BpAP1 directly regulates BpDEF to promote male inflorescence formation in Betula platyphylla × B. pendula

2019 ◽  
Vol 39 (6) ◽  
pp. 1046-1060 ◽  
Author(s):  
Shuo Wang ◽  
Haijiao Huang ◽  
Rui Han ◽  
Jiying Chen ◽  
Jing Jiang ◽  
...  
Keyword(s):  
Chromatin Immunoprecipitation ◽  
Target Gene ◽  
Regulatory Mechanism ◽  
Function Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Male Inflorescence ◽  
Carg Box ◽  
Gene Regulatory ◽  
Gene Function Analysis

Abstract Flowering is a crucial process for plants that is under complex genetic control. AP1 acts as an organizer and a switch for the transition from vegetative to reproductive growth. In our previous study, we found that overexpression of BpAP1 significantly promoted the formation of male inflorescence in birch (Betula platyphlla × B. pendula). In this study, we aimed at investigating the molecular regulatory mechanism of BpAP1 during the process of male inflorescence formation in birch. We found that overexpression of BpAP1 affected the expression of many flowering-related genes, and had significant effect on B class MADS-box genes. A BpAP1-mediated gene regulatory network was constructed and B class gene BpDEF was finally predicted as a key target gene of BpAP1. Chromatin immunoprecipitation results indicated that BpAP1 could directly regulate BpDEF during the process of male inflorescence formation. Yeast one-hybrid assays and its validation in tobacco results suggested that BpAP1 regulated BpDEF via binding to a consensus DNA sequence known as CArG box. Gene function analysis of BpDEF indicated that BpDEF may function in sex-determination, and in particular specify the identity of male inflorescence in birch. Our results provide valuable clues for our understanding of the molecular mechanism of BpAP1 during the process of male inflorescence formation in birch.

scholarly journals Independent origin of MIRNA genes controlling homologous target genes by partial inverted duplication of antisense-transcribed sequences

2019 ◽  
Author(s):  
Lydia Gramzow ◽  
Dajana Lobbes ◽  
Sophia Walter ◽  
Nathan Innard ◽  
Günter Theißen
Keyword(s):  
Transcription Factors ◽  
Target Gene ◽  
Target Genes ◽  
Mirna Biogenesis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Developmental Processes ◽  
Inverted Duplication ◽  
The Future ◽  
Transcribed Sequences

AbstractSome microRNAs (miRNAs) are key regulators of developmental processes, mainly by controlling the accumulation of transcripts encoding transcription factors that are important for morphogenesis. MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants. Here we study the convergent evolution of two MIRNA (MIR) gene families, named MIR444 and MIR824, targeting members of the same clade of MIKCC-group MADS-box genes. We show that these two MIR genes most likely originated independently in monocots (MIR444) and in Brassicales (eudicots, MIR824). We provide evidence that in both cases the future target gene was transcribed in antisense prior to the evolution of the MIR genes. Both MIR genes then likely originated by a partial inverted duplication of their target genes, resulting in natural antisense organization of the newly evolved MIR gene and its target gene at birth. We thus propose a new model for the origin of MIR genes, MEPIDAS (MicroRNA Evolution by Partial Inverted Duplication of Antisense-transcribed Sequences). MEPIDAS is a refinement of the inverted duplication hypothesis. According to MEPIDAS, a MIR gene evolves at a genomic locus at which the future target gene is also transcribed in the antisense direction. A partial inverted duplication at this locus causes the antisense transcript to fold into a stem-loop structure that is recognized by the miRNA biogenesis machinery to produce a miRNA that regulates the gene at this locus. Our analyses exemplify how to elucidate the origin of conserved miRNAs by comparative genomics and will guide future studies.

scholarly journals Extending the Toolkit for Beauty: Differential Co-Expression of DROOPING LEAF-Like and Class B MADS-Box Genes during Phalaenopsis Flower Development

2021 ◽  
Vol 22 (13) ◽  
pp. 7025
Author(s):  
Francesca Lucibelli ◽  
Maria Carmen Valoroso ◽  
Günter Theißen ◽  
Susanne Nolden ◽  
Mariana Mondragon-Palomino ◽  
...  
Keyword(s):  
Differential Expression ◽  
Flower Development ◽  
Differential Expression Analysis ◽  
Mads Box ◽  
Wild Type ◽  
Mads Box Genes ◽  
Regulatory Interactions ◽  
Class B ◽  
Gene Regulatory ◽  
Orchid Flower

The molecular basis of orchid flower development is accomplished through a specific regulatory program in which the class B MADS-box AP3/DEF genes play a central role. In particular, the differential expression of four class B AP3/DEF genes is responsible for specification of organ identities in the orchid perianth. Other MADS-box genes (AGL6 and SEP-like) enrich the molecular program underpinning the orchid perianth development, resulting in the expansion of the original “orchid code” in an even more complex gene regulatory network. To identify candidates that could interact with the AP3/DEF genes in orchids, we conducted an in silico differential expression analysis in wild-type and peloric Phalaenopsis. The results suggest that a YABBY DL-like gene could be involved in the molecular program leading to the development of the orchid perianth, particularly the labellum. Two YABBY DL/CRC homologs are present in the genome of Phalaenopsis equestris, PeDL1 and PeDL2, and both express two alternative isoforms. Quantitative real-time PCR analyses revealed that both genes are expressed in column and ovary. In addition, PeDL2 is more strongly expressed the labellum than in the other tepals of wild-type flowers. This pattern is similar to that of the AP3/DEF genes PeMADS3/4 and opposite to that of PeMADS2/5. In peloric mutant Phalaenopsis, where labellum-like structures substitute the lateral inner tepals, PeDL2 is expressed at similar levels of the PeMADS2-5 genes, suggesting the involvement of PeDL2 in the development of the labellum, together with the PeMADS2-PeMADS5 genes. Although the yeast two-hybrid analysis did not reveal the ability of PeDL2 to bind the PeMADS2-PeMADS5 proteins directly, the existence of regulatory interactions is suggested by the presence of CArG-boxes and other MADS-box transcription factor binding sites within the putative promoter of the orchid DL2 gene.

Molecular Cloning and Function Analysis of Two SQUAMOSA -Like MADS-Box Genes From Gossypium hirsutum L.

2013 ◽  
Vol 55 (7) ◽  
pp. 597-607 ◽  
Author(s):  
Wenxiang Zhang ◽  
Shuli Fan ◽  
Chaoyou Pang ◽  
Hengling Wei ◽  
Jianhui Ma ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Molecular Cloning ◽  
Function Analysis ◽  
Mads Box ◽  
Mads Box Genes ◽  
Gossypium Hirsutum L ◽  
And Function

Comparative evolutionary analysis of MADS-box genes inArabidopsisthalianaand A.lyrata

2010 ◽  
Vol 18 (2) ◽  
pp. 109 ◽  
Author(s):  
Xue Haoyue ◽  
Xu Guixia ◽  
Guo Chunce ◽  
Shan Hongyan ◽  
Kong Hongzhi
Keyword(s):  
Evolutionary Analysis ◽  
Mads Box ◽  
Mads Box Genes

Genome-wide identification and analysis of the MADS-box gene family and its potential role in fruit ripening in black raspberry (Rubus occidentalis L.)

2021 ◽  
pp. 1-15
Author(s):  
Yaqiong Wu ◽  
Chunhong Zhang ◽  
Wenlong Wu ◽  
Weilin Li ◽  
Lianfei Lyu
Keyword(s):  
Gene Family ◽  
Fruit Ripening ◽  
Fruit Development ◽  
Expression Patterns ◽  
Type I ◽  
Black Raspberry ◽  
Mads Box ◽  
Mads Box Genes ◽  
Genome Wide ◽  
Mads Box Gene

BACKGROUND: Black raspberry is a vital fruit crop with a high antioxidant function. MADS-box genes play an important role in the regulation of fruit development in angiosperms. OBJECTIVE: To understand the regulatory role of the MADS-box family, a total of 80 MADS-box genes were identified and analyzed. METHODS: The MADS-box genes in the black raspberry genome were analyzed using bioinformatics methods. Through an analysis of the promoter elements, the possible functions of different members of the family were predicted. The spatiotemporal expression patterns of members of the MADS-box family during black raspberry fruit development and ripening were systematically analyzed. RESULTS: The genes were classified into type I (Mα: 33; Mβ: 6; Mγ: 10) and type II (MIKC *: 2; MIKCC: 29) genes. We also obtained a complete overview of the RoMADS-box gene family through phylogenetic, gene structure, conserved motif, and cis element analyses. The relative expression analysis showed different expression patterns, and most RoMADS-box genes were more highly expressed in fruit than in other tissues of black raspberry. CONCLUSIONS: This finding indicates that the MADS-box gene family is involved in the regulation of fruit ripening processes in black raspberry.

scholarly journals The Relationship between AGAMOUS and Cytokinin Signaling in the Establishment of Carpeloid Features

Plants ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 827
Author(s):  
Andrea Gómez-Felipe ◽  
Daniel Kierzkowski ◽  
Stefan de Folter
Keyword(s):  
Regulatory Network ◽  
Dependent Manner ◽  
Mads Box ◽  
Type B ◽  
Cytokinin Signaling ◽  
Reproductive Structures ◽  
Carpel Development ◽  
Gene Regulatory ◽  
The Relationship ◽  
Gynoecium Development

Gynoecium development is dependent on gene regulation and hormonal pathway interactions. The phytohormones auxin and cytokinin are involved in many developmental programs, where cytokinin is normally important for cell division and meristem activity, while auxin induces cell differentiation and organ initiation in the shoot. The MADS-box transcription factor AGAMOUS (AG) is important for the development of the reproductive structures of the flower. Here, we focus on the relationship between AG and cytokinin in Arabidopsis thaliana, and use the weak ag-12 and the strong ag-1 allele. We found that cytokinin induces carpeloid features in an AG-dependent manner and the expression of the transcription factors CRC, SHP2, and SPT that are involved in carpel development. AG is important for gynoecium development, and contributes to regulating, or else directly regulates CRC, SHP2, and SPT. All four genes respond to either reduced or induced cytokinin signaling and have the potential to be regulated by cytokinin via the type-B ARR proteins. We generated a model of a gene regulatory network, where cytokinin signaling is mainly upstream and in parallel with AG activity.

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