpression of SlMBF1c decreased the resistance of tomato to B. cinerea through enhancing the gene expression of the SA-mediated signaling pathway and depressing JA/ET-mediated signaling pathways. These results will facilitate future functional studies of the transcriptional co-activator family.

scholarly journals Genome-Wide Study of NOT2_3_5 Protein Subfamily in Cotton and Their Necessity in Resistance to Verticillium wilt

2021 ◽  
Vol 22 (11) ◽  
pp. 5634
Author(s):  
Pei Zhao ◽  
Tengfei Qin ◽  
Wei Chen ◽  
Xiaohui Sang ◽  
Yunlei Zhao ◽  
...  
Keyword(s):  
Verticillium Wilt ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Protein Family ◽  
Expansion Process ◽  
Promoter Regions ◽  
Mrna Metabolism ◽  
Genome Wide ◽  
Development Processes ◽  
Genome Wide Study

The Negative on TATA-less (NOT) 2_3_5 domain proteins play key roles in mRNA metabolism and transcription regulation, but few comprehensive studies have focused on this protein family in plants. In our study, a total of 30 NOT2_3_5 genes were identified in four cotton genomes: Gossypium. arboretum, G. raimondii, G. hirsutum and G. barbadense. Phylogenetic analysis showed that all the NOT2_3_5 domain proteins were divided into two classes. The NOT2_3_5 genes were expanded frequently, and segmental duplication had significant effects in their expansion process. The cis-regulatory elements analysis of NOT2_3_5 promoter regions indicated that NOT2_3_5 domain proteins might participate in plant growth and development processes and responds to exogenous stimuli. Expression patterns demonstrated that all of the GhNOT2_3_5 genes were expressed in the majority of tissues and fiber development stages, and that these genes were induced by multiple stresses. Quantitative real-time PCR showed that GbNOT2_3_5 genes were up-regulated in response to verticillium wilt and the silencing of GbNOT2_3_5-3/8 and GbNOT2_3_5-4/9 led to more susceptibility to verticillium wilt than controls. Identification and analysis of the NOT2_3_5 protein family will be beneficial for further research on their biological functions.

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