A common trick for transferring bacterial DNA

Why do mobile genetic elements transfer DNA of their hosts?

The prokaryote world is replete with mobile genetic elements (MGEs) - self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex.

The bacteriophage decides own tracks: When they are with or against the bacteria

Bacteriophages, bacteria-infecting viruses, are considered by many researchers a promising solution for antimicrobial resistance. On the other hand, some phages have shown contribution to bacterial resistance phenomenon by transducing antimicrobial resistance genes to their bacterial hosts. Contradictory consequences of infections are correlated to different phage lifecycles. Out of four known lifecycles, lysogenic and lytic pathways have been riddles since the uncontrolled conversion between them could negatively affect the intended use of phages. However, phages still can be engineered for applications against bacterial and viral infections to ensure high efficiency. This review highlights two main aspects: (1) the different lifecycles as well as the different factors that affect lytic-lysogenic switch are discussed, including the intracellular and molecular factors control this decision. In addition, different models which describe the effect of phages on the ecosystem are compared, besides the approaches to study the switch. (2) An overview on the contribution of the phage in the evolution of the bacteria, instead of eating them, as a consequence of different mode of actions. As well, how phage display has helped in restricting phage cheating and how it could open new gates for immunization and pandemics control will be tacked.

Lateral transduction is inherent to the life cycle of the archetypical Salmonella phage P22

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with early prophage excision followed by DNA replication and packaging (ERP). This temporal program is considered universal for P22-like temperate phages, though there is no direct evidence to support the timing and sequence of these events. Here we report that the long-standing ERP program is an observation of the experimentally favored Salmonella phage P22 tsc229 heat-inducible mutant, and that wild-type P22 actually follows the replication-packaging-excision (RPE) program. We find that P22 tsc229 excises early after induction, but P22 delays excision to just before it is detrimental to phage production. This allows P22 to engage in lateral transduction. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation.

The Age of Phage: Friend or Foe in the New Dawn of Therapeutic and Biocontrol Applications?

Extended overuse and misuse of antibiotics and other antibacterial agents has resulted in an antimicrobial resistance crisis. Bacteriophages, viruses that infect bacteria, have emerged as a legitimate alternative antibacterial agent with a wide scope of applications which continue to be discovered and refined. However, the potential of some bacteriophages to aid in the acquisition, maintenance, and dissemination of negatively associated bacterial genes, including resistance and virulence genes, through transduction is of concern and requires deeper understanding in order to be properly addressed. In particular, their ability to interact with mobile genetic elements such as plasmids, genomic islands, and integrative conjugative elements (ICEs) enables bacteriophages to contribute greatly to bacterial evolution. Nonetheless, bacteriophages have the potential to be used as therapeutic and biocontrol agents within medical, agricultural, and food processing settings, against bacteria in both planktonic and biofilm environments. Additionally, bacteriophages have been deployed in developing rapid, sensitive, and specific biosensors for various bacterial targets. Intriguingly, their bioengineering capabilities show great promise in improving their adaptability and effectiveness as biocontrol and detection tools. This review aims to provide a balanced perspective on bacteriophages by outlining advantages, challenges, and future steps needed in order to boost their therapeutic and biocontrol potential, while also providing insight on their potential role in contributing to bacterial evolution and survival.

Evolutionary Diversity of Prophage DNA in Klebsiella pneumoniae Chromosomes

Mobile gene elements play an important role in the continuous evolution of the prophage DNA of bacteria, promoting the emergence of new gene structures. This study explored the evolution of four strains of Klebsiella pneumoniae harboring prophages, 19051, 721005, 911021, and 675920, and 16 genomes of K. pneumoniae from GenBank. The results revealed a wide range of genetic variation in the prophage DNA inserted into the sap sites of K. pneumoniae chromosomes. From analysis and comparison of the sequences of the 20 prophage DNAs determined from the four strains and the 16 GenBank genomes of K. pneumoniae using high-throughput sequencing and antimicrobial susceptibility tests, we identified a novel transposon, Tn6556. We also identified at least nine large genetic structures with massive genetic acquisitions or losses and five hotspot sites showing a tendency to undergo insertion of gene elements such as IS1T, IS1R, IS26, ISKpn26, ISKpn28, Tn6556, MDR, and In27-related regions as variable regions; however, the only highly conserved core genes were int and umuCD among the 20 prophage DNAs. These findings provide important insights into the evolutionary diversity of bacteriophage DNA contained in K. pneumoniae.

Comparative genomics groups phages of Negativicutes and classical Firmicutes despite different Gram-staining properties

Negativicutes are gram-negative bacteria characterized by two cell membranes, but they are phylogenetically a side-branch of gram-positive Firmicutes that contain only a single membrane. We asked whether viruses (phages) infecting Negativicutes were horizontally acquired from gram-negative Proteobacteria, given the shared outer cell structure of their bacterial hosts, or if Negativicute phages co-evolved vertically with their hosts and thus resemble gram-positive Firmicute prophages. We predicted and characterized 485 prophages (mostly Caudovirales) from gram-negative Firmicute genomes plus 2977 prophages from other bacterial clades, and we used virome sequence data from 183 human stool samples to support our predictions. The majority of identified Negativicute prophages were lambdoids closer related to prophages from other Firmicutes than Proteobacteria by sequence relationship and genome organization (position of the lysis module). Only a single Mu-like candidate prophage and no clear P2-like prophages were identified in Negativicutes, both common in Proteobacteria. Given this collective evidence, it is unlikely that Negativicute phages were acquired from Proteobacteria. Sequence-related prophages, which occasionally harboured antibiotic resistance genes, were identified in two distinct Negativicute orders (Veillonellales and Acidaminococcales), possibly suggesting horizontal cross-order phage infection between human gut commensals. Our results reveal ancient genomic signatures of phage and bacteria co-evolution despite horizontal phage mobilization.

"FAGOMA: Spanish Network of Bacteriophages and Transducer Elements"-V Meeting Report

The Spanish Network of Bacteriophages and Transducer Elements (FAGOMA) was created to answer the need of Spanish scientists working on phages to exchange knowledge and find synergies. Seven years and five meetings later, the network has become a fruitful forum where groups working on distinct aspects of phage research (structural and molecular biology, diversity, gene transfer and evolution, virus–host interactions, clinical, biotechnological and industrial applications) present their work and find new avenues for collaboration. The network has recently increased its visibility and activity by getting in touch with the French Phage Network (Phages.fr) and with different national and international scientific institutions. Here, we present a summary of the fifth meeting of the FAGOMA network, held in October 2018 in Alcalá de Henares (Madrid), in which the participants shared some of their latest results and discussed future challenges of phage research.