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Characterization of the Tomato ARF Gene Family Uncovers a Multi-Levels Post-Transcriptional Regulation Including Alternative Splicing 总被引:1,自引:0,他引:1
Mohamed Zouine Yongyao Fu Anne-Laure Chateigner-Boutin Isabelle Mila Pierre Frasse Hua Wang Corinne Audran Jean-Paul Roustan Mondher Bouzayen 《PloS one》2014,9(1)
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Auxin response factors (ARFs), member of the plant-specific B3 DNA binding superfamily, target specifically to auxin response
elements (AuxREs) in promoters of primary auxin-responsive genes and heterodimerize with Aux/IAA proteins in auxin signaling
transduction cascade. In previous research, we have isolated and characterized maize Aux/IAA genes in whole-genome scale. Here, we report the comprehensive analysis of ARF genes in maize. A total of 36 ARF genes were identified and validated from the B73 maize genome through an iterative strategy. Thirty-six maize ARF genes are distributed in all maize chromosomes except chromosome 7. Maize ARF genes expansion is mainly due to recent segmental duplications. Maize ARF proteins share one B3 DNA binding domain which
consists of seven-stranded β sheets and two short α helixes. Twelve maize ARFs with glutamine-rich middle regions could be as activators in modulating expression of auxin-responsive
genes. Eleven maize ARF proteins are lack of homo- and heterodimerization domains. Putative cis-elements involved in phytohormones and light signaling responses, biotic and abiotic stress adaption locate in promoters
of maize ARF genes. Expression patterns vary greatly between clades and sister pairs of maize ARF genes. The B3 DNA binding and auxin response factor domains of maize ARF proteins are primarily subjected to negative selection
during selective sweep. The mixed selective forces drive the diversification and evolution of genomic regions outside of B3
and ARF domains. Additionally, the dicot-specific proliferation of ARF genes was detected. Comparative genomics analysis indicated that maize, sorghum and rice duplicate chromosomal blocks containing
ARF homologs are highly syntenic. This study provides insights into the distribution, phylogeny and evolution of ARF gene
family. 相似文献
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Liyan Su Ming Xu Jiudong Zhang Yihang Wang Yushan Lei Qiang Li 《Physiology and Molecular Biology of Plants》2021,27(6):1261
Auxin response factor (ARF) acts as a vital component of auxin signaling and participates in growth, development, and stress responses in plants. In the present study, we comprehensively analyzed kiwifruit’s (Actinidia chinensis) ARF genes (AcARFs) and their involvement in abiotic stress response. We identified a total of 41 AcARFs encoding ARFs in the A. chinensis genome. AcARF genes were characterized by the classic ARF_resp and a B3 domain and primarily localized on the cytoplasm and nucleus. AcARFs were categorized into eight subgroups as per the phylogenetic analysis. Synteny analysis showed that 35 gene pairs in AcARF family underwent segmental and whole genome duplication events. Promoter cis-element prediction revealed that AcARFs might be involved in abiotic factors related to stress response, which was later assessed and validated by qRT-PCR based expression analysis. Additionally, AcARFs showed tissue-specific expression. These findings extend our understanding of the functional roles of AcARFs in stress responses. Taken together, the systematic annotation of the AcARF family genes provides a platform for the functional and evolutionary study, which might help in elucidating the precise roles of the AcARFs in stress responses.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-01011-4. 相似文献
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Yan Liu HaiYang Jiang Wenjuan Chen Yexiong Qian Qing Ma Beijiu Cheng Suwen Zhu 《Plant Growth Regulation》2011,63(3):225-234
Auxin response factors (ARFs) are an important family involved in auxin-mediated response through specific binding to auxin
response elements (AuxREs). A few members of the ARF family have been functionally characterized in Arabidopsis, rice (Oryza sativa), Poplar (Populous trichocarpa). However, little is known about ARF genes in maize (Zea mays). We performed a comprehensive bioinformatics analysis of the maize ARF gene family including analysis of the genome sequence, conserved domains, chromosomal locations, phylogenetic relationships,
gene duplication, and expression profiles. 35 ZmARF genes were identified and categorized into four groups (Class I, II, III, and IV). In addition, a segmental ZmARF duplication event was shown to play an important role in maize ARF gene expansion. 7 ZmARF genes had no expression in specific tissues we obtained, but presented in mixed tissues according to the NCBI EST database,
respectively. These studies have laid the theoretical foundation for further functional verification of these ZmARF genes. 相似文献
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Genome-wide identification and expression analysis of peach auxin response factor gene families 总被引:1,自引:0,他引:1
Huifeng Li Kun Ran Qingrong Sun 《Journal of plant biochemistry and biotechnology.》2016,25(4):349-357
Plant auxin response factors (ARFs) are involved in plant growth, development and multiple other processes. In this study, the ARF gene family in the peach genome was identified by bioinformatics software and RT-PCR. In total, 18 PpARF candidate genes were found in the peach genome. The DNA-binding and ARF domains, as well as motif III and IV of the PpARF gene family were highly conserved. The phylogenetic analysis revealed that PpARF gene family was divided into five classes: Class I (three members), Class II (four members), Class III (five members), Class IV (three members) and Class V (three members). The results of an intron-exon structure analysis indicated that PpARF gene family members were composed of 2–15 exons. A chromosome mapping analysis revealed that PpARF genes were distributed with different densities over eight chromosomes, with the largest number of PpARF genes on chromosome 1 (four genes), followed by chromosome 4 and 6 (three genes each). Only one gene was located on each of chromosome 3, 7 and 8. A conserved motif analysis revealed that the DNA-binding and ARF domains were observed in all PpARF proteins (except for PpARF18). Class I contained no motifs III or IV (except for PpARF7). RT-PCR results indicated that all of the PpARF genes, with the exception of PpARF15 and PpARF17, were expressed in at least one of the tissues (roots, stems, leaves, flowers and five stages of fruit development). These results suggested that the PpARF gene family members are highly and structurally conserved, and are involved in various aspects of peach growth and development, especially in fruit development. 相似文献
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INK4a/ARF基因位于人染色体9p21,是人类肿瘤中最常见的基因失活位点之一.INK4a/ARF基因有两套各自独立的启动子,通过可变阅读框,能够编码两种蛋白质:p16INK4a和p14ARF(ARF在鼠细胞中为p19ARF).p16作为CDK4/6的抑制因子,能够阻断pRb磷酸化,将细胞周期阻断在G1期;而ARF可结合原癌蛋白MDM2,稳定p53,将细胞周期阻断在G1期和G2/M转换期,或诱导细胞凋亡.因此ARF蛋白和p16一样也是一种肿瘤抑制因子. 相似文献
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Auxin response factors 总被引:7,自引:0,他引:7
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The F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants 总被引:3,自引:0,他引:3
Yang X Kalluri UC Jawdy S Gunter LE Yin T Tschaplinski TJ Weston DJ Ranjan P Tuskan GA 《Plant physiology》2008,148(3):1189-1200
F-box proteins are generally responsible for substrate recognition in the Skp1-Cullin-F-box complexes that are involved in protein degradation via the ubiquitin-26S proteasome pathway. In plants, F-box genes influence a variety of biological processes, such as leaf senescence, branching, self-incompatibility, and responses to biotic and abiotic stresses. The number of F-box genes in Populus (Populus trichocarpa; approximately 320) is less than half that found in Arabidopsis (Arabidopsis thaliana; approximately 660) or Oryza (Oryza sativa; approximately 680), even though the total number of genes in Populus is equivalent to that in Oryza and 1.5 times that in Arabidopsis. We performed comparative genomics analysis between the woody perennial plant Populus and the herbaceous annual plants Arabidopsis and Oryza in order to explicate the functional implications of this large gene family. Our analyses reveal interspecific differences in genomic distribution, orthologous relationship, intron evolution, protein domain structure, and gene expression. The set of F-box genes shared by these species appear to be involved in core biological processes essential for plant growth and development; lineage-specific differences primarily occurred because of an expansion of the F-box genes via tandem duplications in Arabidopsis and Oryza. The number of F-box genes in the newly sequenced woody species Vitis (Vitis vinifera; 156) and Carica (Carica papaya; 139) is similar to that in Populus, supporting the hypothesis that the F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. This study provides insights into the relationship between the structure and composition of the F-box gene family in herbaceous and woody species and their associated developmental and physiological features. 相似文献