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TOBFAC: The database of tobacco transcription factors

Family: C2H2

Minimum number of tobacco C2H2 genes: 161

Count of tobacco C2H2 sequences: 199

Pfam accession: C2H2

SHOULD possess zf-C2H2 domain but SHOULD NOT possess JmjC JmjN PHD domains

The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger. #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter.

C2H2 zinc fingers (ZF) display a wide range of functions, from DNA or RNA binding to the involvement in protein-protein interactions. Therefore ZFPs not only act in transcriptional regulation, either directly or through site-specific modification and/or regulation of chromatin, but also participate in RNA metabolism and in other cellular functions that probably require specific protein contacts of the ZF domain.

Through in silico analysis 176 zinc finger proteins in Arabidopsis thaliana that hence constitute the most abundant family of putative transcriptional regulators in this plant were found. Only a minority of 33 A. thaliana zinc finger proteins are conserved in other eukaryotes. In contrast, the majority of these proteins (81%) are plant specific. They are derived from extensive duplication events and form expanded families. We assigned the proteins to different subgroups and families and focused specifically on the two largest and evolutionarily youngest families (A1 and C1) that are suggested to be primarily involved in transcriptional regulation. The newly defined family A1 (24 members) comprises proteins with tandemly arranged zinc finger domains. Family C1 (64 members), earlier described as the EPF-family in Petunia, comprises proteins with one isolated or two to five dispersed fingers and a mostly invariant QALGGH motif in the zinc finger helices. Based on the amino acid pattern in these helices we could describe five different signature sequences prevalent in C1 zinc finger domains. We also found a number of non-finger domains that are conserved in these families.

Analysis of the few evolutionarily conserved zinc finger proteins of A. thaliana suggests that most of them could be involved in ancient biological processes like RNA metabolism and chromatin-remodeling. In contrast, the majority of the unique A. thaliana zinc finger proteins are known or suggested to be involved in transcriptional regulation. They exhibit remarkable differences in the features of their zinc finger sequences and zinc finger arrangements compared to animal zinc finger proteins. The different zinc finger helix signatures found in family C1 may have important implications for the sequence specific DNA recognition and allow inferences about the evolution of the members in this family.

Papers

Iuchi, S. Three classes of C2H2 zinc finger proteins. Cell. Mol. Life Sci. 2001. 58(4):625-35 PMID: 11361095

Takatsuji, H. Zinc-finger proteins: the classical zinc finger emerges in contemporary plant science. Plant Mol. Biol. 1999 39(6):1073-8 PMID: 10380795

Englbrecht, CC; Schoof, H; Böhm, S. Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome. BMC Genomics 2004. 5(1):39 PMID: 15236668

Sakamoto, H; Maruyama, K; Sakuma, Y; Meshi, T; Iwabuchi, M; Shinozaki, K; Yamaguchi-Shinozaki, K. Arabidopsis Cys2/His2-type zinc-finger proteins function as transcription repressors under drought, cold, and high-salinity stress conditions. Plant Physiol. 2004. 136(1):2734-46 PMID: 15333755

Number of contigs: 149

Number of singlets: 50

Minimum numbner 40 + 34 + 18 + 37 + 1 + 1 + 2 + 3 + 1 + 1 +23* = 161 minimum

Searched with:

A1a At1g03840 (whole protein)

A1b At1g68130 (whole protein)

A1c AT1g34370 (whole protein)

A1d At1g51220 (whole protein)

A3 At2g23740 (region spanning the 4 fingers)

A4 at1g30970 (two fingers)

B1 at1g72050 (whole protein)

C1-1i At1g640 (single finger)

C1-Sa AT2G15740 (single finger)

C1-Q At2g36475 (single finger)

C1-2i AT2G37430 (two fingers)

C1-3i AT1G02030 (whole finger)

C1-4i AT1G49900 (two searches with the two double finger regions)

C1-5i AT3G29340 (whole protein - six fingers)

C2-B AT1G65110 (single finger)

C2-sb AT4G26030 (single finger)

C2-pairs AT4G12240 (single finger)

C2-unique AT1G04445 (single finger)

C2-cons SF AT2G27100 (single finger)

C3-PL SF AT1G01350 (single finger)

Results:

A1 23 + 3 + 1 + 2 = 40 minimum

N-terminal half 34

C-terminal half 11

Second finger 3

Central part 1

Full 2

C1-2i 32 + 2 = 34 minimum

Full 32

First finger 2

Second finger 1

C1-3i 13 + 4 + 1 = 18 minimum

Full 13

1 + 2 fingers 4

2 + 3 fingers 1

First finger 1

C1-1i = 37 minimum

Full 37

C2 cons = 1 minimum

Full 1

C2 pairs = 1 minimum

Full = 1

B cons 1 + 1 = 2 minimum

Full 1

C-terminal 1

N-terminal 1

C-4i 2 + 1 = 3 minimum

Full 2

First three fingers 1

C1-Q = 1 minimum

Full 1

A4 cons = 1 minimum

First finger 1

Multiple C2H2 fingers but no hits to plant proteins: 23

As we have no basis for comparison, then all 23 are included.

Search sequences and info

Transcription factor sequences

Tobacco published genes related to transcription factor family C2H2

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