Skip to main content

Advertisement

SpringerLink
Log in

Genome-wide analysis of the bHLH transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis)

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Basic helix-loop-helix (bHLH) transcription factors are widely distributed in eukaryotic organisms and are thought to be one of the largest families of regulatory proteins. This important family of transcriptional regulators plays crucial roles in plant development. However, a systematic analysis of the bHLH transcription factor family has not been reported in Chinese cabbage. In this study, 230 bHLH transcription factors were identified from the whole Chinese cabbage genome and compared with proteins from other representative plants, fungi and metazoans. The Chinese cabbage bHLH (BrabHLH) gene family could be classified into 24 subfamilies. Phylogenetic analysis of BrabHLHs along with bHLHs from Arabidopsis and rice indicated 26 subfamilies. The identification, classification, phylogenetic reconstruction, conserved motifs, chromosome distribution, functional annotation, expression patterns and interaction networks of BrabHLHs were analyzed. Distribution mapping showed that BrabHLHs were non-randomly located on the ten Chinese cabbage chromosomes. One hundred and twenty-four orthologous bHLH genes were identified between Chinese cabbage and Arabidopsis, and the interaction networks of the orthologous genes were constructed in Chinese cabbage. Quantitative RT-PCR analysis showed that expressions of BrabHLH genes varied widely under different abiotic stress treatments for different times. Thus, this comprehensive analysis of BrabHLHs represents a rich resource, aiding the elucidation of the roles of bHLH family members in plant growth and development. Furthermore, the comparative genomics analysis deepened our understanding of the evolution of this gene family after a polyploidy event.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  • Atchley WR, Fitch WM (1997) A natural classification of the basic helix-loop-helix class of transcription factors. Proc Natl Acad Sci USA 94:5172–5176

    Article  CAS  PubMed  Google Scholar 

  • Atchley WR, Terhalle W, Dress A (1999) Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J Mol Evol 48:501–516

    Article  CAS  PubMed  Google Scholar 

  • Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS (2009) MEME SUITE: tools for motif discovery and searching. Nucl Acids Res 37:W202–W208

    Article  CAS  PubMed  Google Scholar 

  • Beilstein MA, Nagalingum NS, Clements MD, Manchester SR, Mathews S (2010) Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana. Proc Natl Acad Sci USA 107:18724–18728

    Article  CAS  PubMed  Google Scholar 

  • Carretero-Paulet L, Galstyan A, Roig-Villanova I, Martinez-Garcia JF, Bilbao-Castro JR, Robertson DL (2010) Genome-wide classification and evolutionary analysis of the bHLH family of transcription factors in Arabidopsis, poplar, rice, moss, and algae. Plant Physiol 153:1398–1412

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Dang C, Wang Y, Zhang D, Yao Q, Chen K (2011) A genome-wide survey on basic helix-loop-helix transcription factors in giant panda. PLoS ONE 6:e26878

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Douzery EJ, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution: does a relaxed molecular clock reconcile proteins and fossils? Proc Natl Acad Sci USA 101:15386–15391

    Article  CAS  PubMed  Google Scholar 

  • Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC (2003) The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol Biol Evol 20:735–747

    Article  CAS  PubMed  Google Scholar 

  • Jiang FL, Wang F, Wu Z, Li Y, Shi GJ, Hu JD, Hou XL (2011) Components of the Arabidopsis CBF Cold-Response Pathway Are Conserved in Non-heading Chinese Cabbage. Plant Mol Biol Rep 29:525–532

    Article  CAS  Google Scholar 

  • Jiao Y, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang H, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW (2011) Ancestral polyploidy in seed plants and angiosperms. Nature 473:97–100

    Article  CAS  PubMed  Google Scholar 

  • Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645

    Article  CAS  PubMed  Google Scholar 

  • Ledent V, Vervoort M (2001) The basic helix-loop-helix protein family: comparative genomics and phylogenetic analysis. Genome Res 11:754–770

    Article  CAS  PubMed  Google Scholar 

  • Ledent V, Paquet O, Vervoort M (2002) Phylogenetic analysis of the human basic helix-loop-helix proteins. Genome Biol 3: RESEARCH0030

  • Lee S, Yang KY, Kim YM, Park SY, Kim SY, Soh MS (2006) Overexpression of PRE1 and its homologous genes activates Gibberellin-dependent responses in Arabidopsis thaliana. Plant Cell Physiol 47:591–600

    Article  CAS  PubMed  Google Scholar 

  • Lee TH, Tang HB, Wang XY, Paterson AH (2013) PGDD: a database of gene and genome duplication in plants. Nucl Acids Res 41:D1152–D1158

    Article  CAS  PubMed  Google Scholar 

  • Li L, Stoeckert CJ Jr, Roos DS (2003) OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 13:2178–2189

    Article  CAS  PubMed  Google Scholar 

  • Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, Guo J, Liang W, Chen L, Yin J, Ma H, Wang J, Zhang D (2006) Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol 141:1167–1184

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Li X, Chen L, Hong M, Zhang Y, Zu F, Wen J, Yi B, Ma C, Shen J, Tu J, Fu T (2012) A large insertion in bHLH transcription factor BrTT8 resulting in yellow seed coat in Brassica rapa. PLoS ONE 7:e44145

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Liu WY, Zhao CJ (2010) Genome-wide identification and analysis of the chicken basic helix-loop-helix factors. Comp Funct Genomics 2010:1–12

  • Mara CD, Huang T, Irish VF (2010) The Arabidopsis floral homeotic proteins APETALA3 and PISTILLATA negatively regulate the BANQUO genes implicated in light signaling. Plant Cell 22:690–702

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Massari ME, Murre C (2000) Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol Cell Biol 20:429–440

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Murre C, McCaw PS, Baltimore D (1989) A new DNA binding and dimerization motif in immunoglobulin enhancer binding, daughterless, MyoD, and myc proteins. Cell 56:777–783

    Article  CAS  PubMed  Google Scholar 

  • Peterson KJ, Lyons JB, Nowak KS, Takacs CM, Wargo MJ, McPeek MA (2004) Estimating metazoan divergence times with a molecular clock. Proc Natl Acad Sci USA 101:6536–6541

    Article  CAS  PubMed  Google Scholar 

  • Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucl Acids Res 29:e45

    Article  CAS  PubMed  Google Scholar 

  • Pires N, Dolan L (2010) Origin and diversification of basic-helix-loop-helix proteins in plants. Mol Biol Evol 27:862–874

    Article  CAS  PubMed  Google Scholar 

  • Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD (2012) The Pfam protein families database. Nucl Acids Res 40:D290–D301

    Article  CAS  PubMed  Google Scholar 

  • Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 13:2498–2504

    Article  CAS  PubMed  Google Scholar 

  • Simionato E, Ledent V, Richards G, Thomas-Chollier M, Kerner P, Coornaert D, Degnan BM, Vervoort M (2007) Origin and diversification of the basic helix-loop-helix gene family in metazoans: insights from comparative genomics. BMC Evol Biol 7:33

    Article  PubMed Central  PubMed  Google Scholar 

  • Skinner MK, Rawls A, Wilson-Rawls J, Roalson EH (2010) Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation 80:1–8

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Stevens JD, Roalson EH, Skinner MK (2008) Phylogenetic and expression analysis of the basic helix-loop-helix transcription factor gene family: genomic approach to cellular differentiation. Differentiation 76:1006–1022

    CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  Google Scholar 

  • Tang H, Bowers JE, Wang X, Paterson AH (2010) Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci USA 107:472–477

    Article  CAS  PubMed  Google Scholar 

  • Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 25:4876–4882

    Article  CAS  PubMed  Google Scholar 

  • Toledo-Ortiz G, Huq E, Quail PH (2003) The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15:1749–1770

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang H, Zhu Y, Fujioka S, Asami T, Li J (2009a) Regulation of Arabidopsis brassinosteroid signaling by atypical basic helix-loop-helix proteins. Plant Cell 21:3781–3791

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wang Y, Chen K, Yao Q, Zheng X, Yang Z (2009b) Phylogenetic analysis of zebrafish basic helix-loop-helix transcription factors. J Mol Evol 68:629–640

    Article  CAS  PubMed  Google Scholar 

  • Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun JH, Bancroft I, Cheng F (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43:1035–1039

    Article  CAS  PubMed  Google Scholar 

  • Yu SC, Zhang FL, Yu YJ, Zhang DS, Zhao XY, Wang WH (2012) Transcriptome profiling of dehydration stress in the Chinese cabbage (Brassica rapa L. ssp pekinensis) by tag sequencing. Plant Mol Biol Rep 30:17–28

    Article  CAS  Google Scholar 

  • Zhang H, Jin J, Tang L, Zhao Y, Gu X, Gao G, Luo J (2011) PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucl Acids Res 39:D1114–D1117

    Article  CAS  PubMed  Google Scholar 

  • Zheng X, Wang Y, Yao Q, Yang Z, Chen K (2009) A genome-wide survey on basic helix-loop-helix transcription factors in rat and mouse. Mamm Genome 20:236–246

    Article  CAS  PubMed  Google Scholar 

  • Zuo K, Zhao J, Wang J, Sun X, Tang K (2004) Molecular cloning and characterization of GhlecRK, a novel kinase gene with lectin-like domain from Gossypium hirsutum. DNA Seq 15:58–65

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was supported by the National High Technology Research and Development Program of China (863 Program, No. 2012AA100101), China Agriculture Research System CARS-25-A-12, the Fundamental Research Funds for the Central Universities of China (KYZ201111), and a Project Funded by the Priority Academic Program Development of Jiansu Higher Education Institutions.

Author information

Authors and Affiliations

  1. State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China

    Xiao-Ming Song, Zhi-Nan Huang, Wei-Ke Duan, Jun Ren, Tong-Kun Liu, Ying Li & Xi-Lin Hou

Authors
  1. Xiao-Ming Song
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Zhi-Nan Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wei-Ke Duan
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jun Ren
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Tong-Kun Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ying Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Xi-Lin Hou
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Xi-Lin Hou.

Additional information

Communicated by Y. Van de Peer.

Electronic supplementary material

Below is the link to the electronic supplementary material.

438_2013_791_MOESM1_ESM.eps

Supplementary Figure 1 Alignment of all the bHLH domain of Chinese cabbage proteins. Shown at the top are the boundaries used in this study to distinguish the DNA-binding basic region, the two a-helixes and the variable loop region. (EPS 7155 kb)

438_2013_791_MOESM2_ESM.eps

Supplementary Figure 2 Alignment of all the bHLH domain of Arabidopsis proteins. Shown at the top are the boundaries used in this study to distinguish the DNA-binding basic region, the two a-helixes and the variable loop region. (EPS 5271 kb)

438_2013_791_MOESM3_ESM.eps

Supplementary Figure 3 Alignment of all the bHLH domain of rice proteins. Shown at the top are the boundaries used in this study to distinguish the DNA-binding basic region, the two a-helixes and the variable loop region. (EPS 5598 kb)

438_2013_791_MOESM4_ESM.eps

Supplementary Figure 4 The predicted DNA-binding characteristics of the bHLH domains of BrabHLH, AthbHLH and OsabHLH proteins. (EPS 5593 kb)

438_2013_791_MOESM5_ESM.eps

Supplementary Figure 5 Alignment of all the bHLH domain of Chinese cabbage, Arabidopsis and rice proteins. Shown at the top are the boundaries used in this study to distinguish the DNA-binding basic region, the two a-helixes and the variable loop region. (EPS 15641 kb)

438_2013_791_MOESM6_ESM.eps

Supplementary Figure 6 Logos of BrabHLH protein motifs. Logos are a visualization tool for motifs. The height of a letter indicates its relative frequency at the given position. (EPS 4580 kb)

438_2013_791_MOESM7_ESM.eps

Supplementary Figure 7 The NJ phylogenetic tree and BrabHLH gene structure of Chinese cabbage. The yellow blocks indicate introns and the green blocks indicate exons. The bHLH domains are shown as red blocks. (EPS 7626 kb)

438_2013_791_MOESM8_ESM.eps

Supplementary Figure 8 The NJ phylogenetic tree of the bHLH domain in plants, metazoans and fungi. (a) The NJ phylogenetic tree of the 3,242 bHLH protein domain in 25 representative plants. The phylogenetic classification was mainly according to Pires and Dolan (2010). (b) The NJ phylogenetic tree of the 698 bHLH protein domain in 12 representative metazoans. The phylogenetic classification was mainly according to a previous report (Ledent et al. 2002). (c) The NJ phylogenetic tree of the 3,948 bHLH protein domain in all the plants, metazoans and fungi used in this study. (d) The NJ phylogenetic tree of the 188 bHLH protein domain in the blended group. This group contained several bHLH proteins of plants, metazoans and fungi. (EPS 13901 kb)

438_2013_791_MOESM9_ESM.eps

Supplementary Figure 9 The relative expression levels of the significantly upregulated bHLH genes during (A) cold, (B) ABA, (c) PEG and (d) GA treatments (relative expression level > 5). The expression value was calculated using the 2−ΔΔCT method. Error bars represent standard errors from three independent replicates. (EPS 6475 kb)

438_2013_791_MOESM10_ESM.eps

Supplementary Figure 10 The NJ phylogenetic tree and the schematic diagram of amino acid motifs of bHLH proteins in Chinese cabbage. (EPS 8263 kb)

Supplementary material 10 (XLS 246 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Song, XM., Huang, ZN., Duan, WK. et al. Genome-wide analysis of the bHLH transcription factor family in Chinese cabbage (Brassica rapa ssp. pekinensis). Mol Genet Genomics 289, 77–91 (2014). https://doi.org/10.1007/s00438-013-0791-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-013-0791-3

Keywords

Search

Navigation