In Silico Identification and Expression Analysis of Nuclear Factor Y (Nf-Y) Transcription Factors in Cucumber

The nuclear factor Y (NF-Y) transcription factors (TFs) play vital regulatory roles in diverse developmental processes and responses to abiotic stresses in plants. However, the NF-Y genes remain largely unknown in cucumber. In this study, based on phylogenetic and protein structure analyses, we identified 27 CsaNF-Y members of this gene family in the cucumber genome, including 7 NF-YAs, 13 NF-YBs, and 7 NF-YCs. Their chromosome locations, gene structures, conserved domains, gene duplication, and promoter regions containing stress- and hormone-responsive cis-elements were also analyzed. As reported earlier, RNA-seq data showed that the expression of some CsaNF-Y genes was tissue-specific and varied during fruit development. The qRT-PCR results showed that all the detected CsaNF-Y genes were differentially regulated by drought and salt stress. Taken together, our findings provide a comprehensive understanding of CsaNF-Y genes in the development and abiotic stress response of cucumber and lay the foundation for future crop improvement.

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Identification, expression, and putative target gene analysis of nuclear factor-Y (NF-Y) transcription factors in tea plant (Camellia sinensis)

Planta ◽

10.1007/s00425-019-03256-6 ◽

2019 ◽

Vol 250 (5) ◽

pp. 1671-1686 ◽

Cited By ~ 8

Author(s):

Pengjie Wang ◽

Yucheng Zheng ◽

Yongchun Guo ◽

Xuejin Chen ◽

Yun Sun ◽

...

Keyword(s):

Transcription Factors ◽

Camellia Sinensis ◽

Target Gene ◽

Tea Plant ◽

Gene Analysis ◽

Nuclear Factor ◽

Putative Target Gene ◽

Nuclear Factor Y ◽

Putative Target

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Genome-wide characterization and expression analysis of citrus NUCLEAR FACTOR-Y (NF-Y) transcription factors identified a novel NF-YA gene involved in drought-stress response and tolerance

PLoS ONE ◽

10.1371/journal.pone.0199187 ◽

2018 ◽

Vol 13 (6) ◽

pp. e0199187 ◽

Cited By ~ 7

Author(s):

Suzam L. S. Pereira ◽

Cristina P. S. Martins ◽

Aurizangela O. Sousa ◽

Luciana R. Camillo ◽

Caroline P. Araújo ◽

...

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Stress Response ◽

Expression Analysis ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Genome Wide

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Identification, Characterization and Expression Analysis Reveal the Potential Function of Annexin Genes in Response to Abiotic stress, Calcium and Hormones in Cassava (Manihot esculeta Crantz)

10.21203/rs.2.11537/v1 ◽

2019 ◽

Author(s):

Ruimei Li ◽

Yuqing Wang ◽

Yangjiao Zhou ◽

Tingting Qiu ◽

Yu Song ◽

...

Keyword(s):

Salt Stress ◽

Abiotic Stress ◽

Expression Patterns ◽

Membrane Lipid ◽

Pcr Analysis ◽

Abiotic Stress Response ◽

Promoter Regions ◽

Manihot Esculenta Crantz ◽

Diverse Range ◽

Drought And Salt Stress

Abstract Background The calcium (Ca2+)-dependent phospholipid binding protein annexin gene family, which is known to be related to membrane lipid and cytoskeletal components, is involved in a diverse range of biological functions. However, in cassava (Manihot esculenta Crantz), no studies focusing on the roles of annexin genes in response to abiotic stresses, calcium, and hormones have been informed. Results 12 annexin genes were found and assigned to eight chromosomes in the cassava genome. All of the MeAnns contain a typical annexin domain with four 70-amino acid repeats. The MeAnns are classified into six groups in the phylogenetic tree. In their promoter regions, MeAnns possess at least 3 hormone response-related cis-elements and 1 abiotic stress response-related cis-acting element. MeAnn1, MeAnn2 and MeAnn5 exhibit very high levels of expression in each tested organs or tissues. By contrast, MeAnn12 exhibits very low levels in all the tested organs or tissues. qRT-PCR analysis indicates that both MeAnn5 and MeAnn9 have significantly high expression in leaves after cold, drought, and salt treatments and are highly responsive to CaCl2, GA and JA treatments. MeAnn2 and MeAnn10 are significantly downregulated in leaves by cold, drought and salt stress and negatively respond to CaCl2, GA and JA. The expression patterns of MeAnns under cold, drought, and salt stress are irregular in shoots. In roots, MeAnn1 and MeAnn9 are downregulated by cold, CaCl2 and JA treatments, while their other gene expression patterns are irregular. Conclutions In this study, we identified annexin genes in cassava and our expression profiling analysis demonstrated that cassava annexin genes responded to multiple stresses. Our results laid the foundation for further study of the function of cassava anesxin genes and provided an entry point for understanding the response mechanism of cassava to abiotic stress.

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NUCLEAR FACTOR Y, Subunit C (NF-YC) Transcription Factors Are Positive Regulators of Photomorphogenesis in Arabidopsis thaliana

PLoS Genetics ◽

10.1371/journal.pgen.1006333 ◽

2016 ◽

Vol 12 (9) ◽

pp. e1006333 ◽

Cited By ~ 23

Author(s):

Zachary A. Myers ◽

Roderick W. Kumimoto ◽

Chamindika L. Siriwardana ◽

Krystal K. Gayler ◽

Jan R. Risinger ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factors ◽

Nuclear Factor ◽

Subunit C ◽

Nuclear Factor Y ◽

Positive Regulators

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Modulation of DNA topoisomerase IIα promoter activity by members of the Sp (specificity protein) and NF-Y (nuclear factor Y) families of transcription factors

Biochemical Journal ◽

10.1042/bj20030032 ◽

2003 ◽

Vol 374 (3) ◽

pp. 723-729 ◽

Cited By ~ 20

Author(s):

Natisha MAGAN ◽

Agnieszka P. SZREMSKA ◽

Richard J. ISAACS ◽

Kathryn M. STOWELL

Keyword(s):

Transcription Factors ◽

Functional Significance ◽

Regulatory Elements ◽

Resistant Cell ◽

Nuclear Factor ◽

Drug Resistant ◽

Topoisomerase Iiα ◽

Nuclear Factor Y ◽

Specificity Protein ◽

Drug Resistant Cell

topo IIα (topoisomerase IIα) is a major target of several commonly used anticancer drugs and is subject to down-regulation at the transcriptional level in some drug-resistant cell lines and tumours in response to chemotherapy. Clinical resistance to such drugs has been correlated with down-regulation of topo IIα at transcription in some drug-resistant cell lines and tumours. Putative binding sites for a variety of transcription factors, including Sp1 (specificity protein 1) and NF-Y (nuclear factor Y) have previously been identified in the topo IIα promoter, but their functional significance and interactions have not been described following exposure to anti-cancer drugs. The binding of these factors to specific putative regulatory elements in the topo IIα promoter was studied using electrophoretic-mobility-shift assays. Sp1 was found to bind strongly to both distal and proximal GC-rich elements and NF-Y to ICB1 (the first inverted CCAAT box). The functional significance of transcription-factor binding was studied using transient transfection of HeLa cells using a luciferase reporter driven by a 617-bp minimal promoter containing point mutations in putative regulatory elements. Sp1 and NF-Y were both found to be transcriptional modulators with activator or repressor functions depending on protein/DNA context. Moreover, a functional interaction between Sp1 and NF-Y bound at proximal elements was observed.

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The Arabidopsis thaliana Nuclear Factor Y Transcription Factors

Frontiers in Plant Science ◽

10.3389/fpls.2016.02045 ◽

2017 ◽

Vol 07 ◽

Cited By ~ 27

Author(s):

Hang Zhao ◽

Di Wu ◽

Fanying Kong ◽

Ke Lin ◽

Haishen Zhang ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factors ◽

Nuclear Factor ◽

Nuclear Factor Y

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Genomic Organization, Phylogenetic Comparison, and Differential Expression of the Nuclear Factor-Y Gene Family in Apple (Malus Domestica)

Plants ◽

10.3390/plants10010016 ◽

2020 ◽

Vol 10 (1) ◽

pp. 16

Author(s):

Yanjie Qu ◽

Yaping Wang ◽

Jun Zhu ◽

Yugang Zhang ◽

Hongmin Hou

Keyword(s):

Abiotic Stress ◽

Malus Domestica ◽

Growth And Development ◽

Expression Patterns ◽

Specific Response ◽

Nuclear Factor ◽

Element Analysis ◽

Nuclear Factor Y ◽

Gene Structures ◽

Y Family

The nuclear factor Y (NF-Y) as a transcription factor plays an important role in plants growth and development, and response to stress. However, few genome-wide analyzes and functional research of the NF-Y family has been undertaken in apple (Malus domestica Borkh.) so far. In this study, we comprehensively identified the 43 MdNF-Y genes in apple, which dispersedly distributed among the three subgroups based on their sequence alignment analysis, including 11 MdNF-YAs, 22 MdNF-YBs and 10 MdNF-YCs. The members in the same subgroups had similar evolution relationships, gene structures, and conserved motifs. The gene duplication analysis suggested that all the genes were dispersed followed by 27 segmental duplication. Moreover, based on synteny analysis of MdNF-Ys with eight plant species results suggested that some ortholog genes were preserved during the evolution of these species. Cis-element analysis showed potential functions of MdNF-Ys in apple growth and development and responded to abiotic stress. Furthermore, the interaction among MdNF-Ys protein were investigated in yeast two-hybrid assays. The expression patterns of MdNF-Ys in tissue-specific response reveled divergence and might play important role in apple growth and development. Subsequently, whole MdNF-Y genes family was carried out for RT-PCR in response to five abiotic stress (ABA, drought, heat, cold, and salinity) to identify their expression patterns. Taken together, our study will provide a foundation for the further study to the molecular mechanism of apple in growing development and response to abiotic stresses.

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NUCLEAR FACTOR Y, subunit C (NF-YC) transcription factors are positive regulators of photomorphogenesis in Arabidopsis thaliana

10.1101/067462 ◽

2016 ◽

Author(s):

Zachary A. Myers ◽

Roderick W. Kumimoto ◽

Chamindika L. Siriwardana ◽

Krystal K. Gayler ◽

Jan R. Risinger ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Transcription Factors ◽

Leucine Zipper ◽

Complete Picture ◽

Nuclear Factor ◽

Light Perception ◽

Basic Leucine Zipper ◽

Nuclear Factor Y ◽

Positive Regulators ◽

Early Seedling

AbstractRecent reports suggested that NF-Y transcription factors are positive regulators of skotomorphogenesis in Arabidopsis thaliana. Three NF-YC genes (NF-YC3, NF-YC4, and NF-YC9) are known to have overlapping functions in photoperiod dependent flowering and previous studies demonstrated that they interact with basic leucine zipper (bZIP) transcription factors. This included ELONGATED HYPOCOTYL 5 (HY5), which has well-demonstrated roles in photomorphogenesis. Similar to hy5 mutants, we report that nf-yc3 nf-yc4 nf-yc9 triple mutants failed to inhibit hypocotyl elongation in all tested light wavelengths. Surprisingly, nf-yc3 nf-yc4 nf-yc9 hy5 mutants had synergistic defects in light perception, suggesting that NF-Ys represent a parallel light signaling pathway. As with other photomorphogenic transcription factors, nf-yc3 nf-yc4 nf-yc9 triple mutants also partially suppress the short hypocotyl and dwarf rosette phenotypes of CONSTITUTIVE PHOTOMORPHOGENIC 1 (cop1) mutants. Thus, our data strongly suggest that NF-Y transcription factors have important roles as positive regulators of photomorphogenesis, and in conjunction with other recent reports implies that the NF-Y are multifaceted regulators of early seedling development.Author SummaryLight perception is critically important for the fitness of plants in both natural and agricultural settings. Plants not only use light for photosynthesis, but also as a cue for proper development. As a seedling emerges from soil it must determine the light environment and adopt an appropriate growth habit. When blue and red wavelengths are the dominant sources of light, plants will undergo photomorphogenesis. Photomorphogenesis describes a number of developmental responses initiated by light in a seedling, and includes shortened stems and establishing the ability to photosynthesize. The genes regulating photomorphogenesis have been studied extensively, but a complete picture remains elusive. Here we describe the finding that NUCLEAR FACTOR-Y (NF-Y) genes are positive regulators of photomorphogenesis - i.e., in plants where NF-Y genes are mutated, they display some characteristics of dark grown plants, even though they are in the light. Our data suggests that the roles of NF-Y genes in light perception do not fit in easily with those of other described pathways. Thus, studying these genes promises to help develop a more complete picture of how light drives plant development.

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NF-YB-Mediated Active Responses of Plant Growth under Salt and Temperature Stress in Eucalyptus grandis

Plants ◽

10.3390/plants10061107 ◽

2021 ◽

Vol 10 (6) ◽

pp. 1107

Author(s):

Jia-Hao Dai ◽

An-Qi Hu ◽

Jia-Shuo Zhang ◽

Wen-Hai Liao ◽

Hua-Yan Ma ◽

...

Keyword(s):

Plant Growth ◽

Stress Responses ◽

Expression Profiles ◽

Expression Patterns ◽

Eucalyptus Grandis ◽

Nuclear Factor ◽

Nuclear Factor Y ◽

Gene Structures ◽

Genetic Structures ◽

Y Family

The transcription factor NF-YB (nuclear factor-YB) family is a subfamily of the nuclear factor Y (NF-Y), which plays an important role in regulating plant growth, development and participates in various stress responses. Although the NF-Y family has been studied in many species, it is still obscure in Eucalyptus grandis. In this study, 23 EgNF-YB genes in eucalyptus were identified and unevenly distributed on 11 chromosomes. Phylogenetic analysis showed the EgNF-YB genes were divided into two clades, LEC-1 type and non-LEC1 type. The evolution of distinct clades was relatively conservative, the gene structures were analogous, and the differences of genetic structures among clades were small. The expression profiles showed that the distinct EgNF-YB genes were highly expressed in diverse tissues, and EgNF-YB4/6/13/19/23 functioned in response to salinity, heat and cold stresses. Our study characterized the phylogenetic relationship, gene structures and expression patterns of EgNF-YB gene family and investigated their potential roles in abiotic stress responses, which provides solid foundations for further functional analysis of NF-YB genes in eucalyptus.

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