scholarly journals Genome-wide identification of ZmSnRK2 genes and functional analysis of ZmSnRK2.10 in ABA signaling pathway in maize (Zea mays L)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Tiandan Long ◽  
Binjie Xu ◽  
Yufeng Hu ◽  
Yayun Wang ◽  
Changqing Mao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Expression Patterns ◽  
Functional Study ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Aba Signaling ◽  
Genome Database ◽  
Wide Range ◽  
Duplication Events ◽  
Aba Insensitive

Abstract Background Phytohormone abscisic acid (ABA) is involved in the regulation of a wide range of biological processes. In Arabidopsis, it has been well-known that SnRK2s are the central components of the ABA signaling pathway that control the balance between plant growth and stress response, but the functions of ZmSnRK2 in maize are rarely reported. Therefore, the study of ZmSnRK2 is of great importance to understand the ABA signaling pathways in maize. Results In this study, 14 ZmSnRK2 genes were identified in the latest version of maize genome database. Phylogenetic analysis revealed that ZmSnRK2s are divided into three subclasses based on their diversity of C-terminal domains. The exon-intron structures, phylogenetic, synteny and collinearity analysis indicated that SnRK2s, especially the subclass III of SnRK2, are evolutionally conserved in maize, rice and Arabidopsis. Subcellular localization showed that ZmSnRK2 proteins are localized in the nucleus and cytoplasm. The RNA-Seq datasets and qRT-PCR analysis showed that ZmSnRK2 genes exhibit spatial and temporal expression patterns during the growth and development of different maize tissues, and the transcript levels of some ZmSnRK2 genes in kernel are significantly induced by ABA and sucrose treatment. In addition, we found that ZmSnRK2.10, which belongs to subclass III, is highly expressed in kernel and activated by ABA. Overexpression of ZmSnRK2.10 partially rescued the ABA-insensitive phenotype of snrk2.2/2.3 double and snrk2.2/2.3/2.6 triple mutants and led to delaying plant flowering in Arabidopsis. Conclusion The SnRK2 gene family exhibits a high evolutionary conservation and has expanded with whole-genome duplication events in plants. The ZmSnRK2s expanded in maize with whole-genome and segmental duplication, not tandem duplication. The expression pattern analysis of ZmSnRK2s in maize offers important information to study their functions. Study of the functions of ZmSnRK.10 in Arabidopsis suggests that the ABA-dependent members of SnRK2s are evolutionarily conserved in plants. Our study elucidated the structure and evolution of SnRK2 genes in plants and provided a basis for the functional study of ZmSnRK2s protein in maize.

scholarly journals Effect of Daidzein on the Proliferation of Lung Cancer Cells Involved in the Apoptotic Signaling Pathway

2020 ◽  
Author(s):  
Hui Liu ◽  
Xiaobo Wang ◽  
Ouyang Jin ◽  
Denggang Fu ◽  
You Peng ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Signaling Pathway ◽  
Tp53 Gene ◽  
Cell Counting ◽  
Pcr Analysis ◽  
Human Embryonic Lung ◽  
Bioactive Substances ◽  
Apoptosis Pathway ◽  
Wide Range ◽  
Proliferation And Apoptosis

Abstract Background: Daidzein is one of the key bioactive substances of soybean isoflavones that has a wide range of health benefits includes antineoplastic. Epidemiological evidence suggests that soy glycogen is associated with the incidence and prognosis of lung cancer. we purposed to assess the effect and molecular mechanism of daidzein on lung cancer, and to maximize therapy outcome for individualized treatment. Methods: In this report, H1299 were cultured in a medium with 10 μM daidzein for 6 hours , we detected the expression level of apoptosis-related genes in H1299 by cDNA microarray analysis. The selected genes were further validated by using RT-PCR analysis and Western blot. Finally, We usedflow cytometry to detect cell cycle alterations, and apoptosis the proliferation and apoptosis in HELF and H1299 cells were detected by Cell counting kit-8 assays. Results: These results indicate that low concentrations of isoflavone crude extract and daidzein could significantly affect the proliferation of H1299 (Human lung adenocarcinoma) and HELF (Human embryonic lung fibroblast) cells. The results of microarray in our study suggest that apoptosis-related genes are up-regulated induced by daidzein in H1299 cells and verified by RT-qPCR, particularly TP53 and caspase9. Western blotting shows the effect of daidzein on P53 and caspase9 in HELF cells be more obvious than it in H1299 cells. While the expression of TP53 was suppressed by pifithrin-α (PFTα) in HELF and H1299 cells, the mRNA and protein expression of TP53 still increase induced by daidzein, also, the effect of apoptosis induced by daidzein is involved in the P53 apoptosis pathway through inhibition of TP53 gene expression by PFTα. Conclusions: In conclusion, daidzein affected proliferation and apoptosis in HELF and H1299 cells, and the mechanism of apoptosis involved in the P53 signaling pathway.

scholarly journals Genome-wide identification of the 14-3-3 gene family and its participation in floral transition by interacting with TFL1/FT in Apple

2020 ◽  
Author(s):  
Xiya Zuo ◽  
Shixiang Wang ◽  
Wen Xiang ◽  
Huiru Yang ◽  
Muhammad Mobeen Tahir ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Floral Transition ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Transcriptional Responses ◽  
Genome Database ◽  
Reverse Transcription Pcr ◽  
Conserved Core

Abstract Background: Apple (Malus domestica Borkh.) is one of the most popular cultivated fruit crops in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members play vital roles in flowering. However, little information was available about the 14-3-3 members in apple.Results: In the current study, we identified eighteen 14-3-3 gene family members from the apple genome database, designated MdGF14a to MdGF14r. The isoforms possess a conserved core region comprising nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3 proteins could be classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative real-time reverse transcription PCR analysis showed diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormone treatments during the floral transition phase. Four Md14‑3-3 isoforms (MdGF14a, MdGF14d, MdGF14i, and MdGF14j) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus.Conclusion: We identified the Md14-3-3s family in apple comprehensively. Certain Md14-3-3 genes are expressed predominantly during the apple floral transition stage, and may participate in the regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s in floral transition.

scholarly journals Genome-wide identification of the 14-3-3 gene family and its participation in floral transition by interacting with TFL1/FT in Apple

2020 ◽  
Author(s):  
Xiya Zuo ◽  
Shixiang Wang ◽  
Wen Xiang ◽  
Huiru Yang ◽  
Muhammad Mobeen Tahir ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Economic Value ◽  
Floral Transition ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Transcriptional Responses ◽  
Genome Database ◽  
Reverse Transcription Pcr

Abstract Background: Apple (Malus domestica Borkh.) is a popular cultivated fruit crop with high economic value in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members play vital roles in flowering. However, little information was available about the 14-3-3 members in apple.Results: In the current study, we identified eighteen 14-3-3 gene family members from the apple genome database, designated MdGF14a to MdGF14r. The isoforms possess a conserved core region comprising nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3 proteins could be classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative real-time reverse transcription PCR analysis showed diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormone treatments during the floral transition phase. Four Md14‑3-3 isoforms (MdGF14a, MdGF14d, MdGF14i, and MdGF14j) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus.Conclusion: We identified the Md14-3-3s family in apple comprehensively. Certain Md14-3-3 genes are expressed predominantly during the apple floral transition stage, and may participate in the regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s in floral transition.

Versatile physiological functions of the Nudix Hydrolase family in berry development and stress response in grapevine

2020 ◽  
Author(s):  
Zhaoke Wang ◽  
Peipei Wang ◽  
Le Guan ◽  
Muhammad Salman Haider ◽  
Maazullah Nasim ◽  
...  
Keyword(s):  
Stress Response ◽  
Expression Patterns ◽  
Leaf Roll ◽  
Pcr Analysis ◽  
Berry Development ◽  
Abiotic And Biotic Stresses ◽  
Physiological Functions ◽  
Biotic Stresses ◽  
Wide Range ◽  
Nudix Hydrolases

Abstract Background Nudix hydrolases are widely distributed across all classes of organisms and provide the potential capacity to hydrolyze a wide range of organic pyrophosphates. Although Nudix hydrolases are involved in plants detoxification processes in response to abiotic and biotic stresses, the biological functions of Nudix hydrolases remain largely unclear in grapevine. Results A total of 25 putative grapevine Nudix hydrolases ( VvNUDXs ) were identified by bioinformatics analysis and classified into eight subfamilies based to their preferred substrates. Both tandem and segmental duplications were responsible for the evolution and expansion of NUDX gene family in grapevine. To investigate into their regulatory roles of VvNUDX genes during growth and development as well as in response to abiotic and biotic stress in grapevine, the expression patterns were revealed in publicly available microarray data. The spatial and temporal expression patterns of VvNUDX genes indicated that these genes might play important roles in multiple developmental processes. Transcriptome and qRT-PCR analysis exhibited that ten VvNUDX genes were specifically expressed in grapevine berries, suggesting the potential roles in grapevine berry development. Expression and phylogenetic analysis demonstrated that VvNUDX1 and VvNUDX3 might be involved in terpenoid biosynthesis in grapevine. Futhermore, most VvNUDX genes toward the ADP-ribose/NADH were different patterns in response to various abiotic and biotic stresses, such as salinity and drought, as well as different types of biotic treatments, such as Erysiphe necator , Bois Noir phytoplasma and leaf-roll-associated virus-3 (GLRaV-3). Conclusions These results showed that VvNUDX were associated with plant detoxification processes in response to abiotic and biotic stresses, and regulate disease immunity and resistance pathways. The present informations may provide good opportunities to explore the physiological functions of VvNUDX genes in berry development and stress response networks in grapevine.

scholarly journals Genome-Wide Analysis of the YABBY Transcription Factor Family in Rapeseed (Brassica napus L.)

Genes ◽  
2021 ◽  
Vol 12 (7) ◽  
pp. 981
Author(s):  
Jichun Xia ◽  
Dong Wang ◽  
Yuzhou Peng ◽  
Wenning Wang ◽  
Qianqian Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Expression Patterns ◽  
Purifying Selection ◽  
Brassica Species ◽  
Pcr Analysis ◽  
Sequencing Data ◽  
Functional Identification ◽  
Brassica Napus L ◽  
Intron Structure ◽  
Duplication Events

The YABBY family of plant-specific transcription factors play important regulatory roles during the development of leaves and floral organs, but their functions in Brassica species are incompletely understood. Here, we identified 79 YABBY genes from Arabidopsis thaliana and five Brassica species (B. rapa, B. nigra, B. oleracea, B. juncea, and B. napus). A phylogenetic analysis of YABBY proteins separated them into five clusters (YAB1–YAB5) with representatives from all five Brassica species, suggesting a high degree of conservation and similar functions within each subfamily. We determined the gene structure, chromosomal location, and expression patterns of the 21 BnaYAB genes identified, revealing extensive duplication events and gene loss following polyploidization. Changes in exon–intron structure during evolution may have driven differentiation in expression patterns and functions, combined with purifying selection, as evidenced by Ka/Ks values below 1. Based on transcriptome sequencing data, we selected nine genes with high expression at the flowering stage. qRT-PCR analysis further indicated that most BnaYAB family members are tissue-specific and exhibit different expression patterns in various tissues and organs of B. napus. This preliminary study of the characteristics of the YABBY gene family in the Brassica napus genome provides theoretical support and reference for the later functional identification of the family genes.

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 Identification and Expression Analysis of Two allene oxide cyclase (AOC) Genes in Watermelon

Agriculture ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 225 ◽  
Author(s):  
Jingwen Li ◽  
Yelan Guang ◽  
Youxin Yang ◽  
Yong Zhou
Keyword(s):  
Functional Divergence ◽  
Expression Patterns ◽  
Red Light ◽  
Pcr Analysis ◽  
Infected Leaf ◽  
Allene Oxide ◽  
Primary Role ◽  
Root Knot Nematode ◽  
Allene Oxide Cyclase ◽  
Wide Range

Allene oxide cyclase (AOC, EC 5.3.99.6) catalyzes the most important step in the jasmonic acid (JA) biosynthetic pathway and mediates plant defense response to a wide range of biotic and abiotic stresses. In this study, two AOC genes were identified from watermelon. Sequence analysis revealed that each of ClAOC1 and ClAOC2 contained an allene oxide cyclase domain and comprised eight highly conserved β-strands, which are the typical characteristics of AOC proteins. Phylogenetic analysis showed that ClAOC1 and ClAOC2 were clustered together with AOCs from dicotyledon, with the closest relationships with JcAOC from Jatropha curcas and Ljaoc1 from Lotus japonicus. Different intron numbers were observed in ClAOC1 and ClAOC2, which may result in their functional divergence. qRT-PCR analysis revealed that ClAOC1 and ClAOC2 have specific and complex expression patterns in multiple organs and under hormone treatments. Both ClAOC1 and ClAOC2 displayed the highest transcriptional levels in stem apex and fruit and exhibited relatively lower expression in stem. JA, salicylic acid (SA), and ethylene (ET) could enhance the expression of ClAOC1 and ClAOC2, particularly that of ClAOC2. Red light could induce the expression of ClAOC2 in root-knot nematode infected leaf and root of watermelon, indicating that ClAOC2 might play a primary role in red light-induced resistance against root-knot nematodes through JA signal pathway. These findings provide important information for further research on AOC genes in watermelon.

scholarly journals Genome-wide identification of the 14-3-3 gene family and its participation in response to floral transition by interacting with TFL1/FT in Apple

2020 ◽  
Author(s):  
Xiya Zuo ◽  
Shixiang Wang ◽  
Wen Xiang ◽  
Huiru Yang ◽  
Muhammad Mobeen Tahir ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Floral Transition ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Transcriptional Responses ◽  
Genome Database ◽  
Reverse Transcription Pcr ◽  
Conserved Core

Abstract Background: Apple ( Malus domestica Borkh.) is one of the most popular cultivated fruit crops in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members have been identified to play vital roles in flowering. However, little information was available about the 14-3-3 members in apple. Results: In the current study, we identified eighteen 14-3-3 gene family members from apple genome database, designated MdGF14a to MdGF14r . The isoforms possess a conserved core region composed of nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3s classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative reverse-transcription PCR (qRT-PCR) analysis exhibited diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormones treatments during floral transition phase. Four Md14-3-3 isoforms ( MdGF14a , MdGF14d , MdGF14i and MdGF14j ) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus. Conclusion: We comprehensively identified Md14-3-3s family in apple. Some Md14-3-3 genes are predominantly expressed during apple floral transition stage, and may participate in regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s for floral transition.

scholarly journals Genome-wide identification of the 14-3-3 gene family and its participation in response to floral transition by interacting with TFL1/FT in Apple

2020 ◽  
Author(s):  
Xiya Zuo ◽  
Shixiang Wang ◽  
Wen Xiang ◽  
Muhammad Mobeen Tahir ◽  
Huiru Yang ◽  
...  
Keyword(s):  
Gene Family ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Floral Transition ◽  
Bimolecular Fluorescence Complementation ◽  
Pcr Analysis ◽  
Transcriptional Responses ◽  
Genome Database ◽  
Reverse Transcription Pcr ◽  
Conserved Core

Abstract Background: Apple ( Malus domestica Borkh.) is one of the most popular cultivated fruit crops in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The 14-3-3 proteins are involved in regulating diverse biological processes in plants, and some 14-3-3 members have been identified to play vital roles in flowering. However, little information was available about the 14-3-3 members in apple. Results: In the current study, we identified eighteen 14-3-3 gene family members from apple genome database, designated MdGF14a to MdGF14r , 17 of them are transcribed. The isoforms possess a conserved core region composed of nine antiparallel α-helices and divergent N and C termini. According to their structural and phylogenetic features, Md14-3-3s classified into two major evolutionary branches, the epsilon (ɛ) group and the non-epsilon (non-ɛ) group. Moreover, expression profiles derived from transcriptome data and quantitative reverse-transcription PCR (qRT-PCR) analysis exhibited diverse expression patterns of Md14-3-3 genes in various tissues and in response to different sugars and hormones treatments during floral transition phase. Four Md14-3-3 isoforms ( MdGF14a , MdGF14d , MdGF14i and MdGF14j ) exhibiting prominent transcriptional responses to sugars and hormones were selected for further investigation. Subcellular localization of four selected Md14-3-3 proteins demonstrated their localization in both the cytoplasm and nucleus. Furthermore, yeast two-hybrid and bimolecular fluorescence complementation (BiFC) experiments showed that the four Md14-3-3 proteins interact with key floral integrators, MdTFL1 (TERMINAL FLOWER1) and MdFT (FLOWERING LOCUS T). Conclusion: We comprehensively identified Md14-3-3s family in apple. Some Md14-3-3 genes are predominantly expressed during apple flowering transition stage, and may participate in regulation of flowering through association with flower control genes. Our results provide a preliminary framework for further investigation into the roles of Md14-3-3s for flower transition.

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