Bacteriophages of Lactobacillus

In this review, we are listing Lactobacillus phages that have been reported in peer-reviewed articles published since 1960. Putative phages that are defective or have not been shown to be infectious, such as phage-like particles, are not discussed. Our literature searches led to the identification of 231 Lactobacillus phages, 186 of which have been observed by electron microscopy, with 109 belonging to the Siphoviridae family, 76 to the Myoviridae family, and 1 to the Podoviridae family. Model phages infecting Lb delbrueckii, casei, rhamnosus, plantarum, and gasseri are highlighted, as well as prophages of Lactobacillus hosts. To date, nine complete Lactobacillus phage genomes are available for comparisons and evolution studies. Features such as phage receptors and endolysins are also reviewed, as well as phage-derived genetic tools. Lactobacillus phage research has progressed significantly over the past decade but a thorough understanding of their biology is still lacking. Because of the risks they represent and the knowledge gaps that need to be filled, the outlook for research on Lactobacillus phages is bright

Caractérisation des recombinases XerC et XerD de Proteus mirabilis

Thèse numérisée par la Direction des bibliothèques de l'Université de Montréal

CRISPR-Cas and restriction–modification systems are compatible and increase phage resistance

Bacteria have developed a set of barriers to protect themselves against invaders such as phage and plasmid nucleic acids. Different prokaryotic defence systems exist and at least two of them directly target the incoming DNA: restriction–modification (R-M) and CRISPR-Cas systems. On their own, they are imperfect barriers to invasion by foreign DNA. Here, we show that R-M and CRISPR-Cas systems are compatible and act together to increase the overall phage resistance of a bacterial cell by cleaving their respective target sites. Furthermore, we show that the specific methylation of phage DNA does not impair CRISPR-Cas acquisition or interference activities. Taken altogether, both mechanisms can be leveraged to decrease phage contaminations in processes relying on bacterial growth and/or fermentation

A reverse transcriptase-related protein mediates phage resistance and polymerizes untemplated DNA in vitro

Reverse transcriptases (RTs) are RNA-dependent DNA polymerases that usually function in the replication of selfish DNAs such as retrotransposons and retroviruses. Here, we have biochemically characterized a RT-related protein, AbiK, which is required for abortive phage infection in the Grampositive bacterium Lactococcus lactis. In vitro, AbiK does not exhibit the properties expected for an RT, but polymerizes long DNAs of ‘random’ sequence, analogous to a terminal transferase. Moreover, the polymerized DNAs appear to be covalently attached to the AbiK protein, presumably because an amino acid serves as a primer. Mutagenesis experiments indicate that the polymerase activity resides in the RT motifs and is essential for phage resistance in vivo. These results establish a novel biochemical property and a non-replicative biological role for a polymerase

P087, a lactococcal phage with a morphogenesis module similar to an Enterococcus faecalis prophage

The virulent lactococcal phage P087 was isolated from a dairy environment in 1978. This phage was then recognized as the reference member for one of the ten phage groups currently known to infect Lactococcus lactis strains. The double-stranded DNA genome of this Siphoviridae phage is composed of 60,074 bp and is circularly permuted. Five tRNA and 88 orfs were found within an uncommon genome architecture. Eleven structural proteins were also identified through SDS-PAGE and LC-MS/MS analyses. Of note, 11 translated orfs from the structural module of phage P087 have identities to gene products found in a prophage located in the genome of Enterococcus faecalis V583. The alignment of both genomic sequences suggests that DNA exchanges could occur between these two phages which are infecting low G+C bacteria found in similar ecological niches

Investigative approach to improve hot water system hydraulics through temperature monitoring to reduce building environmental quality hazard associated to Legionella

Several countries have promulgated control measures and design guidelines to limit the proliferation of Legionella within hot water distribution systems (HWDS). However, there is little information on how to assess and improve existing HWDS unable to maintain water temperatures >= 55 degrees C throughout the system. A 50-year old hot water system of a 10 story hospital was investigated in terms of temperature distribution and Legionella pneumophila prevalence. Concentrations of L. pneumophila were correlated with the maximum temperature reached at the tap, with a significant decrease observed at T >= 55 degrees C. Continuous temperature and flow monitoring was performed on the overall HWDS, characterizing the principal and secondary horizontal return loops for all 9 wings, and detailed investigations of the secondary vertical return loops was completed in Wing 3. Results indicated the system inability to systematically maintain desired operating temperatures of 55 degrees C. The deficient hydraulic distribution was the root cause of the poor temperature maintenance throughout the secondary loops, but defective devices were also identified as playing an important role in sectorial temperature failure. A simple stepwise investigative approach was developed to identify hydraulic deficiencies. The implementation of flow restrictions on identified recirculation loops and increased pumping efficiency was conducted within a short period of 2 months, with no major system upgrade. These corrective measures resulted in a balanced system with increased flow velocities (>0.2 m/s). As a result, the proportion of taps achieving 55 degrees C within 2 min increased from 11% to 74% and L. pneumophila prevalence decreased from 93.1% to 46.1% after 4 weeks. (C) 2016 The Authors. Published by Elsevier Ltd

The double-edged sword of CRISPR-Cas systems

A recent paper gives the details on how specific small RNAs can program a protein to cleave an undesired piece of DNA and to provide immunity to a microbial cell

Energy conservation and the promotion of Legionella pneumophila growth: The probable role of heat exchangers in a nosocomial outbreak

OBJECTIVE To determine the source of a Legionella pneumophila serogroup 5 nosocomial outbreak and the role of the heat exchanger installed on the hot water system within the previous year. SETTING A 400-bed tertiary care university hospital in Sherbrooke, Canada. METHODS Hot water samples were collected and cultured for L. pneumophila from 25 taps (baths and sinks) within wing A and 9 taps in wing B. Biofilm (5) and 2 L water samples (3) were collected within the heat exchangers for L. pneumophila culture and detection of protists. Sequence-based typing was performed on strain DNA extracts and pulsed-field gel electrophoresis patterns were analyzed. RESULTS Following 2 cases of hospital-acquired legionellosis, the hot water system investigation revealed a large proportion of L. pneumophila serogroup 5 positive taps (22/25 in wing A and 5/9 in wing B). High positivity was also detected in the heat exchanger of wing A in water samples (3/3) and swabs from the heat exchanger (4/5). The outbreak genotyping investigation identified the hot water system as the source of infections. Genotyping results revealed that all isolated environmental strains harbored the same related pulsed-field gel electrophoresis pattern and sequence-based type. CONCLUSIONS Two cases of hospital-acquired legionellosis occurred in the year following the installation of a heat exchanger to preheat hospital hot water. No cases were reported previously, although the same L. pneumophila strain was isolated from the hot water system in 1995. The heat exchanger promoted L. pneumophila growth and may have contributed to confirmed clinical cases. Infect. Control Hosp. Epidemiol. 2016;1475-1480

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM (-/-) patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors