Maize Genetics Cooperation Newsletter vol 81 2007
Maize and Sorghum Research Institute
Bg transposon sequence and probable Bg-encoded proteins. Analysis of the Bg transposon sequence suggests that this mobile element encodes several proteins (designated as PPBg1-PPBg3), described previously (MNL 79:32-35; MNL 80, submitted). The analysis also shows certain regions of Bg sequence may form Z-DNA and that Bg-encoded proteins have Z-DNA binding properties, indicating a possible autoregulation of this transposon at the transcriptional level (MNL 80, submitted). Structure of all above-mentioned proteins was deduced from the strand of Bg transposon containing the two longest ORFs. However, some mobile elements (e.g., the maize MuDR autonomous element) are transcribed from both strands (Hershberger et al., Genetics 140:1087-1098, 1995). Further analysis of the other sstrand for Bg indicates this mobile element may encode 2 further transcription and chromatin modulation proteins.
An 87 amino acid protein encoded by the second strand of Bg element is similar to Nuclear Factor I family of transcriptional regulators. The ORF of the second strand of Bg, from position 724 to 460 (positions for both strands according to the first strand, the sequence of GenBank accession X56877.1), encodes an 87 amino acid protein, designated hereafter as PPBg4 (Fig. 1a). It is unusually rich in tryptophan (7 residues) and has several PS dipeptide residues.
This
protein shows significant similarity with the transcription regulators of the
nuclear factor I (NFI) family (Fig. 1a), using CLUSTALW analysis at the
European Bioinformatics Institute (http://www.ebi.ac.uk) using default
parameters. In the human genome,
the promoter sites of NFI and Z-DNA forming regions (ZDRs) are near
transcriptional start sites (Champ et al., Nucl. Acids Res.
32:6501-6510, 2004). In the
case of the PPBg4 gene, possible ZDRs
are located just downstream of the PPBg4 gene
at positions 120 and 402. In
addition, a perfect canonical NFI binding site (5�-TGG(N)6GCCAA-3�; Zorbas et
al., J. Biol. Chem. 267:8478-8484) is present at position 1775 of the Bg sequence; i.e., at -1051 bp upstream
on the opposite strand in relation to the translation start site of PPBg4. The SP-rich stretch S29-S35 of PPBg4 (SPSPSTS, Fig. 1b) is
similar to the SPTSPSYSP motif contained in the NFI transcriptional activation
domain (Wendler et al., Nucl.
a)
PPBg4 1 MRQQLQWS-CAAWRQQPHLP------WRR---------------TCWFWLSPSPSTS---- 35
NFI 109 MEEDVDTSPGGDYYTSPNSPTSSSRNWTEDIEGGISSPVKKTEMDKSPFNSPSPQDSPRLS 169
PPBg4 36 ----------CCSRGLA-TPRGT-----PQTDLHVNEVAVSWS-----LP---EPSSTLT- 47
NFI 170 SFTQHHRPVIAVHSGIARSPHPTSALHFPATPILPQTASTYFPHTAIRYPPHLNPQDPLKD 230
PPBg4 48 LWEMELLSRRVADGD----G 87
NFI 231 LVSLACDPATQQPGPSWYLG 250
b)
NFI -SPTSPSYSP
PolII YSPTSPS---
PPBg4 29 -SP-SPSTS- 35
Figure
1. (a) Alignment
of PPBg4 with the transcription factor NF I of Mus musculus (GenBank accession AAK21332.1). The T23-S35 sequence similar to the P-4 peptide
(Fujii et al., 2003) is underlined.
(b) Similarity of the S29-S35 region of PPBg78 with the SPTSPSYSP motif
of NFI transcription factor (NFI) and with repeat
YSPTSPS of the RNA polymerase II (PolII).
Identical residues are shown in a black background, similar ones are in
a grey background.
PPBg5 1 MSCTGLPCNVWIQSNELSTCLLIVGPIICNNLNDILHPNLINNHLSNT 48
CAG25109.1 3427
NNMNNMNNIMNNIMNNNMNNIMN-NIMNNNMNNI 3459
PPBg5 49 IINKFCILNTTSCIYRLVKKHPSIAIYHEINNAHHGRT 86
CAG25109.1 3460
INNNNIFNNDVSNNVDMQHKSDQICIFNS-NNIH 3492
Figure
2. Similarity of
PPBg5 with a SET-domain protein of Plasmodium
falciparum (GenBank accession CAG25109.1). Identical residues are shown in a black background,
similar ones are in a grey background.
Acids Res. 22:2601-2603, 1994). Another indication that PPBg4 regulates transcription is an unanticipated similarity between the PPBg4 sequence TCWFWLSPSPSTS (residues T23-S35) and the P-4 peptide (TWFWPYPYPHLP) which is known to inhibit transcriptional regulation (Fujii et al., Clin. Cancer Res. 9:5423-5428, 2003).
An 86 amino acid protein, PPBg5, encoded
by the second strand of the Bg element is similar to SET-domain proteins. The ATG codon on the Bg second strand, starting from position
2350, may determine the translational start site of another second strand Bg encoded protein. BLAST analysis of this 86 amino acid
protein (referred to as PPBG5) revealed its similarity with SET-domain proteins
(Fig. 2). Based on known SET domain involvement in histone methylation,
transcription activation of repression (reviewed in Schotta et al., Genes Dev. 18:1251-1262, 2004) and
transcription elongation in Saccharomyces cerevisiae (Krogan et al., Mol. Cell. Biol.
23:4207-4218, 2003), the SET domain in PPBg5 may be involved in
chromatin remodeling processes connected with transcription of Bg.
Please Note: Notes submitted to the Maize Genetics Cooperation
Newsletter may be cited only with consent of authors.