Читать книгу Basic Virology - Martinez J. Hewlett - Страница 23

In the last decade or so, molecular biologists have developed a number of powerful techniques to amplify and sequence the genome of any organism or virus of interest. The correlation between sequence data; classical physiological, biochemical, and morphological analyses; and the geological record has provided one of the triumphs of modern biology. We now know that the biosphere is made up of three domains, the eubacteria (bacteria), the eukaryotes (nucleated cells), and the archaebacteria – the latter only discovered through the ribosomal RNA(rRNA) sequence studies of Woese and his colleagues in the past 30 years or so. Further, analysis of genetic changes in conserved sequences of critical proteins as well as rRNA confirms that eukaryotes are more closely related to (and thus derived from) the ancestors of archaea than they are to eubacteria.

Carefully controlled statistical analysis of the frequency and numbers of base changes in genes encoding conserved enzymes and proteins mediating essential metabolic and other cellular processes can be used to both measure the degree of relatedness between greatly divergent organisms, and provide a sense of when in the evolutionary time scale they diverged from a common ancestor. This information can be used to generate a phylogenetic tree, which graphically displays such relationships. An example of such a tree showing the degree of divergence of some index species in the three domains is shown in Figure 1.1.

Although there is no geological record of viruses (they do not form fossils in any currently useful sense), analyses of the relationship between the amino acid sequences of viral and cellular proteins and of the nucleotide sequences of the genes encoding them provide ample genetic evidence that the association between viruses and their hosts is as ancient as the origin of the hosts themselves. Some viruses (e.g., retroviruses) integrate their genetic material into the cell they infect, and if this cell happens to be germ line, the viral genome (or its relict) can be maintained essentially forever. Analysis of the sequence relationship between various retroviruses found in mammalian genomes demonstrates integration of some types before major groups of mammals diverged.

While the geological record cannot provide evidence of when or how viruses originated, genetics offers some important clues. First, the vast majority of viruses do not encode genes for ribosomal proteins or genetic evidence of relicts of such genes. Second, this same vast majority of viruses do not contain genetic evidence of ever having encoded enzymes involved in energy metabolism. This is convincing evidence that the viruses currently investigated did not evolve from free‐living organisms. This finding distinctly contrasts with two eukaryotic organelles, the mitochondrion and the chloroplast, which are known to be derived from free‐living organisms.

Figure 1.1 A phylogenetic tree of selected species from the three domains of life: Eukaryota (or Eukarya), Eubacteria, and Archaea. The tree is based upon statistical analysis of sequence variation in seven universally conserved protein sequences: arginyl‐t‐RNA synthetase, methionyl‐t‐RNA synthetase, tyrosyl‐t‐RNA synthetase, RNA pol II largest subunit, RNA pol II second largest subunit, PCNA, and 5′‐3′ exonuclease.

Source: Based upon Raoult, D., Audic, S., Robert, C., et al. (2004). The 1.2‐megabase genome sequence of mimivirus. Science306: 1344–1350.

Genetics also demonstrates that a large number of virus‐encoded enzymes and proteins have a common origin with cellular ones of similar or related function. For example, many viruses containing DNA as their genetic material have viral‐encoded DNA polymerases that are related to all other DNA polymerase isolated from plants, animals, and archaea.

Statistical analysis of the divergence in three highly conserved regions of eukaryotic DNA polymerases suggests that the viral enzymes, including those from herpesviruses and from poxviruses and relatives (including mimiviruses), have existed as long as the three domains themselves. Indeed, convincing arguments exist that the viral enzymes are more similar to the ancestral form. This, in turn, implies that viruses or virus‐like self‐replicating entities (replicons) had a major role, if not the major role, in the origin of DNA‐based genetics. The phylogenetic tree of relationships between two forms of eukaryotic DNA polymerase (alpha and delta), two forms of the enzyme found in archaebacteria, as well as those of three groups of large DNA viruses and some other DNA viruses infecting algae and protists is shown in Figure 1.2.

Another example of the close genetic interweaving of early cellular and viral life forms is seen in the sequence analysis of the reverse transcriptase enzyme encoded by retroviruses, which is absolutely required for converting retroviral genetic information contained in RNA to DNA. This enzyme is related to an important eukaryotic enzyme involved in reduplicating the telomeres of chromosomes upon cell division – an enzyme basic to the eukaryotic mode of genome replication. Reverse transcriptase is also found in cellular transposable genetic elements (retrotransposons), which are circular genetic elements that can move from one chromosomal location to another. Thus, the relationship between certain portions of the replication cycle of retroviruses and mechanisms of gene transposition and chromosome maintenance in cells is so intimately involved that it is impossible to say which occurred first.

A major complication to a complete and satisfying scheme for the origin of viruses is that a large proportion of viral genes have no known cellular counterparts, and viruses themselves may be a source of much of the genetic variation seen between different free‐living organisms. In an extensive analysis of the relationship between groups of viral and cellular genes, L. P. Villarreal points out that the deduced size of the Last Universal Common Ancestor(LUCA) of eukaryotic and prokaryotic cells is on the order of 300 genes – no bigger than a large virus – and provides some very compelling arguments for viruses having provided some of the distinctive genetic elements that distinguish cells of the eukaryotic and prokaryotic kingdoms. In such a scheme, precursors to both viruses and cells originated in a pre‐biotic environment hypothesized to provide the chemical origin of biochemical reactions leading to cellular life.

At the level explored here, it is probably not terribly useful to spend great efforts to be more definitive about virus origins beyond their functional relationship to the cell and organism they infect. The necessarily close mechanistic relationship between cellular machinery and the genetic manifestations of viruses infecting them makes viruses important biological entities, but it does not make them organisms. They do not grow, they do not metabolize small molecules for energy, and they only “live” when in the active process of infecting a cell and replicating in that cell. The study of these processes, then, must tell as much about the cell and the organism as it does about the virus. This makes the study of viruses of particular interest to biologists of every sort.

Figure 1.2 A phylogenetic tree of selected eukaryotic and archaeal species along with specific large DNA‐containing viruses based upon sequence divergence in conserved regions of DNA polymerase genes.

Source: Based upon Villarreal, L.P. and DeFilippis, V.R. (2000). A hypothesis for DNA viruses as the origin of eukaryotic replication proteins. Journal of Virology74: 7079–7084.