Maize and Sorghum Research Institute

Pascani, Republic of Moldova

 

 

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

 

 

Koterniak V. V.

 

Bg transposon sequence and probable Bg-encoded proteins.

Analysis of Bg transposon sequence suggested that this mobile element may encode several proteins (designated as PPBg1-PPBg3), the primary structure and properties of which have been reported previously (MNL 79: 32-35; MNL 80, submitted). The analysis also shown on the propensities of certain regions of Bg sequence to form Z-DNA and on Z-DNA binding properties of Bg- encoded proteins indicating on the possibility of autoregulation of activity of this transposon on transcriptional level (MNL 80, submitted). Structure of all above mentioned proteins was deduced from one strand of Bg transposon containing two longest ORFs. It is known however that some mobile elements (e. g. maize MuDR autonomous element) are transcribed from both strands (see for example Hershberger RJ et al, Genetics 140: 1087-1098, 1995). Further analysis of Bg sequence indicates on the possibility of transcription of this mobile element from both strands encoding at least two products similar to 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 Bg second strand ORF from position 724 to 460 (positions in both strands of Bg sequence are indicated according to its first strand sequence of the GenBank accession number X56877.1) encodes an 87 amino acid protein (designated hereafter as PPBg4, fig. 1, a). It is unusually rich in tryptophane (7 residues) and has several PS dipeptide residues. BLAST analysis of this protein (carried out on NCBI server with default parameters) showed similarity of this protein with FAD/FMN-containing dehydrogenases of Ralstonia solanacearum (ZP_00945305.1); Oxidoreductase/nitrogenase of Rhodopseudomonas palustris (ZP_00810380.1); myosin, heavy polypeptide 7B of Bos taurus (XP_875978.1).

Further analysis of this Bg encoded protein sequence revealed some characteristics indicating on its involvement in transcription machinery. Firstly this protein shows significant similarity with the transcription regulators of the nuclear factor I (NFI) family (fig. 1a). (The CLUSTALW analysis was carried out on the server of European Bioinformatics Institute (http://www.ebi.ac.uk) using default parameters.) It has been shown that in human genome promoter site of NFI and Z-DNA forming regions (ZDRs) near transcriptional start sites of known genes (Champ PC et al, Nucleic Acids Research 32: 6501-6510, 2004). This correlation seems also to be true to the PPBg4 gene. Thus, the probable ZDRs of Bg transposon (starting from positions 120 and 402, MNL 80, submitted) are located near and downstream of the PPBg4 gene. A perfect canonical NFI binding site (5’-TGG(N)₆GCCAA-3’, see for review Zorbas H et al, The Journal of Biological Chemistry 267: 8478-8484) is present in position 1775 of Bg sequence (i.e. at -1051 bp upstream on the opposite strand in relation to translation start site of PPBg4).

The SP-rich stretch S29-S35 of PPBg4 (SPSPSTS, fig. 1b) is similar to the SPTSPSYSP motif containing in the NFI transcriptional activation domain (Wendler w et al, Nucleic Acids Research, 22: 2601-2603, 1994) and the latter is strongly related to heptapeptide repeat YSPTSPS of the RNA polymerase II carboxyterminal domain (Wendler w et al, Nucleic Acids Research, 22: 2601-2603, 1994). It was observed that “SPXX” elements are characteristic for DNA binding proteins (Suzuki M, EMBO J, 8: 797-804; 1989; Suzuki M, J. Mol. Biol., 207: 61-84, 1989). Another indication on the transcription regulation properties of PPBg4 is an unanticipated similarity between the PPBg4 sequence TCWFWLSPSPSTS (residues T23-S35) with the P-4 peptide (TWFWPYPYPHLP, Fujii T et al, Clinical Cancer Research, 9: 5423-5428, 2003) the latter inhibiting transcriptional regulatory function on the papillomavirus E2 protein (Fujii T et al, Clinical Cancer Research, 9: 5423-5428, 2003). (It will be also interesting to test the E2 inhibitory function of the TCWFWLSPSPSTS peptide.)

Different assumption can be made about the role of PPBg4 in transcription regulation. Similarity of this protein with NFI family transcription factors may indicate that it can participate in the transcription complexes which include these factors. For example, it was shown that CTF1 activator, a member of mentioned family of transcription regulators, interacts with TFIIB (Kim TK et al, PNAS, 91: 4170-4174, 1994).

 

 

 

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

 

Fig. 1. (a) Alignment of PPBg4 (upper line) with the transcription factor NF I of Mus musculus (NFI, lower line; GenBank accession number AAK21332.1). The T23-S35 sequence similar to the P-4 peptide (Fujii T et al, Clinical Cancer Research, 9: 5423-5428, 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 black background, the similar ones are in grey background.

 

An 86 amino acid protein encoded by the second strand of Bg element is similar to SET-domains proteins.

               The ATG codon on the Bg second strand starting from position 2350 can determine translational start site of another second strand Bg encoded protein. BLAST analysis of this 86 amino acid protein (further referred to as PPBg5) revealed its similarity with SET-domains proteins (fig. 2).

 

 

 

 

 

 

 

 

 

 

PPBg5 1 MSCTGLPCNVWIQSNELSTCLLIVGPIICNNLNDILHPNLINNHLSNT 48

CAG25109.1 3427 NNMNNMNNIMNNIMNNNMNNIMN-NIMNNNMNNI 3459

 

PPBg5 49 IINKFCILNTTSCIYRLVKKHPSIAIYHEINNAHHGRT 86

CAG25109.1 3460 INNNNIFNNDVSNNVDMQHKSDQICIFNS-NNIH 3492

 

Fig. 2. Similarity of PPBg5 with a SET-domain protein of Plasmodium falciparum (GenBank accession number CAG25109.1). Identical residues are shown in black background, the similar ones are in grey background.

 

 

 

               SET-domain containing methyltransferases participate in histone methylation. It is known that histone methylation can lead to both transcription activation of repression (reviewed in Schotta G et al, Genes & Dev., 18: 1251-1262, 2004). It was also shown the involvement of SET domain proteins in transcription elongation in Saccharomyces cerevisiae (Krogan NJ et al, Molecular and Cellular Biology, 23: 4207-4218, 2003). A connection between histone and DNA methylation was established (Malagnac F et al, EMBO J, 24: 6642-6852, 2002; Tariq M et al, PNAS 100: 8823-8827, 2003). All this indicate that SET domain in PPBg5 may be involved in chromatin remodeling processes connected with transcription of Bg. The transcription of Bg encoding genes should effect both its own transposition and transposition of nonautonomous rbg element (possible only in presence of autonomous Bg element). Proceeding from this, determination of the character of interaction between proteins encoded from both Bg strands could be considered as an important aspect of transcription and activity of this transposon.