The Evolution of Viruses - Zhdanov, V. M. 1990

Special Section
Tailed Phages

A large group of highly specialized Viruses infecting prokaryotes (Bacteria) and lower eukaryotes (Fungi) is represented by tailed phages (phages with a tail). In Virus Classification [Matthews R., 1982], 3 groups of these viruses are schematically presented, corresponding to 3 families: phages with a long contractile tail (Myoviridae), phages with a long non-contractile tail (Sfyloviridae), and phages with a short tail (Podoviridae). Upon a more detailed description, the number of these forms becomes significantly larger, and phages are divided into smaller taxonomic groups [Liss A. et al., 1981; Reanney D., Ackermann Н., 1981]. All of them are viruses with a fairly large genome in the form of double-stranded linear or circular RNA. The Molecular Weight of the myovirus genome is about 120×10⁶, with RNA containing hydroxymethylcytosine instead of thymine. Within this family, groups of phages with an isometric HEAD (phage P2 group) and an elongated head (even-T phages) are distinguished. Accordingly, The Genome of these phages has 10 genes, and 15–20 Proteins are detected in the composition of virions.

In isometric phages, the head has an icosahedral shape. Head diameters range from 40 to 180 nm. In phages with an oblong head, the size of the latter is 100×80 nm. The tail is long (80–450 nm) and consists of a collar, a tube, a contractile sheath, and fibrils.

Upon interaction with bacteria, the phage attaches to the bacterial Cell via its tail equipped with fibrils; the Lysozyme located at the end of the tail degrades The Cell wall, the sheath contracts, and the tail penetrates into the Cytoplasm, where the phage DNA is subsequently delivered. Replication is a very complex and strictly regulated process, and the assembly of virions—which leave the bacterial cell after its lysis—is equally complex. Alongside replicative (lytic) interaction (virulent phages), an integrative process can occur (formation of a temperate virus prophage). Finally, phages can exist in the form of Plasmids. This group comprises hundreds of viruses infecting many hundreds of different bacterial species.

In styloviruses (phage λ group), the genome has a size of about 33×10⁶, the DNA has sticky ends, and virions contain about 10 structural proteins. Two groups of phages are also distinguished—those with an isometric head and those with an elongated head. The tail is not equipped with a contractile sheath. This is also a numerous group. The viruses can cause either lytic or integrative infection (virulent and temperate phages, respectively).

Class="center">

Fig. 45. Organization OF THE T7 phage genome.

1 — percentage of T7 genomes; 2 — METABOLISM/31.html">Transcription; 3 — T7 DNA and number of genes; 4 — Functional groups of genes.

In podoviruses, the genome has a molecular weight of about 25×10⁶. Virions contain up to 12 proteins. The diameter of the virion head is 65 nm, the length of the short tail is 17 nm, and fibrils are present. This group also includes subgroups with isometric and oblong heads. These virus groups are characterized by the presence of a terminal protein covalently attached by a phosphodiester bond to the 5'-ends of the DNA. In the Bacillus subtilis phage φ29, such a protein is p28. Similar terminal proteins have been found in phages Cp-1, PRD1, and others.

An extremely extensive literature is dedicated to the considered phage groups; therefore, there is no need to briefly outline the basic data on the Morphology and architecture of bacteriophage virions, their chemical composition, Structural and functional proteins, reproduction cycle, and the specifics of their interactions with "host" Cells. Consequently, we will limit ourselves to a few illustrations that provide a general idea of these phages.

Phage P22 has a short tail [Suskind M., Bottstein D., 1978], and phages T3 and T7 are closely related [Krueger D., Schroeder С., 1981]. The molecular weight of the DNA of these phages is 25×10⁶—30×10⁶; A number of genes have been identified on the DNA (Fig. 45). The order of their "action" is similar in Podoviridae and lambda Styloviridae groups. These data indicate The complexity of the genome Structure in the group under consideration and the strict Introduction/30.html">Regulation of Gene Expression encoding the synthesis of structural and functional proteins. Phage DNA replication is schematically shown in Fig. 46. The entire replication cycle is driven by the viral DNA Synthesis system (unwinding protein, primase, polymerase, ligase) and generally mirrors the synthesis of "host" DNA.

Fig. 46. Stages of T7 phage DNA replication.

L — light and H — heavy strands; I — primary initiation; 2 — "eye-shaped" intermediate form; 3 — Replication fork; 4 — concatemers.

The process of virion formation (morphogenesis) has been studied in detail using the T4 phage model (Myoviridae). As can be seen from Fig. 47 [Wood W., 1978; 1980; Kellenberger Е., 1980; Tsugita A. et al., 1980], 14 proteins participate in this process. The phages described belong to highly specialized viruses.

Now let us attempt to summarize the data on the ORIGIN AND EVOLUTION of the phage group under consideration. Unfortunately, just as with viruses from most other groups, one cannot even speculate on THE ORIGIN OF tailed phages; they appeared like Deus ex machina, without the slightest "hint" of their possible sources of origin. Of course, tailed phages are ancient forms whose evolution spanned many hundreds of millions of years, if not more. On the one hand, they infect practically all Major Groups of bacteria, including cyanobacteria; on the other hand, the most diverse forms of tailed phages can be found within the same bacterial group (e.g., Pseudomonas and Bacillus phages). Thus, when studying 62 Pseudomonas phages, 17 morphological groups of tailed phages were isolated, while among 99 Bacillus phages, 10 groups were identified.

Fig. 47. Assembly pathways of bacteriophage T4. Dashed lines indicate stages not detected in vitro; numbers indicate gene numbers.

Over the course of long evolution, highly specialized structures have emerged that have no analogues among later-appearing viruses infecting eukaryotic organisms. It is to be hoped that in the coming years criteria will be found that will make it possible to determine the evolutionary relationship and construct a genealogical tree for at least some of these numerous viruses.

Much more information can be obtained regarding potential connections within the groups under consideration. First of all, however, it should be noted that these groups are clearly not isolated from one another and are interrelated. Thus, gene 13 of phage P22 (a podovirus) encodes the synthesis of a protein with a molecular weight of 11,500, which shares 89% Homology with protein 5 of phage λ (a stylovirus). Gene 19 of phage P22 encodes the synthesis of a protein with a molecular weight of 16,000, exhibiting some homology with the lysozyme of phage T4 (a myovirus), although it is not homologous to the R and RZ proteins of phage λ that perform analogous Functions [Rennell D., Poteete A., 1985]. These data can be interpreted in different ways. Firstly, there are still insufficient morphological criteria for delineating taxonomic groups, let alone higher ones such as families. In this case, tail length, flexibility or rigidity, and the presence or absence of a contractile sheath are apparently insufficient for assigning the respective virus groups within a family. Secondly, since the same cell can be simultaneously inhabited by multiple phages, recombination processes—gene exchange between different viruses—are possible. Therefore, divergent dichotomy was hardly the sole pathway of speciation in phages.

Phage evolution should be viewed not only as the evolution of parasites pathogenic to bacteria, but also as the coevolution of two partners, each contributing to the success of the species. It is precisely from this perspective that The phenomenon of Lysogeny and lysogenic phages should be considered [Herskowitz I., Hagen D., 1980]. The additional Genetic information introduced into the "host" cell genome, on the one hand, provides Immunity against a related virulent phage and, on the other hand, can introduce Other types of information (Antibiotic Resistance, new Enzymes, toxins, etc.) that were "captured" by the phage upon "excisision" from a lysogenic bacterial culture. Phages can become sources of plasmids, which frequently carry these beneficial traits in their "pure" form, without additional genetic baggage.

Of particular interest are phages carrying toxin genes in their genome (diphtheria phages, clostridial tetanus and botulinum phages, enterobacterial and cholera vibrio phages, staphylococcal phages). The phages of diphtheria corynebacteria producing diphtheria toxin have been studied in the greatest detail. Diphtheria bacteria themselves are non-toxigenic and become toxigenic upon infection with temperate Bacteriophages (β, cγ, etc.) carrying the diphtheria toxin gene. Being temperate, these bacteriophages integrate with the corynebacterial genome, and expression of the toxin gene ensures toxin production by the bacterial cell [Rappuoli R. et al., 1983]. The nucleotide sequence of the gene has been determined for both β [Greenfield L. et al., 1983] and cγ [Ratti G. et al., 1983] bacteriophages. During Biosynthesis, the polypeptide chain undergoes proteolytic Cleavage into subunits A (21,000) and B (40,000), followed by the joining of the subunits via Disulfide Bonds. Furthermore, both PARTS OF THE toxin—the addressing and toxophoric moieties—acquire their final conformation. The addressing component (fragment B) interacts with cell membranes, and the toxin molecule penetrates into the Cytosol via acidic vesicles [Donovan et al., 1981], whereas the toxophoric component (fragment A) inactivates elongation factor 2, thereby terminating Protein Synthesis in The Cell and leading to cell death [Zalman L., Wisnieski B., 1984].

Exotoxins structurally similar (two functionally distinct subunits) are widespread among bacteria, although the "target" of the toxophoric component can be different cellular systems. Most similar to diphtheria toxin are the neurotoxins of Clostridium botulinum and Clostridium tetani [Hoch D. et al., 1985]. The exotoxins of Pseudomonas aeruginosa and Shigella dysenteriae also target the Protein Biosynthesis system, the cholera enterotoxin and the heat-labile toxin of Escherichia coli act on the adenylate cyclase system, and staphylococcal toxin possesses NAD-glycohydrolase activity [Yeremchuk Yu. V., 1985], although some toxins have a different structure, such as pertussis toxin [Brandt S. et al., 1985]. Although these toxins are generally specific to different phages and their bacterial "hosts", species barriers are surmountable using Recombinant DNA technology (e.g., The production of diphtheria toxin by Escherichia coli) [Leong D. et al., 1985].

The origin of exotoxins and toxigenic phages remains far from clear. Firstly, not all of the aforementioned toxins are introduced into bacterial cells by phages; rather, the reverse is true: introduction into bacterial cells by bacterial viruses has been proven for only a few toxins. Secondly, it is quite probable that exotoxins originally arose in bacterial cells, and only secondarily were their genes captured by phages and incorporated into their genomes. Additionally, toxins may be produced by plasmids (see Chapter 6).

The Significance of toxigenic phages can be illustrated by the example of toxigenic diphtheria phages. The diphtheria corynebacterium itself is non-toxigenic, lacks invasive properties, and persists on mucous membranes. Upon infection with a temperate toxigenic diphtheria phage, the produced toxin causes Necrosis of the mucous membranes and dramatically improves the conditions for corynebacterial proliferation, thereby compensating for the additional genetic burden caused by the Integration of the viral genome into the cellular one. If these considerations are correct, then in the presence of high antitoxic immunity in the population against diphtheria intoxication, toxigenic corynebacteria will be gradually displaced by non-toxigenic ones, since the additional genetic burden in the form of a prophage will not confer any advantage to toxigenic bacteria, given that Tissues are protected from the toxin by antitoxic immunity.

In the course of evolution, integrated proviruses containing genes for exotoxins could have undergone Mutations that rendered their excision impossible, and in such cases, we attribute the toxicity to a bacterial gene if we fail to detect a defective yet toxigenic prophage. Here, we should also examine the inhibition of bacteriophage replication by lysogens and extrachromosomal elements [Dinkworth D. et al., 1981]. This phenomenon was first discovered during The Study of E. coli phage λ. In the lysogenic state, the phage suppresses the reproduction of even-T phages (T2, T4, T6)—more specifically, their rII mutants—without affecting the pre-early and Cytology/cytology/16.html">Early stages of their synthesis, but halting The formation of late products and virion assembly. This effect is associated with the rex gene of phage λ. This gene also suppresses the reproduction of phages T1 and T5. Other lysogenic phages, such as enterobacterial phages P1 and P2, possess a similar action, although the mechanisms of such inhibition differ. The prophage P22 of salmonellae also suppresses the reproduction of both its own and many other superinfecting phages. In this case, the corresponding gene responsible for the inhibition has likewise been identified.

It was subsequently demonstrated that the inhibition of replication and abortive infection by virulent phages can be caused by extrachromosomal factors such as plasmids, specifically the F factor. In this case, complex interactions take place between the phages and the "host" cells. The propagation of T7, ФІ, ФІI, W31, and λ phages, which possess extensive DNA homology regions, undergoes inhibition. Some of these phages adsorb preferentially to male (W31) cells, while others adsorb to female (ФII, T7) cells. Under these conditions, late syntheses are suppressed: during the synthesis of all mRNA classes (I–III), only class I mRNAs are translated (translational control).

The inhibitory effect of R factors on the propagation of certain phages (λ, P22, T7) has also been described. The inhibitory action of colicinogens on T5, BF23, T7, and W31 phages appears to be associated with the general suppression of host cell synthesis.

Summarizing the above, Three Main Mechanisms of phage replication inhibition by lysogenic phages and extrachromosomal elements can be distinguished: cell resistance, superinfection exclusion, and restriction.