WT Phenotype Research Articles

Mapping the rubella virus subgenomic promoter.

Rubella virus (RUB), the sole member of the Rubivirus genus in the Togaviridae family of positive-strand RNA viruses, synthesizes a single subgenomic (SG) RNA containing sequences from the 3' end of the genomic RNA including the open reading frame (ORF) that encodes the virion proteins. The synthesis of SG RNA is initiated internally on a negative-strand, genome-length template at a site known as the SG promoter (SGP). Mapping the RUB SGP was initiated by using an infectious cDNA vector, dsRobo402/GFP, in which the region containing the SGP was duplicated (K. V. Pugachev, W.-P. Tzeng, and T. K. Frey, J. Virol. 74:10811-10815, 2000). In dsRobo402/GFP, the 5'-proximal nonstructural protein ORF (NS-ORF) is followed by the first SGP (SGP-1), the green fluorescent protein (GFP) gene, the second SGP (SGP-2), and the structural protein ORF. The duplicated SGP, SGP-2, contained nucleotides (nt) -175 to +76 relative to the SG start site, including the 3' 127 nt of the NS-ORF and 47 nt between the NS-ORF and the SG start site. 5' Deletions of SGP-2 to nt -40 (9 nt beyond the 3' end of the NS-ORF) resulted in a wild-type (wt) phenotype in terms of virus replication and RNA synthesis. Deletions beyond this point impaired viability; however, the analysis was complicated by homologous recombination between SGP-1 and SGP-2 that resulted in deletion of the GFP gene and resurrection of viable virus with one SGP. Since the NS-ORF region was not necessary for SGP activity, subsequent mapping was done by using both replicon vectors, RUBrep/GFP and RUBrep/CAT, in which the SP-ORF is replaced with the reporter GFP and chloramphenical acetyltransferase genes, respectively, and the wt infectious clone, Robo402. In the replicon vectors, 5' deletions to nt -26 resulted in the synthesis of SG RNA. In the infectious clone, deletions through nt -28 gave rise to viable virus. A series of short internal deletions confirmed that the region between nt -28 and the SG start site was essential for viability and showed that the repeated UCA triplet at the 5' end of SG RNA was also required. Thus, the minimal SGP maps from nt -26 through the SG start site and appears to extend to at least nt +6, although a larger region is required for the generation of virus with a wt phenotype. Interestingly, while the positioning of the RUB SGP immediately adjacent the SG start site is thus similar to that of members of the genus Alphavirus, the other genus in the Togaviridae family, it does not include a region of nucleotide sequence homology with the alphavirus SGP that is located between nt -48 and nt -23 with respect to the SG start site in the RUB genome.

Contribution of the human parainfluenza virus type 3 HN-receptor interaction to pathogenesis in vivo.

The envelope of human parainfluenza virus type 3 (HPF3) contains two viral glycoproteins, the hemagglutinin-neuraminidase (HN) protein and the fusion (F) protein. In a previous study, highly fusogenic variant HPF3 viruses were isolated, including two, C-0 and C-22, that exhibit increased avidity for sialic acid receptors due to single amino acid changes in the HN protein and one, C-28, that has decreased neuraminidase activity relative to that of the wild type (wt) and is delayed in the release of virus particles into the supernatant fluid. These variants form very large plaques and destroy a cell monolayer more rapidly than does wt HPF3 in cell culture. These variant viruses allowed us to formulate hypotheses about the roles of HN in pathogenesis. We investigated the behavior of wt HPF3 and the three variant viruses in the cotton rat model. In the cotton rat, there was no delayed clearance of any of the variant viruses compared to that of the wt. The variant plaque morphology was preserved in vivo, and there was no reversion to the wt phenotype in the infected animals. In spite of a slight advantage of wt virus in viral titer, there were no differences in the severities of peribronchiolitis between wt viruses and the variants. However, there were marked differences in severities in alveolitis and interstitial pneumonitis when each of the three variants was compared to the wt, with the variants causing enhanced disease. Thus, despite similar or lower viral titers and similar clearance rates, the variants caused more extensive disease in the lung. The results show that mutations in HN conferring altered fusion properties in cell culture also confer striking differences in the ability of HPF3 to cause extensive disease in the cotton rat lung and that this effect is dissociated from any effect on viral replication.

The residues between the two transformation effector sites of Epstein-Barr virus latent membrane protein 1 are not critical for B-lymphocyte growth transformation.

Epstein-Barr virus (EBV) latent membrane protein 1 (LMP1) is essential for EBV-mediated transformation of primary B lymphocytes. LMP1 spontaneously aggregates in the plasma membrane and enables two transformation effector sites (TES1 and TES2) within the 200-amino-acid cytoplasmic carboxyl terminus to constitutively engage the tumor necrosis factor receptor (TNFR)-associated factors TRAF1, TRAF2, TRAF3, and TRAF5 and the TNFR-associated death domain proteins TRADD and RIP, thereby activating NF-kappaB and c-Jun N-terminal kinase (JNK). To investigate the importance of the 60% of the LMP1 carboxyl terminus that lies between the TES1-TRAF and TES2-TRADD and -RIP binding sites, an EBV recombinant was made that contains a specific deletion of LMP1 codons 232 to 351. Surprisingly, the deletion mutant was similar to wild-type (wt) LMP1 EBV recombinants in its efficiency in transforming primary B lymphocytes into lymphoblastoid cell lines (LCLs). Mutant and wt EBV-transformed LCLs were similarly efficient in long-term outgrowth and in regrowth after endpoint dilution. Mutant and wt LMP1 proteins were also similar in their constitutive association with TRAF1, TRAF2, TRAF3, TRADD, and RIP. Mutant and wt EBV-transformed LCLs were similar in steady-state levels of Bcl2, JNK, and activated JNK proteins. The wt phenotype of recombinants with LMP1 codons 232 to 351 deleted further demarcates TES1 and TES2, underscores their central importance in B-lymphocyte growth transformation, and provides a new perspective on LMP1 sequence variation between TES1 and TES2.

Intraclonal polymorphism in the bacterium Streptomyces ambofaciens ATCC23877: evidence for a high degree of heterogeneity of the wild type clones

In Streptomyces ambofaciens a genetic instability generates a high degree of polymorphism consisting of four main phenotypes: pigmented colonies (Pig + qualified as WT phenotype), pigment-defective colonies, pigmented colonies with pigment-defective sector and pigmented colonies with pigment-defective papillae. Molecular analysis of Pig col − and Pig sec − (pigment-defective mutant derived from a colony and a sector, respectively) produced by genetic instability and isolated in five Pig + subclones progenies revealed a new aspect of polymorphism in S. ambofaciens ATCC23877. Frequencies of Pig col − and Pig sec − mutants deleted at the chromosome ends varied from one WT progeny to another. Two main types of deleted mutants were observed: deleted for one or both chromosomal extremities. The relative proportion of these two categories differed according to the WT progeny. These results argue for heterogeneity of the WT clones, i.e., Pig + colonies, originated from S. ambofaciens ATCC23877.

The Deinococcus radiodurans uvrA gene: identification of mutation sites in two mitomycin-sensitive strains and the first discovery of insertion sequence element from deinobacteria

Deinococcus radiodurans ( Dr) possesses a prominent ability to repair the DNA injury induced by various DNA-damaging agents including mitomycin C (MC), ultraviolet light (UV) and ionizing radiation. DNA damage resistance was restored in MC sensitive (MC S) mutants 2621 and 3021 by transforming with DNAs of four cosmid clones derived from the gene library of strain KD8301, which showed wild type (wt) phenotype to DNA-damaging agents. Gene affected by mutation ( mtcA or mtcB) in both mutants was cloned and its nucleotide (nt) sequence was determined. The deduced amino acid (aa) sequence of the gene product consists of 1016 aa and shares homology with many bacterial UvrA proteins. The mutation sites of both mutants were identified by analyzing the polymerase chain reaction (PCR) fragments derived from the genomic DNA of the mutants. A 144-base pair (bp) deletion including the start codon for the uvrA gene was observed in DNA of the mutant 3021, causing a defect in the gene. On the other hand, an insertion sequence (IS) element intervened in the uvrA gene of the mutant 2621, suggesting the insertional inactivation of the gene. The IS element comprises 1322-bp long, flanked by 19-bp inverted terminal repeats (ITR), and generated a 6-bp target duplication (TD). Two open reading frames (ORFs) were found in the IS element. The deduced aa sequences of large and small ORFs show homology to a putative transposase found in IS 4 of Escherichia coli ( Ec) and to a resolvase found in IS Xc5 of Xanthomonas campestris ( Xc), respectively. This is the first discovery of IS element in deinobacteria, and the IS element was designated IS 2621.

Sequence of a novel virulence-mediating gene, virC, from Vibrio anguillarum

Previously, the double-transposon (Tn) mutant VAN20 of Vibrio anguillarum (Va) 775.17B was isolated. This mutant lacked a major surface antigen (MSA) suggested to be a lipopolysaccharide (LPS) and showed a 10 5-fold increase in the 50% lethal dose (LD 50) when fish were infected intraperitoneally. In this study, the two Tn insertion sites within the chromosome were identified, a plasmid insertion mutation was made at each locus in a more virulent strain of Va, NB10, and the virulence was analyzed. One mutant displayed a 10 4-fold increase in LD 50, whereas the second mutant showed the wild-type (wt) phenotype. However, both mutants still expressed the MSA, suggesting that there may be more than two Tn insertions in VAN20 or that a double mutation is required to prevent production of the MSA. The DNA locus for the virulent phenotype was cloned and sequenced. A potential transcriptional unit consisting of three putative open reading frames (ORFs) was identified. The Tn was located in the second ORF, virC (virulence). The first ORF (34.8 kDa) showed 30% homology to the Escherichia coli and Salmonella typhimurium cysG (cysteine) genes. The virC gene (51.4 kDa) and the third ORF (24 kDa) showed no homology to other proteins in GenBank. Plasmid insertion mutants were made within each of these ORFs and the virulence was assayed. Only the virC mutant showed a loss in virulence, indicating that virC is a novel gene that is essential for the virulence of Va.

Ac/Ds transposon mutagenesis in Arabidopsis thaliana: mutant spectrum and frequency of Ds insertion mutants.

Using a two-component Ac/Ds system consisting of a stabilized Ac element (Acc1) and a non-autonomous element (DsA), 650 families of plants carrying independent germinal DsA excisions/transpositions were isolated. Progenies of 559 of these Acc1/DsA families, together with 43 families of plants selected for excision/transposition of wild-type (wt) Ac, were subjected to a broad screening program for mutants exhibiting visible alterations. This resulted in the identification of 48 mutants showing a wide variety of mutant phenotypes, including embryo lethality (24 mutants), chlorophyll defects (5 mutants), defective seedlings (2 mutants), reduced fertility (5 mutants), reduced size (3 mutants), altered leaf morphology (2 mutants), dark green, unexpanded rosette leaves (3 mutants), and aberrant flower or shoot morphology (4 mutants). To whether these mutants were due to transposon insertions, a series of Southern blot experiments was performed on 28 families, comparing in each case several mutant plants with others showing the wild-type phenotype. A preliminary analysis revealed in 4 of the 28 families analyzed a common, novel DsA fragment in all mutant plants, which was present only in heterozygous plants with wt phenotype, as expected for DsA insertion mutations. These four mutants included two showing embryo lethality, one with dark green, unexpanded rosette leaves and stunted inflorescences, and one with curly growth of stems, leaves and siliques. Further evidence for DsA insertion mutations was obtained for one embryo lethal mutant and for the stunted mutant, while in case of the second embryo lethal mutant, the DsA insertion could be separated from the mutant locus by genetic recombination.

Amino Acid Changes in the L Polymerase Protein of Vesicular Stomatitis Virus Which Confer Aberrant Polyadenylation and Temperature-Sensitive Phenotypes

TsG16(I) is a temperature-sensitive mutant of vesicular stomatitis virus . In vitro, at the permissive temperature (31°), it makes long poly(A) tracts, shows a larger increase in polyadenylation in the presence of S-adenosyl-homocysteine than its parental wt(Glasgow) virus, and makes an excess of polycistronic mRNA. In vitro transcription is also more thermosensitive than that of wt virus. Previous work suggested that there are at least two mutations in the L gone of tsG16(I), one effecting the poly(A)-associated phenotypes, the polycistronic phenotype, and the ability to grow at 34.7°, the other affecting in vitro thermosensitivity for transcription and ability to grow at 37°. We report further characterization of two revertants: 35G16p25, which grows at 34.7° and has regained the wt poly(A), SAH and polycistronic RNA phenotypes; and 37G16p25, isolated from 35G16p25 based on growth at 37°, which has regained the wt phenotype for in vitro thermosensitivity of transcription. Both revertants were shown to be due to intracistronic reversion[s] in the L gene. Sequencing of the L genes indicated that the ts G16(I) poly(A), SAH, polycistronic RNA, and growth at 34.7° phenotypes were associated with amino acid 1488 phenylalanine → serine and that transcription thermosensitivity and growth at 37° were associated with changes in cysteine 1291.

Carbohydrate cycling in signal transduction: parafusin, a phosphoglycoprotein and possible Ca(2+)-dependent transducer molecule in exocytosis in Paramecium.

Parafusin, a cytosolic phosphoglycoprotein of M(r) 63,000, is dephosphorylated and rephosphorylated rapidly in a Ca(2+)-dependent manner upon stimulation of exocytosis in vivo in wild-type (wt) Paramecium. In contrast, the temperature-sensitive exocytosis mutant nd9, grown at the nonpermissive temperature (27 degrees C), does not exocytose or dephosphorylate parafusin upon stimulation in the presence of Ca2+; grown at the permissive temperature (18 degrees C), nd9 cells show a wt phenotype. Parafusin contains two types of phosphorylation sites: one where glucose 1-phosphate is added by an alpha-glucose-1-phosphate phosphotransferase and removed by a phosphodiesterase and one where phosphate from ATP is added directly to a serine residue by a protein kinase and removed by a phosphatase. We show here that, in cell fractions from wt Paramecium, both reactions can be carried out in vitro by using uridine(5'-[beta-[35S]thio])diphospho(1)-glucose (UDP[beta 35S]-Glc) and [gamma-32P]ATP, respectively. The characteristics of these pathways are different. Specifically, in the presence of Ca2+, the amount of UDP[beta 35S]-Glc label in parafusin is reduced. In contrast, identical labeling experiments with [gamma-32P]ATP show that Ca2+ enhances labeling of parafusin. Mg2+ had no appreciable effect on either labeling. Removal of the UDP[beta 35S]-Glc label on parafusin in the presence of Ca2+ correlates with the in vivo dephosphorylation seen upon exocytosis. Incubations with UDP[beta 35S]-Glc were then performed with homogenates and nd9 cell fractions grown at 27 degrees C under the ionic conditions used for wt cells. These labelings were not affected by Ca2+, in contrast to results from wt cells but in accord with those obtained earlier with nd9-27 mutant cells in vivo. Factors responsible for both dephosphorylation and Ca2+ sensitivity were found in the high-speed pellet (P2) in wt cells, suggesting that the putative phosphodiesterase is in this fraction and that the defect in the mutant nd9-27 residues in the Ca2+ activation of the phosphodiesterase. We conclude that the in vivo dephosphorylation of parafusin that occurs upon exocytosis is a dephosphoglucosylation due to removal of the alpha-glucose 1-phosphate and more generally that carbohydrates on cytoplasmic glycoproteins may be cyclically added and/or removed in response to extracellular stimuli.

Revertants of a mutant of vesicular stomatitis virus which has an aberrant polyadenylation activity and a temperature-sensitive transcriptase

tsG16(I), a temperature-sensitive mutant of vesicular stomatitis virus, in vitro has at least three phenotypic differences from its parental wild-type ( wt) virus due to mutation of the L gene. It was not known whether (i) the temperature sensitivity of the transcriptase, (ii) the aberrant polyadenylation phenotype, and (iii) the extent of increased polyadenylation in response to S-adenosylhomocysteine (SAH) were associated with a single mutation. Spontaneous partial revertants were selected from tsG16(I) on the basis of the ability to form plaques at 34.7° (351316 revenants) or from 35G16 revertants on the basis of the ability to form plaques at 37° (371316 revenants). All six 351316 revertants had fully (five) or partially (one) recovered the wt polyadenylation phenotype and the former five had also fully recovered the wt polyadenylation response to SAH. This suggested that a single mutation in tsG16(I) was probably associated with both of these phenotypes and also probably conferred the inability to grow at 34.7°. None of the 351316 revertants regained the wt phenotype for thermosensitivity of the transcriptase, although both of the 371316 revenants did. This suggested that in vitro temperature-sensitivity of transcription by tsG16(I) might be due to a mutation different than the one affecting polyadenylation in the absence or presence of SAH.

Genetic analysis of in vivo-selected viral variants causing chronic infection: importance of mutation in the L RNA segment of lymphocytic choriomeningitis virus.

Viral variants with different biological properties are present in the central nervous systems (CNS) and lymphoid tissues of mice persistently infected with lymphocytic choriomeningitis virus (LCMV). Viral isolates from the CNS are similar to the original Armstrong LCMV strain and induce potent virus-specific T-cell responses in adult mice, and the infection is rapidly cleared. In contrast, LCMV isolates derived from spleens of carrier mice cause persistent infections in adult mice. This chronic infection is associated with low levels of antiviral T-cell responses. In this study, we genetically characterized two independently derived spleen variants by making recombinants (reassortants) between the spleen isolates and wild-type (wt) LCMV and showed that the ability to persist in adult mice and the associated suppression of T-cell responses segregates with the large (L) RNA segment. In addition, we analyzed a revertant (isolated from the CNS) derived from one of the spleen variants. By comparing the biological properties of three reassortants that contained the same S segment but had the L segment of either the original wt Armstrong LCMV, the spleen variant derived from it, or the CNS revertant derived from the spleen variant, we were able to show unequivocally that biologically relevant mutations occurred in the L segment not only during generation of the spleen variant from wt LCMV but also in reversion of the spleen variant to the wt phenotype. Thus, our results showed that (i) genetic alterations in the L genomic segment were involved in organ-specific selection of viral variants, and (ii) these mutations profoundly affected the ability of LCMV to cause chronic infections in adult mice.

Developmental control of the excitability of muscle: transplantation experiments on a myotonic mouse mutant.

Developmental aspects of an animal model of myotonia, the mouse mutant called "arrested development of righting response" (ADR phenotype), were studied. Adult ADR muscle is characterized by a low chloride conductance of the membrane, leading to hyperexcitability, and by a low parvalbumin content. The myotonic hyperexcitability (as measured by the extent of "aftercontractions") of ADR muscle increased steeply between postnatal days 9 and 18, by which time it had approached the adult level. To study the tissue autonomy of the myotonic phenotype, muscle grafts were performed in all four combinations between ADR and wildtype (WT phenotype) donors and hosts. In most experiments, the relative contributions of donor and host to the regenerated muscles were determined by an allelic marker (glucose phosphate isomerase). In WT and ADR hosts, ADR grafts showed myotonic responses that in WT nude mouse hosts were incomplete and similar to those of juvenile ADR muscle. In no case did grafts from WT donors show any myotonia. This shows that the myotonic ADR phenotype is based on an intrinsic muscle property most likely related to the plasma membrane. The parvalbumin contents of grafted muscles, when compared with those of untransplanted muscles, indicated graft-host interaction in the expression of this secondary phenotypic property.

Alfalfa mosaic virus temperature-sensitive mutants IV. Tbts 7, a coat protein mutant defective in an early function

Tbts 7 is coat protein mutant of alfalfa mosaic virus (AIMV) which replicates in tobacco leaf disks at 23° but not at 30°, whereas the wild-type (wt) replicates at both temperatures. To analyze the temperature-sensitive step in virus multiplication, the replication of Tbts 7 in protoplasts was investigated. The data indicated that poly- l-ornithine (PLO), when present in the inoculum, selectively interfered with the uncoating in cowpea protoplasts of the mutant virions containing RNA 3 (top component b, Tb) whereas uncoating of virions containing RNAs 1 and 2 was not noticably affected. When PLO in the inoculum was replaced by polyethylene glycol (PEG), Tbts 7 was able to replicate in cowpea and in tobacco protoplasts at 25° but not at 30°. At the restrictive temperature the replication of mutant RNA 3 was selectively defective. An infection induced by an inoculum containing a mixture of Tbts 7 genomic RNAs and wt coat protein was similarly temperature sensitive in RNA synthesis, indicating that a defect in uncoating of Tb is not responsible for the temperature-sensitive behavior. Addition of wild-type Tb to a Tbts 7 inoculum restored the wt phenotype. Under these conditions, at both 25 and 30°, only wt RNA 3 was replicated and not the mutant RNA 3 present in the inoculum. The results are discussed in respect of the early function of AIMV coat protein in the virus replication cycle.

An alfalfa mosaic virus RNA 2 mutant, which does not induce a hypersensitive reaction in cowpea plants, is multiplied to a high concentration in cowpea protoplasts

A mutant of alfalfa mosaic virus (AMV), which in contrast to wild type (wt) can invade cowpea plants systemically, is replicated more efficiently in cowpea protoplasts than the wt. Mutant preparations isolated from infected cowpea protoplasts contained a higher amount of middle component (M, containing RNA 2) than wt preparations. Both in cowpea plants and in cowpea protoplasts a wt phenotype is obtained upon addition of wt M to this mutant, suggesting a correlation between the type of plant reaction evoked by the virus infection and the regulation of viral RNA synthesis.

Complementation analysis of hormone-sensitive adenylate cyclase

PLASMA membranes of most animal cells respond to specific hormonal signals by synthesising adenosine 3′,5′ cyclic monophosphate (cyclic AMP) from ATP, a reaction catalysed by adenylate cyclase. The precise molecular basis of this membrane response has not been defined. In particular, we do not know the number of molecular species required for transduction of hormonal signals into stimulation of cyclic AMP synthesis. Catalytic adenylate cyclase and specific hormone binding activities can be separated on the basis of their physical properties1–3. However, hormonal stimulation may require one or more other molecules necessary for coupling the two activities in membranes. One of these may contain a guanyl nucleotide regulatory site, as guanyl trinucleotides are strictly required for hormonal stimulation of cyclase in several membrane systems4–8. Genetic complementation analysis can help to define the minimum number of gene products involved in a complex biochemical function. Although subject to qualifications, the principle is simple : if a cross between two mutant cells bearing a recessive phenotype fails to reconstitute the wild-type (WT or normal) phenotype, both mutant parental cells must bear a lesion in a common gene product; if the cross produces a WT phenotype, the two parental mutations must affect different gene products. Here we apply this method of analysis to the hormone-sensitive cyclase system of the S49 lymphoma tissue culture line, in which two distinct classes of variant clones with stable deficiencies in hormonal stimulation of cyclase have been selected9–10. We have constructed viable hybrid clones by crossing each of these variants with WT, and with each other. We describe the resulting hybrid phenotypes and their implications regarding the molecular components of hormone-sensitive adenylate cyclase.

RNA- temperature-sensitive mutants of vesicular stomatitis virus: L-protein thermosensitivity accounts for transcriptase restriction of group I mutants

In vitro transcriptase activity of three group I temperature-sensitive (ts) mutants of vesicular stomatitis virus restricted at 39 C was restored by L-protein fractions derived from wild-type (wt) vesicular stomatitis virion nucleo-capsids. Soluble NS protein from wt nucleocapsids did not reconstitute restricted transcriptions of the group I RNA-ts mutants. NS protein activity, but not L protein activity, was purified from the group I ts mutants; this NS fraction always displayed the wt phenotype in reconstitution assays. Neither the L nor the NS protein was capable of restoring the defective transcriptive activity of the group IV vesicular stomatitis virus mutant ts W16B.