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TOBFAC: The database of tobacco transcription factors

Family: bHLH

Minimum number of tobacco bHLH genes: 190

Count of tobacco bHLH sequences: 191

Pfam accession: HLH

SHOULD possess HLH domain

The basic helix-loop-helix (bHLH) transcription factors form one of the largest families of transcription factors in plants . The bHLH domain is approximately 60 amino acids long and contains two functionally distinct regions . Typically, there are 18 hydrophilic and basic amino acids at the N-terminus, followed by two regions of hydrophobic residues predicted to form amphipathic -helices separated by an intervening loop . These -helices can interact with other proteins, allowing the formation of homodimers or heterodimers with MYB, bHLH, WD40 or other proteins . The basic region determines the DNA binding activity of the protein . A small number of bHLH proteins do not bind DNA, whereas the other bHLHs can be subdivided into two categories: the E Box binders (CANNTG) and the G box binders (CACGTG). The subdivision is based on the presence or absence of Glu-13 and Arg-16 in the basic region .

In Zea mays a group of bHLH genes (R, B, Lc, Sn and R-ch Hopi) are required for the production of the purple anthocyanin pigments . These genes interact with the products of the R2R3MYB proteins C1 and P and together control pigmentation. bHLH/MYB complexes are also involved in trichome development in Arabidopsis through the interaction of the bHLH protein GLABRA3 and the R2R3MYB protein GLABROUS1 . One of most important roles of bHLH proteins in plants is in light sensing and studies have shown that related bHLHs play key roles in phytochrome signaling . The bHLHs involved in light signaling are found in subgroup E and several specifically interact with light-activated phytochrome. These bHLH proteins are called phytochrome interacting factors (PIFs) or phytochrome interacting factor-like (PILs). They vary in their specificity for the phytochromes phyA-E and primarily act as negative regulators of phytochrome signaling.

Phylogenetic analysis of the bHLH family is considerably more difficult than for most of the other families. This is illustrated by two recent publications, that sought to analyse the complete bHLH gene family in Arabidopsis . Using slightly different search strategies, Toledo-Ortiz and co-workers reported the discovery of 147 bHLH genes, whereas Heim and co-workers reported the discovery of 133 genes. Both groups then cooperated in producing a combined dataset and arrived at a final total of 162 bHLH genes . There were several reasons for these problems and some became apparent when we studied the bHLH family in tobacco. One major problem is that the bHLH genes are relatively divergent and there are disagreements as to what exactly constitutes a bHLH domain. This resulted in no single search ever isolating all 162 Arabidopsis genes . Another problem is the presence of up to three introns in many bHLH domains, particularly very short introns in the loop domain. This was a significant source of false negatives in the Arabidopsis analyses and was also a problem with the tobacco gene family.

Papers

Toledo-Ortiz G, Huq E, Quail PH. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell. 2003 Aug;15(8):1749-70 PMID: 12897250

Buck, MJ; Atchley, WR. Phylogenetic analysis of plant basic helix-loop-helix proteins. J. Mol. Evol. 2003 56(6):742-50 PMID: 12911037

Heim, MA; Jakoby, M; Werber, M; Martin, C; Weisshaar, B; Bailey, PC. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol. Biol. Evol. 2003 20(5):735-47 PMID: 12679534

Littlewood, TD; Evan, GI. Transcription factors 2: helix-loop-helix. Protein Profile 1995 2(6):621-702 PMID: 7553065

Massari, ME; Murre, C. Helix-loop-helix proteins: regulators of transcription in eucaryotic organisms. Mol. Cell. Biol. 2000 20(2):429-40 PMID: 10611221

Quattrocchio, F; Wing, JF; van der Woude, K; Mol, JN; Koes, R. Analysis of bHLH and MYB domain proteins: species-specific regulatory differences are caused by divergent evolution of target anthocyanin genes. Plant J. 1998 13(4):475-88 PMID: 9680994

Bailey, PC; Martin, C; Toledo-Ortiz, G; Quail, PH; Huq, E; Heim, MA; Jakoby, M; Werber, M; Weisshaar, B. Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana. Plant Cell 2003. 15(11):2497-502 PMID: 14600211

Heim, M.A., Jakoby, M., Werber, M., Martin, C., Weisshaar, B., and Bailey, P.C. The basic helix-loop-helix transcription factor family in plants: A genome-wide study of protein structure and functional diversity. MOLECULAR BIOLOGY AND EVOLUTION 20, 735-747 2003

Toledo-Ortiz, G., Huq, E., and Quail, P.H. The Arabidopsis basic/helix-loop-helix transcription factor family. PLANT CELL 15, 1749-1770 2003

Quail, P.H. Phytochrome photosensory signalling networks. NATURE REVIEWS MOLECULAR CELL BIOLOGY 3, 85-93 2002

Massari, M.E., and Murre, C. Helix-loop-helix proteins: Regulators of transcription in eucaryotic organisms. MOLECULAR AND CELLULAR BIOLOGY 20, 429-440 2000

Payne, C.T., Zhang, F., and Lloyd, A.M. GL3 encodes a bHLH protein that regulates trichome development in arabidopsis through interaction with GL1 and TTG1. GENETICS 156, 1349-1362 2000

Hu, J.P., Anderson, B., and Wessler, S.R. Isolation and characterization of rice R genes: Evidence for distinct evolutionary paths in rice and maize. GENETICS 142, 1021-1031 1996

Murre, C., Bain, G., Vandijk, M.A., Engel, I., Furnari, B.A., Massari, M.E., Matthews, J.R., Quong, M.W., Rivera, R.R., and Stuiver, M.H. Structure and Function of Helix-Loop-Helix Proteins. Biochimica Et Biophysica Acta-Gene Structure and Expression 1218, 129-135 1994

Murre, C., McCaw, P.S., Vaessin, H., Caudy, M., Jan, L.Y., Jan, Y.N., Cabrera, C.V., Buskin, J.N., Hauschka, S.D., Lassar, A.B., Weintraub, H., and Baltimore, D. Interactions between Heterologous Helix-Loop-Helix Proteins Generate Complexes That Bind Specifically to a Common DNA-Sequence. CELL 58, 537-544 1989

Number of contigs: 156

Number of singlets: 37

Number of N terminal – 2

Number of C terminal – 20

Number of full – 169

There is one published bHLH gene that did not appear in the GSSs search and was added to the data set manually.

Total minimum number – 190

Search sequences and info

Transcription factor sequences

Tobacco published genes related to transcription factor family bHLH

Authors of this site:

Paul J Rushton
Marta T. Bokowiec
Xianfeng (Jeff) Chen
Thomas (Tom) W Laudeman
Jennifer F. Brannock
Michael P. Timko

Contact:

pr8y@virginia.edu