scholarly journals Aux/IAA and ARF Gene Families in Salix suchowensis: Identification, Evolution, and Dynamic Transcriptome Profiling During the Plant Growth Process

2021 ◽  
Vol 12 ◽  
Author(s):  
Suyun Wei ◽  
Yingnan Chen ◽  
Jing Hou ◽  
Yonghua Yang ◽  
Tongming Yin
Keyword(s):  
Plant Growth ◽  
Growth Process ◽  
Transcriptome Profiling ◽  
Gene Families ◽  
Auxin Signaling ◽  
Vascular Differentiation ◽  
Auxin Signaling Pathway ◽  
Functional Involvement ◽  
Functional Features ◽  
Gene Structures

The phytohormone auxin plays a pivotal role in the regulation of plant growth and development, including vascular differentiation and tree growth. The auxin/indole-3-acetic acid (Aux/IAA) and auxin response transcription factor (ARF) genes are key components of plant auxin signaling. To gain more insight into the regulation and functional features of Aux/IAA and ARF genes during these processes, we identified 38 AUX/IAA and 34 ARF genes in the genome of Salix suchowensis and characterized their gene structures, conserved domains, and encoded amino acid compositions. Phylogenetic analysis of some typical land plants showed that the Aux/IAA and ARF genes of Salicaceae originated from a common ancestor and were significantly amplified by the ancestral eudicot hexaploidization event and the “salicoid” duplication that occurred before the divergence of poplar and willow. By analyzing dynamic transcriptome profiling data, some Aux/IAA and ARF genes were found to be involved in the regulation of plant growth, especially in the initial plant growth process. Additionally, we found that the expression of several miR160/miR167-ARFs was in agreement with canonical miRNA–ARF interactions, suggesting that miRNAs were possibly involved in the regulation of the auxin signaling pathway and the plant growth process. In summary, this study comprehensively analyzed the sequence features, origin, and expansion of Aux/IAA and ARF genes, and the results provide useful information for further studies on the functional involvement of auxin signaling genes in the plant growth process.

scholarly journals Accelerating structure-function mapping using the ViVa webtool to mine natural variation

2018 ◽  
Author(s):  
Morgan O Hamm ◽  
Britney L Moss ◽  
Alexander R Leydon ◽  
Hardik P Gala ◽  
Amy Lanctot ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Network ◽  
Natural Variation ◽  
Genetic Resource ◽  
Gene Families ◽  
Auxin Signaling ◽  
Human Genetic Variation ◽  
Auxin Signaling Pathway ◽  
Accelerating Structure ◽  
Or Gene

Thousands of sequenced genomes are now publicly available capturing a significant amount of natural variation within plant species; yet, much of this data remains inaccessible to researchers without significant bioinformatics experience. Here, we present a webtool called ViVa (Visualizing Variation) which aims to empower any researcher to take advantage of the amazing genetic resource collected in the Arabidopsis thaliana 1001 Genomes Project (http://1001genomes.org). ViVa facilitates data mining on the gene, gene family or gene network level. To test the utility and accessibility of ViVa, we assembled a team with a range of expertise within biology and bioinformatics to analyze the natural variation within the well-studied nuclear auxin signaling pathway. Our analysis has provided further confirmation of existing knowledge and has also helped generate new hypotheses regarding this well studied pathway. These results highlight how natural variation could be used to generate and test hypotheses about less studied gene families and networks, especially when paired with biochemical and genetic characterization. ViVa is also readily extensible to databases of interspecific genetic variation in plants as well as other organisms, such as the 3,000 Rice Genomes Project (http://snp-seek.irri.org/) and human genetic variation (https://www.ncbi.nlm.nih.gov/clinvar/).

scholarly journals Genome-Wide Identification and Co-Expression Analysis of ARF and IAA Family Genes in Euscaphis konishii: Potential Regulators of Triterpenoids and Anthocyanin Biosynthesis

2022 ◽  
Vol 12 ◽  
Author(s):  
Bobin Liu ◽  
Juanli Zhu ◽  
Lina Lin ◽  
Qixin Yang ◽  
Bangping Hu ◽  
...  
Keyword(s):  
Anthocyanin Biosynthesis ◽  
Southern China ◽  
Gene Families ◽  
Auxin Signaling ◽  
Auxin Response ◽  
Chromosomal Distribution ◽  
Element Analysis ◽  
Genome Wide ◽  
Gene Structures

Euscaphis konishii is an evergreen plant that is widely planted as an industrial crop in Southern China. It produces red fruits with abundant secondary metabolites, giving E. konishii high medicinal and ornamental value. Auxin signaling mediated by members of the AUXIN RESPONSE FACTOR (ARF) and auxin/indole-3-acetic acid (Aux/IAA) protein families plays important roles during plant growth and development. Aux/IAA and ARF genes have been described in many plants but have not yet been described in E. konishii. In this study, we identified 34 EkIAA and 29 EkARF proteins encoded by the E. konishii genome through database searching using HMMER. We also performed a bioinformatic characterization of EkIAA and EkARF genes, including their phylogenetic relationships, gene structures, chromosomal distribution, and cis-element analysis, as well as conserved motifs in the proteins. Our results suggest that EkIAA and EkARF genes have been relatively conserved over evolutionary history. Furthermore, we conducted expression and co-expression analyses of EkIAA and EkARF genes in leaves, branches, and fruits, which identified a subset of seven EkARF genes as potential regulators of triterpenoids and anthocyanin biosynthesis. RT-qPCR, yeast one-hybrid, and transient expression analyses showed that EkARF5.1 can directly interact with auxin response elements and regulate downstream gene expression. Our results may pave the way to elucidating the function of EkIAA and EkARF gene families in E. konishii, laying a foundation for further research on high-yielding industrial products and E. konishii breeding.

scholarly journals The Gene FvTST1 From Strawberry Modulates Endogenous Sugars Enhancing Plant Growth and Fruit Ripening

2022 ◽  
Vol 12 ◽  
Author(s):  
Arif Rashid ◽  
Haixiang Ruan ◽  
Yunsheng Wang
Keyword(s):  
Plant Growth ◽  
Fruit Ripening ◽  
Target Genes ◽  
Developmental Stages ◽  
Sugar Transport ◽  
Biological Significance ◽  
Sugar Accumulation ◽  
Auxin Signaling ◽  
Auxin Signaling Pathway ◽  
Differential Expression Pattern

Sugar is an important carbon source and contributes significantly to the improvement of plant growth and fruit flavor quality. Sugar transport through the tonoplast is important for intracellular homeostasis and metabolic balance in plant cells. There are four tonoplast sugar transporters (FvTST1-4) in strawberry genome. The qRT-PCR results indicated that FvTST1 has a differential expression pattern in different tissues and developmental stages, and exhibited highest expression level in mature fruits. The yeast complementation assay showed that FvTST1 can mediate the uptake of different sugars, such as fructose, glucose, sucrose, and mannose. Subcellular localization analyses revealed that FvTST1 was mainly targeted to the tonoplast. Transient expression of FvTST1 in strawberry fruits enhanced both fruit ripening and sugar accumulation. Furthermore, FvTST1-transformed tomato plants exhibited higher sucrose and auxin content, enhanced seed germination and vegetative growth, higher photosynthetic rate, early flowering, and bore fruit; fructose and glucose levels were higher in transgenic fruits than those in the control. Transcriptomic analysis indicated that the auxin signaling pathway was highly enriched pathway in up-regulated Gene-ontology terms. In transgenic plants, genes encoding transcription factors, such as phytochrome-interacting factors PIF1, -3, and -4, as well as their potential target genes, were also induced. Collectively, the results show that FvTST1 enhances plant growth and fruit ripening by modulating endogenous sugars, and highlight the biological significance of this gene for future breeding purposes.

scholarly journals Genome-Wide Analysis of Auxin Receptor Family Genes in Brassica juncea var. tumida

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 165 ◽  
Author(s):  
Zhaoming Cai ◽  
De-er Zeng ◽  
Jingjing Liao ◽  
Chunhong Cheng ◽  
Zulfiqar Ali Sahito ◽  
...  
Keyword(s):  
Plant Growth ◽  
Brassica Juncea ◽  
Plasmodiophora Brassicae ◽  
Auxin Signaling ◽  
Auxin Receptor ◽  
Biotic Stresses ◽  
Genome Wide ◽  
Gene Structures ◽  
Receptor Family

Transport inhibitor response 1/auxin signaling f-box proteins (TIR1/AFBs) play important roles in the process of plant growth and development as auxin receptors. To date, no information has been available about the characteristics of the TIR1/AFB gene family in Brassica juncea var. tumida. In this study, 18 TIR1/AFB genes were identified and could be clustered into six groups. The genes are located in 11 of 18 chromosomes in the genome of B. juncea var. tumida, and similar gene structures are found for each of those genes. Several cis-elements related to plant response to phytohormones, biotic stresses, and abiotic stresses are found in the promoter of BjuTIR1/AFB genes. The results of qPCR analysis show that most genes have differential patterns of expression among six tissues, with the expression levels of some of the genes repressed by salt stress treatment. Some of the genes are also responsive to pathogen Plasmodiophora brassicae treatment. This study provides valuable information for further studies as to the role of BjuTIR1/AFB genes in the regulation of plant growth, development, and response to abiotic stress.

scholarly journals A chemically induced proximity system engineered from the plant auxin signaling pathway

2018 ◽  
Vol 9 (26) ◽  
pp. 5822-5827 ◽  
Author(s):  
Weiye Zhao ◽  
Huong Nguyen ◽  
Guihua Zeng ◽  
Dan Gao ◽  
Hao Yan ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Auxin Signaling ◽  
Auxin Signaling Pathway ◽  
Chemically Induced

A new chemically induced proximity system is developed by engineering the plant auxin signaling pathway.

Identification of Auxin Activity Like 1, a chemical with weak functions in auxin signaling pathway

2018 ◽  
Vol 98 (3) ◽  
pp. 275-287
Author(s):  
Wenbo Li ◽  
Haimin Li ◽  
Peng Xu ◽  
Zhi Xie ◽  
Yajin Ye ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Auxin Signaling ◽  
Auxin Activity ◽  
Auxin Signaling Pathway

scholarly journals Molecular Rewiring of the Jasmonate Signaling Pathway to Control Auxin-Responsive Gene Expression

Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 641
Author(s):  
Ning Li ◽  
Linggai Cao ◽  
Wenzhuo Miu ◽  
Ruibin Cao ◽  
Mingbo Peng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Signaling Pathway ◽  
Developmental Process ◽  
Expression System ◽  
Transient Gene Expression ◽  
Transcriptional Repressor ◽  
Auxin Signaling ◽  
General Strategy ◽  
Auxin Signaling Pathway ◽  
Responsive Gene

The plant hormone jasmonic acid (JA) has an important role in many aspects of plant defense response and developmental process. JA triggers interaction between the F-box protein COI1 and the transcriptional repressors of the JAZ family that leads the later to proteasomal degradation. The Jas-motif of JAZs is critical for mediating the COI1 and JAZs interaction in the presence of JA. Here, by using the protoplast transient gene expression system we reported that the Jas-motif of JAZ1 was necessary and sufficient to target a foreign reporter protein for COI1-facilitated degradation. We fused the Jas-motif to the SHY2 transcriptional repressor of auxin signaling pathway to create a chimeric protein JaSHY. Interestingly, JaSHY retained the transcriptional repressor function while become degradable by the JA coreceptor COI1 in a JA-dependent fashion. Moreover, the JA-induced and COI1-facilitated degradation of JaSHY led to activation of a synthetic auxin-responsive promoter activity. These results showed that the modular components of JA signal transduction pathway can be artificially redirected to regulate auxin signaling pathway and control auxin-responsive gene expression. Our work provides a general strategy for using synthetic biology approaches to explore and design cell signaling networks to generate new cellular functions in plant systems.

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