A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening

Manning, Kenneth C.; Tör, Mahmut; Poole, Mervin; Hong, Yiguo; Thompson, Andrew J.; King, Graham J.; Giovannoni, James J.; Seymour, Graham B.

doi:10.1038/ng1841

Cited by 1,074 publications

(938 citation statements)

References 29 publications

Supporting

Mentioning

909

Contrasting

Unclassified

Order By: Relevance

“…Several of these were found to be orthologous to genes that are known to be important regulators of flower and fruit development in other species. This suggests that apple fruit development is regulated by epigenetic processes, which is consistent with data obtained in tomato, demonstrating that DNA methylation is important for fruit ripening [56][57][58] .…”

Section: Discussionsupporting

confidence: 89%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

View full text Add to dashboard Cite

Using the latest sequencing and optical mapping technologies, we have produced a high-quality de novo assembly of the apple (Malus domestica Borkh.) genome. Repeat sequences, which represented over half of the assembly, provided an unprecedented opportunity to investigate the uncharacterized regions of a tree genome; we identified a new hyper-repetitive retrotransposon sequence that was over-represented in heterochromatic regions and estimated that a major burst of different transposable elements (TEs) occurred 21 million years ago. Notably, the timing of this TE burst coincided with the uplift of the Tian Shan mountains, which is thought to be the center of the location where the apple originated, suggesting that TEs and associated processes may have contributed to the diversification of the apple ancestor and possibly to its divergence from pear. Finally, genome-wide DNA methylation data suggest that epigenetic marks may contribute to agronomically relevant aspects, such as apple fruit development.

show abstract

Section: Discussionsupporting

confidence: 89%

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

et al. 2017

View full text Add to dashboard Cite

show abstract

“…4). In contrast, CNR 50 , Uniform (Golden-like 2) 51 and HB-1 (ref. 52) showed distinct expression patterns in hot pepper and tomato (Fig.…”

Section: Comparative Fruit Ripeningmentioning

confidence: 99%

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

et al. 2014

Self Cite

View full text Add to dashboard Cite

“…To date, only a few functions for SBP domain proteins have been reported, perhaps due to genetic redundancy of closely related family members. In all cases, SBP domain proteins have been implicated in various aspects of plant growth and development, including metal sensing in algae and directing development of leaves, embryos, and floral organs in higher plants (9,(13)(14)(15)(16)(17)(18)(19)(20)(21)(22). Some of these SBP do-main proteins may also be posttranscriptionally regulated by noncoding microRNAs to control their spatial and temporal expression (23)(24)(25).…”

mentioning

confidence: 99%

Identification of a Consensus DNA-Binding Site for the Arabidopsis thaliana SBP Domain Transcription Factor, AtSPL14, and Binding Kinetics by Surface Plasmon Resonance

2008

View full text Add to dashboard Cite

Proteins with a conserved Cys- and His-rich SQUAMOSA promoter binding protein (SBP) domain are transcription factors restricted to photosynthetic organisms that possess a novel two Zn-finger structure DNA-binding domain. Despite the fact that altered expression of some SBP-encoding genes has profound effects on organism growth and development, little is known about SBP domain protein target genes. Misexpression of the Arabidopsis thaliana AtSPL14 SBP domain gene confers resistance to programmed cell death and modifies plant architecture. A consensus DNA-binding motif for AtSPL14 was identified by systematic evolution of ligands by exponential enrichment (SELEX) or random binding site selection (RBSS). DNA recognized by AtSPL14 contained the core binding motif (GTAC) found for other SBP domain proteins, but mutational analyses indicated that at least one additional flanking nucleotide is necessary for effective AtSPL14−DNA interaction. Comparison of several SBP domain amino acid sequences allows us to hypothesize which specific amino acids might participate in this sequence-specific DNA recognition. Electrophoretic mobility shift assays (EMSA) with mutant AtSPL14 DNA-binding domain proteins indicated that not all of the Zn2+ ion coordinating ligands in the second Zn structure are strictly required for DNA binding. Surface plasmon resonance (SPR) was used to evaluate AtSPL14 in vitro binding kinetics for comparison of equilibrium binding constants with other SBP domain proteins. These data provide a strong basis for further experiments aimed at defining and distinguishing the sets of genes regulated by the closely related SBP domain family members.

show abstract

A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening

Cited by 1,074 publications

References 29 publications

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

Identification of a Consensus DNA-Binding Site for the Arabidopsis thaliana SBP Domain Transcription Factor, AtSPL14, and Binding Kinetics by Surface Plasmon Resonance

Contact Info

Product

Resources

About