Julie E. Samson

Bacteriophage resistance mechanisms

Phages are now acknowledged as the most abundant microorganisms on the planet and are also possibly the most diversified. This diversity is mostly driven by their dynamic adaptation when facing selective pressure such as phage resistance mechanisms, which are widespread in bacterial hosts. When infecting bacterial cells, phages face a range of antiviral mechanisms, and they have evolved multiple tactics to avoid, circumvent or subvert these mechanisms in order to thrive in most environments. In this Review, we highlight the most important antiviral mechanisms of bacteria as well as the counter-attacks used by phages to evade these systems.

Revenge of the phages: defeating bacterial defences

Bacteria and their viral predators (bacteriophages) are locked in a constant battle. In order to proliferate in phage-rich environments, bacteria have an impressive arsenal of defence mechanisms, and in response, phages have evolved counter-strategies to evade these antiviral systems. In this Review, we describe the various tactics that are used by phages to overcome bacterial resistance mechanisms, including adsorption inhibition, restriction–modification, CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems and abortive infection. Furthermore, we consider how these observations have enhanced our knowledge of phage biology, evolution and phage–host interactions.

Bacteriophages in Food Fermentations: New Frontiers in a Continuous Arms Race

Phage contamination represents an important risk to any process requiring bacterial growth, particularly in the biotechnology and food industries. The presence of unwanted phages may lead to manufacturing delays, lower quality product, or, in the worst cases, total production loss. Thus, constant phage monitoring and stringent application of the appropriate control measures are indispensable. In fact, a systematic preventive approach to phage contamination [phage analysis and critical control points (PACCP)] should be put in place. In this review, sources of phage contamination and novel phage detection methods are described, with an emphasis on bacterial viruses that infect lactic acid bacteria used in food fermentations. Recent discoveries related to antiphage systems that are changing our views on phage-host interactions are highlighted. Finally, future directions are also discussed.

Differential morphogenesis of the extraradical mycelium of an arbuscular mycorrhizal fungus grown monoxenically on spatially heterogeneous culture media

A new in vitro experimental system was developed to study the morphogenesis of discrete regions of a single extraradical mycelium of the arbuscular mycorrhizal (AM) fungus Glomus intraradices, growing simultaneously in six different agar-based media. The media were (i) unamended water agar (WA), (ii) WA+PO43− (PO43−), (iii) WA+NO3− (NO3−), (iv) WA+NH4+ (NH4+), (v) WA+NH4++MES (NH4++MES) and (vi) minimal medium (M, complete nutrients). Each medium was amended with the pH indicator bromocresol purple. The extraradical mycelium of the fungus showed between-treatment differences in morphogenesis, architecture, formation of branched absorbing structures (BAS) and sporulation. Extraradical hyphae that developed in WA or PO43− compartments exhibited an economic development pattern, in which runner hyphae radially extended the external colony. Extraradical hyphal growth in the NO3− compartments was characterized by increased formation of runner hyphae, BAS and spores and an alkalinization of the medium. In the two NH4+-amended media (NH4+, NH4++MES), sporulation was suppressed and considerable morphological changes were noted. These results show the plasticity of G. intraradices that lets it efficiently exploit an heterogeneous substrate.

Degradation of 2,4,6-trinitrotoluene by Serratia marcescens

A strain of Serratia marcescens, isolated from the soil of a contaminated site, degraded 2,4,6-trinitrotoluene (TNT) as the sole source of carbon and energy. At an initial concentration of 50mg , TNT was totally degraded in 48h under aerobic conditions in a minimal salt medium. Reduction intermediates (4-amino-2,6-dinitrotoluene and 2-amino-4,6-dinitrotoluene) were observed. The presence of a surfactant (Tween 80) is essential to facilitate rapid degradation.

Cyclohexenone derivative- and phosphate-levels in split-root systems and their role in the systemic suppression of mycorrhization in precolonized barley plants

Summary In a split-root system root colonization by the arbuscular mycorrhizal fungus Glomus mosseae on one side is reduced when roots on the other side are already colonized by G. mosseae . Root colonization by arbuscular mycorrhizal fungi enhances the P-status of plants, thus the observed suppressional effect on further root colonization in precolonized barley plants could be P-level regulated. Split-root systems allow to separate plant mediated P-effects on root colonization by arbuscular mycorrhizal fungi from direct P-effects on arbuscular mycorrhizal fungi. By adding a KH 2 PO 4 -solution to one side of the split-root system of non-mycorrhizal control plants, higher P-levels were obtained as in split-root systems of G. mosseae precolonized plants. Subsequent inoculation with G. mosseae of the P-supplied and the precolonized plants resulted in an inhibition of root colonization in the precolonized plants, but not in the P-supplied plants, discarding the enhanced P-level as the responsible factor for the observed suppression. Cyclohexenone derivatives are secondary plant compounds only found in roots of mycorrhizal plants. Analysis of cyclohexenone derivatives in mycorrhizal and non-mycorrhizal roots in split-root systems revealed that cyclohexenone derivatives can be detected in mycorrhizal roots, but not in non-mycorrhizal roots of mycorrhizal plants. The presented results show clearly that cyclohexenone derivatives are not systemically accumulated and that the P-levels are not the responsible factors for the observed systemic suppression of mycorrhization in roots of precolonized barley plants.

Characterization of Lactococcus lactis Phage 949 and Comparison with Other Lactococcal Phages

ABSTRACT The virulent Lactococcus lactis phage 949 was isolated in 1975 from cheese whey in New Zealand. This phage is a member of the Siphoviridae family and of a rare lactococcal phage group that bears its name (949 group). It has an icosahedral capsid (79-nm diameter) and a very long noncontractile tail (length, 500 nm; width, 12 nm). It infected 7 of 59 tested L. lactis strains, a somewhat expanded host range for a rare lactococcal phage. The abortive phage infection defense mechanisms AbiQ and AbiT strongly inhibited the multiplication of phage 949, but AbiK and AbiV did not. Its double-stranded DNA (dsDNA) genome of 114,768 bp is, to date, the largest among lactococcal phages. Its GC content was calculated at 32.7%, which is the lowest reported for a lactococcal phage. Its 154 open reading frames (ORFs) share limited identity with database sequences. In addition, terminal redundancy was observed as well as the presence of six tRNAs, one group I intron, and putative recombinases. SDS-PAGE coupled with mass spectrometry identified 13 structural proteins. The genomes of the members of the 10 currently known L. lactis phage groups were used to construct a proteomic tree. Each L. lactis phage group separated into distinct genetic clusters, validating the current classification scheme. Of note, members of the polythetic P335 groups were clearly separated into subgroups.

Structure and activity of AbiQ, a lactococcal endoribonuclease belonging to the type III toxin-antitoxin system.

AbiQ is a phage resistance mechanism found on a native plasmid of Lactococcus lactis that abort virulent phage infections. In this study, we experimentally demonstrate that AbiQ belongs to the recently described type III toxin–antitoxin systems. When overexpressed, the AbiQ protein (ABIQ) is toxic and causes bacterial death in a bacteriostatic manner. Northern and Western blot experiments revealed that the abiQ gene is transcribed and translated constitutively, and its expression is not activated by a phage product. ABIQ is an endoribonuclease that specifically cleaves its cognate antitoxin RNA molecule in vivo. The crystal structure of ABIQ was solved and site‐directed mutagenesis identified key amino acids for its anti‐phage and/or its RNase function. The AbiQ system is the first lactococcal abortive infection system characterized to date at a structural level.

Effect of the abortive infection mechanism and type III toxin/antitoxin system AbiQ on the lytic cycle of Lactococcus lactis phages

To survive in phage-containing environments, bacteria have evolved an array of antiphage systems. Similarly, phages have overcome these hurdles through various means. Here, we investigated how phages are able to circumvent the Lactococcus lactis AbiQ system, a type III toxin-antitoxin with antiviral activities. Lactococcal phage escape mutants were obtained in the laboratory, and their genomes were sequenced. Three unrelated genes of unknown function were mutated in derivatives of three distinct lactococcal siphophages: orf38 of phage P008, m1 of phage bIL170, and e19 of phage c2. One-step growth curve experiments revealed that the phage mutations had a fitness cost while transcriptional analyses showed that AbiQ modified the early-expressed phage mRNA profiles. The L. lactis AbiQ system was also transferred into Escherichia coli MG1655 and tested against several coliphages. While AbiQ was efficient against phages T4 (Myoviridae) and T5 (Siphoviridae), escape mutants of only phage 2 (Myoviridae) could be isolated. Genome sequencing revealed a mutation in gene orf210, a putative DNA polymerase. Taking these observations together, different phage genes or gene products are targeted or involved in the AbiQ phenotype. Moreover, this antiviral system is active against various phage families infecting Gram-positive and Gram-negative bacteria. A model for the mode of action of AbiQ is proposed.

Lactococcal Abortive Infection Protein AbiV Interacts Directly with the Phage Protein SaV and Prevents Translation of Phage Proteins

ABSTRACT AbiV is an abortive infection protein that inhibits the lytic cycle of several virulent phages infecting Lactococcus lactis, while a mutation in the phage gene sav confers insensitivity to AbiV. In this study, we have further characterized the effects of the bacterial AbiV and its interaction with the phage p2 protein SaV. First, we showed that during phage infection of lactococcal AbiV+ cells, AbiV rapidly inhibited protein synthesis. Among early phage transcripts, sav gene transcription was slightly inhibited while the SaV protein could not be detected. Analyses of other phage p2 mRNAs and proteins suggested that AbiV blocks the activation of late gene transcription, probably by a general inhibition of translation. Using size exclusion chromatography coupled with on-line static light scattering and refractometry, as well as fluorescence quenching experiments, we also demonstrated that both AbiV and SaV formed homodimers and that they strongly and specifically interact with each other to form a stable protein complex.