@article{dinsmore_dj o'sullivan_klaenhammer_1998, title={A leucine repeat motif in AbiA is required for resistance of Lactococcus lactis to phages representing three species.}, volume={212}, ISSN={["0378-1119"]}, DOI={10.1016/S0378-1119(98)00132-2}, abstractNote={The abiA gene encodes an abortive bacteriophage infection mechanism that can protect Lactococcus species from infection by a variety of bacteriophages including three unrelated phage species. Five heptad leucine repeats suggestive of a leucine zipper motif were identified between residues 232 and 266 in the predicted amino acid sequence of the AbiA protein. The biological role of residues in the repeats was investigated by incorporating amino acid substitutions via site-directed mutagenesis. Each mutant was tested for phage resistance against three phages, phi 31, sk1, and c2, belonging to species P335, 936, and c2, respectively. The five residues that comprise the heptad repeats were designated L234, L242, A249, L256, and L263. Three single conservative mutations of leucine to valine in positions L235, L242, and L263 and a double mutation of two leucines (L235 and L242) to valines did not affect AbiA activity on any phages tested. Non-conservative single substitutions of charged amino acids for three of the leucines (L235, L242, and L256) virtually eliminated AbiA activity on all phages tested. Substitution of the alanine residue in the third repeat (A249) with a charged residue did not affect AbiA activity. Replacement of L242 with an alanine elimination phage resistance against phi 31, but partial resistance to sk1 and c2 remained. Two single proline substitutions for leucines L242 and L263 virtually eliminated AbiA activity against all phages, indicating that the predicted alpha-helical structure of this region is important. Mutations in an adjacent region of basic amino acids had various effects on phage resistance, suggesting that these basic residues are also important for AbiA activity. This directed mutagenesis analysis of AbiA indicated that the leucine repeat structure is essential for conferring phage resistance against three species of lactococcal bacteriophages.}, number={1}, journal={GENE}, author={Dinsmore, PK and DJ O'Sullivan and Klaenhammer, TR}, year={1998}, month={May}, pages={5–11} }
 @misc{klaenhammer_conkling_o'sullivan_djordjevic_walker_taylor_1998, title={Bacteriophage-triggered cell suicide systems and fermentation methods employing the same}, volume={5,792,625}, number={1998 Aug. 11}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Klaenhammer, T. R. and Conkling, M. A. and O'Sullivan, D. and Djordjevic, G. and Walker, S. A. and Taylor, C. G.}, year={1998} }
 @article{dj o'sullivan_klaenhammer_1998, title={Control of expression of LlaI restriction in Lactococcus lactis}, volume={27}, ISSN={["1365-2958"]}, DOI={10.1046/j.1365-2958.1998.00748.x}, abstractNote={The plasmid encoded LlaI R/M system from Lactococcus lactis ssp. lactis consists of a bidomain methylase, with close evolutionary ties to type IIS methylases, and a trisubunit restriction complex. Both the methylase and restriction subunits are encoded on a polycistronic 6.9 kb operon. In this study, the 5′ end of the llaI 6.9 kb transcript was determined by primer extension analysis to be 254 bp upstream from the first R/M gene on the operon, llaIM. Deletion of this promoter region abolished LlaI restriction in L. lactis. Analysis of the intervening sequence revealed a 72‐amino‐acid open reading frame, designated llaIC, with a conserved ribosome binding site and helix–turn–helix domain. Overexpression of llaIC in Escherichia coli with a T7 expression vector produced the predicted protein of 8.2 kDa. Mutation and in trans complementation analyses indicated that C·LlaI positively enhanced LlaI restriction activity in vivo. Northern analysis and transcriptional fusions of the llaI promoter to a lacZ reporter gene indicated that C·LlaI did not enhance transcription of the llaI operon. Databank searches with the deduced protein sequence for llaIC revealed significant homologies to the E. coli Rop regulatory and mRNA stabilizer protein. Investigation of the effect of C·LlaI on enhancement of LlaI restriction in L. lactis revealed that growth at elevated temperatures (40°C) completely abolished any enhancement of restriction activity. These data provide molecular evidence for a mechanism on how the expression of a restriction system in a prokaryote can be drastically reduced during elevated growth temperatures, by a small regulatory protein.}, number={5}, journal={MOLECULAR MICROBIOLOGY}, author={DJ O'Sullivan and Klaenhammer, TR}, year={1998}, month={Mar}, pages={1009–1020} }
 @article{djordjevic_osullivan_walker_conkling_klaenhammer_1997, title={A triggered-suicide system designed as a defense against bacteriophages}, volume={179}, ISSN={["0021-9193"]}, DOI={10.1128/jb.179.21.6741-6748.1997}, abstractNote={A novel bacteriophage protection system for Lactococcus lactis based on a genetic trap, in which a strictly phage-inducible promoter isolated from the lytic phage phi31 is used to activate a bacterial suicide system after infection, was developed. The lethal gene of the suicide system consists of the three-gene restriction cassette LlaIR+, which is lethal across a wide range of gram-positive bacteria. The phage-inducible trigger promoter (phi31P) and the LlaIR+ restriction cassette were cloned in Escherichia coli on a high-copy-number replicon to generate pTRK414H. Restriction activity was not apparent in E. coli or L. lactis prior to phage infection. In phage challenges of L. lactis(pTRK414H) with phi31, the efficiency of plaquing was lowered to 10(-4) and accompanied by a fourfold reduction in burst size. Center-of-infection assays revealed that only 15% of infected cells released progeny phage. In addition to phage phi31, the phi31P/LlaIR+ suicide cassette also inhibited four phi31-derived recombinant phages at levels at least 10-fold greater than that of phi31. The phi31P/LlaIR+-based suicide system is a genetically engineered form of abortive infection that traps and eliminates phages potentially evolving in fermentation environments by destroying the phage genome and killing the propagation host. This type of phage-triggered suicide system could be designed for any bacterium-phage combination, given a universal lethal gene and an inducible promoter which is triggered by the infecting bacteriophage.}, number={21}, journal={JOURNAL OF BACTERIOLOGY}, author={Djordjevic, GM and OSullivan, DJ and Walker, SA and Conkling, MA and Klaenhammer, TR}, year={1997}, month={Nov}, pages={6741–6748} }
 @article{osullivan_walker_west_klaenhammer_1996, title={Development of an expression strategy using a lytic phage to trigger explosive plasmid amplification and gene expression}, volume={14}, ISSN={["0733-222X"]}, DOI={10.1038/nbt0196-82}, abstractNote={A novel plasmid-based expression strategy, exploiting two features of lytic bacteriophages, was developed in Lactococcus lactis. Components of this system include a phage origin of replication and phage expression signals, which were induced to high efficiency upon phage infection of the host. Phage-specific expression signals were cloned from phi 31 in a promoter-screening strategy using the lacZ gene from Streptococcus thermophilus. One clone exhibited a significant induction in beta-galactosidase production and concomitant increase in lacZ mRNA during the phi 31 infection cycle of the host. Molecular characterization of the cloned insert revealed 888 bp positioned near the phi 31 cos site. Primer extension analysis showed that transcription was induced approximately 20 min following phi 31 infection at four points, apparently organized in two sets of tandem promoters on the cloned phage insert. One of these middle phage promoters also showed a basal level of activity prior to phage infection. The phi 31 promoter lacZ cassette was cloned into a low-copy-number vector plasmid containing the phi 31 origin of replication (ori31) and the resulting low-copy-number plasmid exhibited negligible beta-galactosidase production in L. lactis. However, > 2,000 units were detected following a deliberate infection with phi 31. A control expression plasmid without ori31 could only be induced to 85 units. The combination of these phage-inducible expression signals together with ori31 functioned synergistically to drive rapid and high efficiency expression of a heterologous gene in L. lactis.}, number={1}, journal={BIO-TECHNOLOGY}, author={OSullivan, DJ and Walker, SA and West, SG and Klaenhammer, TR}, year={1996}, month={Jan}, pages={82–87} }
 @article{osullivan_zagula_klaenhammer_1995, title={IN-VIVO RESTRICTION BY LLAI IS ENCODED BY 3 GENES, ARRANGED IN AN OPERON WITH LLAIM, ON THE CONJUGATIVE LACTOCOCCUS PLASMID-PTR2030}, volume={177}, ISSN={["0021-9193"]}, DOI={10.1128/jb.177.1.134-143.1995}, abstractNote={The LlaI restriction and modification (R/M) system is encoded on pTR2030, a 46.2-kb conjugative plasmid from Lactococcus lactis. The llaI methylase gene, sequenced previously, encodes a functional type IIS methylase and is located approximately 5 kb upstream from the abiA gene, encoding abortive phage resistance. In this study, the sequence of the region between llaIM and abiA was determined and revealed four consecutive open reading frames (ORFs). Northern (RNA) analysis showed that the four ORFs were part of a 7-kb operon with llaIM and the downstream abiA gene on a separate transcriptional unit. The deduced protein sequence of ORF2 revealed a P-loop consensus motif for ATP/GTP-binding sites and a three-part consensus motif for GTP-binding proteins. Data bank searches with the deduced protein sequences for all four ORFs revealed no homology except for ORF2 with MerB, in three regions that coincided with the GTP-binding motifs in both proteins. To phenotypically analyze the llaI operon, a 9.0-kb fragment was cloned into a high-copy-number lactococcal shuttle vector, pTRKH2. The resulting construct, pTRK370, exhibited a significantly higher level of in vivo restriction and modification in L. lactis NCK203 than the low-copy-number parental plasmid, pTR2030. A combination of deletion constructions and frameshift mutations indicated that the first three ORFs were involved in LlaI restriction, and they were therefore designated llaI.1, llaI.2, and llaI.3. Mutating llaI.1 completely abolished restriction, while disrupting llaI.2 or llaI.3 allowed an inefficient restriction of phage DNA to occur, manifested primarily by a variable plaque phenotype. ORF4 had no discernible effect on in vivo restriction. A frameshift mutation in llaIM proved lethal to L. lactis NCK203, implying that the restriction component was active without the modification subunit. These results suggested that the LlaI R/M system is unlike any other R/M system studied to date and has diverged from the type IIS class of restriction enzymes by acquiring some characteristics reminiscent of type I enzymes.}, number={1}, journal={JOURNAL OF BACTERIOLOGY}, author={OSULLIVAN, DJ and ZAGULA, K and KLAENHAMMER, TR}, year={1995}, month={Jan}, pages={134–143} }
 @article{osullivan_klaenhammer_1993, title={HIGH-COPY-NUMBER AND LOW-COPY-NUMBER LACTOCOCCUS SHUTTLE CLONING VECTORS WITH FEATURES FOR CLONE SCREENING}, volume={137}, ISSN={["0378-1119"]}, DOI={10.1016/0378-1119(93)90011-Q}, abstractNote={High- and low-copy-number shuttle cloning vectors were constructed by incorporating the Escherichia coli P15A plasmid origin of replication into the pAM beta 1-derived vectors, pIL252 and pIL253. The resulting vectors were structurally stable in Lactococcus, which is a common feature of theta-replicating plasmids, and also displayed good structural stability in E. coli, possibly due to lack of a resolvase-encoding gene. All the vectors expressed erythromycin resistance (ErR) in both; brain heart infusion medium allowed clear selection of ErR in E. coli. Some of the vectors provided insertional inactivation of a cat (pTRKH1; pTRKL1) or tet (pTRKH1; pTRKH3; pTRKH5) gene to facilitate screening for clones. Multiple cloning sites in a lacZ gene, which expresses beta-galactosidase in lacZ alpha-complementing E. coli strains, were included in some vectors (pTRKH2/H5 and pTRKL2) to enable blue/white screening of clones on XGal plates. The 'H' and 'L' prefixes signify if the vector exists at high (H) or low (L) copy number in Lactococcus. Successful introduction of these vectors into Lactococcus, Enterococcus, Streptococcus and Lactobacillus highlights their utility for expanding the possibilities for genetic manipulation of these industrially significant bacteria.}, number={2}, journal={GENE}, author={OSULLIVAN, DJ and KLAENHAMMER, TR}, year={1993}, month={Dec}, pages={227–231} }