Non Darwinian Evolution Of Bacteria Biology Essay

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Since Darwin published his theories on evolution in 1859, we have believed that every creature we see on the planet today is the result (and continual product) of a survival of the fittest way of life.

individuals having any advantage, however slight, over others, would have the best chance of surviving and of procreating their kind.....................this preservation of favourable variations and the rejection of injurious variations, I call Natural Selection - The Origin of Species (1859)

Animals typically produce more offspring than can possible survive, so the ones most likely to survive are the ones best suited to the dangers and benefits of the environment it lives in. Because these advantages come from genetic mutations, they start off in low numbers, but over countless generations these small differences progressively alter members of a species. In some cases a group may become so altered that they branch off from the original species.

This theory for the evolution of species works when the genetic information remains confined to the individual, but in bacteria it is transferred easily between species. This essay discusses the impact this has on the definition of a microbial species, but I will start by explaining what we consider a species to be.

There are many ways that a species can be defined and there has been much debate over a unifying way to sort each organism into a definitive species. The huge diversity of life means there are no clear boundaries between organisms, some maybe being different in few ways, but still different nonetheless. So the there may be two organisms that clearly belong to separate species but another organisms half way between the two, what species does this organism belong to?

Even the definition used in most textbooks; "groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups"(2) has its flaws. It does not take into account asexually reproducing organisms and it is not often known whether two similar groups of organisms are potentially capable of mating. In a few cases it may be physically impossible for members of the same species to mate e.g. a Chiwawa and a Great Dane (although this case has involved human-directed alterations that would not occur in the wild).

Implications of HGT for species definition

Horizontal gene transfer is a mechanism by which large amounts of DNA can be incorporated into a host genome from a donor between very similar or dissimilar groups of organisms. Studies have shown transfer from Bacteria to Archaea (Rest & Mindell 2003), Archaea to Bacteria (Gophna et al. 2004), Bacteria to Eukarya (Watkins & Gray 2006), Eukarya to Bacteria (Guljamow et al. 2007), Archaea to Eukarya (Andersson et al. 2003), and even within Eukarya (Nedelcu et al. 2008). However, it is in bacterial and archaeal evolution that horizontal gene transfer has been more widely documented and accepted.

The relationships between organisms are usually determined by the use of genetic markers such as the sequence of 16S RNA genes. Other genes can blur the boundaries between organisms, particularly microbes, by their common appearance in otherwise very dissimilar organisms.

Whatever current definition you chose for a species, evolution involving horizontal gene transfer will conflict with it. This is because they all are based on the assumption that an organism gets all its genes from one or two parents which are very like that organism, horizontal gene transfer makes this assumption false.

HGT for micro-organisms

Despite having small genomes bacteria exhibit a huge degree of variation in characteristics even between closely related organisms. Point mutations can be the cause of a few changes in function and may lead to slow modification of existing genes, but it cant explain the ability of bacteria to rapidly adapt and grow in new environments. Horizontal gene transfer results in immediate and significant alterations that can generate new variants of bacterial strains.

The first example of HGT being a driving evolutionary factor was the spread of antibiotic resistance between the bacteria of different diseases e.g. Mycobacterium tuberculosis and Streptococcus pneumonia. The speed that the resistance appeared ruled out the possibility that these traits were generated by point mutations by each strain, and the fact that the strains were resistant to the same antibiotics show that genes were transferred across these different taxa of microbes.

Not all genes have an equal chance of transfer. The gene must provide some kind of advantageous phenotype or else it will be lost from the genome quickly. Essential genes are unlikely to present in one strain and not in another so they are not expected to be transferred. Rarer genes are much likelier to be new to a strain and provide some beneficial functions, these genes tend to accumulate into operons for more efficient transfer.

How does HGT occur?

Gene transfer can take place via 3 mechanisms: Transformation, Transduction and Conjugation. In order for gene transfer to occur successfully the DNA must be delivered from the donor cell, incorporated into the genome of the recipient and be expressed by the transcriptional and translational machinery.

Transformation: Uptake of naked DNA by competent cells. Double-stranded DNA binds to the cell surface, taken up and incorporated into the genome. Some species are naturally competent, others can be made artificially competent. Through this mechanism even distantly related organisms can share DNA.

Transduction: Transducing particles arise by accidental packaging of chromosomal DNA. Phage-encoded proteins can promote the integration of the transferred sequence into the host chromosome to protect it from degradation by host restriction endonucleases. The amount of DNA that can be transferred in a single event is limited by the size of the phage capsid, but can range upwards of 100 kilo bases (kb).

Conjugation: In this mechanism, DNA is transferred from a donor to a recipient strain in the form of a plasmid that integrates into the chromosome to form a High Frequency Recombinant. Conjugation may also take place through transposons. By conjugation, genetic materials can be exchanged even between different domains provided the donor and recipient cells are in physical contact with one another.

Detecting lateral transfer

How can it be established that a new sequence of DNA is in the genome because of HGT? The most conclusive way would be to observe the transfer as it occurs, but this is impossible when sampling genomes of microbes from the wild. It is important to remember that point mutations do cause changes in function so how do we distinguish between modified, original genes and newly transferred ones?

Genes that have been acquired from a donor genome share the characteristics of the genome sequence and not the hosts. With the recent explosion in genomic sequencing its becoming easier to compare a sequence with the rest of the genome. If the sequence characteristics are found to be different then it indicates that this gene has been transferred into the genome.

Codon bias is the used to compare the GC content of the sequence to the rest of the genome. Bacterial species display a wide degree of variation in their overall G+C content, but the genes in a particular species' genome are fairly similar with respect to their base compositions

In some cases, it is possible to establish the evolutionary history of a gene by analysing its distribution among various lineages. If a gene is confined to one taxon or species, it is more likely to have been acquired through gene transfer than to have been lost independently from multiple lineages. However, one cannot rule out the possibility that a particular phenotypic trait such as resistance to certain antibiotics has evolved independently in diverse lineages through point mutations in existing genes (Ochman et al 2000). Hence, it may not always be possible to distinguish between convergent evolution and horizontal transfer on the basis of phylogenetic analyses alone. In fact, the best clues to the origin and ancestry of any gene within a bacterial chromosome are usually provided by the intrinsic sequence characteristics of the gene itself.

In any chromosome, ancestral (vertically transmitted) genes experience a particular set of directional mutation pressures (Sueoka 1988), mediated by the specific features of the replication machinery of the cell, such as the balance of the dNTP pools, mutational biases of the DNA polymerases, efficiency of mismatch repair systems and so on (Lawrence 1999). Apart from the mutational bias, there are several other characteristic features such as synonymous codon bias (Ikemura 1985; Sharp and Li 1987; Andersson and Kurland 1990; Pan et al 1998), fractal distribution of nucleotides (Jeffrey 1990; Dutta and Das 1992) or dinucleotide relative abundance (Karlin et al 1997) which leave distinct fingerprints on sequences native to that cytoplasm, while the foreign genes, i.e. genes acquired through HGT, retain the characteristics of the donor genome and thus can be distinguished from ancestral DNA (Lawrence and Ochman 1998). Comparative analyses of E. coli and Salmonella enterica chromosomes have revealed that a large number of S. Enteric genes, which are not present in E. coli (and other closely related enteric species), have nucleotide and codon compositions significantly different from the characteristic G + C-content and codon bias of the rest of the chromosome (Groisman et al 1992; Lawrence and Ochman 1997). Regions adjacent to genes identified as being laterally acquired ones often contain relics of sequences that might have helped in their integration, such as remnants of translocation elements, attachment sites of phage integrases, transfer origins of plasmids, which further affirm their recent integration in the genome.

Based on these concepts, various methods have been developed for identification of potential foreign genes. Among them, are the direct methods such as subtractive hybridization (Lan and Reeves 1996) as well as indirect approaches like assessment and comparison of overall G + C-content (Groisman et al 1992), codon-positionspecific nucleotide composition (Lawrence and Ochman 1997, 1998), codon usage pattern (Karlin et al 1998a,b), dinucleotide relative abundance signature (Karlin and Burge 1995) and Markov Chain Analyses of oligonucleotide biases (Hayes and Borodovsky 1998).

Atypical sequence characteristics however, can also be exhibited by genes whose products perform some special functions and therefore have a biased amino acid composition. In order to find out the total number of putative horizontally transferred genes in a genome, appropriate corrections should be made for such native genes that have selectively evolved to atypical compositions. In other words, the genes for which nucleotide sequence characteristics depart from the prevalent features of their resident genome, but where amino acid compositions of the corresponding gene-products are not unusually biased, have a strong potential of being horizontally acquired.

It would appear that bacterial genome is far from fixed, exchanging genomic material, keeping beneficial segments and rejecting

Equally exciting is the realization that viruses have a fundamental role in the biosphere, in both immediate and long-term evolutionary senses. Recent work suggests that viruses are an important repository and memory of a community's genetic information, contributing to the system's evolutionary dynamics and stability. This is hinted at, for example, by prophage induction, in which viruses latent in cells can become activated by environmental influences. The ensuing destruction of the cell and viral replication is a potent mechanism for the dispersal of host and viral genes.

It is becoming clear that microorganisms have a remarkable ability to reconstruct their genomes in the face of dire environmental stresses, and that in some cases their collective interactions with viruses may be crucial to this. In such a situation, how valid is the very concept of an organism in isolation? It seems that there is a continuity of energy flux and informational transfer from the genome up through cells, community, virosphere and environment. We would go so far as to suggest that a defining characteristic of life is the strong dependency on flux from the environment be it of energy, chemicals, metabolites or genes.

Mayr, E. (1942) Systematics and the Origin of Species (Columbia Univ. Press, New York).

Kevin de Queiroz April 25, 2005 Ernst Mayr and the modern concept of species