Alfin Genomic sequences

Minimum number of tobacco Alfin genes: 9

Count of tobacco Alfin sequences: 24

Pfam accession: Alfin-like

SHOULD possess Alfin-like domain and COULD   possess PHD SNF2_N zf-C2H2 zf-C5HC2 zf-CCCH zf-TAZ domains but SHOULD NOT possess DDT Homeobox JmjC JmjN domains

Alfin1 cDNA, obtained by differential screening of a poly(A)+ library from salt-tolerant alfalfa cells, encodes a novel protein with a Cys4 and His/Cys3 putative zinc-binding domain that suggests a possible role for this protein in transcriptional regulation. We have expressed the cDNA in Escherichia coli and show that the recombinant Alfin1 protein binds DNA in a sequence-specific manner. The DNA recognition sequence was determined from individual clones isolated after four rounds of random oligonucleotide selection in gel retardation assays, coupled with PCR amplification of the selected sequences. The consensus binding site for Alfin1 is shown to contain two to five G-rich triplets with the conserved core of GNGGTG or GTGGNG in clones showing high-efficiency binding. DNA binding of the recombinant Alfin1 was inhibited by EDTA. Alfin1 mRNA was found predominantly in alfalfa roots. Growth of salt-sensitive Medicago sativa L on 171 mM NaCl led to a slight decrease in Alfin1 mRNA, while the salt-tolerant plants showed no decrease in Alfin1 mRNA levels. Interestingly, recombinant Alfin1 binds efficiently to three fragments of the MsPRP2 promoter, each containing consensus sequences identified by the random oligonucleotide selection. Since MsPRP2 transcripts were shown to be root-specific and accumulated in alfalfa roots in a salt-inducible manner, Alfin1 may play a role in the regulated expression of MsPRP2 in alfalfa roots and contribute to salt tolerance in these plants .

The Cys-rich sequence Cys-X2-Cys-X11-Cys-Cys-X2-Cys-X4-His-X2-Cys-X9-His-X5-Cys-X2-Cys- encoded by Alfin-1 contains one putative Cys4 zinc finger structure and another His/Cys3 structure, thus making it a good candidate for a new category of zinc finger nucleic adid-binding protein in plants .

Papers

Bastola, DR; Pethe, VV; Winicov, I. Alfin1, a novel zinc-finger protein in alfalfa roots that binds to promoter elements in the salt-inducible MsPRP2 gene. Plant Mol. Biol. 1998. 38(6):1123-35 PMID: 9869418

Winicov I. cDNA encoding putative zinc finger motifs from salt-tolerant alfalfa (Medicago sativa L.) cells. Plant Physiol. 1993 June; 102 (2): 681¨C682 PMID: 8108516



Number of contigs: 33

Number of singlets: 0

N terminus (up to 50th amino acid) – 9

50 aa – 110 aa – 7

120 aa – 185 – 3

C terminus including finger – 5

Total minimum number – 9




Search sequences and info


Transcription factor sequences
Locus
Description
NCBI
Alfin_2 [comment=first 20 amino acids] ET045429
ET051351
Alfin_3 [comment=5 prime 50 - 110] ET046047
ET044034
Alfin_4 [comment=5 prime quarter of gene] ET048660
ET047233
Alfin_5 [comment=C terminal finger] ET047637
ET047638
Alfin_6 [comment=N-terminal 30 amino acids] ET047005
ET047006
Alfin_7 [comment=N-terminal 30 amino acids] ET044241
ET051763
Alfin_8 [comment=N-terminal 50 amino acids] ET048172
ET046863
Alfin_9 [comment=N terminal 40 amino acids] ET043645
ET051262
Alfin_10 [comment=50 - 110 amino acids] ET042222
ET043407
Alfin_11 [comment=120-185 amino acids] ET048262
ET048518
Alfin_13 [comment=50 - 110 amino acids] ET043582
ET042170
ET042882
Alfin_14 [comment=C terminal 70 amino acids] ET045008
ET051747
ET044483
Alfin_15 [comment=N terminal 40 amino acids] ET044259
ET051621
ET051620
Alfin_17 [comment=50 - 110 amino acids] ET050037
ET049019
ET047645
Alfin_18 [comment=N terminal 40 amino acids] ET042206
ET046249
ET042532
ET042533
Alfin_20 [comment=C terminal 100 amino acids] ET048747
ET050932
ET049963
ET050933
ET045242
Alfin_21 [comment=50 - 110 amino acids] ET044776
ET044108
ET043526
ET042224
ET046026
Alfin_22 [comment=50 - 110 amino acids] ET047663
ET047664
ET047665
ET044488
ET049132
Alfin_24 [comment=C terminal 130 amino acids] ET048519
ET042254
ET048263
ET046379
ET048544
ET042255
Alfin_26 [comment=N terminal 35 amino acids] ET043474
Alfin_28 [comment=130-160 amino acids (short middle bit)] ET048479
Alfin_29 [comment=C terminal half] ET045975
Alfin_31 [comment=130-160 amino acids (short middle bit)] ET044302
Alfin_33 [comment=75 - 120 amino acids] ET049307


Tobacco published genes related to transcription factor family Alfin
Family Genbank ID Name
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