Evolutionary origins and functional diversification of Auxin Response Factors

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Дек. 30, 2024

The Auxin Response Factors (ARFs) family of transcription factors are the central mediators auxin-triggered transcriptional regulation. Functionally different classes extant ARFs operate as antagonistic auxin-dependent and -independent regulators. While part evolutionary trajectory to present auxin response functions has been reconstructed, it is unclear how emerged, early diversification led functionally proteins. Here, we use in silico vivo analyses revisit molecular events that origin subsequent evolution ARFs. We reveal shared from preexisting domains, uncovering a protein fold homologous ARF DNA-binding conserved eukaryotic chromatin regulator. Building on this, reconstruct complete history ARFs, including divergence leading appearance defining main targets for their functional diversification. derive emergence nuclear signalling pathway.

Язык: Английский

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Pan-genome analysis and expression verification of the maize ARF gene family

Frontiers in Plant Science, Год журнала: 2025, Номер 15

Опубликована: Фев. 11, 2025

Auxin transcription factors regulate auxin responses and play crucial roles in plant growth, development, to abiotic stress. Utilizing the maize pan-genome data, this study identified 35 ARF family members maize, comprising 21 core genes, 10 near-core 4 non-essential genes; no private genes were detected. The construction of a phylogenetic tree using Arabidopsis thaliana revealed that G3 subfamily comprises highest number with total 10, exhibits relative stability throughout evolution maize. calculation Ka/Ks ratios for across 26 genomes indicated that, aside from ARF8 ARF11 , which subjected positive selection, remaining underwent purifying selection. Analysis structural variation expression level ARF4 gene significantly differed as result variation. Simultaneously, also influenced conserved domain cis-acting elements gene. Further combining transcriptome data RT-qPCR found levels higher at early stage embryo grain each member complementary, plays an important role In summary, utilizes bioinformatics methods investigate evolutionary relationships functional thereby providing novel theoretical framework further research on family.

Язык: Английский

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Comparative mutant analyses reveal a novel mechanism of ARF regulation in land plants

Nature Plants, Год журнала: 2025, Номер unknown

Опубликована: Апрель 11, 2025

Язык: Английский

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Genome-Wide Identification and Analysis of Auxin Response Factor Transcription Factor Gene Family in Populus euphratica

Plants, Год журнала: 2025, Номер 14(8), С. 1248 - 1248

Опубликована: Апрель 19, 2025

Auxin response factor (ARF) is a plant-specific transcription that responds to changes in auxin levels, regulating various biological processes plants such as flower development, senescence, lateral root formation, stress response, and secondary metabolite accumulation. In this study, we identified the ARF gene family Populus euphratica Oliv. using bioinformatics analysis, examining their conserved structural domains, structure, expression products, evolutionary relationships. We found 34 PeARF genes were unevenly distributed on 19 chromosomes of P. euphratica. All 56 proteins hydrophilic unstable localized nucleus, with structures containing α-helices, extended strands, random coils, β-turns but lacking transmembrane helices (TM-helices) signal peptides. Evolutionary analysis divided into five subfamilies (A–E), high conservation observed order number motifs, other characteristics within each subfamily. Expression pattern revealed 17 upregulated during cell growth heterophylly development. This comprehensive provides insights molecular mechanisms growth, serving basis for further studies signaling pathway

Язык: Английский

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Auxin response factors: important keys for understanding regulatory mechanisms of fleshy fruit development and ripening

Horticulture Research, Год журнала: 2024, Номер 11(10)

Опубликована: Июль 31, 2024

Auxin response transcription factors (ARFs) form a large gene family, many of whose members operate at the final step auxin signaling pathway. ARFs participate directly in aspects plant growth and development. Here we summarize recent advances understanding roles regulating fleshy fruit development ripening. play crucial role size, color, nutrients, texture, yield, other properties that ultimately influence ripening quality important crops such as tomato, apple, strawberry, peach. impact these processes acting positive, negative, or bidirectional regulators via phytohormone-dependent -independent mechanisms. In pathway, act central hub linking interactions with multiple phytohormones generating diverse effects. The three domains within ARFs, namely DNA-binding domain, middle region, carboxy-terminal dimerization exhibit distinct yet overlapping functions, contributing to range mechanisms mediated by ARFs. These findings not only provide profound ARF but also raise new questions. Further exploration can lead more comprehensive regulatory

Язык: Английский

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Analysis of auxin responses in the fern Ceratopteris richardii identifies the developmental phase as a major determinant for response properties

Development, Год журнала: 2024, Номер 151(20)

Опубликована: Сен. 26, 2024

ABSTRACT The auxin signaling molecule regulates a range of plant growth and developmental processes. core transcriptional machinery responsible for auxin-mediated responses is conserved across all land plants. Genetic, physiological molecular exploration in bryophyte angiosperm model species have shown both qualitative quantitative differences responses. Given the highly divergent ontogeny dominant gametophyte (bryophytes) sporophyte (angiosperms) generations, however, it unclear whether such derive from distinct phylogeny or ontogeny. Here, we address this question by comparing physiological, to generations fern Ceratopteris richardii. We find that response gametophytes closely resembles thalloid bryophyte, whereas mimics flowering This resemblance manifests at phenotypic levels. Furthermore, show disrupting transport can lead ectopic induction on gametophyte, suggesting role alternation generations. Our study thus identifies phase, rather than phylogeny, as major determinant properties

Язык: Английский

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Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Frontiers in Microbiology, Год журнала: 2023, Номер 14

Опубликована: Сен. 7, 2023

Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved variety of plant biological processes. Here, gene members 24 SpapARFs and 39 SpnpARFs were identified two genomes Saccharum spontaneum clones AP85-441 Np-X, respectively. Phylogenetic analysis showed that all ARF genes clustered into four clades, which identical to those maize (Zea mays) sorghum (Sorghum bicolor). The structure domain composition this family are conserved large degree across species. SpapARF SpnpARF unevenly distributed on chromosomes 1-8 1-10 Segmental duplication events may also contribute expansion S. spontaneum. post-transcriptional regulation likely involves sugarcane against various stressors through miRNA-medicated pathway. Expression levels six representative ShARF analyzed by qRT-PCR assays cultivars [LCP85-384 (resistant leaf scald) ROC20 (susceptible scald)] triggered Acidovorax avenae subsp. (Aaa) Xanthomonas albilineans (Xa) infections salicylic acid (SA) treatment. ShARF04 functioned as positive under Xa Aaa stress, whereas it was negative SA ShARF07/17 played roles both pathogenic bacteria stresses. Additionally, ShARF22 negatively modulated stimuli cultivars, particularly LCP85-384. These findings imply ARFs exhibit functional redundancy divergence stressful conditions. This work lays foundation for further research functions diverse environmental stressors.

Язык: Английский

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Evolutionary Origins and Functional Diversification of Auxin Response Factors

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Авг. 15, 2024

Abstract The Auxin Response Factors (ARFs) family of transcription factors are the central mediators auxin-triggered transcriptional regulation. Functionally different classes extant ARFs operate as antagonistic auxin-dependent and -independent regulators. While part evolutionary trajectory to present auxin response functions has been reconstructed, it is unclear how emerged, early diversification led functionally proteins. Here, we use in silico vivo analyses revisit molecular events that origin subsequent evolution ARFs. We reveal shared from preexisting domains, uncovering a protein fold homologous ARF DNA-binding conserved eukaryotic chromatin regulator. Building on this, reconstruct complete history ARFs, including divergence leading appearance defining main targets for their functional diversification. derive emergence nuclear signalling pathway.

Язык: Английский

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N6-adenosine methylation of mRNA integrates multilevel auxin response and ground tissue development in Arabidopsis

Development, Год журнала: 2023, Номер 150(19)

Опубликована: Сен. 19, 2023

N6-methyl adenosine (m6A) is a widespread internal mRNA modification impacting the expression of numerous genes. Here, we characterize auxin-related defects among pleiotropic phenotypes hypomorphic Arabidopsis thaliana mutants with impaired m6A status and reveal that they show strong resistance to exogenously applied auxin. By combining major published datasets, propose high-confidence target transcripts emerge those encoding main components required for auxin signaling, including TIR1/AFB receptors ARF transcriptional regulators. We also observe subtle changes in endogenous levels indole-3-acetic acid metabolites these lines, which correlate methylation amidohydrolase transcripts. In addition, reduced lead endodermal patterning primary root arising from timing periclinal cell divisions. These can be reverted by inhibition signaling. Together, our data underline likely affects auxin-dependent processes at multiple levels.

Язык: Английский

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Analysis of auxin responses in the fern Ceratopteris richardii identifies tissue ontogeny as a major determinant for response properties

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Май 8, 2024

Abstract The auxin signalling molecule regulates a range of plant growth and developmental processes. core transcriptional machinery responsible for auxin-mediated responses is conserved across all land plants. Genetic, physiological molecular exploration in bryophyte angiosperm model species have shown both qualitative quantitative differences responses. Given the highly divergent ontogeny dominant gametophyte (bryophytes) sporophyte (angiosperms) generations, however, it unclear whether such derive from distinct phylogeny or ontogeny. Here, we address this question by comparing physiological, to generations fern Ceratopteris richardii . We find that response gametophytes closely resembles thalloid bryophyte, whereas mimics flowering This resemblance manifests at phenotypic level. Furthermore, show disrupting transport can lead ectopic induction on gametophyte, suggesting role alternation generations. Our study thus identifies ontogeny, rather than phylogeny, as major determinant properties Summary statement Studies angiosperms bryophytes left unresolved roles tissue response. problem characterizing fern.

Язык: Английский

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