Reinhard Klein

Natrialba magadii virus φCh1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon

The double‐stranded (ds)DNA virus φCh1 infects the haloalkaliphilic archaeon Natrialba magadii. The complete DNA sequence of 58 498 bp of the temperate virus was established, and the probable functions of 21 of 98 φCh1‐encoded open reading frames (ORFs) have been assigned. This knowledge has been used to propose functional modules each required for specific functions during virus development. The φCh1 DNA is terminally redundant and circularly permuted and therefore appears to be packaged by the so‐called headful mechanism. The presence of ORFs encoding homologues of proteins involved in plasmid replication as well as experimental evidence indicate a plasmid‐mediated replication strategy of the virus. Results from nanosequencing of virion components suggest covalent cross‐linking of monomers of at least one of the structural proteins during virus maturation. A comparison of the φCh1 genome with the partly sequenced genome of Halobacterium salinarum virus φH revealed a close relationship between the two viruses, although their host organisms live in distinct environments with respect to the different pH values required for growth.

Characterization of Natronobacterium magadii phage ΦCh1, a unique archaeal phage containing DNA and RNA

A novel archaeal bacteriophage, ΦCh1, was isolated from a haloalkalophilic archaeon Natronobacterium magadii upon spontaneous lysis. The phage‐cured strain N. magadii (L13) was used to demonstrate infectivity of phage ΦCh1. The turbid‐plaque morphology and the fact that N. magadii cells isolated from plaques were able to produce phage indicated that ΦCh1 is a temperate phage. The phage morphology resembles other members of Myoviridae‐infecting Halobacterium species. In solution below 2 M NaCl, the phage lost its morphological stability and infectivity. One‐ and two‐dimensional SDS–PAGE of phage particles revealed at least four major and five minor proteins with molecular masses ranging from 15 to 80 kDa and acidic isoelectric points. Southern blot analysis of chromosomal DNA of a lysogenic N. magadii strain showed that ΦCh1 exists as a chromosomally integrated prophage. The phage particles contain both double‐stranded, linear DNA (approx. 55 kbp) as well as several RNA species (80–700 nucleotides). Hybridization of labelled RNA fragments to total DNA from N. magadii and ΦCh1 showed that the virion‐associated RNA is host encoded. Part of the phage DNA population is modified and restriction analysis revealed evidence for adenine methylation. Phage ΦCh1 is the first virus described for the genus Natronobacterium, and the first phage containing DNA and RNA in mature phage particles.

Pigs aerogenously immunized with genetically inactivated (ghosts) or irradiated Actinobacillus pleuropneumoniae are protected against a homologous aerosol challenge despite differing in pulmonary cellular and antibody responses

Aerosol immunization is a safe way to induce complete protection against pleuropneumonia in pigs caused by the lung pathogenic bacterium Actinobacillus pleuropneumoniae. In order to determine the local immune responses of vaccinees in concomitant with protection, lung lining fluid before and 3 weeks after immunization from pigs immunized three times with aerosols of either genetically inactivated ghosts which represent whole cell envelope preparations, or irradiated bacteria were examined following an homologous aerosol challenge. Specific antibody isotypes in the bronchoalveolar lavage were assayed by whole cell ELISAs. Total and relative numbers of cells including lymphocyte subsets were determined. In both vaccinated groups a net influx of plasma cells and lymphocytes, as well as a significant increase of specific IgG occurred. Concurrently, the CD4+/CD8+ ratio was found to increase after aerosol immunization. The lymphocyte subsets of IgG+ and IgA+ cells were found significantly higher in the group immunized with irradiated bacteria when compared to pigs immunized with bacterial ghosts. The latter group showed a significant increase of IgA, IgM, and a net influx of lymphoid blasts and granulocytes in the bronchoalveolar lining fluid. Although differences between the local immune responses of both immunized groups occurred, a significant increase of specific IgG and a net influx of plasma cells and lymphocytes were found to be associated with complete protection against a homologous aerosol challenge infection.

The archaeal halophilic virus-encoded Dam-like methyltransferase M. phiCh1-I methylates adenine residues and complements dam mutants in the low salt environment of Escherichia coli.

The genome of the archaeal virus φCh1, infecting Natrialba magadii (formerly Natronobacterium magadii), is composed of 58.5 kbp linear ds DNA. Virus particles contain several RNA species in sizes of 100–800 nucleotides. A fraction of φCh1 genomes is modified within 5′‐GATC‐3′ and related sequences, as determined by various restriction enzyme digestion analyses. High performance liquid chromatography revealed a fifth base, in addition to the four nucleosides, which was identified as N6‐methyladenosine. Genetic analyses and subsequent sequencing led to the identification of a DNA (N6‐adenine) methyltransferase (mtase) gene. The protein product was designated M.φCh1‐I. By the localization of the most conserved motifs (a DPPY motif occurring before FxGxG), the enzyme was placed within the β‐subgroup of the (N6‐adenine) methyltransferase class. The mtase gene of φCh1 was classified as a ‘late’ gene, as determined by measuring the kinetics of mRNA and protein expression in N. magadii during the lytic cycle of φCh1. After infection of cells, M.φCh1‐I mRNA and protein could be detected in lower amounts than in the situation of virus induction from lysogenic cells. Consequently, only about 5% of the φCh1 progeny genomes after infection of N. magadii carry the M.φCh1‐I methylation in contrast to 50% of virus genomes generated by induction of φCh1‐lysogenic N. magadii cells. Heterologous expression of the mtase from a halophile with 3 M cytoplasmic salt concentration showed an unexpected feature: the protein was active in the low environment of Escherichia coli and was able to methylate DNA in vivo. Interestingly, it seemed to exhibit a higher sequence specificity in E. coli that resulted in adenine methylation exclusively in the sequence 5′‐GATC‐3′. Additionally, expression of M.φCh1‐I in dam–E. coli cells led to a complete substitution of the function of M.Dam in DNA mismatch repair.

Haloarchaeal myovirus φCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities.

The φCh1 myovirus, which infects the haloalkaliphilic archaeon Natrialba magadii, contains an invertible region that comprises the convergent open reading frames (ORFs) 34 and 36, which code for the putative tail fibre proteins gp34 and gp36 respectively. The inversion leads to an exchange of the C‐termini of these proteins, thereby creating different types of tail fibres. Gene expression experiments revealed that only ORF34 is transcribed, indicating that φCh1 produces tail fibre proteins exclusively from this particular ORF. Only one of the two types of tail fibres encoded by ORF34 is able to bind to Nab. magadii in vitro. This is reflected by the observation that during the early phases of the infection cycle, the lysogenic strain L11 carries its invertible region exclusively in the orientation that produces that specific type of tail fibre. Obviously, Nab. magadii can only be infected by viruses carrying this particular type of tail fibre. By mutational analysis, the binding domain of gp34 was localized to the C‐terminal part of the protein, particularly to a galactose‐binding domain. The involvement of galactose residues in cell adhesion was supported by the observation that the addition of α‐D‐galactose to purified gp34 or whole virions prevented their attachment to Nab. magadii.

Inversion within the haloalkaliphilic virus φCh1 DNA results in differential expression of structural proteins

The sequence of φCh1 contains an open reading frame (int1) in the central part of its genome that belongs to the λ integrase family of site‐specific recombinases. Sequence similarities to known integrases include the highly conserved tetrad R‐H‐R‐Y. The flanking sequences of int1 contain several direct repeats of 30 bp in length (IR‐L and IR‐R), which are orientated in an inverted direction. Here, we show that a recombination active region exists in the genome of φCh1: the number of those repeats, non‐homologous regions within the repeat clusters IR‐L and IR‐R and the orientation of the int1 gene vary in a given virus population. Within this study, we identified circular intermediates, composed of the int1 gene and the inwards orientated repeat regions IR‐L and IR‐R, which could be involved in the recombination process itself. IR‐L and IR‐R are embedded within ORF34 and ORF36 respectively. As a consequence of the inversion within this region of φCh1, the C‐terminal parts of the proteins encoded by ORF34 and 36 are exchanged. Both proteins, expressed in Escherichia coli, interact with specific antisera against whole virus particles, indicating that they could be parts of φCh1 virions. Expression of the protein(s) in Natrialba magadii could be detected 98 h after inoculation, which is similar to other structural proteins of φCh1. Taken together, the data show that the genome of φCh1 contains an invertible region that codes for a recombinase and structural proteins. Inversion of this segment results in a variation of these structural proteins.

The lysogenic region of virus φCh1: identification of a repressor-operator system and determination of its activity in halophilic Archaea

AbstractφCh1 is a temperate virus infecting the haloalkaliphilic archaeon Natrialba magadii. As for all temperate viruses, a control of the lysogenic state versus the lytic life cycle is essential. Two open reading frames (ORFs) have been identified as putative repressor encoding genes: ORF48 and ORF49. The protein of ORF48 showed sequence similarities to putative repressor molecules. ORF49 was identified by the analysis of a mutant of φCh1: the lysogenic strain carrying mutant φCh1-1 showed a different lysis behavior than wild type virus φCh1, indicating a dysfunction in the regulation of gene expression. Here, we show that the intergenic region between ORF48 and ORF49 comprises a promoter/operator sequence that is a transcriptionally active region in the model system Haloferax volcanii. Transcription from this region can be repressed by the activity of the ORF48 gene product. Gp43/gp44 has an enhancing effect on this regulatory sequence. Evidence is given for a possible binding site of Rep and gp43/gp44 within the coding region of the rep gene.

The Viral Gene ORF79 Encodes a Repressor Regulating Induction of the Lytic Life Cycle in the Haloalkaliphilic Virus ϕCh1

ABSTRACT In this study, we describe the construction of the first genetically modified mutant of a halovirus infecting haloalkaliphilic Archaea. By random choice, we targeted ORF79, a currently uncharacterized viral gene of the haloalkaliphilic virus ϕCh1. We used a polyethylene glycol (PEG)-mediated transformation method to deliver a disruption cassette into a lysogenic strain of the haloalkaliphilic archaeon Natrialba magadii bearing ϕCh1 as a provirus. This approach yielded mutant virus particles carrying a disrupted version of ORF79. Disruption of ORF79 did not influence morphology of the mature virions. The mutant virus was able to infect cured strains of N. magadii, resulting in a lysogenic, ORF79-disrupted strain. Analysis of this strain carrying the mutant virus revealed a repressor function of ORF79. In the absence of gp79, onset of lysis and expression of viral proteins occurred prematurely compared to their timing in the wild-type strain. Constitutive expression of ORF79 in a cured strain of N. magadii reduced the plating efficiency of ϕCh1 by seven orders of magnitude. Overexpression of ORF79 in a lysogenic strain of N. magadii resulted in an inhibition of lysis and total absence of viral proteins as well as viral progeny. In further experiments, gp79 directly regulated the expression of the tail fiber protein ORF34 but did not influence the methyltransferase gene ORF94. Further, we describe the establishment of an inducible promoter for in vivo studies in N. magadii. IMPORTANCE Genetic analyses of haloalkaliphilic Archaea or haloviruses are only rarely reported. Therefore, only little insight into the in vivo roles of proteins and their functions has been gained so far. We used a reverse genetics approach to identify the function of a yet undescribed gene of ϕCh1. We provide evidence that gp79, a currently unknown protein of ϕCh1, acts as a repressor protein of the viral life cycle, affecting the transition from the lysogenic to the lytic state of the virus. Thus, repressor genes in other haloviruses could be identified by sequence homologies to gp79 in the future. Moreover, we describe the use of an inducible promoter of N. magadii. Our work provides valuable tools for the identification of other unknown viral genes by our approach as well as for functional studies of proteins by inducible expression.

Genomic manipulations in alkaliphilic haloarchaea demonstrated by a gene disruption in Natrialba magadii.

Alkaliphilic haloarchaea, a distinct physiological group from the closely related neutrophilic haloarchaea, represent an underutilized resource for basic research and industrial applications. In contrast to the neutrophilic haloarchaea, no reports on genomic manipulations in haloalkaliphiles have been published until now. Genomic manipulations via homologous recombination are useful for basic research. In this study, we demonstrate the possibility for this strategy in alkaliphilic haloarchaea for the first time. In a previous study, we developed a PEG-mediated transformation technique for alkaliphilic haloarchaea that was deployed in this study to deliver a gene disruption cassette into the model organism Natrialba magadii. The gene encoding for the well-studied Natrialba extracellular protease was successfully disrupted by a recombination marker gene, demonstrating a proof of principle for the usability of homologous recombination for genomic manipulations in alkaliphilic haloarchaea. Since halo(alkali)philic Archaea are polyploid, a selection process was applied in order to obtain a mutant strain containing exclusively disrupted genes. The resulting strain exhibited no proteolytic activity measurable by an azo-casein assay. Complementation was able to restore proteolytic activity. The expression pattern of the Natrialba extracellular protease was different in the complemented strain.