Viruses has now published two Special Issues on phage–host interactions, the latest under the name Phage–Host Interactions 2021 [...

Skurnik, Mikael

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Helsingin yliopiston digitaalinen arkisto

https://helda.helsinki.fiþÿ E d i t o r i a l   o f   V i r u s e s   S p e c i a l   I s s u e   o n   P h a g e  H o s t   I n t e r a c t i o n s   2 0 2 1Skurnik, MikaelMultidisciplinary Digital Publishing Institute2022-01-25þÿ S k u r n i k ,   M .   E d i t o r i a l   o f   V i r u s e s   S p e c i a l   I s s u e   o n   P h a g e  H o s t   I n t e r a c t i o n s   2 0 2 1 .   V i r u s e s2022, 14, 236.http://hdl.handle.net/10138/349211Downloaded from Helda, University of Helsinki institutional repository.This is an electronic reprint of the original article.This reprint may differ from the original in pagination and typographic detail.Please cite the original version.Citation: Skurnik, M. Editorial ofViruses Special Issue on Phage–HostInteractions 2021. Viruses 2022, 14,236. https://doi.org/10.3390/v14020236Received: 20 January 2022Accepted: 24 January 2022Published: 25 January 2022Publisher’s Note: MDPI stays neutralwith regard to jurisdictional claims inpublished maps and institutional affil-iations.Copyright: © 2022 by the author.Licensee MDPI, Basel, Switzerland.This article is an open access articledistributed under the terms andconditions of the Creative CommonsAttribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).virusesEditorialEditorial of Viruses Special Issue on Phage–HostInteractions 2021Mikael Skurnik 1,21 Department of Bacteriology and Immunology, Medicum, Human Microbiome Research Program,Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland; mikael.skurnik@helsinki.fi2 Division of Clinical Microbiology, HUSLAB, University of Helsinki and Helsinki University Hospital,00290 Helsinki, FinlandViruses has now published two Special Issues on phage–host interactions, the latestunder the name Phage–Host Interactions 2021. In the present Special Issue we have13 papers that study the topic from different angles. We have several papers that describecharacterizations of new phages, their genomes, host ranges, identification of host receptorsand receptor-binding proteins, phage proteomes and other properties. Some papers dealwith conditions that influence the life cycles of phages. Additionally, prophages playdifferent roles.Shchurova et al. investigated the biological properties, genomic organization, andvirus–bacterial host-interaction strategy of novel myovirus TaPaz, isolated using a K47capsule strain of Acinetobacter baumannii. The authors identified two different tailspikedepolymerases (TSDs) and tested the purified proteins against a collection of A. baumanniistrains belonging to 56 different K types. One TSD was identified as a specific K47 CPSglycosidase. Feng et al. described a novel Alteromonas phage vB_AmeP-R8W (R8W) thathas a wide host range, mainly infecting Alteromonas strains isolated from deep waters. Theauthors show that R8W possesses two receptor-binding proteins that likely contribute tothe wide host range.Three papers describe detailed characterizations of Yersinia phages. Happonenet al. describe the proteogenomic characterization and host-receptor identification of thesiphovirus vB_YenS_ϕR2-01 (ϕR2-01) that infects strains representing several Yersinia ente-rocolitica serotypes. Of the 154 predicted genes, 117 are homologous to those of Escherichiabacteriophage T5. The outer membrane vitamin B12 receptor BtuB was identified as thehost receptor of the phage. Salem et al. characterized T4-like Yersinia bacteriophages fPS-2,fPS-65, and fPS-90, isolated from pig stools, which were 84–92% identical to each otherand ca 85% identical to phage T4. The phages exhibited relatively wide host ranges amongYersinia pseudotuberculosis and related species. Sequencing of spontaneous phage-resistantmutants revealed mutations in the ompF, galU, hldD, or hldE genes, demonstrating thatthe porin OmpF and the lipopolysaccharide (LPS) inner core function as phage receptors.The host recognition was assigned to the distal β-helices connecting loops of the predictedlong tail-fiber tip protein, a homolog of Gp38 of T-even phages. Skurnik et al. identifiedYersinia pestis phages fEV-1 and fD1 as a dwarf myovirus and a T4-like myovirus, respec-tively. They carried out proteome characterizations for both phages. fEV-1 is the first dwarfmyovirus described for Y. pestis, and its host range was restricted strictly to Y. pestis strains.Phage fD1 showed wider host range, including other members of Enterobacterales such asEscherichia coli and Y. pseudotuberculosis.Duyvejonck et al. evaluated the ability of different buffer and infusion solutions to sup-port phage infectivity when stored at 4 ◦C. They observed wide variability between phagesand between solutions. They also reported on the stability of lyophilized phage preparates.Hosseini et al., when working to design a phage cocktail against Aeromonas salmonicidasubsp. salmonicida, the causative agent of furunculosis, noticed that when five phages wereViruses 2022, 14, 236. https://doi.org/10.3390/v14020236 https://www.mdpi.com/journal/virusesViruses 2022, 14, 236 2 of 2used individually, or as combinations of two to five phages, that the phage cocktail was noteffective against strains bearing Prophage 3, which is present in two-thirds of the strainsfrom the province of Quebec. Their work demonstrated that the prophage content can affectthe efficacy of a cocktail of virulent phages for phage-therapy purposes. McCutcheon et al.review the clinical significance, virulence factors, and antimicrobial resistance mechanismsof Stenotrophomonas maltophilia, all the phages isolated and characterized to date, and strate-gies for their use. They describe the in vivo phage-therapy studies conducted against thisbacterium and discuss future prospects for the use of phages to treat multidrug-resistantS. maltophilia. Zhang et al. isolated a T4-like lytic phage targeting Escherichia coli C600carrying plasmid pHNAH67 encoding 11 antibiotic resistance genes (ARGs). Using NGSthey found that the phage could misload host DNA randomly, including the plasmid ARGs.Hünnefeld et al. characterized the genome of Corynebacterium phage CL31 andanalyzed its infection dynamics in the Corynebacterium glutamicum strain ATCC 13032. CL31efficiently infected a mutant strain lacking the restriction-modification system, and evenmore efficiently the prophage-free C. glutamicum strain MB001. The authors furthermorecarried out proteome analysis of purified phage particles, and transcriptome analysis ofinfected bacteria. Analysis of CL31-resistant strains revealed SNPs in genes involved inmycolic acid biosynthesis, suggesting a role of this cell envelope component in phageadsorption. Bastin et al. report that phage MS2 when propagated in Escherichia coli underaerobic conditions produces mostly non-infectious phage particles. Indeed, only 2% ofthe produced phage particles were infectious. They show that growth under anaerobicconditions and ROS inhibition increases infectious phages to 8 and 25%, respectively. Thus,the authors predict that oxidative damage impacts the molecular replication and assemblyof MS2 phages. Sacher et al. describe the characterization of a Campylobacter jejuni phagethat requires functional flagellar glycosylation and motor genes for infection, although theflagellae are not necessary for adsorption of the phage on the cell surface. The authorsidentify, using sophisticated approaches, a link between oxidative stress, flagellar motility,and phage infectivity, demonstrating that the host oxidative stress state is an important issueto be taken into account in phage–host interaction studies. Skliros et al., using a multiomicsapproach incorporating transcriptome and metabolome analyses of Vibrio alginolyticusphage-resistant strains, showed that the strains had repressed the expression of the ompF,lamB, and btuB genes encoding phage receptors. However, this was accompanied byrepression of the genes encoding natural nutrient channels, such as RbsA, PtsG, TryP, LivH,LysE, and HisP. This suggests that the bacterial cell needs to readjust its biochemistry toachieve phage resistance. Lavysh et al. report that Salmonella phage 7–11, similarly toEscherichia phage phiEco32, encodes a protein similar to the bacterial sigma subunit ofRNA polymerase. They investigated the temporal pattern of phage 7–11 gene expressionduring infection and compared it to the previously determined transcription strategy ofphiEco32. Using sophisticated methods, they identified eight promoters recognized byhost RNA polymerase holoenzyme equipped with the phage 7–11 sigma subunit. Thesepromoters are characterized by a bipartite consensus GTAAtg-(16)-aCTA and are locatedupstream of late phage genes. Interestingly, the transcription profiles of the two relatedphages differ from each other, likely due to the fact that phage 7–11 does not encode theinhibitor of host transcription and early phage transcription or the activator of transcription.Conflicts of Interest: The authors declare no conflict of interest.

Editorial of Viruses Special Issue on Phage–Host Interactions 2021

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Editorial of Viruses Special Issue on Phage–Host Interactions 2021

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Helsingin yliopiston digitaalinen arkisto