Nucleic Acids Research, Vol. 18, No. 14 4253
.::) 1990 Oxford University Press
Nucleotide sequence of 1S904 from Lactococcus lactis subsp. lactis strain NIZO R5 Peter J.G.Rauch, Marke M.Beerthuyzen and Willem M. de Vos Molecular Genetics Group, Netherlands Institute for Dairy Research (NIZO), PO Box 20, 6710 BA Ede, The Netherlands EMBL accession no. X52273
Submitted June 13, 1990 We have determined the nucleotide sequence of an IS-like element (Fig. 1) from the nisin producing Lactococcus lactis subsp. lactis cheese starter strain NIZO R5 (1). This IS-like element is located at or near the left end of a conjugative transposon, encoding nisin production, nisin immunity, and sucrose fermentation (TnS2 76; P. J.G. R. et al., unpublished results). The element is 1245 base pairs (bp) long. Its termini are 39-bp imperfect inverted repeats. A 4-bp direct target repeat (TTAT) was found. The element contains an open reading frame encoding a putative transposase of 253 amino acids. The NIZO R5 IS-like element is almost identical to IS904 that has very recently been found in L. lactis subsp. lactis strain NCFB894 (2). Therefore, we also used the designation IS904 for the NIZO R5 IS-like element. The copy of IS904 described here is 4 bp longer than that from strain NCFB894 and its nucleotide sequence shows eight differences to that of the NCFB894 copy (Fig. 1). These differences result in two amino acid differences in the putative transposase (S77A, Y142C). The inverted repeats of the two copies are identical, as are the 4-bp direct target repeats. The 128 C-terminal amino acids of the putative transposase of IS904 have been described previously (3). The latter sequence was derived from L. lactis subsp. lactis strain ATCC1 1454 and differs from that described here in one amino acid (T202S). It has been reported that IS904 shows homology to IS2 and IS3 from Escherichia coli, to IS600 from Shigella dysenteriae, and to IS629 from S. sonnei (2, 3). We found additional homologies to the putative transposases and inverted repeats of IS150 and IS3411 from E. coli (4), ISSHOJ from S. dysenteriae (4), IS51 from Pseudomonas savastanoi (4), IS136 from Agrobacterium tumefaciens (4), ISLI from Lactobacillus casei (5), IS476 from Xanthomonas campestris pv. vesicatoria (6), IS861 from group B streptococcus type HI (7), and IS6110 from Mycobacterium tuberculosis (8). In addition, an amino-terminal segment in the putative transposase of IS904 shows homology
101
TAAAACTCATTC
201
AAAATCTT ATATGCGAAAGTGC?TTTTCCACACAAT00ACAGCCCTAGCTGATGCCCAA CATAACTTTAAAm
301
501
C;ATMCTAAAAAAGTrCC AGTACAAGTTC CTAGTTT AMACTCTTTC&TGCAG
601
AACTGATGCACTTGATGGGACTTTATOCCAAGGGAACCCGATATAAATATAAACATTACAACAGAAAAGGCAGTTCOCTTTCAAGACCCAATTTAAWTAA
701
TCACATCTTTAACAACAGCTC
801
G?ITTTCACGTAAGATTGTAGGCTGOTCAATGTCTCACGGATCAACATAAACTGGTGAGGGATACTTCrACAAGCTTGTGGGAAAGAACATCCTC
901
A_CGCTATGCAATACA ,GGTCTAATCACTCGTATCAATCACTCTAGTGGTCTCT
1101
ACTCAAGAAATATTTAAATACATTGAGACCTATTACAATACAAAAAGGATGCATTCAGGTCTTGATTACAAGTCTCCAAAAGACTTTGAAAAATATAATT
401
G
CAGGAGGAA
CGTTTTGATrTcTCTCTTAAACATCATGGGAAGATAAAAATTAAGCATGC TCC TTCAAAAACCA0GT0GAGA6AGAAATCTCTCCAGAGAAATA
CTACAACCTACTTCATAATACTGGTATTATGACCAACACGAAACGTGTTGGGA AGCC
CTA A
CCTATATCCCTACCAAAAAGGTACCTTATACTTAGCCGTGAATATCGAC AGCATAGCG
Figure 1. Nucleotide sequence of IS904 from Lactococcus lactis subsp. lactis strain NIZO R5. The imperfect terminal repeats are indicated by broken arrows. The start and stop codon of the 253-aa putative transposase encoded by IS904 are underlined, as are the possible promoter signals. The differences in nucleotide sequence to the already published sequence of IS904 (2) are given above the nucleotide sequence (-: nucleotide absent). 4-
'SB' ISZ.S
ISjQj isina
Is'l Isi-u.
IiaIl ISf=j Is1s.
a-HEuIX
a-HELIX
-*4TU
XDITY IIGI R RI DETY IIX IKG
amino acids
-
DA
73
-
95
SYLYRAI DA
73
-
95
HYLYRAI
JEGT LY LAVN I DV
98 - 120
VADLTYVATQEGFWLYLAGI XDV
113 - 135
DL
131 - 153
LGDNITY I PT
AGDITYLRTDEGHLY LAVVI
1V6
VADFTYVSTWRGFVYVAFI I DV
134 -
VADFTYVSTWQGFVYVAFIIDV
133 - 155
VADLTYVSTWAGFAYVAFV TDA
44 - 66
VTDVTEFavNE1K
L
L
S P V
43 - 65
Figure 2. Partial amino acid sequence alignment of some IS element encoded putative transposases that show homology in a segment, predicted to possess an ca-helix - turn - a-helix motif (8).
4254 Nucleic Acids Research, Vol. 18, No. 14 with the putative transposases that belong to a superfamily of IS elements (9; Fig. 2). This superfamily includes the Staphylococcus aureus IS257 family, the L. lactis ISSJ family, and the ISS5 family from the R plasmids in Enterobacteria. This segment was predicted (9) to possess an (x-helix - turn - athelix secondary structure motif, found in a number of DNAbinding proteins (10).
REFERENCES 1. Galesloot,T.E. and Pette,J.W. (1957) Neth. Milk Dairy J. 11, 144-151. 2. Dodd,H.M, Horn,N. and Gasson,M.J. (1990) J. Gen. Microbiol. 136, 555-566. 3. Buchman,G.W., Banerjee,S. and Hansen,J.N. (1988) J. Bio. Chem. 263, 16260-16266. 4. Galas,D.J. and Chandler,M. (1989) In: D.E.Berg and M.M. Howe (eds) Mobile DNA. American Society for Microbiology, Washington, DC, 109-162. 5. Shiniizu-Kadota,M., Kiwaki,M., Hirokawa,H. and Tsuchida,N. (1985) MoL. Gen. Genet. 200, 193-198. 6. Kearney,B. and Staskawicz,B.J. (1990) J. Bacteriol. 172, 143-148. 7. Rubens,C.E., Heggen,L.M. and Kuypers,J.M. (1989) J. Bacteriol. 171, 5531 -5535. 8. Thierry,D., Cave,M.D., Eisenach,K.D., Crawford,J.T., Bates,J.H., Gicquel,B. and Guesdon,J.L. (1990) Nucd. Acids Res. 18, 188. 9. Rouch,D.R., Messerotti,L.J., Loo,L.S.L., Jackson,C.A. and Skurray,R.A. (1989) Mol. Microbiol. 3, 161-175. 10. Pabo,C.D. and Sauer,R.T. (1984) Annu. Rev. Biochem. 53, 293-321.
.::) 1990 Oxford University Press
Nucleotide sequence of 1S904 from Lactococcus lactis subsp. lactis strain NIZO R5 Peter J.G.Rauch, Marke M.Beerthuyzen and Willem M. de Vos Molecular Genetics Group, Netherlands Institute for Dairy Research (NIZO), PO Box 20, 6710 BA Ede, The Netherlands EMBL accession no. X52273
Submitted June 13, 1990 We have determined the nucleotide sequence of an IS-like element (Fig. 1) from the nisin producing Lactococcus lactis subsp. lactis cheese starter strain NIZO R5 (1). This IS-like element is located at or near the left end of a conjugative transposon, encoding nisin production, nisin immunity, and sucrose fermentation (TnS2 76; P. J.G. R. et al., unpublished results). The element is 1245 base pairs (bp) long. Its termini are 39-bp imperfect inverted repeats. A 4-bp direct target repeat (TTAT) was found. The element contains an open reading frame encoding a putative transposase of 253 amino acids. The NIZO R5 IS-like element is almost identical to IS904 that has very recently been found in L. lactis subsp. lactis strain NCFB894 (2). Therefore, we also used the designation IS904 for the NIZO R5 IS-like element. The copy of IS904 described here is 4 bp longer than that from strain NCFB894 and its nucleotide sequence shows eight differences to that of the NCFB894 copy (Fig. 1). These differences result in two amino acid differences in the putative transposase (S77A, Y142C). The inverted repeats of the two copies are identical, as are the 4-bp direct target repeats. The 128 C-terminal amino acids of the putative transposase of IS904 have been described previously (3). The latter sequence was derived from L. lactis subsp. lactis strain ATCC1 1454 and differs from that described here in one amino acid (T202S). It has been reported that IS904 shows homology to IS2 and IS3 from Escherichia coli, to IS600 from Shigella dysenteriae, and to IS629 from S. sonnei (2, 3). We found additional homologies to the putative transposases and inverted repeats of IS150 and IS3411 from E. coli (4), ISSHOJ from S. dysenteriae (4), IS51 from Pseudomonas savastanoi (4), IS136 from Agrobacterium tumefaciens (4), ISLI from Lactobacillus casei (5), IS476 from Xanthomonas campestris pv. vesicatoria (6), IS861 from group B streptococcus type HI (7), and IS6110 from Mycobacterium tuberculosis (8). In addition, an amino-terminal segment in the putative transposase of IS904 shows homology
101
TAAAACTCATTC
201
AAAATCTT ATATGCGAAAGTGC?TTTTCCACACAAT00ACAGCCCTAGCTGATGCCCAA CATAACTTTAAAm
301
501
C;ATMCTAAAAAAGTrCC AGTACAAGTTC CTAGTTT AMACTCTTTC&TGCAG
601
AACTGATGCACTTGATGGGACTTTATOCCAAGGGAACCCGATATAAATATAAACATTACAACAGAAAAGGCAGTTCOCTTTCAAGACCCAATTTAAWTAA
701
TCACATCTTTAACAACAGCTC
801
G?ITTTCACGTAAGATTGTAGGCTGOTCAATGTCTCACGGATCAACATAAACTGGTGAGGGATACTTCrACAAGCTTGTGGGAAAGAACATCCTC
901
A_CGCTATGCAATACA ,GGTCTAATCACTCGTATCAATCACTCTAGTGGTCTCT
1101
ACTCAAGAAATATTTAAATACATTGAGACCTATTACAATACAAAAAGGATGCATTCAGGTCTTGATTACAAGTCTCCAAAAGACTTTGAAAAATATAATT
401
G
CAGGAGGAA
CGTTTTGATrTcTCTCTTAAACATCATGGGAAGATAAAAATTAAGCATGC TCC TTCAAAAACCA0GT0GAGA6AGAAATCTCTCCAGAGAAATA
CTACAACCTACTTCATAATACTGGTATTATGACCAACACGAAACGTGTTGGGA AGCC
CTA A
CCTATATCCCTACCAAAAAGGTACCTTATACTTAGCCGTGAATATCGAC AGCATAGCG
Figure 1. Nucleotide sequence of IS904 from Lactococcus lactis subsp. lactis strain NIZO R5. The imperfect terminal repeats are indicated by broken arrows. The start and stop codon of the 253-aa putative transposase encoded by IS904 are underlined, as are the possible promoter signals. The differences in nucleotide sequence to the already published sequence of IS904 (2) are given above the nucleotide sequence (-: nucleotide absent). 4-
'SB' ISZ.S
ISjQj isina
Is'l Isi-u.
IiaIl ISf=j Is1s.
a-HEuIX
a-HELIX
-*4TU
XDITY IIGI R RI DETY IIX IKG
amino acids
-
DA
73
-
95
SYLYRAI DA
73
-
95
HYLYRAI
JEGT LY LAVN I DV
98 - 120
VADLTYVATQEGFWLYLAGI XDV
113 - 135
DL
131 - 153
LGDNITY I PT
AGDITYLRTDEGHLY LAVVI
1V6
VADFTYVSTWRGFVYVAFI I DV
134 -
VADFTYVSTWQGFVYVAFIIDV
133 - 155
VADLTYVSTWAGFAYVAFV TDA
44 - 66
VTDVTEFavNE1K
L
L
S P V
43 - 65
Figure 2. Partial amino acid sequence alignment of some IS element encoded putative transposases that show homology in a segment, predicted to possess an ca-helix - turn - a-helix motif (8).
4254 Nucleic Acids Research, Vol. 18, No. 14 with the putative transposases that belong to a superfamily of IS elements (9; Fig. 2). This superfamily includes the Staphylococcus aureus IS257 family, the L. lactis ISSJ family, and the ISS5 family from the R plasmids in Enterobacteria. This segment was predicted (9) to possess an (x-helix - turn - athelix secondary structure motif, found in a number of DNAbinding proteins (10).
REFERENCES 1. Galesloot,T.E. and Pette,J.W. (1957) Neth. Milk Dairy J. 11, 144-151. 2. Dodd,H.M, Horn,N. and Gasson,M.J. (1990) J. Gen. Microbiol. 136, 555-566. 3. Buchman,G.W., Banerjee,S. and Hansen,J.N. (1988) J. Bio. Chem. 263, 16260-16266. 4. Galas,D.J. and Chandler,M. (1989) In: D.E.Berg and M.M. Howe (eds) Mobile DNA. American Society for Microbiology, Washington, DC, 109-162. 5. Shiniizu-Kadota,M., Kiwaki,M., Hirokawa,H. and Tsuchida,N. (1985) MoL. Gen. Genet. 200, 193-198. 6. Kearney,B. and Staskawicz,B.J. (1990) J. Bacteriol. 172, 143-148. 7. Rubens,C.E., Heggen,L.M. and Kuypers,J.M. (1989) J. Bacteriol. 171, 5531 -5535. 8. Thierry,D., Cave,M.D., Eisenach,K.D., Crawford,J.T., Bates,J.H., Gicquel,B. and Guesdon,J.L. (1990) Nucd. Acids Res. 18, 188. 9. Rouch,D.R., Messerotti,L.J., Loo,L.S.L., Jackson,C.A. and Skurray,R.A. (1989) Mol. Microbiol. 3, 161-175. 10. Pabo,C.D. and Sauer,R.T. (1984) Annu. Rev. Biochem. 53, 293-321.
