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Microbiology 148 (2002), 985-1001
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Microbiology (2002), 148, 985-1001.
© 2002 Society for General Microbiology

Research Paper

Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages

Anne-Marie Crutz-Le Coq1, Bénédicte Cesselin2, Jacqueline Commissaire2 and Jamila Anbaa,1

Laboratoire de Génétique Microbienne1 and Unité de Recherches Laitières et de Génétique Appliquée2, INRA, 78352 Jouy-en-Josas cedex, France

Author for correspondence: Anne-Marie Crutz-Le Coq. Tel: +33 1 34 65 21 06. Fax: +33 1 34 65 21 05. e-mail: lecoq{at}jouy.inra.fr

The complete 31754 bp genome of bIL170, a virulent bacteriophage of Lactococcus lactis belonging to the 936 group, was analysed. Sixty-four ORFs were predicted and the function of 16 of them was assigned by significant homology to proteins in databases. Three putative homing endonucleases of the HNH family were found in the early region. An HNH endonuclease with zinc-binding motif was identified in the late cluster, potentially being part of the same functional module as terminase. Three putative structural proteins were analysed in detail and show interesting features among dairy phages. Notably, gpl12 (putative fibre) and gpl20 (putative baseplate protein) of bIL170 are related by at least one of their domains to a number of multi-domain proteins encoded by lactococcal or streptococcal phages. A 110- to 150-aa-long hypervariable domain flanked by two conserved motifs of about 20 aa was identified. The analysis presented here supports the participation of some of these proteins in host-range determination and suggests that specific adsorption to the host may involve a complex multi-component system. Divergences in the genome of phages of the 936 group, that may have important biological properties, were noted. Insertions/deletions of units of one or two ORFs were the main source of divergence in the early clusters of the two entirely sequenced phages, bIL170 and sk1. An exchange of fragments probably affected the regions containing the putative origin of replication. It led to the absence in bIL170 of the direct repeats recognized in sk1 and to the presence of different ORFs in the ori region. Shuffling of protein domains affected the endolysin (putative cell-wall binding part), as well as gpl12 and gpl20.

Keywords: Lactococcus lactis, Siphoviridae, host specificity, transglycosylases, HNH endonucleases

Abbreviations: indel; insertion/deletion

The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are bIL170, AF009630; bIL120, AY054975; bIL15, AY054976; bIL191, AY054977; bIL77, AY054978.

a Present address: U.E.P.S.D., INRA, 78352 Jouy-en-Josas cedex, France.




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