Genome Sequencing Essay, Research Paper
Microbiology has entered the realm of genome sequencing. This biological revolution is opening up new dimensions in our view of life.
In 1995, a report on the entire DNA sequence for the genome of the bacteria Haemophilus influenzae was published . Although the genomes for a number of viruses had been completed before this, H. influenzae was the first free-living organism to have it’s genome sequenced, and as such, this report remains a biological milestone. Since then, the entire genome sequences for over 10 microorganisms have been compiled and released and more are on their way. The completed microbial genomes include:
Haemophilus influenzae finished 1995
Mycoplasma genitalium finished 1995
Methanococcus jannaschii finished 1996
Synechocystis sp. finished 1996
Mycoplasma pneumoniae finished 1996
Saccharomyces cerevisiae finished 1997
Helicobacter pylori finished 1997
Escherichia coli finished 1997
Bacillus subtilis finished 1997
Archaeoglobus fulgidus finished 1997
The benefits of complete genome sequencing projects include a greater understanding of the organisms being sequenced and acknowledgment of the minimum complement of genes necessary for a free-living organism. Of the organisms that have already had their genomes sequenced, a number are of particular importance. For example, Mycoplasma genitalium has a complete nucleotide sequence that is only 580,070 base pairs long, and as such, is believed to be the smallest genome of any free-living organism. Because of it’s unique size, this genome presents a way of studying a minimal functional gene set. In addition, complete genome sequencing projects are currently being carried out on a number of microbial pathogens in an attempt to better understand them. The inference of molecular structures, in particular genome sequences, have direct practical consequences in clinical microbiology. Data and analyses of clinically important microorganisms are being used to develop molecular diognostics as well as to guide research in the nature of these organisms. Information obtained from sequencing is also being used to provide enzymes for biotechnical and industrial applications.
The impact that genome sequencing has had, and will have, on our view of life only begins here. It appears that the time has come to move formal taxonomy and phylogenetic classification into line with the system emerging from molecular data.
Prior to the 1960’s, evolutionary study had been confined to multicellular eucaryotes whose histories, at best, only cover about 20% of the total evolutionary time span. Plants and animals have complex morphologies, which served as the basis for their phylogenetic classification. In contrast, bacteria have morphologies that are too simple to be used in this way. Many early microbiologists avoided the area of phylogenetic classification for this reason, despite the fact that the history of the microbial world spans most of the Earth’s existence. Those who did study the discipline created distorted schemes that are now under review.
Since the 1950’s, molecular studies have been used to determine evolutionary relationships, although microbiology remained blind to the potential of this unique approach until rRNA sequences were shown to provide a key to procaryotic phylogeny in the 1970’s. It would appear that genome sequencing has advanced the science of phylogenetic classification even further.
The failing view of the organisation of life was that all living things were either plant or animal in nature. In 1990, a proposal for a new, natural system of organisms was published, based on the rRNA sequencing revolution. The more recent genome sequencing era has supported this original proposal, and as a result three domains of life are currently recognised; Archaea, Bacteria, and Eucarya, as shown in the universal phylogenetic tree below.
When the first archaeal genome (Methanococcus jannaschii) was sequenced in 1996, it was found that only 44% of the genes were familiar . This phenomenal discovery justified the creation of the three domains, since all are too dissimilar to be included in the same kingdom. It is only on the molecular level that we are able to see the living world divide into three distinct primary groups. For every characterised molecular system there is a characteristic eucaryotic, bacterial and archaeal version, which all members of each particular group share. Genome sequencing ventures are making the recognition of these characteristic systems much easier, as well as making it possible to compare the systems across the three domains.
The discovery that the archaea were in fact a distinct group of organisms from the bacteria challenged the long-standing eucaryote-procaryote dichotomy that has dominated our view of life since it’s proposal in the 1930’s . It has long been recognised that this eucaryote-procaryote scheme was in need of review. While the eucaryotic form of cellular organisation defines a proper phylogenetic unit, procaryotes are only united as a class by their lack of the characteristics that define the eucaryotic cell. As such, the procaryotic definition is a negative one that offers no meaningful phylogenetic information. In the 1950’s it became feasible to define procaryotes positively, on the basis of shared molecular characteristics, although this revolution, as mentioned earlier did take some time to develop.
The sequencing of the M. jannaschii genome has also given some insights into the archaea’s evolutionary relationships to the bacteria and the eucarya. It is important to note that the root of the tree separates the Bacteria from the other two groups. This separation makes the Archaea and the eucaryotes specific (although distant) relatives, evidenced by the observation of many similarities between the two groups. For example, in all information processing systems, that is, translation, transcription and DNA replication, the archaeal and eucaryotic versions resemble each other a great deal more than either genome resembles the bacterial version . Other resemblances between Archaea and eucaryotes include histones, cell division proteins, proteosomes, and protein transport systems. Despite these similarities, the archaea resemble the bacteria in morphology and metabolism. It has been speculated, as a result of comparisons of genome sequences from all domains of life, that extent archaea may be descendants of the long-postulated procaryotic ancestor of the eucaryotes. The primitive nature of the archaea further supports this suggestion. M. jannaschii, for example, is a complete autotroph. That is, the organism requires no organic nutrients for growth. Recent announcements of possible fossils in a Martian meteorite have fuelled suggestions that the original archaea arrived on such a meteorite, and was able to survive in the absence of any organic matter.
The tree does not adopt the old idea of there being two primary categories of bacteria, gram-positive and gram-negative. This division has been shown true only in part, by molecular studies. While the gram-positive is indeed a phylogenetically coherent grouping, gram negative is not. Rather, the gram-negative grouping encompasses 10 distinct groups. A number of other corrections have been made to traditional phylogenetic groupings. Molecular studies have shown that the mycoplasmas, previously believed to be phylogenetically remote from all other bacteria, are in fact degenerate clostridia, while the view that photosynthetic bacteria arose from nonphotosynthetic heterotrophic ancestors gains no support from sequencing data. These inconsistencies reflect not only the accuracy of molecular based classification but also the inaccuracy of phylogenetic classification based on morphology. The early microbiologists who attempted to create a phylogenetic framework cannot be blamed for their misconceptions. The classical microbiologist’s insistence on morphology as the primary criterion for phylogenetic classification did not suit the simple, and at times, uninterpretable microbial morphologies. At the time however, phylogenetic classification was not experimentally viable. An unfortunate consequence of their misleading associations is that they shaped the taxonomy system that is still currently in use (despite its obvious flaws). One of the absurdities to immerge from the flawed system is the taxon Pseudomonas, perhaps one of the best studied ‘representative genus’ which is actually a collection of more than five separate bacterial groups. Ironically, the name Pseudomonas is derived from the Greek pseudes and monus, or false unit.
Molecular studies, in particular, genome sequencing projects are making possible new comparisons. Organisms, like the Pseudomonas, that were once grouped together are now being grouped separately. These changes however are not occurring fluently. For the new taxonomy to be accepted readily it has to be complete, and at the moment it is only just being created. The old system, in contrast, is all but written in stone, and it may take a long time for the winds of evolutionary change to take hold. In contrast, microbial phylogeny has always been a weak, and in a sense immature, discipline, and as such, molecular data is being used readily to develop a new phylogenetic system .
Because the universal phylogenetic tree brings us face to face with the great evolutionary questions, our growing ability to formulate these in molecular and genetic terms is particularly exciting. We can now inquire about the origins of not only the eucaryotic cell, but also parts of the eucaryotic genome. In particular we can now ask for what fraction of eucaryotic genes is the most similar homolog an archaeal gene or a bacterial gene and for what fraction is there no detectable homolog? We can also inquire about the genetic processes that were involved in the evolution of extant life. The origins of key cellular functions can now also be addressed. In particular, the extent to which we can trace genes back to a basic genetic complement is expanding as more and more organisms have their complete genomes sequenced. The answers to all of these questions are vital in shaping the microbial phylogeny that is developing.
The mapping of the genomes of model organisms has been likened to the work carried out by the map-makers during the Age of Exploration . What is important in this comparison is that sequencing project are opening up new worlds, that are not only of concern to microbiologists, but also to evolutionists and biologists alike. Developing microbial phylogeny is not just the long awaited completion of the Darwinian program. It increases the current time span of evolution by almost an order of magnitude. It is possible that it will even revolutionise the way we view selection. Rather than providing the few missing links, bacterial evolution is indeed itself the puzzle and the ‘Pandora’s box’ of phylogeny has only just been opened.