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Host range phenotype induced by mutations in the internal ribosomal entry site of poliovirus RNA.

Most poliovirus strains infect only primates. The host range (HR) of poliovirus is thought to be primarily determined by a cell surface molecule that functions as poliovirus receptor (PVR), since it has been shown that transgenic mice are made poliovirus sensitive by introducing the human PVR gene into the genome. The relative levels of neurovirulence of polioviruses tested in these transgenic mice were shown to correlate well with the levels tested in monkeys (H. Horie et al., J. Virol. 68:681-688, 1994). Mutants of the virulent Mahoney strain of poliovirus have been generated by disruption of nucleotides 128 to 134, at stem-loop II within the 5' noncoding region, and four of these mutants multiplicated well in human HeLa cells but poorly in mouse TgSVA cells that had been established from the kidney of the poliovirus-sensitive transgenic mouse. Neurovirulence tests using the two animal models revealed that these mutants were strongly attenuated only in tests with the mouse model and were therefore HR mutants. The virus infection cycle in TgSVA cells was restricted by an internal ribosomal entry site (IRES)-dependent initiation process of translation. Viral protein synthesis and the associated block of cellular protein synthesis were not observed in TgSVA cells infected with three of four HR mutants and was evident at only a low level in the remaining mutant. The mutant RNAs were functional in a cell-free protein synthesis system from HeLa cells but not in those from TgSVA and mouse neuroblastoma NS20Y cells. These results suggest that host factor(s) affecting IRES-dependent translation of poliovirus differ between human and mouse cells and that the mutant IRES constructs detect species differences in such host factor(s). The IRES could potentially be a host range determinant for poliovirus infection.

Animals↗

Lymantria dispar nucleopolyhedrovirus hrf-1 expands the larval host range of Autographa californica nucleopolyhedrovirus.

The gypsy moth (Lymantria dispar) is nonpermissive for Autographa californica nucleopolyhedrovirus (AcNPV) infection. We previously isolated a gene, host range factor 1 (hrf-1), from L. dispar nucleopolyhedrovirus that promotes AcNPV replication in Ld652Y cells, a nonpermissive L. dispar cell line (S. M. Thiem, X. Du, M. E. Quentin, and M. M. Berner, J. Virol. 70:2221-2229, 1996). In the present study, we investigated the ability of hrf-1 to alter the larval host range of AcNPV. Bioassays using recombinant AcNPV bearing hrf-1 were conducted with insect larvae by use of oral infection. AcNPV bearing hrf-1 was infectious for neonate L. dispar larvae, with a 50% lethal concentration of 1.2 x 10(5) polyhedral inclusion bodies/ml of diet, which is similar to that of wild-type AcNPV for permissive hosts. AcNPV can kill neonate L. dispar larvae at high doses, but it does not kill third-instar larvae. However, electron microscopy studies of AcNPV-inoculated third-instar larvae revealed virus replication in the midgut cells. PCR analyses indicated that the virus was AcNPV. These results suggest that the block for AcNPV infection of L. dispar larvae is its inability to spread systematically from primary infection sites in the midgut epithelium and that this barrier is leaky in neonates. hrf-1 allows AcNPV to overcome this barrier. AcNPV recombinants bearing hrf-1 were also significantly more infectious for Helicoverpa zea, a resistant species, suggesting that the blocks for AcNPV infection of L. dispar and H. zea larvae may be similar.

Animals↗

Transposon mutagenesis in Legionella pneumophila. I.--Persistence of suicide and broad host-range plasmids.

Two of three highly virulent strains of Legionella pneumophila could act as recipients at high frequencies in conjugation experiments with Escherichia coli donor strains carrying broad host-range plasmids belonging to incompatibility groups N, P and W. All broad host-range and most transposon-delivery plasmids persisted within transconjugants with high stability. Only one (pSUP1021) of several vehicles designed for the delivery of transposons into the chromosome of Gram-negative bacteria was found to yield transposon mutants of Legionella at a detectable frequency.

Blotting, Southern↗

Conservation of the genetic switch between replication and transfer genes of IncP plasmids but divergence of the replication functions which are major host-range determinants.

The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trb operon encodes most of the apparatus for mating pair formation, the first step in conjugative transfer. Comparison of the nucleotide sequence of the IncP beta plasmid R751 presented here with the equivalent IncP alpha sequence identifies conserved features of the organization and regulation of the trfA operon and the region controlling expression of the trb operon. As in IncP alpha plasmids, these operons are transcribed from a bidirectional promoter region consisting of trfAp for the trfA operon and trbAp and trbBp for the trb operon. The KorA-dependent switch between the trfA and trbA promoters is conserved as is the trbA gene encoding the third IncP global regulator. The intergenic region between trbA and trbB shows very little sequence identity between the two plasmids but the spacing, the KorB operator, the trbB promoter, and the existence of a hairpin loop (albeit of different actual sequence) which sequesters the trbB ribosome binding site are all conserved. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa. A TcR derivative of R751 was constructed and shown not to establish itself efficiently in P. aeruginosa at 37 degrees C, although it did establish itself inefficiently at lower temperatures, underlining the importance of this region in the adaptation of the plasmid to the host.

Amino Acid Sequence↗

Functional features of oriV of the broad host range plasmid RSF1010 in Pseudomonas aeruginosa.

The broad host range plasmid RSF1010 requires for its replication in Escherichia coli three plasmid-encoded proteins and specific nucleotide sequences ssiA, ssiB, and iterons in the oriVRSF1010. In Pseudomonas aeruginosa, a recombinant mini-RSF1010 plasmid lacking ssiB lost its replication ability, but a miniplasmid lacking ssiA or carrying a primosome assembly site in place of ssiA could replicate. Moreover, ssiA, as a sole ssi signal, in the orientation that ssiB had originally taken was sufficient for replication of the miniplasmid. These results indicated that only one RSF1010-specific ssi signal in the orientation that ssiB takes in wild-type oriVRSF1010 was essential for replication of RSF1010. Replication of the miniplasmids was dependent on the three plasmid-encoded proteins, RepA, B', and C, as in E. coli.

Bacteriophage phi X 174↗

Comparison of promoter activities in Escherichia coli and Pseudomonas aeruginosa: use of a new broad-host-range promoter-probe plasmid.

The broad-host-range plasmid, pRW2, is a derivative of pRK 2501 carrying the Escherichia coli lac operon without a promoter, downstream of a polylinker sequence. We have cloned a number of DNA fragments carrying promoters into this plasmid and measured promoter activity in both E. coli and Pseudomonas aeruginosa. Promoters carrying consensus -10 and -35 sequences were active in both backgrounds and the dependence of activity on the nucleotide sequence of the 35 region was the same in both cases. We also measured the activity of two promoters at which transcription in E. coli was totally dependent on the E. coli activators CRP and FNR: both promoters were found to be active in P. aeruginosa.

Base Sequence↗

Functional difference between the two oppositely oriented priming signals essential for the initiation of the broad host-range plasmid RSF1010 DNA replication.

The broad host-range plasmid RSF1010 contains two oppositely oriented priming signals, ssiA and ssiB, for DNA synthesis dependent on the origin of vegetative DNA replication (oriV). If either ssiA or ssiB was deleted or inverted, the RSF1010 miniplasmids containing engineered oriVs were maintained at low copy numbers, replicated abnormally as dimers, and accumulated specific single strands in the Escherichia coli strain supplying the three RSF1010-encoded RepA, RepB', and RepC proteins. Interestingly, an additional intracellular supply of the Sog primase (the sog gene product of plasmid CoIIb-P9) reversed the replication deficiency of these miniplasmids with respect to all three aspects described above. These were also true for the RSF1010 miniplasmids in which either ssiA or ssiB was replaced by the primosome assembly site (PAS) or by the G4-type ssi signal (G site). Furthermore, comparative analysis of the functional contribution of the two oppositely oriented ssi signals to the DNA replication of RSF1010 showed that, irrespective of their types, ssi signals conducting the initiation of DNA chain elongation away from the iterons were functionally more important than ones in the inverted orientation. We consider that this functional difference reflects the inherent properties of the initiation mechanism of RSF1010 DNA replication.

Bacterial Proteins↗

A 26-kDa outer membrane protein, OmpK, common to Vibrio species is the receptor for a broad-host-range vibriophage, KVP40.

KVP40 is a broad-host-range vibriophage forming plaques on strains of at least eight Vibrio and one Photobacterium species. A spontaneous KVP40-resistant mutant, R4000, derived from Vibrio parahaemolyticus 1010 lacked a 26-kDa outer membrane protein designated OmpK. KVP40 was inactivated by outer membrane and OmpK prepared from 1010, but not by outer membrane from R4000. These results strongly suggest that OmpK is the receptor for KVP40. Immunoblotting analyses using an anti-OmpK rabbit serum revealed that OmpK or its homologs of molecular masses 25-29 kDa were distributed widely among Vibrio and Photobacterium strains including those naturally resistant to KVP40.

Adsorption↗

Transformation of Actinomyces spp. by a gram-negative broad-host-range plasmid.

The gram-negative broad-host-range vector pJRD215 was transferred by electroporation into strains of Actinomyces viscosus or Actinomyces naeslundii at efficiencies which ranged from 10(2) to 10(7) transformants per microgram of plasmid DNA. The Actinomyces transformants expressed pJRD215-encoded resistance to kanamycin and streptomycin. Moreover, the transforming plasmid DNA had not undergone any deletions or rearrangements, nor had it integrated into the genomes of these strains.

Actinomyces↗

Integration and expression of viral DNA in cells transformed by host range mutants of adenovirus type 5.

Group I host range (hr) mutants of adenovirus type 5 are unable to transform rat embryo or rat embryo brain cells but induce an abnormal transformation of baby rat kidney cells. We established several transformed rat kidney cell lines and characterized them with respect to the transformed phenotype and the structure of the integrated viral DNA. The hr mutant-transformed cells, unlike wild-type virus transformants, were fibroblastic rather than epithelial, failed to grow in soft agar, and were also less tumorigenic in nude mice. Studies on the structure of the integrated viral DNA sequences showed that hr-transformed cells always contained the left end of the adenovirus DNA, but the size of the integrated DNA fragment varied among different lines, and a high percentage of the lines contained the entire viral genome colinearly integrated. The patterns of integration were maintained after prolonged growth in culture and after subcloning. Attempts to rescue infectious virus from lines which contained the entire genome were unsuccessful. Using immunoprecipitation and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, we analyzed the viral proteins expressed in hr-transformed cells. Results of these studies indicated that, like wild type-transformed cells, hr transformants expressed E1B proteins of molecular weight 58,000 and 19,000.

Adenoviridae↗

Broad host range cosmid pLAFR1 and non-mucoid mutant XCP20 provide a suitable vector-host system for cloning genes in Xanthomonas campestris pv. campestris.

For many gram-negative bacteria, whose transformation systems have yet developed, following a two stage manipulation for gene cloning is a common choice. Following this strategy, DNAs are cloned in Escherichia coli, using a mobilizable vector, and the recombinant plasmids conjugally transferred into the original host. In this study, transfer of the broad-host range plasmid pLAFR1 (a 21.6 kb cosmid, TcR, derived from RK2 replicon) from E. coli to Xanthomonas campestris pv. campestris, by the help of plasmid pRK2013, was carried out to optimize the working conditions for gene cloning experiments in this phytopathogenic bacterium. Among several mating procedures tested, the highest frequencies of transfer were found by dropping the mixtures of the donor, helper and recipient cells (at ratios 1:1:10) to a nitrocellulose filter on an agar plate, with all the cells used from the cultures between OD550 0.3 to 0.5. When the non-mucoid mutant P20 was used as the recipient instead of its parental mucoid strain XC11A, 14-fold more transconjugants were obtained. In addition, the plasmid was found to be quite stable in the X. campestris cells. Further experiments showed that pLTA1, which is pLAFR1 with a cloned DNA fragment (4.4 kb) encoding alpha-amylase activity from XC11A, was not only maintained stably but also found to contribute a 8.3-fold over-production of enzyme activity to the transconjugant cells. From these studies, it has been demonstrated that cosmid pLAFR1 and the non-mucoid mutant P20 together provide a suitable vector/host system for cloning genes in X. campestris.

Cloning, Molecular↗

Characterization of host-range mutants of cyanophage N-1.

Fifteen host-range (h) mutants of cyanophage N-1 were characterized with reference to their efficiency of plating, time of appearance, morphology and size of plaques on Nostoc muscorum and its three phage-resistant (Nm 1/N-1, Nm 2/N-1 and Nm 8/N-1) mutants. While phage N-1 did not adsorb to the three phage-resistant mutants, the h mutants differed one from the other in having lower or higher adsorption rate constants on N. muscorum or the phage-resistant mutants. The inability of majority of h mutants isolated on Nm 1/N-1 to grow in Nm 8/N-1 was shown to be due to a failure of adsorption. The h mutants also differed one from the other in their reversion (back mutation) frequencies. The lethal doses (LD37) required to kill 37% of free phage particles after UV-irradiation, heating and ethylenediamine tetraacetate (EDTA) treatment greatly varied. Most of the h mutants were found to be considerably more sensitive to UV and thermic inactivation than N-1 while they were resistant to EDTA. The h mutants except five of them were unable to multiply at 40 degrees C. The significance of these features is discussed.

Bacteriophages↗

Adaptation of chimeric retroviruses in vitro and in vivo: isolation of avian retroviral vectors with extended host range.

We have designed and characterized two new replication-competent avian sarcoma/leukosis virus-based retroviral vectors with amphotropic and ecotropic host ranges. The amphotropic vector RCASBP-M2C(797-8), was obtained by passaging the chimeric retroviral vector RCASBP-M2C(4070A) (6) in chicken embryos. The ecotropic vector, RCASBP(Eco), was created by replacing the env-coding region in the retroviral vector RCASBP(A) with the env region from an ecotropic murine leukemia virus. It replicates efficiently in avian DFJ8 cells that express murine ecotropic receptor. For both vectors, permanent cell lines that produce viral stocks with titers of about 5 x 10(6) CFU/ml on mammalian cells can be easily established by passaging transfected avian cells. Some chimeric viruses, for example, RCASBP(Eco), replicate efficiently without modifications. For those chimeric viruses that do require modification, adaptation by passage in vitro or in vivo is a general strategy. This strategy has been used to prepare vectors with altered host range and could potentially be used to develop vectors that would be useful for targeted gene delivery.

Animals↗

Complete genome sequence of the broad-host-range vibriophage KVP40: comparative genomics of a T4-related bacteriophage.

The complete genome sequence of the T4-like, broad-host-range vibriophage KVP40 has been determined. The genome sequence is 244,835 bp, with an overall G+C content of 42.6%. It encodes 386 putative protein-encoding open reading frames (CDSs), 30 tRNAs, 33 T4-like late promoters, and 57 potential rho-independent terminators. Overall, 92.1% of the KVP40 genome is coding, with an average CDS size of 587 bp. While 65% of the CDSs were unique to KVP40 and had no known function, the genome sequence and organization show specific regions of extensive conservation with phage T4. At least 99 KVP40 CDSs have homologs in the T4 genome (Blast alignments of 45 to 68% amino acid similarity). The shared CDSs represent 36% of all T4 CDSs but only 26% of those from KVP40. There is extensive representation of the DNA replication, recombination, and repair enzymes as well as the viral capsid and tail structural genes. KVP40 lacks several T4 enzymes involved in host DNA degradation, appears not to synthesize the modified cytosine (hydroxymethyl glucose) present in T-even phages, and lacks group I introns. KVP40 likely utilizes the T4-type sigma-55 late transcription apparatus, but features of early- or middle-mode transcription were not identified. There are 26 CDSs that have no viral homolog, and many did not necessarily originate from Vibrio spp., suggesting an even broader host range for KVP40. From these latter CDSs, an NAD salvage pathway was inferred that appears to be unique among bacteriophages. Features of the KVP40 genome that distinguish it from T4 are presented, as well as those, such as the replication and virion gene clusters, that are substantially conserved.

Bacteriophage T4↗

Structural analysis of a mutation in canine parvovirus which controls antigenicity and host range.

A single mutation in canine parvovirus (CPV) of VP2 residue 300 from alanine to aspartic acid causes a loss of canine host range and alters the antigenic properties of the virus. The three-dimensional structure of this mutant has been solved to 3.25 A resolution. Crystals of full particles were triclinic, with cell dimensions of a = 267.6, b = 268.5, c = 274.3 A. alpha = 61.9, beta = 62.6, and gamma = 60.2 degrees. The native structure of CPV was used as an initial model. Phases were improved by real-space electron density averaging. In spite of the relative low percentage of observed reflections (32.5% of the data between 15.0 and 3.25 A resolution), the presence of 60-fold noncrystallographic redundancy allowed the averaging procedure to converge smoothly. The mutant aspartic acid at residue 300 forms a salt bridge with Arg81 in an icosahedrally threefold-related subunit, inducing local changes within the antigenic site B on the CPV surface. In addition, the loop between residues 359 and 374 adopts a conformation similar to that displayed by feline panleukopenia virus. The ability of the Ala300-->Asp mutant to evade antibody binding can be associated with the change of charge distribution and structure in the antigenic binding site. The variation in host range behavior may be due to the increased stability as a result of formation of the salt bridge between adjacent subunits.

Animals↗

Mapping of host range restriction of the rakkyo strain of tobacco mosaic virus in Nicotiana tabacum cv. bright yellow.

The rakkyo strain (TMV-R) and the common strain (TMV-U1) of tobacco mosaic virus exhibit distinct host range differences. TMV-R infects rakkyo plants, a monocot host that TMV-U1 is unable to infect. However, TMV-R causes only latent infection in Nicotiana tabacum cv. Bright Yellow (BY) in inoculated leaves, whereas TMV-U1 infects BY systemically and induces mosaic symptoms. Complete nucleotide sequencing of the TMV-R genomic RNA revealed amino acid changes in the 130K/ 180K replicase proteins, the 30K protein, and the coat protein and nucleotide changes in the 5' and 3' noncoding regions compared to TMV-U1. To identify viral components involved in determination of differences in host range, we have mapped determinants for the differential infection phenotype in BY plants by constructing chimeric viruses between the two strains in the present study. Examination of the infection phenotypes of the 14 constructed chimeric viruses in BY showed that determinants defining the differential infection phenotype in BY reside in the 130K/180K replicase proteins and the 3' noncoding region. Cognate combination of the 130K/180K replicase proteins and the 3' noncoding region of TMV-U1 origin is required to produce systemic infection in BY plants.

DNA-Directed DNA Polymerase↗

The Rhizobium meliloti host range nodQ gene encodes a protein which shares homology with translation elongation and initiation factors.

The Rhizobium meliloti nod region IIb is involved in host-range determination: (i) the presence of region IIb is necessary for transfer of alfalfa root hair curling ability to Rhizobium leguminosarum biovar trifolii; (ii) a mutation in region IIb extends the R. meliloti infection host range to Vicia sativa nigra; (iii) dominance of R. meliloti nod genes over R. leguminosarum biovar viciae nod genes is abolished by mutations in region IIb. The nucleotide sequence of this region has been determined. Genes corresponding to the two open reading frames identified are designated nodP and nodQ. The predicted amino acid sequence of the NodQ protein shows homology with translation initiation and elongation factors. The consensus sequence involved in the GTP-binding domain is conserved.

Amino Acid Sequence↗

Broad-host-range plasmid pJB658 can be used for industrial-level production of a secreted host-toxic single-chain antibody fragment in Escherichia coli.

In industrial scale recombinant protein production it is often of interest to be able to translocate the product to reduce downstream costs, and heterologous proteins may require the oxidative environment outside of the cytoplasm for correct folding. High-level expression combined with translocation to the periplasm is often toxic to the host, and expression systems that can be used to fine-tune the production levels are therefore important. We previously constructed vector pJB658, which harbors the broad-host-range RK2 minireplicon and the inducible Pm/xylS promoter system, and we here explore the potential of this unique system to manipulate the expression and translocation of a host-toxic single-chain antibody variable fragment with affinity for hapten 2-phenyloxazol-5-one (phOx) (scFv-phOx). Fine-tuning of scFv-phOx levels was achieved by varying the concentrations of inducers and the vector copy number and also different signal sequences. Our data show that periplasmic accumulation of scFv-phOx leads to cell lysis, and we demonstrate the importance of controlled and high expression rates to achieve high product yields. By optimizing such parameters we show that soluble scFv-phOx could be produced to a high volumetric yield (1.2 g/liter) in high-cell-density cultures of Escherichia coli.

Biotechnology↗