Maize Genetics Cooperation Newsletter vol 81 2007

 

Pascani, Republic of Moldova

Maize and Sorghum Research Institute

 

Bg transposon transcription from both strands: two products similar to NFI and SET domain proteins may be involved in transcription and chromatin modulation

--Koterniak, VV

 

          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.

 

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