scholarly journals Genome-wide Survey of the bHLH Super Gene Family in Brassica napus

2020 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Bhlh Transcription Factor ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Helix Loop Helix

Abstract Background: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus . Results : We identified 602 potential bHLHs in the B. napus genome ( BnabHLHs ) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs . Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs . Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA 3 , gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus . Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research. Keywords: Brassica napus ; bHLH transcription factor; root; gene expression

Genome-wide Survey of the bHLH Super Gene Family in Brassica napus and its Role in Roots

2020 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
Organization Analysis

Abstract Background: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. Results: We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

scholarly journals Genome-wide Survey of the bHLH Super Gene Family in Brassica napus

2020 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
Organization Analysis

Abstract Background: The basic helix-loop-helix (bHLH) gene family is one of the largest transcription factor families in plants and is functionally characterized in diverse species. However, less is known about its functions in the economically important allopolyploid oil crop, Brassica napus. Results: We identified 602 potential bHLHs in the B. napus genome (BnabHLHs) and categorized them into 35 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure, and exon-intron organization analysis. The intron insertion patterns of this gene family were analyzed and a total of eight types were identified in the bHLH regions of BnabHLHs. Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnabHLHs. Expression analyses showed that BnabHLHs were widely in different plant tissues and formed seven main patterns, suggesting they may participate in various aspects of B. napus development. Furthermore, when roots were treated with five different hormones (IAA, auxin; GA3, gibberellin; 6-BA, cytokinin; ABA, abscisic acid and ACC, ethylene), the expression profiles of BnabHLHs changed significantly, with many showing increased expression. The induction of five candidate BnabHLHs was confirmed following the five hormone treatments via qRT-PCR. Up to 246 BnabHLHs from nine subfamilies were predicted to have potential roles relating to root development through the joint analysis of their expression profiles and homolog function. Conclusion: The 602 BnabHLHs identified from B. napus were classified into 35 subfamilies, and those members from the same subfamily generally had similar sequence motifs. Overall, we found that BnabHLHs may be widely involved in root development in B. napus. Moreover, this study provides important insights into the potential functions of the BnabHLHs super gene family and thus will be useful in future gene function research.

Genome-wide Survey of bHLH Super Gene Family in Brassica napus and Their Roles in Roots

2019 ◽  
Author(s):  
Yunzhuo Ke ◽  
Yunwen Wu ◽  
Hongjun Zhou ◽  
Ping Chen ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Expression Profiles ◽  
Joint Analysis ◽  
Pcr Analysis ◽  
Sequence Motifs ◽  
Intron Insertion ◽  
Under Five ◽  
Helix Loop Helix ◽  
Root Hair Development

Abstract Background: Basic helix-loop-helix (bHLH) gene family is one of the largest transcription factors in plants and are functionally characterized in diverse species. However, less is known about their functions in the economically important allopolyploid oil crop, Brassica napus . Results : We identified 602 potential bHLHs in B. napus genome ( BnbHLHs ) and categorized them into 36 subfamilies, including seven newly separated subfamilies, based on phylogeny, protein structure and exon-intron organization analysis. The intron insertion patterns of this gene family were corrected and a total of eight types were identified in the bHLH regions of BnbHLHs . Chromosome distribution and synteny analyses revealed that hybridization between Brassica rapa and Brassica oleracea was the main expansion mechanism for BnbHLHs . Expression analyses showed that BnbHLHs were wide and formed six main patterns, suggesting they may participate in various aspects in B. napus during the development. The expression profiles under five hormone treatments (IAA, ABA, ACC, GA3, 6-BA) in roots further revealed the active response of BnbHLHs with a large proportion of which being induced. qRT-PCR analysis confirmed the expression profiles of five candidate BnbHLHs under five hormone inductions. Up to 246 BnbHLHs from nine subfamilies were predicted to have potential roles relating to root development by joint analysis of expression profile and homolog function. Further, the MYB/bHLH/WD40 (MBW) protein complex regulating root hair development were verified in B. napus by yeast two-hybrid experiment. Conclusion: The 602 BnbHLHs identified from B. napus could be classed into 36 subfamilies, and those members from the same subfamily generally have similar sequence motifs. BnbHLHs may widely involve in root biological process in B. napus . Overall, this study provides important insights into the characterization and potential functions of B. napus bHLH super gene family and thus will be useful in future gene function research.

scholarly journals Global Analysis of WOX Transcription Factor Gene Family in Brassica napus Reveals Their Stress- and Hormone-Responsive Patterns

2018 ◽  
Vol 19 (11) ◽  
pp. 3470 ◽  
Author(s):  
Mang-Mang Wang ◽  
Ming-Ming Liu ◽  
Feng Ran ◽  
Peng-Cheng Guo ◽  
Yun-Zhuo Ke ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Brassica Napus ◽  
Gene Family ◽  
Gene Structure ◽  
Stress Responses ◽  
Expression Profiles ◽  
Global Analysis ◽  
Transcription Factor Gene ◽  
Factor Gene ◽  
Transcription Factor Gene Family

The plant-specific WUSCHEL-related homeobox (WOX) transcription factor gene family is important for plant growth and development but little studied in oil crops. We identified and characterized 58 putative WOX genes in Brassica napus (BnWOXs), which were divided into three major clades and nine subclades based on the gene structure and conserved motifs. Collinearity analysis revealed that most BnWOXs were the products of allopolyploidization and segmental duplication events. Gene structure analysis indicated that introns/exons and protein motifs were conserved in each subclade and RNA sequencing revealed that BnWOXs had narrow expression profiles in major tissues and/or organs across different developmental stages. The expression pattern of each clade was highly conserved and similar to that of the sister and orthologous pairs from Brassica rapa and Brassica oleracea. Quantitative real-time polymerase chain reaction showed that members of the WOX4 subclade were induced in seedling roots by abiotic and hormone stresses, indicating their contribution to root development and abiotic stress responses. 463 proteins were predicted to interact with BnWOXs, including peptides regulating stem cell homeostasis in meristems. This study provides insights into the evolution and expression of the WOX gene family in B. napus and will be useful in future gene function research.

Hxt encodes a basic helix-loop-helix transcription factor that regulates trophoblast cell development

Development ◽  
1995 ◽  
Vol 121 (8) ◽  
pp. 2513-2523 ◽  
Author(s):  
J.C. Cross ◽  
M.L. Flannery ◽  
M.A. Blanar ◽  
E. Steingrimsson ◽  
N.A. Jenkins ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Gene Promoter ◽  
Giant Cells ◽  
Placental Lactogen ◽  
Specific Gene ◽  
Bhlh Transcription Factor ◽  
Trophoblast Cells ◽  
Positive Role ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix

Trophoblast cells are the first lineage to form in the mammalian conceptus and mediate the process of implantation. We report the cloning of a basic helix-loop-helix (bHLH) transcription factor gene, Hxt, that is expressed in early trophoblast and in differentiated giant cells. A separate gene, Hed, encodes a related protein that is expressed in maternal deciduum surrounding the implantation site. Overexpression of Hxt in mouse blastomeres directed their development into trophoblast cells in blastocysts. In addition, overexpression of Hxt induced the differentiation of rat trophoblast (Rcho-1) stem cells as assayed by changes in cell adhesion and by activation of the placental lactogen-I gene promoter, a trophoblast giant cell-specific gene. In contrast, the negative HLH regulator, Id-1, inhibited Rcho-1 differentiation and placental lactogen-I transcription. These data demonstrate a role for HLH factors in regulating trophoblast development and indicate a positive role for Hxt in promoting the formation of trophoblast giant cells.

scholarly journals Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

Genes ◽  
2019 ◽  
Vol 10 (11) ◽  
pp. 914
Author(s):  
Shan ◽  
Zhang ◽  
Yu ◽  
Wang ◽  
Li ◽  
...  
Keyword(s):  
Brassica Oleracea ◽  
Expression Profiles ◽  
Phylogenetic Analyses ◽  
Chilling Stress ◽  
Expression Patterns ◽  
Comprehensive Analysis ◽  
Bhlh Transcription Factor ◽  
Specific Expression ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

scholarly journals FIT, a regulatory hub for iron deficiency and stress signaling in roots, and FIT-dependent and -independent gene signatures

2020 ◽  
Vol 71 (5) ◽  
pp. 1694-1705 ◽  
Author(s):  
Birte Schwarz ◽  
Petra Bauer
Keyword(s):  
Transcription Factor ◽  
Protein Interactions ◽  
Fe Deficiency ◽  
Bhlh Transcription Factor ◽  
Root Cells ◽  
Gene Signatures ◽  
Helix Loop Helix ◽  
Independent Gene ◽  
Fe Uptake ◽  
Fe Acquisition

Abstract Iron (Fe) is vital for plant growth. Plants balance the beneficial and toxic effects of this micronutrient, and tightly control Fe uptake and allocation. Here, we review the role of the basic helix–loop–helix (bHLH) transcription factor FIT (FER-LIKE FE DEFICIENCY-INDUCED TRANSCRIPTION FACTOR) in Fe acquisition. FIT is not only essential, it is also a central regulatory hub in root cells to steer and adjust the rate of Fe uptake by the root in a changing environment. FIT regulates a subset of root Fe deficiency (–Fe) response genes. Based on a combination of co-expression network and FIT-dependent transcriptome analyses, we defined a set of FIT-dependent and FIT-independent gene expression signatures and co-expression clusters that encode specific functions in Fe regulation and Fe homeostasis. These gene signatures serve as markers to integrate novel regulatory factors and signals into the –Fe response cascade. FIT forms a complex with bHLH subgroup Ib transcription factors. Furthermore, it interacts with key regulators from different signaling pathways that either activate or inhibit FIT function to adjust Fe acquisition to growth and environmental constraints. Co-expression clusters and FIT protein interactions suggest a connection of –Fe with ABA responses and root cell elongation processes that can be explored in future studies.

scholarly journals Tomato bHLH132 Transcription Factor Controls Growth and Defense and Is Activated by Xanthomonas euvesicatoria Effector XopD During Pathogenesis

2019 ◽  
Vol 32 (12) ◽  
pp. 1614-1622 ◽  
Author(s):  
Jung-Gun Kim ◽  
Mary Beth Mudgett
Keyword(s):  
Transcription Factor ◽  
Protease Activity ◽  
Transcriptional Profiling ◽  
Bhlh Transcription Factor ◽  
Transcription Activator ◽  
Tal Effectors ◽  
Sumo Protease ◽  
Tal Effector ◽  
Helix Loop Helix ◽  
Xanthomonas Euvesicatoria

Effector-dependent manipulation of host transcription is a key virulence mechanism used by Xanthomonas species causing bacterial spot disease in tomato and pepper. Transcription activator-like (TAL) effectors employ novel DNA-binding domains to directly activate host transcription, whereas the non-TAL effector XopD uses a small ubiquitin-like modifier (SUMO) protease activity to represses host transcription. The targets of TAL and non-TAL effectors provide insight to the genes governing susceptibility and resistance during Xanthomonas infection. In this study, we investigated the extent to which the X. euvesicatoria non-TAL effector strain Xe85-10 activates tomato transcription to gain new insight to the transcriptional circuits and virulence mechanisms associated with Xanthomonas euvesicatoria pathogenesis. Using transcriptional profiling, we identified a putative basic helix-loop-helix (bHLH) transcription factor, bHLH132, as a pathogen-responsive gene that is moderately induced by microbe-associated molecular patterns and defense hormones and is highly induced by XopD during X. euvesicatoria infection. We also found that activation of bHLH132 transcription requires the XopD SUMO protease activity. Silencing bHLH132 mRNA expression results in stunted tomato plants with enhanced susceptibility to X. euvesicatoria infection. Our work suggests that bHLH132 is required for normal vegetative growth and development as well as resistance to X. euvesicatoria. It also suggests new transcription-based models describing XopD virulence and recognition in tomato.

scholarly journals Genome-wide survey and expression analyses of the GRAS gene family in Brassica napus reveals their roles in root development and stress response

Planta ◽  
2019 ◽  
Vol 250 (4) ◽  
pp. 1051-1072 ◽  
Author(s):  
Pengcheng Guo ◽  
Jing Wen ◽  
Jin Yang ◽  
Yunzhuo Ke ◽  
Mangmang Wang ◽  
...  
Keyword(s):  
Stress Response ◽  
Brassica Napus ◽  
Gene Family ◽  
Root Development ◽  
Genome Wide ◽  
Genome Wide Survey ◽  
Gras Gene
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