Genome-Wide Identification of the Transcription Factors Involved in Citrus Fruit Ripening from the Transcriptomes of a Late-Ripening Sweet Orange Mutant and Its Wild Type

Abstract Background: Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results: In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions: These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

Download Full-text

Genome-wide regulation of light-controlled seedling morphogenesis by three families of transcription factors

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1803861115 ◽

2018 ◽

Vol 115 (25) ◽

pp. 6482-6487 ◽

Cited By ~ 27

Author(s):

Hui Shi ◽

Mohan Lyu ◽

Yiwen Luo ◽

Shoucheng Liu ◽

Yue Li ◽

...

Keyword(s):

Transcription Factors ◽

Continuous Light ◽

Specific Protein ◽

Bhlh Protein ◽

Wild Type ◽

Morphological Aspects ◽

Genome Wide ◽

Wide Range ◽

Transcriptional Changes ◽

Bzip Proteins

Three families of transcription factors have been reported to play key roles in light control of Arabidopsis seedling morphogenesis. Among them, bHLH protein PIFs and plant-specific protein EIN3/EIN3-LIKE 1 (EIN3/EIL1) accumulate in the dark to maintain skotomorphogenesis. On the other hand, HY5 and HY5 HOMOLOG (HYH), two related bZIP proteins, are stabilized in light and promote photomorphogenic development. To systemically investigate the transcriptional regulation of light-controlled seedling morphogenesis, we generated HY5ox/pifQein3eil1, which contained mutations of EIN3/EIL1 and four PIF genes (pifQein3eil1) and overexpression of HY5. Our results show that dark-grown HY5ox/pifQein3eil1 seedlings display a photomorphogenesis highly similar to that of wild-type seedlings grown in continuous light, with remarkably enhanced photomorphogenic phenotypes compared with the pifQ mutants. Consistent with the genetic evidence, transcriptome analysis indicated that PIFs, EIN3/EIL1, and HY5 are dominant transcription factors in collectively mediating a wide range of light-caused genome-wide transcriptional changes. Moreover, PIFs and EIN3/EIL1 independently control the expression of light-regulated genes such as HLS1 to cooperatively regulate apical hook formation, hypocotyl elongation, and cotyledon opening and expansion. This study illustrates a comprehensive regulatory network of transcription activities that correspond to specific morphological aspects in seedling skotomorphogenesis and photomorphogenesis.

Download Full-text

Genome-Wide Characterization of R2R3-MYB Transcription Factors in Pitaya Reveals a R2R3-MYB Repressor HuMYB1 Involved in Fruit Ripening through Regulation of Betalain Biosynthesis by Repressing Betalain Biosynthesis-Related Genes

Cells ◽

10.3390/cells10081949 ◽

2021 ◽

Vol 10 (8) ◽

pp. 1949

Author(s):

Fangfang Xie ◽

Qingzhu Hua ◽

Canbin Chen ◽

Zhike Zhang ◽

Rong Zhang ◽

...

Keyword(s):

Transcription Factors ◽

Gene Family ◽

Fruit Ripening ◽

Phylogenetic Analyses ◽

Luciferase Reporter ◽

Molecular Characteristics ◽

Genome Data ◽

Genome Wide ◽

Hylocereus Undatus ◽

R2r3 Myb

The MYB (myeloblastosis) superfamily constitutes one of the most abundant transcription factors (TFs) regulating various biological processes in plants. However, the molecular characteristics and functions of MYB TFs in pitaya remain unclear. To date, no genome-wide characterization analysis of this gene family has been conducted in the Cactaceae species. In this study, 105 R2R3-MYB members were identified from the genome data of Hylocereus undatus and their conserved motifs, physiological and biochemical characteristics, chromosome locations, synteny relationship, gene structure and phylogeny were further analyzed. Expression analyses suggested that three up-regulated HuMYBs and twenty-two down-regulated HuMYBs were probably involved in fruit ripening of pitaya. Phylogenetic analyses of R2R3-MYB repressors showed that seven HuMYBs (HuMYB1, HuMYB21, HuMYB48, HuMYB49, HuMYB72, HuMYB78 and HuMYB101) were in clades containing R2R3-MYB repressors. HuMYB1 and HuMYB21 were significantly down-regulated with the betalain accumulation during fruit ripening of ‘Guanhuahong’ pitaya (H. monacanthus). However, only HuMYB1 had R2 and R3 repeats with C1, C2, C3 and C4 motifs. HuMYB1 was localized exclusively to the nucleus and exhibited transcriptional inhibition capacities. Dual luciferase reporter assay demonstrated that HuMYB1 inhibited the expression of betalain-related genes: HuADH1, HuCYP76AD1-1 and HuDODA1. These results suggested that HuMYB1 is a potential repressor of betalain biosynthesis during pitaya fruit ripening. Our results provide the first genome-wide analyses of the R2R3-MYB subfamily involved in pitaya betalain biosynthesis and will facilitate functional analysis of this gene family in the future.

Download Full-text

Citrus sinensis CBF1 Functions in Cold Tolerance by Modulating Putrescine Biosynthesis Through Regulation of ARGININE DECARBOXYLASE

Plant and Cell Physiology ◽

10.1093/pcp/pcab135 ◽

2021 ◽

Author(s):

Jie Song ◽

Hao Wu ◽

Feng He ◽

Jing Qu ◽

Yue Wang ◽

...

Keyword(s):

Transcription Factors ◽

Stress Response ◽

Transgenic Plants ◽

Cold Stress ◽

Cold Tolerance ◽

Citrus Sinensis ◽

Sweet Orange ◽

Arginine Decarboxylase ◽

Wild Type ◽

Shed Light

Abstract C-repeat (CRT) binding factors (CBFs) are well known to act as crucial transcription factors that function in cold stress response. Arginine decarboxylase (ADC)-mediated putrescine biosynthesis has been reported to be activated in plants exposed to cold conditions, but it remains elusive whether CBFs can regulate ADC expression and putrescine accumulation. In this study, we show that cold up-regulated ADC gene (CsADC) and elevation of endogenous putrescine content in sweet orange (Citrus sinensis). Promoter of CsADC contains two CRT sequences that are canonical elements recognized by CBFs. Sweet orange genome contains four CBFs (CsCBF1-4), in which CsCBF1 was significantly induced by cold. CsCBF1, located in the nucleus, was demonstrated to bind directly and specifically to the promoter of CsADC and acted as a transcriptional activator. Overexpression of CsCBF1 led to notable elevation of CsADC and putrescine level in sweet orange transgenic plants, along with remarkably enhanced cold tolerance, relative to the wild type (WT). However, pretreatment with D-arginine, an ADC inhibitor, caused prominent reduction of endogenous putrescine level in the overexpressing lines, accompanied by greatly compromised cold tolerance. Taken together, these results demonstrate that CBF1 of sweet orange directly regulates ADC expression and modulates putrescine synthesis for orchestrating the cold tolerance. Our findings shed light into the transcriptional regulation of putrescine accumulation through targeting the ADC gene in the presence of cold stress. Meanwhile, this study illustrates a new mechanism underlying the CBF-mediated cold stress response.

Download Full-text

Genome-Wide Analysis of Basic Helix-Loop-Helix Transcription Factors to Elucidate Candidate Genes Related to Fruit Ripening and Stress in Banana (Musa acuminata L. AAA Group, cv. Cavendish)

Frontiers in Plant Science ◽

10.3389/fpls.2020.00650 ◽

2020 ◽

Vol 11 ◽

Author(s):

Zhuo Wang ◽

Caihong Jia ◽

Jing-Yi Wang ◽

Hong-Xia Miao ◽

Ju-Hua Liu ◽

...

Keyword(s):

Transcription Factors ◽

Candidate Genes ◽

Fruit Ripening ◽

Musa Acuminata ◽

Genome Wide Analysis ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Genome Wide

Download Full-text

Genome-Wide Identification of WRKY Transcription Factors in Chinese jujube (Ziziphus jujuba Mill.) and Their Involvement in Fruit Developing, Ripening, and Abiotic Stress

Genes ◽

10.3390/genes10050360 ◽

2019 ◽

Vol 10 (5) ◽

pp. 360 ◽

Cited By ~ 3

Author(s):

Xin Chen ◽

Ruihong Chen ◽

Yanfeng Wang ◽

Cuiyun Wu ◽

Jian Huang

Keyword(s):

Transcription Factors ◽

Fruit Ripening ◽

Transcript Abundance ◽

Northern China ◽

Tissue Expression ◽

Chinese Jujube ◽

Wrky Transcription Factors ◽

Genome Wide ◽

Jujube Fruit ◽

Ziziphus Jujuba

Chinese jujube (Ziziphus jujuba Mill.) is an economically important fruit crop in China and mainly cultivated on land with high salinity and drought conditions in northern China. WRKY transcription factors (TFs) are involved in plant development and in responses to multiple abiotic stresses. In this study, we identified 61 and 52 putative ZjWRKY TFs in ‘Junzao’ and ‘Dongzao’ at the genome-wide level. Tissue expression profiling showed that 7 genes were constitutively expressed at high level in all tissues of ‘Junzao’. Transcriptome analysis revealed that 39 ZjWRKY genes were expressed during ‘Junzao’ jujube fruit ripening. Among these genes, the transcript abundance of 19 genes were differentially expressed between ‘Junzao’ and ‘Qingjiansuanzao’ fruit. In addition, RT-qPCR analyses revealed that 30, 14, and 18 ZjWRKY genes responded to drought, NaCl, and ABA treatments, respectively. Taken together, ZjWRKY genes expression dynamics during jujube fruit development, ripening, and their differences between jujube and wild jujube would provide insights into their possible roles regulating fruit ripening. In addition, those ZjWRKY genes responded strongly to drought and salt stress, which provide candidate ZjWRKY genes for facilitating tolerance breeding.

Download Full-text

An integrative analysis of the transcriptome and proteome of the pulp of a spontaneous late-ripening sweet orange mutant and its wild type improves our understanding of fruit ripening in citrus

Journal of Experimental Botany ◽

10.1093/jxb/eru044 ◽

2014 ◽

Vol 65 (6) ◽

pp. 1651-1671 ◽

Cited By ~ 78

Author(s):

Juxun Wu ◽

Zhilong Xu ◽

Yajian Zhang ◽

Lijun Chai ◽

Hualin Yi ◽

...

Keyword(s):

Fruit Ripening ◽

Sweet Orange ◽

Integrative Analysis ◽

Wild Type

Download Full-text

Genome-wide analysis of the AREB/ABF gene lineage in land plants and functional analysis of TaABF3 in Arabidopsis

BMC Plant Biology ◽

10.1186/s12870-020-02783-9 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Fangfang Li ◽

Fangming Mei ◽

Yifang Zhang ◽

Shumin Li ◽

Zhensheng Kang ◽

...

Keyword(s):

Transcription Factors ◽

Phylogenetic Relationship ◽

Developmental Stages ◽

Land Plants ◽

Wild Type ◽

Abiotic Stress Response ◽

Genome Wide ◽

Protein Properties ◽

Relationship Of ◽

Signaling Components

Abstract Background Previous studies have shown that ABFs (abscisic acid-responsive transcription factors) are important ABA-signaling components that participate in abiotic stress response. However, little is known about the function of ABFs in Triticum aestivum. In addition, although various ABFs have been identified in other species, the phylogenetic relationship between ABF transcription factors has not been systemically investigated in land plants. Results In this study, we systemically collected ABFs from land plants and analyzed the phylogenetic relationship of these ABF genes. The ABF genes are present in all the land plants we investigated, including moss, lycophyte, monocots, and eudicots. Furthermore, these ABF genes are phylogenetically divided into seven subgroups, differentiations that are supported by variation in the gene structure, protein properties, and motif patterns. We further demonstrated that the expression of ABF genes varies among different tissues and developmental stages, and are induced by one or more environmental stresses. Furthermore, we found that three wheat ABFs (TaABF1, TaABF2, and TaABF3) were significantly induced by drought stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaABF3 displayed enhanced drought tolerance. Conclusions These results provide important ground work for understanding the phylogenetic relationships between plant ABF genes. Our results also indicate that TaABFs may participate in regulating plant response to abiotic stresses.

Download Full-text