Molecular evolution of the AP2 subfamily

Shigyo, Mikao; Hasebe, Mitsuyasu; Itô, Motomi

doi:10.1016/j.gene.2005.08.009

Cited by 172 publications

(158 citation statements)

References 56 publications

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“…Total RNA from A. majus inflorescences was isolated with the RNeasy Maxi Kit (Qiagen), and polyA + RNA was obtained using magnetic beads (Dynabeads Oligo(dT) 25 , Invitrogen). To determine the 5¢ end of the MIRFIS transcript (pri-MIRFIS in Fig.…”

Section: Methodsmentioning

confidence: 99%

“…As in the miR169/NF-YA pairs, the P. hybrida and A. majus AP2 orthologs also contain the recognition site for miR172 (ref. 25), and miR172 is conserved from ferns to higher plants 1 . The function of miR172 has not been assessed in P. hybrida and A. majus, but in a phylogenetically related species, Nicotiana benthamiana, the miR172/AP2 module does not seem to have a role in C gene control comparable to that in A. thaliana 26 .…”

Section: E T T E R Smentioning

confidence: 99%

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A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity

et al. 2007

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It is commonly thought that deep phylogenetic conservation of plant microRNAs (miRNAs) and their targets 1,2 indicates conserved regulatory functions. We show that the blind (bl) mutant of Petunia hybrida 3 and the fistulata (fis) mutant of Antirrhinum majus 4,5 , which have similar homeotic phenotypes, are recessive alleles of two homologous miRNA-encoding genes. The BL and FIS genes control the spatial restriction of homeotic class C genes 6,7 to the inner floral whorls, but their ubiquitous early floral expression patterns are in contradiction with a potential role in patterning C gene expression. We provide genetic evidence for the unexpected function of the MIRFIS and MIRBL genes in the center of the flower and propose a dynamic mechanism underlying their regulatory role. Notably, Arabidopsis thaliana, a more distantly related species, also contains this miRNA module but does not seem to use it to confine early C gene expression to the center of the flower.The spatial partitioning of floral homeotic gene expression is crucial for wild-type flower development. Several transcription factors participate in this control, which aims at transcriptional silencing of the so-called 'C genes' outside their genuine expression domain in the inner two whorls of the flower, where they govern reproductive organ (stamen and carpel) development 6,7 . The functions of orthologous repressor genes, constituting the A function of the floral ABCs 6 , are, in part, comparable between different species 8 , as are some of the cis-acting regulatory regions within the large second intron of their structurally and functionally related target C genes AGAMOUS (AG) in Arabidopsis thaliana 7 , pMADS3 in P. hybrida 9 and PLENA and FARINELLI (PLE and FAR) in A. majus 10 . There are also exceptions to these overall similarities among species. For instance, orthologs of the A. thaliana APETALA2 (AP2) gene have no role in C gene regulation in P. hybrida 11 or A. majus 12 , raising the question of whether other genes fulfill this role. Candidates are the BL gene in P. hybrida and FIS in A. majus, which, when mutated, show markedly similar homeotically converted stamenoid petals in their second floral whorls 4,5 (Fig. 1).By a combination of transposon tagging and map-based cloning strategies, we cloned the BL and FIS genes and found that they encode homologous bona fide miRNAs (miRBL and miRFIS), related in their core sequences to members of the large miR169 family 13,14 (Fig. 2). The bl-1 and fis-1 alleles lie within large genomic deletions and thus represent null alleles; bl-2 and fis-2 are transposon induced and genetically unstable alleles (Fig. 2a). miRNA-encoding genes are relatively small targets for mutation, and therefore, recessive mutants are infrequent; bl and fis thus offer a rare opportunity to study and compare the function of potential orthologs in two plant species. miRNAs control gene expression by recognizing short complementary sequences in their transcripts (miRNA-recognition elements, or MREs), which are then post-transcrip...

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Section: Methodsmentioning

confidence: 99%

Section: E T T E R Smentioning

confidence: 99%

A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity

et al. 2007

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“…In past decade, AP2/ERF family has become more attentional gene family. AP2/ERF superfamily originated as a result of horizontal transfer from bacteria/viruses to plants (Magnani, 2004;Shigyo et al, 2006). This is one of the most important transcription factors having AP2-DNA binding domain (Kim et al, 2011), which consists of 60 to 70 amino acid residues first discovered in Arabidopsis thaliana (Jofuku et al, 1994).…”

Section: Introductionmentioning

confidence: 99%

“…AP2 family have two AP2/ERF domain and possess very important function in regulation of developmental process like leaf formation, flower (Elliott et al, 1996), embryo, ovule (Boutilier et al, 2002;Song et al, 2013) and fruit development . AP2 family is further classified into AP2 and ANT subfamilies (Shigyo et al, 2006). ERF family have single AP2/ERF domain and carry crucial function in ethylene signal transduction in response to environmental stresses (Takagi and Shinshi, 1995; Dubouzet et al, 2003), pathogen related stimuli and regulated pathogenesis-related gene expression (Zarei et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Genome–wide Analysis of Ethylene Responsive Factor in Maize: An in Silico Approach

Hussain¹

2016

Appl Ecol Env Res

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Abstract. Transcription factors are usually considered as key player for gene regulation. Among various transcription factor families, AP2/ERF superfamily is well known for regulating various stress responses in plants. The family encompasses AP2/ERF domain, which is involved in DNA binding comprises of about 60 to 70 amino acids. To date, there is no detailed report presenting structural and functional prediction of ERF genes in Zea mays (L.). The current study presents a comprehensive genome-wide analysis of 105 ERF genes in maize (ZmERF) using several computational techniques. We performed phylogenetic analysis, conserved motif analysis, chromosomal localization, gene structure analysis and multiple sequence alignment of ERF genes. The phylogenetic analysis led to classification of these ERF members into 10 major groups and various subgroups and inferred evolutionary relationship among the groups on the basis of various protein motifs as well as intron/exon structure. The mapping of ERF genes on 10 maize chromosomes revealed their existence on all chromosomes with most number (17 genes) carried by chromosome 1 and least number (8 genes) found on chromosome 3. Interestingly, a very limited intron frequency was resulted in gene structure analysis. Gene ontology analysis concludes that ZmERF are involved in responses to various stresses including both biotic and abiotic. The results of the present study provide important structural information to design functional analyses of the ERF genes in Z. mays.

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“…ESR1 encodes a transcription factor belonging to the ETHYLENE-RESPONSIVE FACTOR (ERF) family. The ERF family is the largest branch in the AP2/ERF superfamily of transcription factors containing 1 or 2 AP2/ERF domains, which are plant-specific DNAbinding motifs (McGrath et al 2005;Nakano et al 2006;Shigyo et al 2006). The Arabidopsis genome has more than 100 ERF family genes, which are implicated in diverse physiological events such as hormone signaling (Guo and Ecker 2004;Ohme-Takagi and Shinshi 1995;Song et al 2005;van der Fits and Memelink 2000), biotic and abiotic stress tolerance (Agarwal et al 2006;Gutterson and Reuber 2004), cuticular wax biosynthesis (Aharoni et al 2004;Broun et al 2004;Zhang et al 2005), and developmental processes (Banno et al 2001;Chandler et al 2007;Hirota et al 2007;Ikeda et al 2006;Kirch et al 2003;van der Graaff et al 2000).…”

mentioning

confidence: 99%

A domain containing the ESR motif in ENHANCER OF SHOOT REGENERATION 1 functions as a transactivation domain

Nomura

Matsuo

Banno

2009

Plant Biotechnology

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The Arabidopsis ENHANCER OF SHOOT REGENERATION 1 (ESR1) gene is thought to regulate the initiation of in vitro shoot regeneration. ESR1 encodes a transcriptional activator belonging to the ETHYLENE-RESPONSIVE FACTOR family. In this study, we investigated the functions of the C-terminal domain of the ESR1 protein. Effectorreporter assays using the GAL4 DNA-binding domain fused with portions of the C-terminal domain revealed that the ESR motif, which is a short amino acid sequence commonly seen in the C-terminal domain of ESR1 and ESR2, functions as a transactivation domain. We also examined the effects of partial deletions of the C-terminal domain on the in vitro shoot regeneration-enhancing effects of ESR1 overexpression. The results revealed that the ESR motif and a region between the AP2/ERF domain and the ESR motif were required for the shoot regeneration-enhancing effects of ESR1. The region between the AP2/ERF domain and the ESR motif appeared to have an essential function other than nuclear localization, DNA-binding, and transactivation. Substitution of the ESR motif by the VP16 transactivation domain abolished the ability of ESR1 to enhance shoot regeneration, suggesting that the ESR motif not only has transactivation activity but also has other functions.

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Molecular evolution of the AP2 subfamily

Cited by 172 publications

References 56 publications

A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity

A conserved microRNA module exerts homeotic control over Petunia hybrida and Antirrhinum majus floral organ identity

Genome–wide Analysis of Ethylene Responsive Factor in Maize: An in Silico Approach

A domain containing the ESR motif in ENHANCER OF SHOOT REGENERATION 1 functions as a transactivation domain

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