scholarly journals The Bacillus phage SPβ and its relatives: A temperate phage model system reveals new strains, species, prophage integration loci, conserved proteins and lysogeny management components

2021 ◽  
Author(s):  
Katharina Kohm ◽  
Valentina A. Floccari ◽  
Veronika T. Lutz ◽  
Birthe Nordmann ◽  
Carolin Mittelstaedt ◽  
...  
Keyword(s):  
Phage Genome ◽  
Genome Replication ◽  
Genome Packaging ◽  
Virion Release ◽  
Replication Strategy ◽  
Conserved Genes ◽  
Core Proteome ◽  
Bacillus Phage ◽  
Plaque Phenotype ◽  
Type Strains

The Bacillus phage SPβ has been known for about 50 years, but only a few strains are avalible. We isolated four new wild type strains of the SPbeta species. Phage vB_BsuS-Goe14 introduces its prophage into the spoVK locus, previously not observed to be used by SPβ-like phages. We could also reveal the SPβ-like phage genome replication strategy, the genome packaging mode, and the phage genome opening point. We extracted 55 SPβ-like prophages from public Bacillus genomes, thereby discovering three more integration loci and one additional type of integrase. The identified prophages resembled four new species clusters and three species orphans in the genus Spbetavirus. The determined core proteome of all SPβ-like prophages consists of 38 proteins. The integration cassette proved to be not conserved even though present in all strains. It consists of distinct integrases. Analysis of SPβ transcriptomes revealed three conserved genes, yopQ, yopR, and yokI, to be transcribed from a dormant prophage. While yopQ and yokI could be deleted from the prophage without activating the prophage, damaging of yopR led to a clear-plaque phenotype. Under the applied laboratory conditions, the yokI mutant showed an elevated virion release implying the YokI protein being a component of the arbitrium system.

scholarly journals Resistance in marine cyanobacteria differs against specialist and generalist cyanophages

2019 ◽  
Vol 116 (34) ◽  
pp. 16899-16908 ◽  
Author(s):  
Sophia Zborowsky ◽  
Debbie Lindell
Keyword(s):  
Phage Genome ◽  
Marine Cyanobacteria ◽  
Genome Replication ◽  
Genome Transcription ◽  
Infection Cycles ◽  
Resistance To Infection ◽  
Partial Genome ◽  
Stage Infection ◽  
Genome Degradation

Long-term coexistence between unicellular cyanobacteria and their lytic viruses (cyanophages) in the oceans is thought to be due to the presence of sensitive cells in which cyanophages reproduce, ultimately killing the cell, while other cyanobacteria survive due to resistance to infection. Here, we investigated resistance in marine cyanobacteria from the genera Synechococcus and Prochlorococcus and compared modes of resistance against specialist and generalist cyanophages belonging to the T7-like and T4-like cyanophage families. Resistance was extracellular in most interactions against specialist cyanophages irrespective of the phage family, preventing entry into the cell. In contrast, resistance was intracellular in practically all interactions against generalist T4-like cyanophages. The stage of intracellular arrest was interaction-specific, halting at various stages of the infection cycle. Incomplete infection cycles proceeded to various degrees of phage genome transcription and translation as well as phage genome replication in numerous interactions. In a particularly intriguing case, intracellular capsid assembly was observed, but the phage genome was not packaged. The cyanobacteria survived the encounter despite late-stage infection and partial genome degradation. We hypothesize that this is tolerated due to genome polyploidy, which we found for certain strains of both Synechococcus and Prochlorococcus. Our findings unveil a heavy cost of promiscuous entry of generalist phages into nonhost cells that is rarely paid by specialist phages and suggests the presence of unknown mechanisms of intracellular resistance in the marine unicellular cyanobacteria. Furthermore, these findings indicate that the range for virus-mediated horizontal gene transfer extends beyond hosts to nonhost cyanobacterial cells.

scholarly journals Host-dependent differences in replication strategy of the Sulfolobus Spindle-shaped Virus strain SSV9 (a.k.a., SSVK1): Lytic replication in hosts of the family Sulfolobaceae

2020 ◽  
Author(s):  
Ruben Michael Ceballos ◽  
Coyne Drummond ◽  
Carson Len Stacy ◽  
Elizabeth Padilla Crespo ◽  
Kenneth Stedman
Keyword(s):  
High Temperature ◽  
Virus Strain ◽  
Molecular Mechanisms ◽  
Transmission Rate ◽  
Lytic Replication ◽  
Host Interactions ◽  
Virion Release ◽  
The Family ◽  
Replication Strategy ◽  
Geographic Separation

ABSTRACTThe Sulfolobus Spindle-shaped Virus (SSV) system has become a model for studying thermophilic virus biology, including archaeal host-virus interactions and biogeography. Several factors make the SSV system amenable to studying archaeal genetic mechanisms (e.g., CRISPRs) as well as virus-host interactions in high temperature acidic environments. First, it has been shown that endemic populations of Sulfolobus, the reported SSV host, exhibit biogeographic structure. Second, the acidic (pH<4.5) high temperature (65-88°C) SSV habitats have low biodiversity, thus, diminishing opportunities for host switching. Third, SSVs and their hosts are readily cultured in liquid media and on gellan gum plates. Fourth, given the wide geographic separation between the various SSV-Sulfolobus habitats, the system is amenable for studying allopatric versus sympatric virus-host interactions. Previously, we reported that SSVs exhibit differential infectivity on allopatric and sympatric hosts. We also noticed a wide host range for virus strain SSV9 (a.k.a., SSVK1). For decades, SSVs have been described as “non-lytic” dsDNA viruses that infect species of the genus Sulfolobus and release virions via “blebbing” or “budding” as a preferred strategy over host lysis. Here, we show that SSVs infect more than one genus of the family Sulfolobaceae and, in allopatric hosts, SSV9 does not appear to release virions by blebbing. Instead, SSV9 appears to lyse all susceptible allopatric hosts tested, while exhibiting canonical non-lytic viral release via “blebbing” (historically reported for all other SSVs), on a single sympatric host. Lytic versus non-lytic virion release does not appear to be driven by multiplicity of infection (MOI). Greater relative stability of SSV9 compared to other SSVs (i.e., SSV1) in high temperature, low pH environments may contribute to higher transmission rates. However, neither higher transmission rate nor relative virulence in SSV9 infection drives replication profile (i.e., lytic versus non-lytic) in susceptible hosts. Although it is known that CRISPR-Cas systems offer protection against viral infection in prokaryotes, CRISPRS are not reported to be a determinant virus replication strategy. Thus, the genetic/molecular mechanisms underlying SSV9-induced lysis are unknown. These results suggest that there are unknown genetic elements, resulting from allopatric evolution, that drive virion release strategy in specific host strain-SSV strain pairings.

scholarly journals EpitoCore: mining conserved epitope vaccine candidates in the core proteome of multiple bacteria strains

2019 ◽  
Author(s):  
T.S. Fiuza ◽  
J.P.M.S. Lima ◽  
G.A. de Souza
Keyword(s):  
Peptide Vaccine ◽  
Computational Prediction ◽  
Reverse Vaccinology ◽  
Automated Identification ◽  
Single Strain ◽  
Vaccine Candidates ◽  
The Core ◽  
Core Proteins ◽  
Conserved Genes ◽  
Core Proteome

ABSTRACTIn reverse vaccinology approaches, complete proteomes of bacteria are submitted to multiple computational prediction steps in order to filter proteins that are possible vaccine candidates. Most available tools perform such analysis only in a single strain, or a very limited number of strains. But the vast amount of genomic data had shown that most bacteria contain pangenomes, i.e. their genomic information contains core, conserved genes, and random accessory genes specific to each strain. Therefore, it is of the utmost importance to define core proteins, and also core epitopes, in reverse vaccinology methods. EpitoCore is a decision-tree pipeline developed to fulfill that need. It provides surfaceome prediction of proteins from related strains, defines clusters of core proteins within those, calculate the immunogenicity of such clusters, predicts epitopes for a given set of MHC alleles defined by the user, and then reports if epitopes are located extracellularly and if they are conserved among the core homologues. Pipeline performance is illustrated by mining peptide vaccine candidates in Mycobacterium avium hominissuis strains. From a total proteome of approximately 4,800 proteins per strain, EpitoCore mined 103 highly immunogenic core homologues located at cell surface, many of those related to virulence and drug resistance. Conserved epitopes identified among these homologues allows the users to define sets of peptides with potential to immunize the largest coverage of tested HLA alleles using peptide-based vaccines. Therefore, EpitoCore is able to provide automated identification of conserved epitopes in bacterial pangenomic datasets.

scholarly journals Analysis of bifidobacterial evolution using a multilocus approach

2006 ◽  
Vol 56 (12) ◽  
pp. 2783-2792 ◽  
Author(s):  
Marco Ventura ◽  
Carlos Canchaya ◽  
Antonio Del Casale ◽  
Franco Dellaglio ◽  
Erasmo Neviani ◽  
...  
Keyword(s):  
Bacterial Genome ◽  
Evolutionary Process ◽  
Housekeeping Gene ◽  
Pharmaceutical Products ◽  
Gene Sequences ◽  
Genome Sequences ◽  
Functional Ingredients ◽  
Conserved Genes ◽  
Multilocus Approach ◽  
Type Strains

Bifidobacteria represent one of the most numerous groups of bacteria found in the gastrointestinal tract of humans and animals. In man, gastrointestinal bifidobacteria are associated with health effects and for this reason they are often used as functional ingredients in food and pharmaceutical products. Such applications may benefit from or require a clear and reliable bifidobacterial species identification. The increasing number of available bacterial genome sequences has provided a large amount of housekeeping gene sequences that can be used both for identification of bifidobacterial species as well as for understanding bifidobacterial evolution. In order to assess their relative positions in the evolutionary process, fragments from seven conserved genes, clpC, dnaB, dnaG, dnaJ1, purF, rpoC and xfp, were sequenced from each of the currently described type strains of the genus Bifidobacterium. The results demonstrate that the concatenation of these seven gene sequences for phylogenetic purposes allows a significant increase in the discriminatory power between taxa.

scholarly journals Hepatitis E Virus Replication

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 719 ◽  
Author(s):  
Robert LeDesma ◽  
Ila Nimgaonkar ◽  
Alexander Ploss
Keyword(s):  
Hepatitis E Virus ◽  
Rna Virus ◽  
Hypervariable Region ◽  
Hepatitis E ◽  
Open Reading Frames ◽  
Health Concern ◽  
Viral Gene ◽  
Genome Replication ◽  
Replication Strategy ◽  
Viral Gene Product

Hepatitis E virus (HEV) is a small quasi-enveloped, (+)-sense, single-stranded RNA virus belonging to the Hepeviridae family. There are at least 20 million HEV infections annually and 60,000 HEV-related deaths worldwide. HEV can cause up to 30% mortality in pregnant women and progress to liver cirrhosis in immunocompromised individuals and is, therefore, a greatly underestimated public health concern. Although a prophylactic vaccine for HEV has been developed, it is only licensed in China, and there is currently no effective, non-teratogenic treatment. HEV encodes three open reading frames (ORFs). ORF1 is the largest viral gene product, encoding the replicative machinery of the virus including a methyltransferase, RNA helicase, and an RNA-dependent RNA polymerase. ORF1 additionally contains a number of poorly understood domains including a hypervariable region, a putative protease, and the so-called ‘X’ and ‘Y’ domains. ORF2 is the viral capsid essential for formation of infectious particles and ORF3 is a small protein essential for viral release. In this review, we focus on the domains encoded by ORF1, which collectively mediate the virus’ asymmetric genome replication strategy. We summarize what is known, unknown, and hotly debated regarding the coding and non-coding regions of HEV ORF1, and present a model of how HEV replicates its genome.

scholarly journals Role of Annexin A2 in the Production of Infectious Hepatitis C Virus Particles

2010 ◽  
Vol 84 (11) ◽  
pp. 5775-5789 ◽  
Author(s):  
Perdita Backes ◽  
Doris Quinkert ◽  
Simon Reiss ◽  
Marco Binder ◽  
Margarita Zayas ◽  
...  
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Infectious Hepatitis ◽  
Annexin A2 ◽  
Host Factor ◽  
Genome Replication ◽  
Nonstructural Proteins ◽  
Virion Release ◽  
Domain Iii ◽  
Positive Strand Rna

ABSTRACT Hepatitis C virus (HCV) is an important human pathogen affecting 170 million chronically infected individuals. In search for cellular proteins involved in HCV replication, we have developed a purification strategy for viral replication complexes and identified annexin A2 (ANXA2) as an associated host factor. ANXA2 colocalized with viral nonstructural proteins in cells harboring genotype 1 or 2 replicons as well as in infected cells. In contrast, we found no obvious colocalization of ANXA2 with replication sites of other positive-strand RNA viruses. The silencing of ANXA2 expression showed no effect on viral RNA replication but resulted in a significant reduction of extra- and intracellular virus titers. Therefore, it seems likely that ANXA2 plays a role in HCV assembly rather than in genome replication or virion release. Colocalization studies with individually expressed HCV nonstructural proteins indicated that NS5A specifically recruits ANXA2, probably by an indirect mechanism. By the deletion of individual NS5A subdomains, we identified domain III (DIII) as being responsible for ANXA2 recruitment. These data identify ANXA2 as a novel host factor contributing, with NS5A, to the formation of infectious HCV particles.

scholarly journals Interplay between Host tRNAs and HIV-1: A Structural Perspective

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1819
Author(s):  
Jinwei Zhang
Keyword(s):  
Small Molecules ◽  
Viral Genome ◽  
Molecular Mechanisms ◽  
Genome Replication ◽  
Structural Protein ◽  
Genome Packaging ◽  
Major Structural Protein ◽  
Viral Genome Replication ◽  
Hiv 1 ◽  
Structural Perspective

The cellular metabolism of host tRNAs and life cycle of HIV-1 cross paths at several key virus–host interfaces. Emerging data suggest a multi-faceted interplay between host tRNAs and HIV-1 that plays essential roles, both structural and regulatory, in viral genome replication, genome packaging, and virion biogenesis. HIV-1 not only hijacks host tRNAs and transforms them into obligatory reverse transcription primers but further commandeers tRNAs to regulate the localization of its major structural protein, Gag, via a specific interface. This review highlights recent advances in understanding tRNA–HIV-1 interactions, primarily from a structural perspective, which start to elucidate their underlying molecular mechanisms, intrinsic specificities, and biological significances. Such understanding may provide new avenues toward developing HIV/AIDS treatments and therapeutics including small molecules and RNA biologics that target these host–virus interfaces.

scholarly journals Ebolavirus polymerase uses an unconventional genome replication mechanism

2019 ◽  
Vol 116 (17) ◽  
pp. 8535-8543 ◽  
Author(s):  
Laure R. Deflubé ◽  
Tessa N. Cressey ◽  
Adam J. Hume ◽  
Judith Olejnik ◽  
Elaine Haddock ◽  
...  
Keyword(s):  
Rna Viruses ◽  
Rna Virus ◽  
Replication Initiation ◽  
Genome Replication ◽  
Terminal Nucleotide ◽  
Nucleotide Addition ◽  
Replication Strategy ◽  
Virus Genomes ◽  
High Degree

Most nonsegmented negative strand (NNS) RNA virus genomes have complementary 3′ and 5′ terminal nucleotides because the promoters at the 3′ ends of the genomes and antigenomes are almost identical to each other. However, according to published sequences, both ends of ebolavirus genomes show a high degree of variability, and the 3′ and 5′ terminal nucleotides are not complementary. If correct, this would distinguish the ebolaviruses from other NNS RNA viruses. Therefore, we investigated the terminal genomic and antigenomic nucleotides of three different ebolavirus species, Ebola (EBOV), Sudan, and Reston viruses. Whereas the 5′ ends of ebolavirus RNAs are highly conserved with the sequence ACAGG-5′, the 3′ termini are variable and are typically 3′-GCCUGU, ACCUGU, or CCUGU. A small fraction of analyzed RNAs had extended 3′ ends. The majority of 3′ terminal sequences are consistent with a mechanism of nucleotide addition by hairpin formation and back-priming. Using single-round replicating EBOV minigenomes, we investigated the effect of the 3′ terminal nucleotide on viral replication and found that the EBOV polymerase initiates replication opposite the 3′-CCUGU motif regardless of the identity of the 3′ terminal nucleotide(s) and of the position of this motif relative to the 3′ end. Deletion or mutation of the first residue of the 3′-CCUGU motif completely abolished replication initiation, suggesting a crucial role of this nucleotide in directing initiation. Together, our data show that ebolaviruses have evolved a unique replication strategy among NNS RNA viruses resulting in 3′ overhangs. This could be a mechanism to avoid antiviral recognition.

scholarly journals STUDIES ON THE MECHANISM OF TRANSDUCTION BY BACTERIOPHAGE ϕγ. II. FORMATION OF TRANSDUCING ELEMENTS

Genetics ◽  
1980 ◽  
Vol 95 (3) ◽  
pp. 525-544
Author(s):  
Jean-Pierre Gratia
Keyword(s):  
Phage Genome ◽  
Initiation Site ◽  
Specific Point ◽  
Genome Packaging ◽  
Linear Fashion ◽  
A Site

ABSTRACT The formation of the transducing elements (TE) of bacteriophage ɸγ, analyzed in lysogens of the thermo-inducible derivative ɸγhyI, has been found to parallel the formation of plaque-forming particles with a frequency of 2 × 10-2 TE/PFU, but is more sensitive to temperature and to UV. Deletion of one of the prophage termini (attR) prevents normal excision and formation of plaque-forming particles, but does not affect the formation of transducing elements, which arise at a rate of nearly 10-1 TE per induced bacterium. Transducing elements would be formed by in situ encapsulation of a hybrid segment from a specific point in the induced prophage, possibly the presumed packaging initiation site of the normal phage genome, before excision of the latter has occurred. Analysis of the mechanism of transduction to partly heterologous lysogens has revealed the participation of a co-infecting genome arranged in a linear fashion and has given evidence for a permutation in the sequence of transducing and nontransducing genomes. The data are consistent with a mechanism of encapsidation distinct from the Ter system even for hybrids inheriting part of the ɸ80 genome, but endowed with the property to form transducing elements like those of ɸγ. Upon infection, transducing elements are formed after one cycle of lytic development with the same characteristics as those resulting from induction, but with a frequency 50 to 100 times lower. This process is dependent on the efficiency of Int promoted recombination. Superinfection experiments performed under conditions preventing Int promoted recombination reveal that any superinfecting ɸγ can promote the formation of transducing particles, depending on the presence within the host prophage of a site from which transducing genome packaging initiates.

scholarly journals Temporal compartmentalization of viral infection in bacterial cells

2021 ◽  
Vol 118 (28) ◽  
pp. e2018297118
Author(s):  
Audrey Labarde ◽  
Lina Jakutyte ◽  
Cyrille Billaudeau ◽  
Beatrix Fauler ◽  
Maria López-Sanz ◽  
...  
Keyword(s):  
Genome Replication ◽  
Bacterial Cells ◽  
Biosynthetic Activity ◽  
Genome Packaging ◽  
Viral Dna ◽  
Particle Assembly ◽  
Protein Cage ◽  
Host Cytoplasm ◽  
Total Dna ◽  
Viral Particle Assembly

Virus infection causes major rearrangements in the subcellular architecture of eukaryotes, but its impact in prokaryotic cells was much less characterized. Here, we show that infection of the bacterium Bacillus subtilis by bacteriophage SPP1 leads to a hijacking of host replication proteins to assemble hybrid viral–bacterial replisomes for SPP1 genome replication. Their biosynthetic activity doubles the cell total DNA content within 15 min. Replisomes operate at several independent locations within a single viral DNA focus positioned asymmetrically in the cell. This large nucleoprotein complex is a self-contained compartment whose boundaries are delimited neither by a membrane nor by a protein cage. Later during infection, SPP1 procapsids localize at the periphery of the viral DNA compartment for genome packaging. The resulting DNA-filled capsids do not remain associated to the DNA transactions compartment. They bind to phage tails to build infectious particles that are stored in warehouse compartments spatially independent from the viral DNA. Free SPP1 structural proteins are recruited to the dynamic phage-induced compartments following an order that recapitulates the viral particle assembly pathway. These findings show that bacteriophages restructure the crowded host cytoplasm to confine at different cellular locations the sequential processes that are essential for their multiplication.

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