Origin and Evolution of Viruses (eBook)

Esteban Domingo, John J. Holland, Colin R. Parrish (Herausgeber)

eBook Download: EPUB

2008 | 2. Auflage
560 Seiten
Elsevier Science (Verlag)
978-0-08-056496-8 (ISBN)

Infos

New viral diseases are emerging continuously. Viruses adapt to new environments at astounding rates. Genetic variability of viruses jeopardizes vaccine efficacy. For many viruses mutants resistant to antiviral agents or host immune responses arise readily, for example, with HIV and influenza.These variations are all of utmost importance for human and animal health as they have prevented us from controlling these epidemic pathogens.

This book focuses on the mechanisms that viruses use to evolve, survive and cause disease in their hosts. Covering human, animal, plant and bacterial viruses, it provides both the basic foundations for the evolutionary dynamics of viruses and specific examples of emerging diseases explained by the evolutionary flexibility of the viral agents that circulate in a continuously changing earth environment.

* NEW to this edition - chapters on the molecular basis of copying fidelity of viral polymerases, methods to establish phylogenetic relationships among viruses, and the mechanisms of cellular RNA interference and editing functions as they affect virus evolution.

* UNIQUE - combines theoretical concepts in evolution with detailed analyses of the evolution of important virus groups.

* Bacterial, plant, animal and human viruses are compared regarding their interaction with their hosts.

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New viral diseases are emerging continuously. Viruses adapt to new environments at astounding rates. Genetic variability of viruses jeopardizes vaccine efficacy. For many viruses mutants resistant to antiviral agents or host immune responses arise readily, for example, with HIV and influenza. These variations are all of utmost importance for human and animal health as they have prevented us from controlling these epidemic pathogens. This book focuses on the mechanisms that viruses use to evolve, survive and cause disease in their hosts. Covering human, animal, plant and bacterial viruses, it provides both the basic foundations for the evolutionary dynamics of viruses and specific examples of emerging diseases. - NEW - methods to establish relationships among viruses and the mechanisms that affect virus evolution- UNIQUE - combines theoretical concepts in evolution with detailed analyses of the evolution of important virus groups- SPECIFIC - Bacterial, plant, animal and human viruses are compared regarding their interation with their hosts

Textauszug

CHAPTER 1 Early Replicons: Origin and Evolution*

Peter Schuster, Peter F. Stadler

ABSTRACT

RNA and protein molecules have been found to be both templates for replication and specific catalysts for biochemical reactions. RNA molecules, although very difficult to obtain via plausible synthetic pathways under prebiotic conditions, are the only candidates for early replicons. Only they are obligatory templates for replication, which can conserve mutations and propagate them to forthcoming generations. RNA-based catalysts, called ribozymes, act with high efficiency and specificity for all classes of reactions involved in the interconversion of RNA molecules such as cleavage and template-assisted ligation. The idea of an RNA world was conceived for a plausible prebiotic scenario of RNA molecules operating upon each other and constituting thereby a functional molecular organization. A theoretical account of molecular replication making precise the conditions under which one observes parabolic, exponential, or hyperbolic growth is presented. Exponential growth is observed in a protein-assisted RNA world where plus–minus (±) duplex formation is avoided by the action of an RNA replicase. Error propagation to forthcoming generations is analyzed in the absence of selective by neutral mutants as well as for predefined degrees of neutrality. The concept of an error threshold for sufficiently precise replication and survival of populations derived from the theory of molecular quasispecies is discussed. Computer simulations are used to model the interplay between adaptive evolution and random drift. A model of evolution is proposed that allows for explicit handling of phenotypes.

WHAT IS A REPLICON?

Biology, and evolution in particular, are based on reproduction or multiplication and on variation. Reproduction pure has the property of self-enhancement and leads to exponential growth. Self-enhancement in chemical reactions under isothermal conditions is tantamount to autocatalysis that, in its simplest form, corresponds to a reaction mechanism of the kind:

     (1)

where A is the substrate and Y the autocatalyst. Being just an autocatalyst is certainly not enough for playing a role at the origin of life or in evolution. An additional conditio sine qua non is the property to act as an encoded instruction for the reproduction process. It is useful to remain rather vague as far as the nature of this instruction is concerned, because there are many possible solutions for template action at the molecular level. In reality the most straightforward candidates for useful templates are heteropolymers built from a few classes of monomers with specific interactions. The proper physical basis for such interactions are charge patterns, patterns of hydrogen bonds, space-filling hydrophobic interactions, and others. We may summarize the first paragraph by saying: “A replicon is an entity that carries the instruction for its own replication in some encoded form.”

Precise asexual reproduction gives rise to perfect inheritance. This is essentially true for prokaryotes: bacteria, archaebacteria, and viruses. In sexually reproducing eukaryotes, recombination introduces variation already into the error-free reproduction process.1 Mutation in the form of unprecise or error-prone reproduction represents the universal kind of variation, which occurs in all organisms and can be sketched by a single overall reaction step:

     (2)

Here, the mutant is denoted by Y’. The rate parameters k and k’ refer to two parallel reaction channels. This can be indicated by replacing the two parameters with a single rate constant and reaction (channel) frequencies:

     (3)

In the (improbable) case that Y’ is the only mutant of Y, the two channel frequencies add up to unity: Q + Q’ = l. In general, there will be many mutations, Yj → Yi, that give rise to variants and conservation of probabilities then leads to the conservation relation:

     (4)

which expresses that a copy is either error free or contains errors.

It is useful further to distinguish two classes of replicons: (i) obligatory replicons and (ii) optional replicons. All error copies of obligatory replicons can be replicated and thus are replicons themselves. Examples of obligatory replicons are nucleic acid molecules under suitable conditions (Figure 1.1). In Nature practically no restrictions on the initiation and chain propagation of replication are known apart from recognition sites at replication origins and a few other general requirements for replication. An example of a laboratory system is the polymerase chain reaction (PCR), which allows for amplification of DNA templates with (almost) any sequence. Optional replicons are, for example, autocatalytically growing oligonucleotides (von Kiedrowski, 1986) and oligopeptides (Lee et al., 1996) (Figure 1.2). These oligomers lose their capability to act as template (almost always) when a particular nucleotide or amino acid residue is exchanged for any other one. In other words, the property to be a replicon is not common feature of the entire class of molecules but a specific property of certain selected molecules only.

FIGURE 1.1 Template-induced replication of nucleic acids molecules. Direct replication (upper part) is primarily occurring with DNA. It represents a highly sophisticated process involving some 20 enzymes. Template-induced DNA synthesis occurs at the “replication fork,” both daughter molecules carry one DNA strand of the parent molecule. Complementary replication (lower part) occurs in Nature with single-stranded RNA molecules. The problem in uncatalyzed complementary replication is complex dissociation. A single enzyme is sufficient for complementary replication of simple RNA bacteriophages, since it causes the separation of plus and minus strands during replication. The two strands separate and form their own single-strand structures before the double helix is completed. Polymerase chain reaction (PCR) follows essentially the same mechanism of complementary replication as shown here. The separation of the two strands of the double helix is accomplished by heating: the complex dissociates spontaneously at higher temperature.

FIGURE 1.2 Oligopeptide and oligonucleotide replicons. (A) An autocatalytic oligopeptide that makes use of the leucine zipper for template action. The upper part illustrates the stereochemistry of oligopeptide template-substrate interaction by means of the helix wheel. The ligation site is indicated by arrows. The lower part shows the mechanism (Lee et al., 1996; Severin et al., 1997). (B) Template-induced self-replication of oligonucleotides (von Kiedrowski (1986)) follows essentially the same reaction mechanism. The critical step is the dissociation of the dimer after bond formation which commonly prevents these systems from exponential growth and Darwinian behavior.

Simple replicons certainly lack the complexity of present-day organisms and are defined best as molecular entities that are capable of replication by means of some mechanism based on interaction with a template. Almost all known replicons are oligomers or polymers composed from a few classes of monomers. Two extreme types of replicons are distinguished: obligatory replicons, for which exchange of individual monomeric units yields other replicons with different monomer sequences, and optional replicons where the capability of replication is restricted to certain specific sequences.

More complex replicons (not discussed in detail here) including DNA and protein, compartment structure, and metabolism have been considered as well (Eigen and Schuster, 1982; Gánti, 1997; Szathmáry and Maynard Smith, 1997; Rasmussen et al., 2003; Luisi, 2004). A successful experimental approach to self-reproduction of micelles and vesicles highlights one of the many steps on the way towards a primitive cell: prebiotic formation of vesicle structures (Bachmann et al., 1992). The basic reaction leading to autocatalytic production of amphiphilic materials is the hydrolysis of ethyl caprate. The combination of vesicle formation with RNA replication represents a particularly important step towards the construction of a kind of minimal synthetic cell (Luisi et al., 1994). Primitive forms of metabolism were considered for minimal cells as well (see, e.g., Rasmussen et al., 2004b).

SIMPLE REPLICONS AND THE ORIGIN OF REPLICATION

A large number of successful experimental studies have been conducted to work out plausible chemical scenarios for the origin of early replicons being molecules capable of replication (Mason, 1991). A sketch of such a possible sequence of events in prebiotic evolution is shown in Figure 1.1. Most of the building blocks of present-day biomolecules are available from different...

Produkt-Details

• Erscheint lt. Verlag: 23.6.2008
• Sprache: englisch
• Themenwelt: Naturwissenschaften ► Biologie ► Evolution
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Themenwelt: Naturwissenschaften ► Biologie ► Ökologie / Naturschutz
• Themenwelt: Technik
• ISBN-10: 0-08-056496-8 / 0080564968
• ISBN-13: 978-0-08-056496-8 / 9780080564968