A group I intron in the terminase gene of Lactobacillus delbrueckii subsp. lactis phage LL-H

Abstract

An 837 nt long group IA intron was discovered in the Ladobacillus delbnreckii subsp. /actis virulent phage LL-H genome. The LL-H intron conforms well to the secondary structure that is common to all group I introns. The only exception is that the extreme 3' nucleotide of the intron is an A residue instead of the usual G; despite this the intron is efficiently spliced in wivo. This LL-H intron contains an ORF, ORF168, which shows homology with endonucleases encoded by ORFs contained in B a c i h s subti/is phage introns. A t present, the LL-H intron is the only one found in the phages of lactic acid bacteria and the first one to be found in a phage belonging to the most abundant taxonomic group, group B or Siphoviridae. The LL-H intron interrupts gene terf., the product of which (505 kDa, Terl) is significantly homologous to the large subunit of B. subtilis phage SPP1 terminase. The product of the upstream gene, terS of LL-H (15.9 kDa, TerS), shows homology to small subunits of B. subtilis phage terminases.

Sequence analysis of the lactococcal bacteriophage bIL170: insights into structural proteins and HNH endonucleases in dairy phages The GenBank/EMBL/DDBJ accession numbers for the sequences reported in this paper are bIL170, AF009630; bIL120, AY054975; bIL15, AY054976; bIL191, AY054977; bIL77, AY054978.

“…Most of them are homing endonucleases, involved in the mobility of their own genes or of the introns\inteins in which they are targeted (for a review see Chevalier & Stoddard, 2001). All phage hits obtained with the bIL170 gene products are intron-encoded homing endonucleases Lazarevic et al, 1998 ;Mikkonen & Alatossava, 1995 ;van Sinderen et al, 1996). Their degree of similarity with the three gene products of bIL170 (25-40 % over at least half of the length of the proteins) and the absence of homologues in sk1 strongly suggest that gpe11, gpe20 and gpe37 are related to homing endonucleases.…”

Barriers to Intron Promiscuity in Bacteria

“…Apart from the td, nrdD, and nrdB introns in T-even phages, no other group I introns have been discovered in any gram-negative bacterial phage. Conversely, group I introns are more abundant in phages of grampositive bacteria (1,24,25,26,45,54,61), exemplified by the Staphylococcus phage Twort, which possesses at least five introns (44). While it is tempting to generalize about group I intron distribution in phages, it is worth noting that only two detailed studies have been performed; one concerned with distribution of the three T4 introns in related T-even phages (18) and the other concerned with the distribution of a lysin intron in Streptococcus thermophilus phages (24).…”

“…Thus, a rationale was provided for the retention of seemingly optional introns in size-constrained genomes subject to pressures of genome streamlining for rapid replication. However, this presumed function for the T4 introns began to lose attractiveness with the discovery that close relatives of T4 lacked introns in these genes (67), with the (unpublished) experimental observation that T4 introns could be deleted without detectable detriment to the phage (18), and with the finding that some phage introns do not interrupt genes of nucleotide metabolism (44,54,61).…”

“…Ironically, precise deletion of the intron from an individual phage within a population would provide positive selection for retention of the endonuclease ORF, because the homing site would be regenerated and become a substrate for endonucleases of other phage within the same population. Of course, no hypothesis is bulletproof, and there are already examples of endonuclease-containing introns interrupting genes not involved in replication or transcription (the lysin gene of S. thermophilus phages [24] and the terminase gene of Lactobacillus phage LL-H [54]). It is possible, however, that these endonucleases are also targeting conserved nucleotide sequences within their respective genes.…”

Widespread Distribution of a Group I Intron and Its Three Deletion Derivatives in the Lysin Gene of Streptococcus thermophilus Bacteriophages

“…Among the eubacteria, the only group I introns described to date occur in several genera of cyanobacteria and purple proteobacteria (3,32). Although group I introns have been described for several T-even bacteriophages of Escherichia coli (30,36), six Bacillus subtilis bacteriophages (1,17,18,22), and one bacteriophage each of Lactococcus lactis (29), Lactobacillus delbrueckii (28), and Staphylococcus aureus (21), none have been reported so far for the genomes of the respective host bacteria. Interestingly, apart from the T-even bacteriophages, all of the intron-containing phages described to date infect a group of evolutionarily related low-GC-content gram-positive bacteria.…”