scholarly journals Genome-wide identification and expression profile analysis of CCH gene family in Populus

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3962 ◽  
Author(s):  
Zhiru Xu ◽  
Liying Gao ◽  
Mengquan Tang ◽  
Chunpu Qu ◽  
Jiahuan Huang ◽  
...  
Keyword(s):  
Gene Family ◽  
Metal Binding ◽  
Function Analysis ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Binding Motif ◽  
Copper Chaperone ◽  
Specific Expression ◽  
Copper Chaperones ◽  
Tissue Specific

Copper plays key roles in plant physiological activities. To maintain copper cellular homeostasis, copper chaperones have important functions in binding and transporting copper to target proteins. Detailed characterization and function analysis of a copper chaperone, CCH, is presently limited to Arabidopsis. This study reports the identification of 21 genes encoding putative CCH proteins in Populus trichocarpa. Besides sharing the conserved metal-binding motif MXCXXC and forming a βαββαβ secondary structure at the N-terminal, all the PtCCHs possessed the plant-exclusive extended C-terminal. Based on their gene structure, conserved motifs, and phylogenetic analysis, the PtCCHs were divided into three subgroups. Our analysis indicated that whole-genome duplication and tandem duplication events likely contributed to expansion of the CCH gene family in Populus. Tissue-specific data from PlantGenIE revealed that PtCCH genes had broad expression patterns in different tissues. Quantitative real-time RT-PCR (qRT-PCR) analysis revealed that PnCCH genes of P. simonii × P. nigra also had different tissue-specific expression traits, as well as different inducible-expression patterns in response to copper stresses (excessive and deficiency). In summary, our study of CCH genes in the Populus genome provides a comprehensive analysis of this gene family, and lays an important foundation for further investigation of their roles in copper homeostasis of poplar.

Functional characterization and expression patterns of PnATX genes under different abiotic stress treatments in Populus

2020 ◽  
Vol 40 (4) ◽  
pp. 520-537
Author(s):  
Zhiru Xu ◽  
Jiahuan Huang ◽  
Chunpu Qu ◽  
Ruhui Chang ◽  
Jinyuan Chen ◽  
...  
Keyword(s):  
Salicylic Acid ◽  
Metal Binding ◽  
Molecular Mechanisms ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Pcr Analysis ◽  
Binding Motif ◽  
Copper Chaperone ◽  
Specific Expression ◽  
Relative Expression Level

Abstract The copper chaperone ATX1 has been investigated previously in the herbaceous plants Arabidopsis and rice. However, the molecular mechanisms of ATX1 underlying copper transport and functional characteristics in the woody plant Populus are poorly understood. In this study, PnATX1 and PnATX2 of Populus simonii × P. nigra were identified and characterized. Sequence analysis showed that PnATXs contained the metal-binding motif MXCXXC in the N-terminus and a lysine-rich region. Phylogenetic analysis of ATX protein sequences revealed that PnATXs were clustered in the same group as AtATX1. PnATX proteins were localized in the cytoplasm and nucleus. Tissue-specific expression analysis showed that PnATX1 and PnATX2 were expressed in all analyzed tissues and, in particular, expressed to a higher relative expression level in young leaves. Quantitative real-time PCR analysis indicated that each PnATX gene was differentially expressed in different tissues under treatments with copper, zinc, iron, jasmonate and salicylic acid (SA). The copper-response element GTAC, methyl jasmonate and salicylic acid responsiveness elements and other cis-acting elements were identified in the PnATX1 and PnATX2 promoters. Expression of β-glucuronidase driven by the PnATX1 promoter was observed in the apical meristem of 7-day-old Arabidopsis transgenic seedlings, and the signal strength was not influenced by deficient or excessive copper conditions. Both PnATX1 and PnATX2 functionally rescued the defective phenotypes of yeast atx1Δ and sod1Δ strains. Under copper excess and deficiency conditions, transgenic Arabidopsis atx1 mutants harboring 35S::PnATX constructs exhibited root length and fresh weight similar to those of the wild type and higher than those of Arabidopsis atx1 mutants. Superoxide dismutase activity decreased in transgenic lines compared with that of atx1 mutants, whereas peroxidase and catalase activities increased significantly under excess copper. The results provide a basis for elucidating the role of Populus PnATX genes in copper homeostasis.

scholarly journals Genome-wide identification of ZF-HD gene family in Triticum aestivum: Molecular evolution mechanism and function analysis

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0256579
Author(s):  
Hongli Niu ◽  
Pengliang Xia ◽  
Yifeng Hu ◽  
Chuang Zhan ◽  
Yiting Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Function Analysis ◽  
Expression Patterns ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Wheat Evolution ◽  
New Perspective ◽  
Almost All ◽  
And Function

ZF-HD family genes play important roles in plant growth and development. Studies about the whole genome analysis of ZF-HD gene family have been reported in some plant species. In this study, the whole genome identification and expression profile of the ZF-HD gene family were analyzed for the first time in wheat. A total of 37 TaZF-HD genes were identified and divided into TaMIF and TaZHD subfamilies according to the conserved domain. The phylogeny tree of the TaZF-HD proteins was further divided into six groups based on the phylogenetic relationship. The 37 TaZF-HDs were distributed on 18 of 21 chromosomes, and almost all the genes had no introns. Gene duplication and Ka/Ks analysis showed that the gene family may have experienced powerful purification selection pressure during wheat evolution. The qRT-PCR analysis showed that TaZF-HD genes had significant expression patterns in different biotic stress and abiotic stress. Through subcellular localization experiments, we found that TaZHD6-3B was located in the nucleus, while TaMIF4-5D was located in the cell membrane and nucleus. Our research contributes to a comprehensive understanding of the TaZF-HD family, provides a new perspective for further research on the biological functions of TaZF-HD genes in wheat.

scholarly journals Insights into the Superoxide Dismutase Gene Family and Its Roles in Dendrobium catenatum under Abiotic Stresses

Plants ◽  
2020 ◽  
Vol 9 (11) ◽  
pp. 1452
Author(s):  
Hui Huang ◽  
Hui Wang ◽  
Yan Tong ◽  
Yuhua Wang
Keyword(s):  
Superoxide Dismutase ◽  
Gene Family ◽  
Abiotic Stresses ◽  
Phylogenetic Analyses ◽  
Expression Patterns ◽  
Light Response ◽  
Vital Role ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Expression Levels

Dendrobium catenatum is a member of epiphytic orchids with extensive range of pharmacological properties and ornamental values. Superoxide dismutase (SOD), a key member of antioxidant system, plays a vital role in protecting plants against oxidative damage caused by various biotic and abiotic stresses. So far, little is known about the SOD gene family in D. catenatum. In this study, eight SOD genes, including four Cu/ZnSODs, three FeSODs and one MnSOD, were identified in D. catenatum genome. Phylogenetic analyses of SOD proteins in D. catenatum and several other species revealed that these SOD proteins can be assigned to three subfamilies based on their metal co-factors. Moreover, the similarities in conserved motifs and gene structures in the same subfamily corroborated their classification and inferred evolutionary relationships. There were many hormone and stress response elements in DcaSODs, of which light responsiveness elements was the largest group. All DcaSODs displayed tissue-specific expression patterns and exhibited abundant expression levels in flower and leaf. According to public RNA-seq data and qRT-PCR analysis showed that the almost DcaSODs, except for DcaFSD2, were highly expressed under cold and drought treatments. Under heat, light, and salt stresses, DcaCSD1, DcaCSD2, DcaCSD3 were always significantly up-regulated, which may play a vital role in coping with various stresses. The expression levels of DcaFSD1 and DcaFSD2 were promoted by high light, suggesting their important roles in light response. These findings provided valuable information for further research on DcaSODs in D. catenatum.

scholarly journals Genome-Wide Analysis of the WOX Gene Family and Function Exploration of GmWOX18 in Soybean

Plants ◽  
2019 ◽  
Vol 8 (7) ◽  
pp. 215 ◽  
Author(s):  
Qingnan Hao ◽  
Ling Zhang ◽  
Yanyan Yang ◽  
Zhihui Shan ◽  
Xin-an Zhou
Keyword(s):  
Abiotic Stress ◽  
Gene Family ◽  
Function Analysis ◽  
Expression Patterns ◽  
Protein Structures ◽  
Pcr Analysis ◽  
Regeneration Ability ◽  
Functional Identification ◽  
Phylogenetic Tree Analysis ◽  
Wox Genes

WUSCHEL-related homeobox (WOX) is a family of transcription factors that are unique to plants and is characterized by the presence of a homeodomain. The WOX transcription factor plays an important role in regulating plant growth and development and the response to abiotic stress. Soybean is one of the most important oil crops worldwide. In this study, based on the available genome data of soybean, the WOX gene family was identified by bioinformatics analysis. The chromosome distribution, gene and protein structures, phylogenetic relationship and gene expression patterns of this family were comprehensively compared. The results showed that a total of 33 putative WOX genes in the soybean genome were found and then designated as GmWOX1- GmWOX33, which were distributed across 19 chromosomes except chromosome 16. Multiple sequence analysis of the GmWOX gene family revealed a highly conserved homeodomain. Phylogenetic tree analysis showed that 33 WOX genes could be divided into three major clades (modern/WUS, intermediate and ancient) in soybean. Of these 33 WOX genes, some showed differential expression patterns in the tested tissues (leaves, pods, unopen and open flowers, nodules, seed, roots, root hairs, stems, shoot apical meristems and shoot tips). In addition, the expression profile and qRT-PCR analysis showed that most of the GmWOX genes responded to different abiotic stress treatments (cold and drought). According to the expression pattern of GmWOX genes in the high regeneration capacity soybean material P3, overexpression of GmWOX18 was selected for function analysis. The overexpression of GmWOX18 increased the regeneration ability of clustered buds. The results will provide valuable information for further studies on the roles of WOX genes in regulating soybean growth, development and responses to abiotic stress, as well as a basis for the functional identification and analysis of WOX genes in soybean.

scholarly journals Genome-Wide Characterization of Glutamine Synthetase Family Genes in Cucurbitaceae and Their Potential Roles in Cold Response and Rootstock-Scion Signaling Communication

Agriculture ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1156
Author(s):  
Xiaojun Li ◽  
Xiaohong Lu ◽  
Mengshuang Liu ◽  
Chenggang Xiang ◽  
Wenqian Liu ◽  
...  
Keyword(s):  
Glutamine Synthetase ◽  
Subcellular Localization ◽  
Gene Family ◽  
Higher Plants ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Pcr Analysis ◽  
Specific Expression ◽  
Cucumis Sativus L ◽  
Cold Response

Glutamine synthetase (GS; EC 6.3.1.2, L-glutamate: ammonia ligase ADP-forming) is the key enzyme responsible for the primary assimilation and reassimilation of nitrogen (N) in higher plants. There are two main isoforms of GS in higher plants, classified as cytosolic GS (GS1) and chloroplastic GS (GS2) by their size and subcellular localization. In order to improve the stress tolerance, quality, and yield of cucurbit crops such as cucumbers (Csa, Cucumis sativus L.), pumpkins (Cmo, Cucurbita moschata var. Rifu) are often used as rootstocks. Here, the GS family of the two species were comprehensively analyzed using bioinformatics in terms of aspects of the phylogenic tree, gene structure, chromosome location, subcellular localization, and evolutionary and expression patterns. Seven and four GS gene family members were screened in pumpkin and cucumber, respectively. GS family genes were divided into three groups (one for GS2 and two for GS1) according to their homology and phylogenetic relationships with other species. The analysis of gene ontology annotation of GS family genes, promoter regulatory elements, and tissue-specific expression patterns indicates the potential different biological roles of GS isoforms in Cucurbitaceae. In particular, we have identified a potentially available gene (GS1: CmoCh08G004920) from pumpkin that is relatively highly expressed and tissue-specifically expressed. RT-PCR analysis showed that most CmoGSs are induced by low temperature, and long-term (day 2 to day 9) cold stress has a more obvious effect on the RNA abundance of CmoGS. Our work presents the structure and expression patterns of all candidate members of the pumpkin and cucumber GS gene family, and to the best of our knowledge, this is the first time such work has been presented. It is worth focusing on the candidate genes with strong capacity for improving pumpkin rootstock breeding in order to increase nitrogen-use efficiency in cold conditions, as well as rootstock-scion communication.

Tissue-specific expression patterns of nuclear receptors

2013 ◽  
Author(s):  
AL Bookout ◽  
Y Jeong ◽  
M Downes ◽  
RT Yu ◽  
RM Evans ◽  
...  
Keyword(s):  
Nuclear Receptors ◽  
Expression Patterns ◽  
Specific Expression ◽  
Tissue Specific ◽  
Tissue Specific Expression

scholarly journals Identification, Expression, and Functions of the Somatostatin Gene Family in Spotted Scat (Scatophagus argus)

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 194
Author(s):  
Peizhe Feng ◽  
Changxu Tian ◽  
Xinghua Lin ◽  
Dongneng Jiang ◽  
Hongjuan Shi ◽  
...  
Keyword(s):  
Gene Family ◽  
Growth Regulation ◽  
Expression Patterns ◽  
Open Reading Frames ◽  
Pcr Analysis ◽  
Sequence Alignments ◽  
Scatophagus Argus ◽  
Gene Structure And Expression ◽  
Liver Fragments

Somatostatins (SSTs) are a family of proteins consisting of structurally diverse polypeptides that play important roles in the growth regulation in vertebrates. In the present study, four somatostatin genes (SST1, SST3, SST5, and SST6) were identified and characterized in the spotted scat (Scatophagus argus). The open reading frames (ORFs) of SST1, SST3, SST5, and SST6 cDNA consist of 372, 384, 321, and 333 bp, respectively, and encode proteins of 123, 127, 106, and 110 amino acids, respectively. Amino acid sequence alignments indicated that all SST genes contained conserved somatostatin signature motifs. Real-time PCR analysis showed that the SST genes were expressed in a tissue specific manner. When liver fragments were cultured in vitro with synthetic peptides (SST1, SST2, or SST6 at 1 μM or 10 μM) for 3 h or 6 h, the expression of insulin-like growth factor 1 and 2 (Igf-1 and Igf-2) in the liver decreased significantly. Treatment with SST5 had no significant effect on Igf-1 and Igf-2 gene expression. This study provides an enhanced understanding of the gene structure and expression patterns of the SST gene family in S. argus. Furthermore, this study provides a foundation for future exploration into the role of SST genes in growth and development.

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