Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter

This study aims to gain insight into the DNA-specific recognition mechanism of c-Myb transcription factor during the regulation of cell early differentiation and proliferation.Therefore,we chose the chicken myeloid gene,mitochondrial import protein 1(mim-1),as a target to study the binding specificity between potential dual-Myb-binding sites.The c-Myb-binding site in mim-1 is a pseudo-palindromic sequence AACGGTT,which contains two AACNG consensuses.Simulation studies in different biological scenarios revealed that c-Myb binding with mim-1 in the forward strand(complex F)is more stable than that in the reverse strand(complex R).The principal component analysis(PCA)dynamics trajectory analyses suggested an opening motion of the recognition helices of R2 and R3(R2R3),resulting in the dissociation of DNA from c-Myb in complex R at 330 K,triggered by the reduced electrostatic potential on the surface of R2R3.Furthermore,the DNA confirmation and hydrogen-bond interaction analyses indicated that the major groove width of DNA increased in complex R,which affected on the hydrogenbond formation ability between R2R3 and DNA,and directly resulted in the dissociation of DNA from R2R3.The steered molecular dynamics(SMD)simulation studies also suggested that the electrostatic potential,major groove width,and hydrogen bonds made major contribution to the DNA-specific recognition.In vitro trials confirmed the simulation results that c-Myb specifically bound to mim-1 in the forward strand.This study indicates that the three-dimensional(3D)structure features play an important role in the DNA-specific recognition mechanism by c-Myb besides the AACNG consensuses,which is beneficial to understanding the cell early differentiation and proliferation regulated by c-Myb,as well as the prediction of novel c-Myb-binding motifs in tumorigenesis.

ZmCOL3, a CCT gene represses flowering in maize by interfering with the circadian clock and activating expression of ZmCCT

Flowering time is a trait vital to the adaptation of flowering plants to different environments. Here, we report that CCT domain genes play an important role in flowering in maize （Zea mays L.）. Among the 53 CCT family genes we identified in maize, 28 were located in flowering time quantitative trait locus regions and 15 were significantly associated with flowering time, based on candidate-gene association mapping analysis. Furthermore, a CCT gene named ZmCOL3 was shown to be a repressor of flowering. Overexpressing ZmCOL3 delayed flowering time by approximately 4 d, in either long-day or short-day conditions. The absence of one cytosine in the ZmCOL3 3＇UTR and the presence of a 551 bp fragment in the promoter region are likely the causal polymorphisms contributing to the maize adaptation from tropical to temperate regions. We propose a modified model of the maize photoperiod pathway, wherein ZmCOL3 acts as an inhibitor of flowering either by transactivating transcription of ZmCCT, one of the key genes regulating maize flowering, or by interfering with the circadian clock.

Resequencing 250 Soybean Accessions:New Insights into Genes Associated with Agronomic Traits and Genetic Networks

The limited knowledge of genomic diversity and functional genes associated with the traits of soybean varieties has resulted in slow progress in breeding.In this study,we sequenced the genomes of 250 soybean landraces and cultivars from China,America,and Europe,and investigated their population structure,genetic diversity and architecture,and the selective sweep regions of these accessions.Five novel agronomically important genes were identified,and the effects of functional mutations in respective genes were examined.The candidate genes GSTT1,GL3,and GSTL3 associated with the isoflavone content,CKX3 associated with yield traits,and CYP85 A2 associated with both architecture and yield traits were found.The phenotype-gene network analysis revealed that hub nodes play a crucial role in complex phenotypic associations.This study describes novel agronomic trait-associated genes and a complex genetic network,providing a valuable resource for future soybean molecular breeding.

Erratum to:Molecular dynamics simulation reveals DNA-specific recognition mechanism via c-Myb in pseudo-palindromic consensus of mim-1 promoter

Erratum to:J Zhejiang Univ-Sci B(Biomed&Biotechnol)202324(10):883-895 https://doi.0rg/10.1631/jzus.B2200634.The original version of this article(Weng et al.,2023)unfortunately contained a mistake.In Acknowledgments,the number(No.226-2022-00213)of the Fundamental Research Funds for the Central Universities is wrong.The correct number should be No.2022FZZX01-33.