| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
|
|
|
|||||||
|
|||||||||
American Society of Plant Biologists
Update on the Basic Helix-Loop-Helix Transcription Factor Gene Family in Arabidopsis thaliana
a John Innes Centre Colney Lane NR4 7UH Norwich, UK
Basic helix-loop-helix (bHLH) transcription factors represent a family of proteins that contain a bHLH domain, a motif involved in binding DNA. Recently, two groups independently analyzed the BHLH gene family of Arabidopsis thaliana (Heim et al., 2003
Cross-referencing between the two data sets and further analysis have extended the total number of detected AtBHLH genes to 162 (Table 1). We assume that this count is very close to the final number of AtBHLH genes present in the Arabidopsis thaliana genome, but clearly, corrections or additions to the  complete Arabidopsis thaliana genome sequence in the future still may cause this number to change. During examination and comparison of the data sets, we observed some common problems that contributed to the discrepancies. These problems arise commonly during the handling of large data sets and are discussed here to aid future attempts at gene family annotation. The main reasons for discrepancies were as follows. (1) Differences between TIGR (www.tigr. org) or TAIR (www.arabidopsis.org) and MIPS (MAtDB; mips.gsf.de/projects/plants). Such differences are not easy to avoid, despite the best efforts of the database providers. Most problematic are differences in Arabidopsis Genome Initiative (AGI) codes for the same gene between the different databases.
(2) Positions on pseudochromosomes that are not stable as a result of corrections in single BAC sequences that affect the entire area (3) BAC identifiers and BAC sequence coordinates that differ for the same gene when either the upper or the lower strand is considered. One option is to keep the gene orientation according to the direction of transcription; the other is to keep the original BAC sequence in its 5' to 3' arrangement. Clearly consistency is very important. (4) Genes located at BAC borders that can result in either double entries of the same gene or failure to detect the gene as a result of the destruction of a continuous signature pattern. (5) Sequence errors in the genome sequence that destroy open reading frames. (6) Differences in the detailed definition of what constitutes a bHLH domain.
Both studies started with a subset of known bHLH domain transcription factors and used a consensus sequence described by Atchley et al. (1999)
Search engines have been greatly improved in the last few years, but they still often are not exact enough to identify certain motifs. This is not necessarily the result of deficiencies in the search algorithms but may result from the structure of matrices that describe known motifs (e.g., AtBHLH125 spanned two separate BAC ends, and two separate predictions had to be fused). Even the continuous optimization of our bHLH domain matrix never resulted in the identification of all 162 AtBHLH genes in one search. Additionally, gene prediction tools are sometimes not flexible enough to respond to variable intron lengths and exon distribution (e.g., the prediction NM_105789 for AtBHLH160 contains an intron that causes an overestimate of the length of the loop structure). It sounds obvious, but it is worth emphasizing that cDNA sequences, even from reverse transcriptase–mediated PCR experiments, should be deposited in GenBank (http://www.ncbi.nlm.nih.gov/) or EMBL (http://www.ebi.ac.uk/Databases/) even if the genomic sequence is already in the database, and the
It is an interesting and critical point that even with a combination of all available BLAST (Basic Local Alignment Search Tool) tools, both groups were unable to obtain a full set of Arabidopsis bHLH domain transcription factors in their initial analyses. Both studies relied on BLAST search capabilities (TBLASTN and BLASTP) and subsequent evaluation of the hits for the respective bHLH consensus sequences. In addition, position-specific iterated BLAST was used by one of the two groups to identify remaining unidentified bHLH domain–encoding sequences. Nevertheless, several true BHLH genes were not detected. Some of these initial false negatives were found by searching for the term We were able to improve gene annotation further by comparing closely related BHLH genes for their exon/intron structures. This powerful similarity-based approach (used here within a single species) led to the correction of some gene annotations and, consequently, to a further increase in the total number of AtBHLH genes detected. Several of the genes that escaped the initial screens by both groups contain short introns in the region that encodes the loop of the HLH region. These comparably short introns, and also short exons that are part of the bHLH open reading frame, resulted in mispredictions that were a significant cause of false negatives in our initial analyses. One example is AtBHLH160, for which we found a formerly unpredicted intron after comparison with the most closely related genes AtBHLH038/ORG2, AtBHLH039/ORG3, AtBHLH100, and AtBHLH101. The combined effort of our two groups and the lessons we have learned from the comparison of the two data sets have resulted in an (almost) complete view of the AtBHLH transcription factor gene family, now provided with unambiguous generic names and reference to synonyms. We hope that this work will serve as a solid foundation for further investigations into the functions of the different members of this interesting gene family in plants. REFERENCES
Abe, H., Urao, T., Ito, T., Seki, M., Shinozaki, K., and Yamaguchi-Shinozaki, K. (2003). Arabidopsis AtMYC2 (bHLH) and AtMYB2 (MYB) function as transcriptional activators in abscisic acid signaling. Plant Cell 15, 63–78. Atchley, W.R., Terhalle, W., and Dress, A. (1999). Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48, 501–516.[CrossRef][ISI][Medline] Buck, M.J., and Atchley, W.R. (2003). Phylogenetic analysis of plant basic helix-loop-helix proteins. J. Mol. Evol. 56, 742–750.[CrossRef][ISI][Medline]
Chinnusamy, V., Ohta, M., Kanrar, S., Lee, B.H., Hong, X., Agarwal, M., and Zhu, J.K. (2003). ICE1: A regulator of cold-induced transcriptome and freezing tolerance in Arabidopsis. Genes Dev. 17, 1043–1054.
Fairchild, C.D., Schumaker, M.A., and Quail, P.H. (2000). HFR1 encodes an atypical bHLH protein that acts in phytochrome A signal transduction. Genes Dev. 14, 2377–2391.
Friedrichsen, D.M., Nemhauser, J., Muramitsu, T., Maloof, J.N., Alonso, J., Ecker, J.R., Furuya, M., and Chory, J. (2002). Three redundant brassinosteroid early response genes encode putative bHLH transcription factors required for normal growth. Genetics 162, 1445–1456.
Heim, M.A., Jakoby, M., Werber, M., Martin, C., Weisshaar, B., and Bailey, P.C. (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. Heisler, M.G., Atkinson, A., Bylstra, Y.H., Walsh, R., and Smyth, D.R. (2001). SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein. Development 128, 1089–1098.[Abstract] Huq, E., and Quail, P.H. (2002). PIF4, a phytochrome-interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis. EMBO J. 21, 2441–2450.[CrossRef][ISI][Medline] Kang, H.G., Foley, R.C., Onate-Sanchez, L., Lin, C., and Singh, K.B. (2003). Target genes for OBP3, a Dof transcription factor, include novel basic helix-loop-helix domain proteins inducible by salicylic acid. Plant J. 35, 362–372.[CrossRef][ISI][Medline]
Nesi, N., Debeaujon, I., Jond, C., Pelletier, G., Caboche, M., and Lepiniec, L. (2000). The TT8 gene encodes a basic helix-loop-helix domain protein required for expression of DFR and BAN genes in Arabidopsis siliques. Plant Cell 12, 1863–1878. Ni, M., Tepperman, J.M., and Quail, P.H. (1998). PIF3, a phytochrome-interacting factor necessary for normal photoinduced signal transduction, is a novel basic helix-loop-helix protein. Cell 95, 657–667.[CrossRef][ISI][Medline]
Payne, C.T., Zhang, F., and Lloyd, A.M. (2000). GL3 encodes a bHLH protein that regulates trichome development in Arabidopsis through interaction with GL1 and TTG1. Genetics 156, 1349–1362. Rajani, S., and Sundaresan, V. (2001). The Arabidopsis myc/bHLH gene ALCATRAZ enables cell separation in fruit dehiscence. Curr. Biol. 11, 1914–1922.[CrossRef][ISI][Medline]
Smolen, G.A., Pawlowski, L., Wilensky, S.E., and Bender, J. (2002). Dominant alleles of the basic helix-loop-helix transcription factor ATR2 activate stress-responsive genes in Arabidopsis. Genetics 161, 1235–1246. Sorensen, A.M., Krober, S., Unte, U.S., Huijser, P., Dekker, K., and Saedler, H. (2003). The Arabidopsis ABORTED MICROSPORES (AMS) gene encodes a MYC class transcription factor. Plant J. 33, 413–423.[CrossRef][ISI][Medline]
Toledo-Ortiz, G., Huq, E., and Quail, P.H. (2003). The Arabidopsis basic/helix-loop-helix transcription factor family. Plant Cell 15, 1749–1770. Urao, T., Yamaguchi-Shinozaki, K., Mitsukawa, N., Shibata, D., and Shinozaki, K. (1996). Molecular cloning and characterization of a gene that encodes a MYC-related protein in Arabidopsis. Plant Mol. Biol. 32, 571–576.[CrossRef][ISI][Medline]
Yamashino, T., Matsushika, A., Fujimori, T., Sato, S., Kato, T., Tabata, S., and Mizuno, T. (2003). A link between circadian-controlled bHLH factors and the APRR1/TOC1 quintet in Arabidopsis thaliana. Plant Cell Physiol. 44, 619–629.
Zhang, F., Gonzalez, A., Zhao, M., Payne, C.T., and Lloyd, A.M. (2003). A network of redundant bHLH proteins functions in all TTG1-dependent pathways of Arabidopsis. Development 130, 4859–4869. This article has been cited by other articles:
|
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HOME | HELP | FEEDBACK | SUBSCRIPTIONS | ARCHIVE | SEARCH | TABLE OF CONTENTS |
| ASPB Publications | THE PLANT CELL | PLANT PHYSIOLOGY | |
|---|---|---|---|
118 AtBHLH genes. Of these, 116 correspond to those listed in 
