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Definitions of “species” and “type species” have been problematic in the taxonomy of different types of biological organisms. For virus taxonomy, the problems have been addressed by the International Committee on Taxonomy of Viruses (ICTV) and the results are compiled in The International Code of Virus Taxonomy and Nomenclature [4, 8]. The Code defines a virus species as a polythetic class of viruses that constitutes a replicating lineage and occupies a particular ecological niche. The application of this definition to virus taxonomy has been reviewed by van Regenmortel [7]. However, although the rules and procedures of virus taxonomy have referred to “type species” in connection with descriptions of genera for a number of years, the virus “type species” has not been explicitly defined. The requirement for virus type species arises from two sections of The Code [4.8]

Bacterial viruses have been classified into 13 families and 1 unassigned genus. A new order, Caudovirales, has now been established, comprising the three families of tailed bacterial viruses, based on similarities in tailed virus morphology, replication, and assembly. In addition, genera have been established for some species in each tailed virus family, based on properties involving viral DNA replication and packaging, and on some features specific to particular genera (e.g., DNA-termini linked proteins, virus-encoded polymerases, and ability to establish temperate infections). At present, there are six genera in the family Myoviridae (viruses with contractile tails), six in the family Siphoviridae (viruses with long, noncontractile tails), and three in the family Podoviridae (viruses with short noncontractile tails). In recognition that the definitions of tailed virus genera represent a “work in progress” and to keep the nomenclature flexible, tailed virus genera have been assigned vernacular names based on their type species.

A recently proposed polythetic definition of virus species appears easily applicable to bacteriophages. Criteria for classification of tailed phages are evaluated. Morphology, DNA homology, and serology are the most important criteria for delineation of species, but no single criterion is satisfactory. Dot-blot hybridization and seroneutralization may suggest false relationships by detecting common sequences in the DNA of otherwise unrelated phages. Species of tailed phages can be defined by a combination of morphology and DNA homology or serology. A procedure for identification of novel phages is outlined. Phage names should include elements of host names.

Microorganisms that cannot be grown in the laboratory can now be tentatively identified, by cloning and sequencing particular nucleic acid segments and then carrying out a comparative sequence analysis with an appropriate database. For bacteria, a few universally distributed genes and gene products have enabled comparative sequence analysis to be used for tentative identification and classification of uncultured bacteria. For viruses, there is no universally distributed viral gene or gene product. However, in a few cases, viruses that could not be propagated in the laboratory have been identified and classified. In these cases, either the entire viral genome sequence was determined or partial sequence information was supplemented with additional data. The Executive Committee of the International Committee on Taxonomy of Viruses (ICTV) has reviewed the issue of identification and classification of viruses that have not been propagated. Under the ICTV system, formal review of any taxonomic proposal is carried out by the relevant ICTV Subcommittee or Study Group. The few examples of unpropagated viruses that have arisen thus far have been readily accommodated within existing viral taxonomy, with the international group of experts comprising each Subcommittee and Study Group determining the necessary and sufficient amount of information needed for classification of an unpropagated virus on a case-by-case basis.

Mycoplasma virus L3 virions are morphologically similar to coliphage T7, contain linear double-stranded DNA of about 39 kilobase pairs, and produce a nonlytic cytocidal infection in Acholeplasma laidlawii host cells. Following nitrous acid mutagenesis, ninety-eight L3 temperature-sensitive (ts) mutants were isolated from a total of 57,000 plaque-forming units (PFU), using 37 degrees C as the permissive temperature and 41 degrees C as the nonpermissive temperature, with reversion frequencies of 10(-5) to 10(-8). Complementation tests allowed fifty-seven of the L3 ts mutants to be placed into twenty-one complementation groups. In mixed infections, recombination frequencies between mutants in different complementation groups were 10(-2) to less than 10(-6). Studies of protein synthesis in L3-infected cells showed synthesis of about twenty virus-specific proteins, including ten L3 virion proteins. After infection with L3 ts mutants from each complementation group, several different patterns of cell- and virus-specific protein synthesis were observed.

Two taxonomically different bacteriophages have unintentionally been given the same name.Alteronomas phage PM2, isolated in 1968, is the type species of the family Corticoviridae, genus Corticovirus: lipid-containing, icosahedral viruses containing circular dsDNA.Aeromonas phage PM2, isolated in 1990, is a tailed virus, with contractile tail, and presumably a member of the family Myoviridae: phages with contractile tails, containing linear DNA. To avoid confusion, the name of Aeromonas phage PM2 is now changed to phage AehPM2.

The morphology of the amorphous, gelatinous, and crystalline varieties of monoclonal IgG cryoglobulins was analyzed by light and transmission and scanning electron microscopy. Each cryoglobulin had a characteristic fine structure that correlated with its gross morphology. Transmission electron microscopy showed that the amorphous precipitates were random and disorganized molecular clumps. In contrast, cryogels were thin-walled, well-organized, and hydrated strawlike clusters, whereas cryocrystals formed tightly compacted, highly structured molecular clusters. Crystals that formed in blood produced rouleaux, and analysis by scanning electron microscopy indicated that the crystals could form thick-walled, branching, macromolecular nets that could physically trap cells. The morphological properties provided visual impressions by which cryoglobulins could cause clinical disease secondary to vascular occlusion produced by self- associated IgG cryoglobulin molecules.

A pulse-labeling protocol has been used to study DNA replication and map replication origins and termini in mycoplasma viruses L2 and L2ins1. The L2 genome is circular, double-stranded DNA of 11.63 kilobase pairs (kb), and the 14.89-kb L2ins1 genome is L2 DNA containing a 3.26-kb insertion. The data show that DNA replication is bidirectional from two origins in L2 and three origins in L2ins1. The extra origin in L2ins1 arises from the fact that one of the L2 origins is in one of the sequences that have been shown to be duplicated and transposed in the generation of L2ins1 from L2.

The morphology of the amorphous, gelatinous, and crystalline varieties of monoclonal IgG cryoglobulins was analyzed by light and transmission and scanning electron microscopy. Each cryoglobulin had a characteristic fine structure that correlated with its gross morphology. Transmission electron microscopy showed that the amorphous precipitates were random and disorganized molecular clumps. In contrast, cryogels were thin-walled, well-organized, and hydrated strawlike clusters, whereas cryocrystals formed tightly compacted, highly structured molecular clusters. Crystals that formed in blood produced rouleaux, and analysis by scanning electron microscopy indicated that the crystals could form thick-walled, branching, macromolecular nets that could physically trap cells. The morphological properties provided visual impressions by which cryoglobulins could cause clinical disease secondary to vascular occlusion produced by self- associated IgG cryoglobulin molecules.

The phylogenetic relationships between the mycoplasmas and bacteria have been established from a comparative analysis of their 16S rRNA oligonucleotide catalogs. The genera Mycoplasma, Spiroplasma, and Acholeplasma arose by degenerative evolution, as a deep branch of the subline of clostridial ancestry that led to Bacillus and Lactobacillus. Thermoplasma has no specific relationship to the other mycoplasmas; it belongs with the archaebacteria.

MVL2, an enveloped double-stranded DNA mycoplasmavirus, causes a nonlytic infection of Acholeplasma laidlawii leading to the establishment of a persistent infection. Persistently infected clones were found to be resistant to superinfection by homologous virus, but could be infected by heterologous virus. Cells in a persistently infected culture had the potential to produce virus and transmitted this potential as a stable heritable trait. Mitomycin C and UV light induced an increase in infectious centers in persistently infected cultures.

L2 is a temperate mycoplasma virus containing 11.8 kilobase pairs of negatively superhelical double-stranded DNA. We observed L2 DNA with less superhelicity in novobiocin-treated cells than that in untreated cells. However, although no change in viral DNA superhelicity could be found in novobiocin-treated novobiocin-resistant cells, L2 production decreased in these novobiocin-treated cells.

Double-stranded DNA from mycoplasma virus L2 can transfect Acholeplasma laidlawii cells in the presence of polyethylene glycol (T. L. Sladek and J. Maniloff, J. Bacteriol. 155:734-741, 1983). We report here that both single-stranded DNA and double-stranded replicative form DNA, from the single-stranded DNA mycoplasma virus L51, are also infectious in this system. For both DNAs transfection frequencies were in the range of 10(-8) transfectants per DNA molecule and 10(-3) transfectants per CFU. An unexpected finding was that both DNAs could transfect A. laidlawii strain REP-, a variant which is a nonpermissive host for single-stranded DNA mycoplasma viruses due to a block in viral DNA replication (Nowak et al., J. Bacteriol. 127:832-836, 1976). The number of viruses produced by transfected REP- cells was comparable to the number produced by both transfected and infected wild-type cells. Therefore, transfected L51 DNAs are able to bypass the replication block in REP- cells that occurs when these cells are infected by L51 virions.

The replication of mycoplasmavirus MVL3 in Acholeplasma laidlawii K2 host cells was studied by analysis of infected-cell lysates using sedimentation in sucrose gradients and DNA-DNA hybridization. Viral DNA replication was found to involve intermediates sedimenting faster than free viral DNA, which is a linear, double-stranded molecule of about 26 x 10(6) daltons. After the shutdown of cellular DNA synthesis, viral DNA synthesis continued for many hours. The fate of cellular and parental viral DNAs was examined.

The kinetics of adsorption and growth of mycoplasmavirus MVL3 in Acholeplasma laidlawii 1305/68 host cells have been studied with one-step growth, premature lysis, and single-burst experiments. The virus was found to kill infected host cells. Virus release starts 90 min after infection and continues for about 10 to 15 h. Hence, virus production is unlike the classical lytic bacteriophages and instead resembles nonlytic cytocidal animal viruses. Structural details of the virus are described, and the molecular weight of the viral linear DNA has beenfound to be 26 x 10(6).

The growth of an enveloped DNA-containing mycoplasmavirus (MVL2 obtained from R.N. Gourlay) has studied, by using the indicator host Acholeplasma laidlawii strain JA1. From virus one-step growth curves, artificial lysis experiments, and infected cell growth curves, it was found that virus infection is nonlytic. Newly infected cells grow slower and are osmotically more stable than uninfected cells. However, 4 to 6 h after infection, the cells reach a carrier state in which cell growth rate and osmotic fragility are indistinguishable from uninfected cells. Carrier cultures contain free virus. Every carrier culture cell gives rise to either a clone of carrier cells or a clone of MVL2-resistant cells.

Intracellular replication of the non-lytic single stranded circular DNA mycoplasmavirus MVL51 has been shown to involve three DNA intermediates: RFI, RFII and SSI. Growth in Eagle's basal medium, rather than richer tryptose medium, has allowed the identification of an intermediate between nascent progeny chromosomes (SSI) and mature virus. This intermediate is a protein associated form of SSI.

We have found that mycoplasma virus L172 is an enveloped globular virion containing circular, single-stranded DNA of 14.0 kilobases. L172 has been reported by other workers to have a double-stranded DNA genome of 13 to 17 kilobase pairs and has been classified as a plasmavirus, a group for which mycoplasma virus L2 is the type member. Mycoplasma viruses L172 and L2 differ in genome size and structure, DNA base composition, and protein composition, and they have no detectable DNA homology. As the only reported enveloped virion containing single-stranded DNA, L172 represents a new group of viruses.

The adsorption properties of the tailed bacteriophage L3 to Acholeplasma laidlawii cells were studied. Adsorption followed a biphasic curve. Reversibility and virus heterogeneity were not sufficient to explain the break in the adsorption curve. Binding studies showed that each colony-forming unit could bind about 350 virions. The electrostatic nature of L3 adsorption was indicated by the effect of cations, pH, and temperature on the adsorption rate constant. L3 adsorption appeared to have a requirement for Ca2+, which could not be replaced by the mono- and divalent cations examined. Ethylene glycol-bis(beta-aminoethyl ether)-N,N-tetraacetic acid inhibition of adsorption was totally reversed by added Ca2+. The effects of EDTA, proteases, and lectins on absorption indicated that membrane proteins are the L3 receptors. The model for L3 adsorption is a multivalent one involving lateral diffusion of adsorbed virions and receptor proteins.

Transfection of Acholeplasma laidlawii strain JA1 with viral DNAs that have been sequence-specifically methylated in vitro has led us to previously postulate that JA1 cells contain an enzyme which cleaves only DNA containing 5-methylcytosine, regardless of the nucleotide sequence containing that base. In this paper we show that an endonuclease activity is present in extracts from JA1 cells but not in extracts from a restriction-deficient variant of JA1. The partially purified enzyme cleaves not only DNA containing 5-methylcytosine, but also DNA containing no methylated bases. We discuss why this endonuclease activity may not have the same in vitro specificity as would be expected from in vivo experiments.

Mycoplasma bacteriophage L51 single-stranded DNA and L2 double-stranded DNA are host cell modified and restricted when they transfect Acholeplasma laidlawii JA1 and K2 cells. The L51 genome has a single restriction endonuclease MboI site (recognition sequence GATC), which contains 5-methylcytosine when the DNA is isolated from L51 phage grown in K2 cells but is unmethylated when the DNA is from phage grown in JA1 cells. This GATC sequence is nonessential, since an L51 mutant in which the MboI site was deleted was still viable. DNA from this deletion mutant phage was not restricted during transfection of either strain K2 or JA1. Therefore, strain K2 restricts DNA containing the sequence GATC, and strain JA1 restricts DNA containing the sequence GAT 5-methylcytosine. We conclude that K2 cells have a restriction system specific for DNA containing the sequence GATC and protect their DNA by methylating cytosine in this sequence. In contrast, JA1 cells (which contain no methylated DNA bases) have a newly discovered type of restriction-modification system. From results of studies of the restriction of specifically methylated DNAs, we conclude that JA1 cells restrict DNA containing 5-methylcytosine, regardless of the nucleotide sequence containing 5-methylcytosine. This is the first report of a DNA restriction activity specific for a single (methylated) base. Modification in this system is the absence of cytosine methylating activity. A restriction-deficient variant of strain JA1, which retains the JA1 modification phenotype, was isolated, indicating that JA1 cells have a gene product with restriction specificity for DNA containing 5-methylcytosine.

For the first time a single experimental approach, 16S ribosomal RNA sequence characterization, has been used to develop an overview of phylogenetic relationships in the bacterial world. The techni...

Chloramphenicol affects several steps in the DNA replication of mycoplasma virus L51, a noncytocidal, naked, bullet-shaped virion containing circular single-stranded (SS) DNA of 1.5 X 10(6) daltons (4.5 kilobases). In the presence of chloramphenicol, adsorption was normal and parental SS DNA was converted to double-stranded replicative forms (RF), but subsequent RF leads to RF replication was inhibited. Chloramphenicol added late in infection, when most viral nascent DNA is in progeny SS molecules, inhibited SS synthesis, but nascent RF molecules were formed. However, a chase experiment showed that these RF molecules could not be converted to SS DNA. Therefore, viral RF molecules made in the presence of chloramphenicol are not functional as SS DNA precursors.

The effect of rifampin on the replication of MVL51, a bullet-shaped mycoplasmavirus with single-stranded circular DNA of molecular weight 2 X 10(6), has been examined in a rifampin-resistant host cell. Rifampin does not block the early steps in MVL51 infection but does decrease the total amount of parental viral DNA taken up. The single-stranded parental viral DNA that enters the cell is found in membrane-associated, double-stranded DNA replicative forms I and II. Rifampin had no significant effect on the synthesis of progeny viral DNA RFI and RFII early in infection and SSI (single-stranded progeny viral chromosomes) later in infection. The rifampin block in virus synthesis was found to be in the step converting SSI into assembled virions. Rifampin was shown to affect the synthesis of virus-specific RNA, Which suggests that viral transcription is necessary for virion assembly.

Mycoplasma virus L2 is subject to host-specific restriction and modification in Acholeplasma laidlawii strains JA1 and K2. We have examined the DNAs from both host cells and viruses propagated on these strains with respect to susceptibility to cleavage by restriction endonucleases and for DNA base modifications. We show that, in strain K2 and L2 virus grown on K2 cells, cytosine in the sequence GATC is methylated to 5-methylcytosine and, although strain K2 and L2 viruses grown on K2 contain N6-methyladenine in their DNA, adenine in the sequence GATC is not methylated. In contrast to K2, strain JA1 and L2 virus grown on JA1 cells contain no detectable methylated bases. It is not known which of the methylated bases in K2 is the basis for the K2 restriction-modification system operative on L2 virus.

The ultraviolet light, photodynamic, and thermal inactivation parameters have been measured for the three groups of mycoplasmaviruses. The differences in these parameters for the three virus groups reflect differences in virion structure and in genome size and structure.

Mycoplasmavirus MVL2 is a nonlytic enveloped virion containing DNA. This DNA has been shown to be a double-stranded circular superhelical molecule of 11.8 kilobase pairs (7.8 X 10(6) daltons). The superhelix density is greater than that of phi X174 RFI but less than that of PM2 phage DNA. A physical map of the MVL2 genome has been obtained using restriction endonucleases.

International audience

International audience

International audience

International audience

International audience

chap. 17; International audience