Q-s-) 1990 Oxford University Press
6458 Nucleic Acids Research, Vol. 18, No. 21
of gene E15 of bacteriophage D108 and comparison with phage Mu Sequence
Martin L.Pato, Mary Banerjee and Barbara T.Wagonner Department of Microbiology and Immunology, University of Colorado Health Sciences Center, Denver, CO 80262, USA EMBL accession
Submitted August 14, 1990 The genomes of bacteriophage Mu and the closely related, heteroimmune bacteriophage D108 are greater than 90% homologous, with three small regions of nonhomology at the left end of the genomes and a 520-bp insertion near the right end of the D108 genome (Gill et al., 1981). The first region of nonhomology encompasses the genes for the two regulatory proteins, repressor (c) and ner, and about 180-bp of the Nterminus of the A, or transposase, gene (Priess et al., 1982; Toussaint et al., 1983; Mizuuchi et al., 1986) and extends from about 200 bp to 1500 bp from the left end of the genomes. The second region of nonhomology between the two genomes contains the 3' portion of gene E6 (in the nomenclature of Priess et al., 1987) and lies between 4817-5044 bp from the left end of the Mu genome (Waggoner et al., 1988). The sequence of gene E15 of D108 is presented in Figure 1 and compared with the Mu E15 sequence (Priess et al., 1987). E15 falls within the third region of nonhomology which spans 515-bp of the Mu genome, between 7676 -8190 bp from the left end, and 605bp of the D108 genome. Mu E15 is 300-bp long; it can encode a protein of 11.68 kDa, as observed in E. coli minicells (Giphart-Gassler et al., 1981). D108 E15 is 288-bp long and can encode a protein of 11.11 kDa. The 5 '-terminal 23-bp
no.
X54298
of the E15 genes and N-terminal 9-aa of the corresponding polypeptides are identical in Mu and D108, reminiscent of E6. The roles of the heterologous c and Ner repressors are clear; the roles of E6 and E15 remain to be determined.
ACKNOWLEDGEMENT Supported by NIH grant GM24270 to M.L.P. REFERENCES Gill,G.S., Hull,R.C. and Curtiss,R.,IIl (1981) J. Virol. 37, 420-430. Giphart-Gassler,M., Reeve,J. and van de Putte,P. (1981) J. Mol. Biol. 145, 165-191. Mizuuchi,M., Weisberg,R.A. and Mizuuchi,K. (1986) Nucl. Acids Res. 14, 3813-3825. Priess,H.D., Kamp,D., Kahmann,R., Brauer,B. and Delius, H. (1982) Mol. Gen. Genet. 186, 315 -321. Priess,H.D., Brauer,B., Schmidt,C. and Kamp,D. (1987) in Symonds,N., Toussaint,A., van de Putte,P. and Howe,M. (eds.) Phage Mu. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 277-296. Toussaint,A., Faelen,M., Desmet,L. and Allet,B. (1983) Mol. Gen. Genet. 190, 70-79. Waggoner,B.T.,Wade,T. and Pato,M.L. (1988) Gene 62, 111-119.
115 D M
ACACGGCGTGCATGAATTGTGAAGGTGAATAATATGAATAATGAAACTAAATTTACGCCTAAAGACCTGGATGAAGAACTGGTGAAAGCTAAGATGCTTG 100 ...A.T..................................................T..CCTTA.TA.T
A.C.TCA
CTG.A.
ThrAlaCysMetAsnCysGluGlyGlu*** M. fAsnAsnGluThrLy3PheThrProLysAspLeuAspGluGluLeuValLysAlaLysMetLeuG
D M
...
LeuAsnIle
AsnValMetAlaGluLy3Gly
D M
AGCGTATGCACGATGTTATTGAGACTGCAATCAGTAAAGGCTTTTCTGCGAGAGAGGCCCTTGAAATTATGACACGGGAAATTCATCTCATACGCGoCGA
D
luArgMetHisA3pValIleGluThrAlaIleSerLysGlyPheSerAlaArgGluAlaLeuGluIleMetThrArgGluIleHi3LeuIleArgA3pGI
ATA.
G.T.G. .C.A.CG
ValArgAlaIleVal
M
.GT.
TyrGly
.T.AGC.TAATC.CA.C.C LysHisAsnLeuThr
AGT. .G
C.
ValArgAsp
C.AC.C IleAsn
MetAsnArgLeuGluThrVa
D M D M
AGTTTTGTTGCATAACAAAAAAGCCCACAACAATATTGTTTGTCGTGAGCTTGGCGTTGATGATTCAGCGGTTATTCCACAGCGTCAGTATCTGTGTGCT
D
CTGATGAGAGGTTCCCGGCATTAACAATATCCTGCCTTGAAGCCCAGAGCTTATTGAGCAGCAGATCAACATACTCATCGGCCTCAAAATCCAGTTCTTC
...GGCAC
A..TG.
C
G.GG.GTACA.CC.C. .CAG
G. .GC.ATCA. .CCAG.ATA. .G. .A.TG.CGC
300
TGTGT.TGAG...
uValLeuLeuHi3AsnLysLysAlaHi3A3nAsnIleValCysArgGluLeuGlyValA3pAspSerAlaValIleProGInArgGlnTyrLeuCy3Ala I
Ala
Gln
GluThr
ArgGluGluTyrIleArg
Arg
LeuSer
M .TC .TCC. CAG .AT .TGGGT .T .ACGAACTGA.AATGT .TTCC.TGA.C. .TGA D LeuMetArqGlySerArgHis**^ M PheLeuIleArgGlnHisLeuGlyLeuThrAsn'** D M D
200
GA.. GTC.GGAAACA.T
GlnAspIleValThrAspAlaHisValPheGlu 400
TT .CAGTTTT .CGCGGCG.CTTGTTCTCATTGCAGGCG.
GAACGTTTTTCGGTTCTTATAGCTGGCCTGTGTATTTCTGATGATGTCATAAGCATCGTGCATGTTGATAACACCGTTTTCAATCAGCTTAATCATCAGA 500 ATCTT..AAAATC.CTGCTG.AGA.CTGAAAA.GGC.T..CCCTCT..TGCG.TGAT.AT.GCC..CT.C..CACAAGGCGC.C...TGCTGATGCA.TC
M
D M D M
TTACCGACCAGCATAAAACCGGTTATACCAAAGAATTTATCCTGGTTATTAACAGGGGTGTCTTTCTGGTTTGTTTCGAAATCTGGGTTTTGTTCATCAT
D
CCGACACCGTATGTTGTTCTTGTTCAGCCATAATATTTCCTTTTATGTTATTACTGAATATGGCGGTGTTGCAGCACCGCCTC-TTTCCGGAGGTACGAT 700
600
M ----------------------------------------------------------------------- C .C D 116
D CATGAGTCGCACATCCCTGATTAAATTAATCCATGTCGCCCGTCGGGAGCTACAACTCGACGACGACACTTACCGCGCTT M ................................................................................ D M. fSerArgThrSerLeuIleLysLeuIleHisValAlaArgArgGluLeuGlnLeuA3pAspA3pThrTyrArgAla M
780
The nucleotide sequences of the coding (non-transcribed) strand of D108 (D) and Mu (M) DNA given from the 5' to 3' direction. Nucleotide position number 1 corresponds to nucleotide 7620 in the Mu sequence of Priess et al. (1987). The predicted amino acid sequences are shown below the DNA The nucleotide and amino acid sequence of Mu are indicated as dots if they are identical to the D108 sequence and only those nucleotides or amino acids which differ specifically written. Below the translational initiation codon, (AUG), the formyl-methionine is written as M.f and each open reading frame is noted above its respective initiation codon. The termination codon sequence is noted with three stars (***). An arbitrary gap has been introduced to obtain maximum homology between the two nucleotide sequences and is indicated with dashes. Vertical arrows indicate the extent of the nonhomologous region. Horizontal arrows indicate an inverted repeat sequence. are
sequences.
are
6458 Nucleic Acids Research, Vol. 18, No. 21
of gene E15 of bacteriophage D108 and comparison with phage Mu Sequence
Martin L.Pato, Mary Banerjee and Barbara T.Wagonner Department of Microbiology and Immunology, University of Colorado Health Sciences Center, Denver, CO 80262, USA EMBL accession
Submitted August 14, 1990 The genomes of bacteriophage Mu and the closely related, heteroimmune bacteriophage D108 are greater than 90% homologous, with three small regions of nonhomology at the left end of the genomes and a 520-bp insertion near the right end of the D108 genome (Gill et al., 1981). The first region of nonhomology encompasses the genes for the two regulatory proteins, repressor (c) and ner, and about 180-bp of the Nterminus of the A, or transposase, gene (Priess et al., 1982; Toussaint et al., 1983; Mizuuchi et al., 1986) and extends from about 200 bp to 1500 bp from the left end of the genomes. The second region of nonhomology between the two genomes contains the 3' portion of gene E6 (in the nomenclature of Priess et al., 1987) and lies between 4817-5044 bp from the left end of the Mu genome (Waggoner et al., 1988). The sequence of gene E15 of D108 is presented in Figure 1 and compared with the Mu E15 sequence (Priess et al., 1987). E15 falls within the third region of nonhomology which spans 515-bp of the Mu genome, between 7676 -8190 bp from the left end, and 605bp of the D108 genome. Mu E15 is 300-bp long; it can encode a protein of 11.68 kDa, as observed in E. coli minicells (Giphart-Gassler et al., 1981). D108 E15 is 288-bp long and can encode a protein of 11.11 kDa. The 5 '-terminal 23-bp
no.
X54298
of the E15 genes and N-terminal 9-aa of the corresponding polypeptides are identical in Mu and D108, reminiscent of E6. The roles of the heterologous c and Ner repressors are clear; the roles of E6 and E15 remain to be determined.
ACKNOWLEDGEMENT Supported by NIH grant GM24270 to M.L.P. REFERENCES Gill,G.S., Hull,R.C. and Curtiss,R.,IIl (1981) J. Virol. 37, 420-430. Giphart-Gassler,M., Reeve,J. and van de Putte,P. (1981) J. Mol. Biol. 145, 165-191. Mizuuchi,M., Weisberg,R.A. and Mizuuchi,K. (1986) Nucl. Acids Res. 14, 3813-3825. Priess,H.D., Kamp,D., Kahmann,R., Brauer,B. and Delius, H. (1982) Mol. Gen. Genet. 186, 315 -321. Priess,H.D., Brauer,B., Schmidt,C. and Kamp,D. (1987) in Symonds,N., Toussaint,A., van de Putte,P. and Howe,M. (eds.) Phage Mu. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp. 277-296. Toussaint,A., Faelen,M., Desmet,L. and Allet,B. (1983) Mol. Gen. Genet. 190, 70-79. Waggoner,B.T.,Wade,T. and Pato,M.L. (1988) Gene 62, 111-119.
115 D M
ACACGGCGTGCATGAATTGTGAAGGTGAATAATATGAATAATGAAACTAAATTTACGCCTAAAGACCTGGATGAAGAACTGGTGAAAGCTAAGATGCTTG 100 ...A.T..................................................T..CCTTA.TA.T
A.C.TCA
CTG.A.
ThrAlaCysMetAsnCysGluGlyGlu*** M. fAsnAsnGluThrLy3PheThrProLysAspLeuAspGluGluLeuValLysAlaLysMetLeuG
D M
...
LeuAsnIle
AsnValMetAlaGluLy3Gly
D M
AGCGTATGCACGATGTTATTGAGACTGCAATCAGTAAAGGCTTTTCTGCGAGAGAGGCCCTTGAAATTATGACACGGGAAATTCATCTCATACGCGoCGA
D
luArgMetHisA3pValIleGluThrAlaIleSerLysGlyPheSerAlaArgGluAlaLeuGluIleMetThrArgGluIleHi3LeuIleArgA3pGI
ATA.
G.T.G. .C.A.CG
ValArgAlaIleVal
M
.GT.
TyrGly
.T.AGC.TAATC.CA.C.C LysHisAsnLeuThr
AGT. .G
C.
ValArgAsp
C.AC.C IleAsn
MetAsnArgLeuGluThrVa
D M D M
AGTTTTGTTGCATAACAAAAAAGCCCACAACAATATTGTTTGTCGTGAGCTTGGCGTTGATGATTCAGCGGTTATTCCACAGCGTCAGTATCTGTGTGCT
D
CTGATGAGAGGTTCCCGGCATTAACAATATCCTGCCTTGAAGCCCAGAGCTTATTGAGCAGCAGATCAACATACTCATCGGCCTCAAAATCCAGTTCTTC
...GGCAC
A..TG.
C
G.GG.GTACA.CC.C. .CAG
G. .GC.ATCA. .CCAG.ATA. .G. .A.TG.CGC
300
TGTGT.TGAG...
uValLeuLeuHi3AsnLysLysAlaHi3A3nAsnIleValCysArgGluLeuGlyValA3pAspSerAlaValIleProGInArgGlnTyrLeuCy3Ala I
Ala
Gln
GluThr
ArgGluGluTyrIleArg
Arg
LeuSer
M .TC .TCC. CAG .AT .TGGGT .T .ACGAACTGA.AATGT .TTCC.TGA.C. .TGA D LeuMetArqGlySerArgHis**^ M PheLeuIleArgGlnHisLeuGlyLeuThrAsn'** D M D
200
GA.. GTC.GGAAACA.T
GlnAspIleValThrAspAlaHisValPheGlu 400
TT .CAGTTTT .CGCGGCG.CTTGTTCTCATTGCAGGCG.
GAACGTTTTTCGGTTCTTATAGCTGGCCTGTGTATTTCTGATGATGTCATAAGCATCGTGCATGTTGATAACACCGTTTTCAATCAGCTTAATCATCAGA 500 ATCTT..AAAATC.CTGCTG.AGA.CTGAAAA.GGC.T..CCCTCT..TGCG.TGAT.AT.GCC..CT.C..CACAAGGCGC.C...TGCTGATGCA.TC
M
D M D M
TTACCGACCAGCATAAAACCGGTTATACCAAAGAATTTATCCTGGTTATTAACAGGGGTGTCTTTCTGGTTTGTTTCGAAATCTGGGTTTTGTTCATCAT
D
CCGACACCGTATGTTGTTCTTGTTCAGCCATAATATTTCCTTTTATGTTATTACTGAATATGGCGGTGTTGCAGCACCGCCTC-TTTCCGGAGGTACGAT 700
600
M ----------------------------------------------------------------------- C .C D 116
D CATGAGTCGCACATCCCTGATTAAATTAATCCATGTCGCCCGTCGGGAGCTACAACTCGACGACGACACTTACCGCGCTT M ................................................................................ D M. fSerArgThrSerLeuIleLysLeuIleHisValAlaArgArgGluLeuGlnLeuA3pAspA3pThrTyrArgAla M
780
The nucleotide sequences of the coding (non-transcribed) strand of D108 (D) and Mu (M) DNA given from the 5' to 3' direction. Nucleotide position number 1 corresponds to nucleotide 7620 in the Mu sequence of Priess et al. (1987). The predicted amino acid sequences are shown below the DNA The nucleotide and amino acid sequence of Mu are indicated as dots if they are identical to the D108 sequence and only those nucleotides or amino acids which differ specifically written. Below the translational initiation codon, (AUG), the formyl-methionine is written as M.f and each open reading frame is noted above its respective initiation codon. The termination codon sequence is noted with three stars (***). An arbitrary gap has been introduced to obtain maximum homology between the two nucleotide sequences and is indicated with dashes. Vertical arrows indicate the extent of the nonhomologous region. Horizontal arrows indicate an inverted repeat sequence. are
sequences.
are
