scholarly journals Mutation of a bHLH transcription factor allowed almond domestication

Science ◽  
2019 ◽  
Vol 364 (6445) ◽  
pp. 1095-1098 ◽  
Author(s):  
R. Sánchez-Pérez ◽  
S. Pavan ◽  
R. Mazzeo ◽  
C. Moldovan ◽  
R. Aiese Cigliano ◽  
...  
Keyword(s):  
Functional Characterization ◽  
Bhlh Transcription Factor ◽  
Dimerization Domain ◽  
P450 Monooxygenase ◽  
Helix Loop Helix ◽  
Cytochrome P450 Genes ◽  
Genome Map ◽  
Kernel Trait ◽  
Wild Almond ◽  
Encoding Genes

Wild almond species accumulate the bitter and toxic cyanogenic diglucoside amygdalin. Almond domestication was enabled by the selection of genotypes harboring sweet kernels. We report the completion of the almond reference genome. Map-based cloning using an F1 population segregating for kernel taste led to the identification of a 46-kilobase gene cluster encoding five basic helix-loop-helix transcription factors, bHLH1 to bHLH5. Functional characterization demonstrated that bHLH2 controls transcription of the P450 monooxygenase–encoding genes PdCYP79D16 and PdCYP71AN24, which are involved in the amygdalin biosynthetic pathway. A nonsynonymous point mutation (Leu to Phe) in the dimerization domain of bHLH2 prevents transcription of the two cytochrome P450 genes, resulting in the sweet kernel trait.

scholarly journals Functional characterization of a liverworts bHLH transcription factor involved in the regulation of bisbibenzyls and flavonoids biosynthesis

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yu Zhao ◽  
Yu-Ying Zhang ◽  
Hui Liu ◽  
Xiao-Shuang Zhang ◽  
Rong Ni ◽  
...  
Keyword(s):  
Vascular Plants ◽  
Functional Characterization ◽  
Bhlh Transcription Factor ◽  
Structural Genes ◽  
Helix Loop Helix ◽  
Family Protein ◽  
Transient Expression Experiment ◽  
Flavonoids Biosynthesis ◽  
Bhlh Transcription Factors

Abstract Background The basic helix-loop-helix (bHLH) transcription factors (TFs), as one of the largest families of TFs, play important roles in the regulation of many secondary metabolites including flavonoids. Their involvement in flavonoids synthesis is well established in vascular plants, but not as yet in the bryophytes. In liverworts, both bisbibenzyls and flavonoids are derived through the phenylpropanoids pathway and share several upstream enzymes. Results In this study, we cloned and characterized the function of PabHLH1, a bHLH family protein encoded by the liverworts species Plagiochasma appendiculatum. PabHLH1 is phylogenetically related to the IIIf subfamily bHLHs involved in flavonoids biosynthesis. A transient expression experiment showed that PabHLH1 is deposited in the nucleus and cytoplasm, while the yeast one hybrid assay showed that it has transactivational activity. When PabHLH1 was overexpressed in P. appendiculatum thallus, a positive correlation was established between the content of bibenzyls and flavonoids and the transcriptional abundance of corresponding genes involved in the biosynthesis pathway of these compounds. The heterologous expression of PabHLH1 in Arabidopsis thaliana resulted in the activation of flavonoids and anthocyanins synthesis, involving the up-regulation of structural genes acting both early and late in the flavonoids synthesis pathway. The transcription level of PabHLH1 in P. appendiculatum thallus responded positively to stress induced by either exposure to UV radiation or treatment with salicylic acid. Conclusion PabHLH1 was involved in the regulation of the biosynthesis of flavonoids as well as bibenzyls in liverworts and stimulated the accumulation of the flavonols and anthocyanins in Arabidopsis.

scholarly journals Cloning, molecular evolution and functional characterization of ZmbHLHl6, the maize ortholog of OsTIP2 (OsbHLH142)

2017 ◽  
Author(s):  
Yongming Liu ◽  
Jia Li ◽  
Gui Wei ◽  
Yonghao Sun ◽  
Yanli Lu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Expression Patterns ◽  
Functional Characterization ◽  
Protein A ◽  
Reproductive Organs ◽  
Male Reproduction ◽  
Yeast Cells ◽  
Bhlh Transcription Factor ◽  
Helix Loop Helix ◽  
A Genome

AbstractAbstract Basic helix-loop-helix (bHLH) transcription factors play key roles in plant male reproduction. More than 14 bHLH proteins related to pollen development have been cloned from rice and Arabidopsis. However, little is known about the role of the bHLH family in maize microspore development. In this study, the bHLH transcription factor ZmbHLH16 was cloned. ZmbHLH16 shares high similarity with the OsTIP2 (OsbHLH142) protein, a master regulator of the developmental coordination of male reproduction in rice. Expression characterization analysis showed that ZmbHLH16 is preferentially expressed in male reproductive organs and is located in the nucleus. Through nucleotide variation analysis, 36 polymorphic sites in ZmbHLH16, including 23 SNPs and 13 InDels, were detected among 78 maize inbred lines. Neutrality tests and linkage disequilibrium analysis showed that ZmbHLH16 experienced no significant evolutionary pressure. A yeast one-hybrid experiment showed that the first 80 residues in the N-terminus of ZmbHLH16 had transactivation activity, whereas the full length did not. To identify potential ZmbHLH16 interactors, 395 genes that shared similar expression patterns in a genome-wide search were obtained through coexpression analysis. Among these genes, the transcription factor ZmbHLH51 had an expression pattern and subcellular localization similar to those of ZmbHLH16. The interaction between ZmbHLH51 and ZmbHLH16 was verified in yeast cells. In addition to the typical bHLH domain, other regions of ZmbHLH16 were necessary and adequate for its heterodimerization with ZmbHLH51. Our results contribute to a solid foundation for further understanding the functions and mechanisms of ZmbHLH16.

scholarly journals SmbHLH37 functions antagonistically with SmMYC2 in regulating jasmonate-mediated biosynthesis of phenolic acids in Salvia miltiorrhiza

2018 ◽  
Author(s):  
Tang-Zhi Du ◽  
Jun-Feng Niu ◽  
Jiao Su ◽  
Sha-Sha Li ◽  
Xiao-Rong Guo ◽  
...  
Keyword(s):  
Target Genes ◽  
Salvia Miltiorrhiza ◽  
Functional Characterization ◽  
Constitutive Expression ◽  
Defense Responses ◽  
Bhlh Transcription Factor ◽  
Bhlh Gene ◽  
Helix Loop Helix ◽  
Jaz Proteins ◽  
Ja Signaling

AbstractJasmonates (JAs) are integral to various defense responses and induce biosynthesis of many secondary metabolites. MYC2, a basic helix-loop-helix (bHLH) transcription factor (TF), acts as a transcriptional activator of JA signaling. MYC2 is repressed by the JASMONATE ZIM-domain (JAZ) proteins in the absence of JA, but de-repressed by the protein complex SCFCOI1 on perception of JA. We previously reported that overexpression of SmMYC2 promotes the production of salvianolic acid B (Sal B) in Salvia miltiorrhiza. However, the responsible molecular mechanism is unclear. Here, we showed that SmMYC2 binds to and activates the promoters of its target genes SmTAT1, SmPAL1, and SmCYP98A14 to activate Sal B accumulations. SmbHLH37, a novel bHLH gene significantly up-regulated by constitutive expression of SmMYC2, was isolated from S. miltiorrhiza for detailed functional characterization. SmbHLH37 forms a homodimer and interacts with SmJAZ3/8. Overexpression of SmbHLH37 substantially decreased yields of Sal B. SmbHLH37 binds to the promoters of its target genes SmTAT1 and SmPAL1 and blocks their expression to suppress the pathway for Sal B biosynthesis. These results indicate that SmbHLH37 negatively regulates JA signaling and functions antagonistically with SmMYC2 in regulating Sal B biosynthesis in S. miltiorrhiza.

scholarly journals Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Qi Wu ◽  
Yiming Luo ◽  
Xiaoyong Wu ◽  
Xue Bai ◽  
Xueling Ye ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Functional Characterization ◽  
Chenopodium Quinoa ◽  
Noncoding Rnas ◽  
Long Noncoding Rnas ◽  
Rna Seq ◽  
Short Day ◽  
Homologous Genes ◽  
The Relationship ◽  
Encoding Genes

Abstract Background Night-break (NB) has been proven to repress flowering of short-day plants (SDPs). Long-noncoding RNAs (lncRNAs) play key roles in plant flowering. However, investigation of the relationship between lncRNAs and NB responses is still limited, especially in Chenopodium quinoa, an important short-day coarse cereal. Results In this study, we performed strand-specific RNA-seq of leaf samples collected from quinoa seedlings treated by SD and NB. A total of 4914 high-confidence lncRNAs were identified, out of which 91 lncRNAs showed specific responses to SD and NB. Based on the expression profiles, we identified 17 positive- and 7 negative-flowering lncRNAs. Co-expression network analysis indicated that 1653 mRNAs were the common targets of both types of flowering lncRNAs. By mapping these targets to the known flowering pathways in model plants, we found some pivotal flowering homologs, including 2 florigen encoding genes (FT (FLOWERING LOCUS T) and TSF (TWIN SISTER of FT) homologs), 3 circadian clock related genes (EARLY FLOWERING 3 (ELF3), LATE ELONGATED HYPOCOTYL (LHY) and ELONGATED HYPOCOTYL 5 (HY5) homologs), 2 photoreceptor genes (PHYTOCHROME A (PHYA) and CRYPTOCHROME1 (CRY1) homologs), 1 B-BOX type CONSTANS (CO) homolog and 1 RELATED TO ABI3/VP1 (RAV1) homolog, were specifically affected by NB and competed by the positive and negative-flowering lncRNAs. We speculated that these potential flowering lncRNAs may mediate quinoa NB responses by modifying the expression of the floral homologous genes. Conclusions Together, the findings in this study will deepen our understanding of the roles of lncRNAs in NB responses, and provide valuable information for functional characterization in future.

scholarly journals Genome-wide identification and transcriptional analyses of MATE transporter genes in root tips of wild Cicer spp. under aluminium stress

2020 ◽  
Author(s):  
Xia Zhang ◽  
Brayden Weir ◽  
Hongru Wei ◽  
Zhiwei Deng ◽  
Xiaoqi Zhang ◽  
...  
Keyword(s):  
Root Growth ◽  
Root Elongation ◽  
Transcriptional Profiling ◽  
Functional Characterization ◽  
Relative Reduction ◽  
Root Tips ◽  
Al Tolerance ◽  
Genome Wide ◽  
Encoding Genes ◽  
Al Treatment

AbstractChickpea is an economically important legume crop with high nutritional value in human diets. Aluminium-toxicity poses a significant challenge for the yield improvement of this increasingly popular crop in acidic soils. The wild progenitors of chickpea may provide a more diverse gene pool for Al-tolerance in chickpea breeding. However, the genetic basis of Al-tolerance in chickpea and its wild relatives remains largely unknown. Here, we assessed the Al-tolerance of six selected wild Cicer accessions by measuring the root elongation in solution culture under control (0 µM Al3+) and Al-treatment (30 µM Al3+) conditions. Al-treatment significantly reduced the root elongation in all target lines compared to the control condition after 2-day’s growth. However, the relative reduction of root elongation in different lines varied greatly: 3 lines still retained significant root growth under Al-treatment, whilst another 2 lines displayed no root growth at all. We performed genome-wide identification of multidrug and toxic compound extrusion (MATE) encoding genes in the Cicer genome. A total of 56 annotated MATE genes were identified, which divided into 4 major phylogeny groups (G1-4). Four homologues to lupin LaMATE (> 50% aa identity; named CaMATE1-4) were clustered with previously characterised MATEs related to Al-tolerance in various other plants. qRT-PCR showed that CaMATE2 transcription in root tips was significantly up-regulated upon Al-treatment in all target lines, whilst CaMATE1 was up-regulated in all lines except Bari2_074 and Deste_064, which coincided with the lines displaying no root growth under Al-treatment. Transcriptional profiling in five Cicer tissues revealed that CaMATE1 is specifically transcribed in the root tissue, further supporting its role in Al-detoxification in roots. This first identification of MATE-encoding genes associated with Al-tolerance in Cicer paves the ways for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.

scholarly journals Cytochrome P450 monooxygenase genes in the wild silkworm, Bombyx mandarina

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10818
Author(s):  
Linrong Wan ◽  
Anlian Zhou ◽  
Wenfu Xiao ◽  
Bangxing Zou ◽  
Yaming Jiang ◽  
...  
Keyword(s):  
Cytochrome P450 ◽  
Enrichment Analysis ◽  
Silk Gland ◽  
P450 Monooxygenase ◽  
Protein Coding ◽  
Bombyx Mandarina ◽  
Physical Maps ◽  
Cytochrome P450 Genes ◽  
In The Wild ◽  
Genome Assemblies

Wild (Bombyx mandarina) and domestic silkworms (B. mori) are good models for investigating insect domestication, as 5000 years of artificial breeding and selection have resulted in significant differences between B. mandarina and B. mori. In this study, we improved the genome assemblies to the chromosome level and updated the protein-coding gene annotations for B. mandarina. Based on this updated genome, we identified 68 cytochrome P450 genes in B. mandarina. The cytochrome P450 repository in B. mandarina is smaller than in B. mori. Certain currently unknown key genes, rather than gene number, are critical for insecticide resistance in B. mandarina, which shows greater resistance to insecticides than B. mori. Based on the physical maps of B. mandarina, we located 66 cytochrome P450s on 18 different chromosomes, and 27 of the cytochrome P450 genes were concentrated into seven clusters. KEGG enrichment analysis of the P450 genes revealed the involvement of cytochrome P450 genes in hormone biosynthesis. Analyses of the silk gland transcriptome identified candidate cytochrome P450 genes (CYP306A) involved in ecdysteroidogenesis and insecticide metabolism in B. mandarina.

scholarly journals ATBS1-INTERACTING FACTOR 2 Negatively Modulates Pollen Production and Seed Formation in Arabidopsis

2021 ◽  
Vol 12 ◽  
Author(s):  
Yoon Kim ◽  
Sun-Ho Kim ◽  
Dong-Min Shin ◽  
Soo-Hwan Kim
Keyword(s):  
Pollen Grains ◽  
Starch Accumulation ◽  
Bhlh Transcription Factor ◽  
Pollen Production ◽  
Sucrose Transport ◽  
Seed Formation ◽  
Helix Loop Helix ◽  
Knockout Mutants ◽  
Auxin Signalling ◽  
Genes Encoding

ATBS1-INTERACTING FACTOR 2 (AIF2) is a non-DNA-binding basic-helix-loop-helix (bHLH) transcription factor. Here, we demonstrate that AIF2 negatively modulates brassinosteroid (BR)-induced, BRASSINAZOLE RESISTANT 1 (BZR1)-mediated pollen and seed formation. AIF2-overexpressing Arabidopsis plants (AIF2ox) showed defective pollen grains and seed production while two AIF2 knockout mutants, aif2-1 and aif2-1/aif4-1, displayed opposite phenotypes. Genes encoding BZR1-regulated positive factors of seed size determination (SHB1, IKU1, MINI3) were suppressed in AIF2ox and genes for negative factors (AP2 and ARF2) were enhanced. Surprisingly, BZR1-regulated pollen genes such as SPL, MS1, and TDF1 were aberrantly up-regulated in AIF2ox plants. This stage-independent abnormal expression may lead to a retarded and defective progression of microsporogenesis, producing abnormal tetrad microspores and pollen grains with less-effective pollen tube germination. Auxin plays important roles in proper development of flower and seeds: genes for auxin biosynthesis such as TCPs and YUCCAs as well as for positive auxin signalling such as ARFs were suppressed in AIF2ox flowers. Moreover, lipid biosynthesis- and sucrose transport-related genes were repressed, resulting in impaired starch accumulation. Contrarily, sucrose and BR repressed ectopic accumulation of AIF2, thereby increasing silique length and the number of seeds. Taken together, we propose that AIF2 is negatively involved in pollen development and seed formation, and that sucrose- and BR-induced repression of AIF2 positively promotes pollen production and seed formation in Arabidopsis.

scholarly journals B-cell- and myocyte-specific E2-box-binding factors contain E12/E47-like subunits

1991 ◽  
Vol 11 (2) ◽  
pp. 1156-1160
Author(s):  
C Murre ◽  
A Voronova ◽  
D Baltimore
Keyword(s):  
Dna Binding ◽  
B Cell ◽  
Dna Sequence ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Dimerization Domain ◽  
Drosophila Development ◽  
Helix Loop Helix ◽  
Nuclear Factors ◽  
Biochemical Function

Recent studies have identified a family of DNA-binding proteins that share a common DNA-binding and dimerization domain with the potential to form a helix-loop-helix (HLH) structure. Various HLH proteins can form heterodimers that bind to a common DNA sequence, termed the E2-box. We demonstrate here that E2-box-binding B-cell- and myocyte-specific nuclear factors contain subunits which are identical or closely related to ubiquitously expressed (E12/E47) HLH proteins. These biochemical function for E12/E47-like molecules in mammalian differentiation, similar to the genetically defined function of daughterless in Drosophila development.

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