scholarly journals Genome-wide Analysis of Basic Helix-Loop-Helix Family Genes and Expression Analysis in Response to Drought and Salt Stresses in Hibiscus hamabo Sieb. et Zucc

2021 ◽  
Vol 22 (16) ◽  
pp. 8748
Author(s):  
Longjie Ni ◽  
Zhiquan Wang ◽  
Zekai Fu ◽  
Dina Liu ◽  
Yunlong Yin ◽  
...  
Keyword(s):  
Stress Responses ◽  
Growth And Development ◽  
Cis Elements ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
Drought And Salt Stresses ◽  
Salt And Drought Stress ◽  
As Stress ◽  
Bhlh Proteins

The basic helix-loop-helix (bHLH) family of transcription factors is one of the most significant and biggest in plants. It is involved in the regulation of both growth and development, as well as stress response. Numerous members of the bHLH family have been found and characterized in woody plants in recent years. However, no systematic study of the bHLH gene family has been published for Hibiscus hamabo Sieb. et Zucc. In this research, we identified 162 bHLH proteins (HhbHLHs) from the genomic and transcriptomic datasets of H. hamabo, which were phylogenetically divided into 19 subfamilies. According to a gene structural study, the number of exon-introns in HhbHLHs varied between zero and seventeen. MEME research revealed that the majority of HhbHLH proteins contained three conserved motifs, 1, 4, and 5. The examination of promoter cis-elements revealed that the majority of HhbHLH genes had several cis-elements involved in plant growth and development and abiotic stress responses. In addition, the overexpression of HhbHLH2 increased salt and drought stress tolerance in Arabidopsis.

scholarly journals Genome-Wide Analysis of Basic Helix-Loop-Helix (bHLH) TFs in Sea Buckthorn (Hippophae rhamnoides)

2020 ◽  
Author(s):  
Songfeng Diao ◽  
Hong Liu ◽  
Zhongrui Lv ◽  
Caiyun He ◽  
Aiguo Duan ◽  
...  
Keyword(s):  
Gene Family ◽  
Stress Responses ◽  
Gene Families ◽  
Sea Buckthorn ◽  
Bhlh Transcription Factor ◽  
Systematic Analysis ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
A Genome

Abstract Background The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and extensively involved in plant growth, organ development, and stress responses. However, limited studies are available on the gene family in sea buckthorn. Results In this study, we focused on 144 HrbHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities, we classified the genes into 15 groups with specific motif structures. In order to explore their expressions, we performed gene expression profiling using RNA-Seq and identified 108 HrbHLH genes that expressed in five sea buckthorn tissue, including root nodule, root, leaf, stem and fruit. Furthermore, we found 11 increased expressed HrbHLH genes during sea buckthorn fruit development. We validated the expression pattern of HrbHLH genes using reverse transcription quantitative real-time PCR. Conclusions This study lays the foundation for future studies on gene cloning, transgenes, and biological mechanisms. We performed a genome-wide, systematic analysis of bHLH proteins in sea buckthorn. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the HrbHLH TFs.

scholarly journals Genome-Wide Analysis of the Trihelix Gene Family and Their Response to Cold Stress in Dendrobium officinale

2021 ◽  
Vol 13 (5) ◽  
pp. 2826
Author(s):  
Yan Tong ◽  
Hui Huang ◽  
YuHua Wang
Keyword(s):  
Stress Responses ◽  
Cold Treatment ◽  
Dendrobium Officinale ◽  
Functional Domain ◽  
Cis Elements ◽  
Genome Wide Analysis ◽  
Functional Studies ◽  
Genome Wide ◽  
Growth Development ◽  
Chinese Medicinal Plant

Trihelix transcription factors play important roles in plant growth, development and various stress responses. In this study, we identified 32 trihelix family genes (DoGT) in the important Chinese medicinal plant Dendrobium officinale. These trihelix genes could be classified into five different subgroups. The gene structure and conserved functional domain of these trihelix genes were similar in the same subfamily but diverged between different subfamilies. Various stresses responsive cis-elements presented in the promoters of DoGT genes, suggesting that the trihelix genes might respond to the environmental stresses. Expressional changes of DoGT genes in three tissues and under cold treatment suggested that trihelix genes were involved in diverse functions during D. officinale development and cold tolerance. This study provides novel insights into the phylogenetic relationships and functions of the D. officinaletrihelix genes, which will aid future functional studies investigating the divergent roles of trihelix genes belonging to other species.

scholarly journals Genome-Wide Analysis of Poplar SQUAMOSA-Promoter-Binding Protein (SBP) Family under Salt Stress

Forests ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 413
Author(s):  
Qing Guo ◽  
Li Li ◽  
Kai Zhao ◽  
Wenjing Yao ◽  
Zihan Cheng ◽  
...  
Keyword(s):  
Salt Stress ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Growth And Development ◽  
Binding Protein ◽  
Gene Segment ◽  
Gene Expression Pattern ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Squamosa Promoter Binding Protein

SQUAMOSA promoter binding protein (SBP) is a kind of plant-specific transcription factor, which plays a crucial role in stress responses and plant growth and development by activating and inhibiting the transcription of multiple target genes. In this study, a total of 30 SBP genes were identified from Populus trichocarpa genome and randomly distributed on 16 chromosomes in poplar. According to phylogenetic analysis, the PtSBPs can be divided into six categories, and 14 out of the genes belong to VI. Furthermore, the SBP genes in VI were proved to have a targeting relationship with miR156. The homeopathic element analysis showed that the promoters of poplar SBP genes mainly contain the elements involved in growth and development, abiotic stress and hormone response. In addition, there existed 10 gene segment duplication events in the SBP gene duplication analysis. Furthermore, there were four poplar and Arabidopsis orthologous gene pairs among the poplar SBP members. What is more, poplar SBP gene family has diverse gene expression pattern under salt stress. As many as nine SBP members were responding to high salt stress and six members possibly participated in growth development and abiotic stress. Yeast two-hybrid experiments indicated that PtSBPs can form heterodimers to interact in the transcriptional regulatory networks. The genome-wide analysis of poplar SBP family will contribute to function characterization of SBP genes in woody plants.

scholarly journals Genome-wide analysis of basic helix-loop-helix superfamily members in peach

PLoS ONE ◽  
2018 ◽  
Vol 13 (4) ◽  
pp. e0195974 ◽  
Author(s):  
Chunhua Zhang ◽  
Ruchao Feng ◽  
Ruijuan Ma ◽  
Zhijun Shen ◽  
Zhixiang Cai ◽  
...  
Keyword(s):  
Genome Wide Analysis ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide

scholarly journals An Examination of the Role of Transcriptional and Posttranscriptional Regulation in Rhabdomyosarcoma

2017 ◽  
Vol 2017 ◽  
pp. 1-10 ◽  
Author(s):  
Alexander J. Hron ◽  
Atsushi Asakura
Keyword(s):  
Skeletal Muscle ◽  
Soft Tissue ◽  
Posttranscriptional Regulation ◽  
Progenitor Cell ◽  
Treatment Options ◽  
Soft Tissue Tumors ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Proteins

Rhabdomyosarcoma (RMS) is an aggressive family of soft tissue tumors that most commonly manifests in children. RMS variants express several skeletal muscle markers, suggesting myogenic stem or progenitor cell origin of RMS. In this review, the roles of both recently identified and well-established microRNAs in RMS are discussed and summarized in a succinct, tabulated format. Additionally, the subtypes of RMS are reviewed along with the involvement of basic helix-loop-helix (bHLH) proteins, Pax proteins, and microRNAs in normal and pathologic myogenesis. Finally, the current and potential future treatment options for RMS are outlined.

A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse

2009 ◽  
Vol 20 (4) ◽  
pp. 236-246 ◽  
Author(s):  
X. Zheng ◽  
Y. Wang ◽  
Q. Yao ◽  
Z. Yang ◽  
K. Chen
Keyword(s):  
Transcription Factors ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

scholarly journals Inhibition of Tcf3 Binding by I-mfa Domain Proteins

2001 ◽  
Vol 21 (5) ◽  
pp. 1866-1873 ◽  
Author(s):  
Lauren Snider ◽  
Hilary Thirlwell ◽  
Jeffrey R. Miller ◽  
Randall T. Moon ◽  
Mark Groudine ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Wnt Signaling ◽  
Binding Sites ◽  
Ectopic Expression ◽  
Wnt Signaling Pathway ◽  
Developmental Pathways ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Dorsal Axis ◽  
Bhlh Proteins

ABSTRACT We have determined that I-mfa, an inhibitor of several basic helix-loop-helix (bHLH) proteins, and XIC, a Xenopusortholog of human I-mf domain-containing protein that shares a highly conserved cysteine-rich C-terminal domain with I-mfa, inhibit the activity and DNA binding of the HMG box transcription factor XTcf3. Ectopic expression of I-mfa or XIC in early Xenopus embryos inhibited dorsal axis specification, the expression of the Tcf3/β-catenin-regulated genessiamois and Xnr3, and the ability of β-catenin to activate reporter constructs driven by Lef/Tcf binding sites. I-mfa domain proteins can regulate both the Wnt signaling pathway and a subset of bHLH proteins, possibly coordinating the activities of these two critical developmental pathways.

Scleraxis: a basic helix-loop-helix protein that prefigures skeletal formation during mouse embryogenesis

Development ◽  
1995 ◽  
Vol 121 (4) ◽  
pp. 1099-1110 ◽  
Author(s):  
P. Cserjesi ◽  
D. Brown ◽  
K.L. Ligon ◽  
G.E. Lyons ◽  
N.G. Copeland ◽  
...  
Keyword(s):  
Connective Tissue ◽  
Expression Pattern ◽  
Consensus Sequence ◽  
Cell Types ◽  
Cell Type ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
E Box ◽  
Cell Type Specific ◽  
Bhlh Proteins

Members of the basic helix-loop-helix (bHLH) family of transcription factors have been shown to regulate growth and differentiation of numerous cell types. Cell-type-specific bHLH proteins typically form heterodimers with ubiquitous bHLH proteins, such as E12, and bind a DNA consensus sequence known as an E-box. We used the yeast two-hybrid system to screen mouse embryo cDNA libraries for cDNAs encoding novel cell-type-specific bHLH proteins that dimerize with E12. One of the cDNAs isolated encoded a novel bHLH protein, called scleraxis. During mouse embryogenesis, scleraxis transcripts were first detected between day 9.5 and 10.5 post coitum (p.c.) in the sclerotome of the somites and in mesenchymal cells in the body wall and limb buds. Subsequently, scleraxis was expressed at high levels within mesenchymal precursors of the axial and appendicular skeleton and in cranial mesenchyme in advance of chondrogenesis; its expression pattern in these cell types foreshadowed the developing skeleton. Prior to formation of the embryonic cartilaginous skeleton, scleraxis expression declined to low levels. As development proceeded, high levels of scleraxis expression became restricted to regions where cartilage and connective tissue formation take place. Scleraxis bound the E-box consensus sequence as a heterodimer with E12 and activated transcription of a reporter gene linked to its DNA-binding site. The expression pattern, DNA-binding properties and transcriptional activity of scleraxis suggest that it is a regulator of gene expression within mesenchymal cell lineages that give rise to cartilage and connective tissue.

scholarly journals mTFE3, an X-linked transcriptional activator containing basic helix-loop-helix and zipper domains, utilizes the zipper to stabilize both DNA binding and multimerization.

1992 ◽  
Vol 12 (2) ◽  
pp. 817-827 ◽  
Author(s):  
C Roman ◽  
A G Matera ◽  
C Cooper ◽  
S Artandi ◽  
S Blain ◽  
...  
Keyword(s):  
Dna Binding ◽  
Heavy Chain ◽  
Leucine Zipper ◽  
Immunoglobulin Heavy Chain ◽  
Functional Roles ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
The Individual ◽  
Bhlh Proteins ◽  
High Degree

Southwestern (DNA-protein) screening of a murine L-cell cDNA library by using a probe for the microE3 site in the immunoglobulin heavy-chain enhancer yielded a clone, mTFE3, which is a member of the subset of basic helix-loop-helix (BHLH) proteins that also contain a leucine zipper (ZIP). Since the individual contribution of these domains is not well understood for proteins which contain them both, mutational analyses were performed to assess the functional roles of the HLH and ZIP regions for DNA binding and multimerization. The HLH region is stringently required for DNA binding but not for multimerization. The ZIP region is not stringently required for binding or multimerization, but stabilizes both multimer formation and DNA binding. A high degree of conservation at both the amino acid and nucleotide levels between the human transcription factor TFE3 and mTFE3 suggests that mTFE3 is the murine homolog of human TFE3. By using fluorescent in situ hybridization, mTFE3 was mapped to mouse chromosome X in band A2, which is just below the centromere. We show that in addition to the immunoglobulin heavy-chain microE3 site, mTFE3 binds to transcriptional elements important for lymphoid-specific, muscle-specific, and ubiquitously expressed genes. Binding of mTFE3 to DNA induces DNA bending.

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