“…Owing to their unique morphology and simple genome amenable to genetic engineering, several inoviruses are widely used for biotechnological applications, including phage display or as drug delivery nanocarriers 4–7 . Ecologically, cultivated inoviruses are known to infect hosts from only 5 bacterial phyla and 10 genera but can have significant effect on the growth and pathogenicity of their host 8–10 . For instance, an inovirus prophage, CTXphi, encodes and expresses the major virulence factor of toxigenic Vibrio cholerae 11,12 , whereas in other bacterial hosts, including Pseudomonas , Neisseria and Ralstonia , inovirus infections indirectly influence pathogenicity by altering biofilm formation and host colonization abilities 8,13–16 .Fig.…”
Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.
“…Owing to their unique morphology and simple genome amenable to genetic engineering, several inoviruses are widely used for biotechnological applications, including phage display or as drug delivery nanocarriers 4–7 . Ecologically, cultivated inoviruses are known to infect hosts from only 5 bacterial phyla and 10 genera but can have significant effect on the growth and pathogenicity of their host 8–10 . For instance, an inovirus prophage, CTXphi, encodes and expresses the major virulence factor of toxigenic Vibrio cholerae 11,12 , whereas in other bacterial hosts, including Pseudomonas , Neisseria and Ralstonia , inovirus infections indirectly influence pathogenicity by altering biofilm formation and host colonization abilities 8,13–16 .Fig.…”
Bacteriophages from the Inoviridae family (inoviruses) are characterized by their unique morphology, genome content and infection cycle. One of the most striking features of inoviruses is their ability to establish a chronic infection whereby the viral genome resides within the cell in either an exclusively episomal state or integrated into the host chromosome and virions are continuously released without killing the host. To date, a relatively small number of inovirus isolates have been extensively studied, either for biotechnological applications, such as phage display, or because of their effect on the toxicity of known bacterial pathogens including Vibrio cholerae and Neisseria meningitidis. Here, we show that the current 56 members of the Inoviridae family represent a minute fraction of a highly diverse group of inoviruses. Using a machine learning approach leveraging a combination of marker gene and genome features, we identified 10,295 inovirus-like sequences from microbial genomes and metagenomes. Collectively, our results call for reclassification of the current Inoviridae family into a viral order including six distinct proposed families associated with nearly all bacterial phyla across virtually every ecosystem. Putative inoviruses were also detected in several archaeal genomes, suggesting that, collectively, members of this supergroup infect hosts across the domains Bacteria and Archaea. Finally, we identified an expansive diversity of inovirus-encoded toxin–antitoxin and gene expression modulation systems, alongside evidence of both synergistic (CRISPR evasion) and antagonistic (superinfection exclusion) interactions with co-infecting viruses, which we experimentally validated in a Pseudomonas model. Capturing this previously obscured component of the global virosphere may spark new avenues for microbial manipulation approaches and innovative biotechnological applications.
“…These P. aeruginosa strains frequently contain prophages, and prophages are important in the CF‐epidemic strains. The filamentous phage Pf is critical for several stages of the P. aeruginosa biofilm life cycle (Rice et al , 2009; Secor et al , 2015) and is a key contributor to the formation of small colony variants and virulence in vivo (Ilyina, 2015; Sweere et al , 2019) . Three putative TA loci have been predicted in the genome of the model strain P. aeruginosa PAO1 by bioinformatic analysis (Williams et al , 2011), and HigB/HigA on the chromosome was shown to be a type II TA system that controls biofilm formation and virulence (Li et al , 2016, Wood and Wood, 2016; Zhang et al, 2018, Guo et al , 2019).…”
Pf prophages are ssDNA filamentous prophages that are prevalent among various Pseudomonas aeruginosa strains. The genomes of Pf prophages contain not only core genes encoding functions involved in phage replication, structure and assembly but also accessory genes. By studying the accessory genes in the Pf4 prophage in P. aeruginosa PAO1, we provided experimental evidence to demonstrate that PA0729 and the upstream ORF Rorf0727 near the right attachment site of Pf4 form a type II toxin/antitoxin (TA) pair. Importantly, we found that the deletion of the toxin gene PA0729 greatly increased Pf4 phage production. We thus suggest the toxin PA0729 be named PfiT for Pf4 inhibition toxin and Rorf0727 be named PfiA for PfiT antitoxin. The PfiT toxin directly binds to PfiA and functions as a corepressor of PfiA for the TA operon. The PfiAT complex exhibited autoregulation by binding to a palindrome (5 0 -AATTCN 5 GTTAA-3 0 ) overlapping the -35 region of the TA operon. The deletion of pfiT disrupted TA autoregulation and activated pfiA expression. Additionally, the deletion of pfiT also activated the expression of the replication initiation factor gene PA0727. Moreover, the Pf4 phage released from the pfiT deletion mutant overcame the immunity provided by the phage repressor Pf4r. Therefore, this study reveals that the TA systems in Pf prophages can regulate phage production and phage immunity, providing new insights into the function of TAs in mobile genetic elements.
“…Other filamentous bacteriophages, such as M13, that do not integrate their genome into the host chromosome, have plasmid‐like vectors as genomes and their DNA is directly converted to RF by host‐encoded enzymes (Stassen et al , ). In this state, the genome of the phage can now be transmitted horizontally when the cell divides like other plasmids or be transferred via conjugation (Rakonjac et al , ; Ilyina, ).…”
With the recently awarded Nobel Prize to the inventor of Phage Display, George Smith, the technique has once more gained attention. However, one should not forget about the biology behind the method. Almost always ignored is how the structure of this bacterial virus is assembled. In contrast to lytic phages, filamentous phages are constantly being extruded through the bacterial membranes without lysis. Such filamentous phages are found in all aquatic environments, such as rivers and lakes, in the deep sea, in arctic ice, in hot springs and, associated with their hosts, in plants and animals including humans. While most filamentous phages infect Gram-negative hosts, inoviruses of Gram-positive hosts have also been described. Despite being among the minority within the phage family with an estimate of less than 5%, filamentous phages are real parasites as they exist at the expense of the host, but do not kill it. In contrast to lytic bacteriophages, filamentous phages are assembled in the host's membrane and extruded across the cellular envelope while the bacterium continues to grow. In this review, we focus on this complex and yet poorly understood process of assembly and secretion of filamentous phages.The fascinating biology behind phage display 1133
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