Pseudomonas aeruginosa is the latest bacterium to have its complete genome sequenced. P. aeruginosa is a gram-negative bacterium that is closely related to E. coli (the work horse of the molecular biologist). It is also responsible for various serious infections in patients with burns, AIDs, and cystic fibrosis that are extremely hard to treat given that these organisms have a long-recognized natural resistance to most front-line antibiotics.

Of greater interest is the versatility of these organisms, as they thrive in a variety of different environments, including the soil, various animal and plant tissues, marshes, and coastal marine habitats. They can even exist as biofilms growing on rocks (as long as the rocks remain wet).

There are several aspects of the genome that might be of interest to teleologists..

1. Size. The genome of P. aeruginosa is the largest one sequenced to date. It contains 6.3 million base pairs, which is interesting because this is larger than some unicellular eukaryotes. In fact, P. aeruginosa is predicted to have 5,570 coding genes, which is slightly less than the 6200 gene products used by baker's yeast. Clearly, eukaryotes are not simply larger procaryotes that have acquired more genes through evolution. The distinction between the two cell types is not so much an issue of complexity or gene copy number, but the inherent system logic employed by both. Both cell types represent two different logical solutions to life.

2. Gene duplication . As mentioned above, P. aeruginosais closely related to E. coli, so the two genomes were compared in great detail. The researchers note, " the median amino-acid identity within the aligned region of the P. aeruginosa-E. coli orthologues is only 40%." The two genomes are organized in essentially the same manner: "Distributions of ORF sizes and inter-ORF spacings are both nearly identical in the two genomes." They also noted the following:

At the level of amino-acid sequence conservation, residual stretches of locally conserved gene order between P. aeruginosa and E. coli are far more evident than are internal duplications in either genome. At the same BLASTP threshold employed for the comparisons between the P. aeruginosa ORFs and those of other bacterial genomes, we searched for clusters of five or more ORFs that are conserved between P. aeruginosa and E. coli, allowing single-ORF insertions or deletions within the clusters. Thirty-three distinct clusters were identified, which included 256 ORFs; seven of these clusters involve ten or more ORFs. This analysis showed only a few gene clusters duplicated within either the E. coli or the P. aeruginosa genome. Hence, with respect to local gene order, evidence of the common ancestry of segments of the P. aeruginosa and E. coli genome is far more abundant than are the vestiges of more recent duplication events of comparable size within either genome.

What does this all mean? First, it looks like the natural frequency of gene duplication is far below the frequency of amino acid substitutions (where the median amino acid identity if 40%). This could pose a problem for evolutionary accounts which rely heavily on multiple gene duplications in a relatively short time period. Secondly, it means that the larger size of the pseudomonad genome is not explained by gene duplications from a simpler E. coli-like ancestor. What makes the two different is that pseudomonas is much more functionally diversified.

3. A model system. According to my ID views, I envision the "origin of life" as the seeding of this planet with a consortium of microbes that involved cells that were more complex than typical extant bacterial. P. aeruginosa provides a rough, but helpful, working model to visualize these original states.

a. It is semi-autonomous. It encodes "most of the genes required for biosynthesis of amino acids, nucleic acids and cofactors" and this helps explain its semi-ubiquitous distribution is various different environments.

b. It is highly versatile. More so than most bacteria, pseudomonas encodes a very large number of outermembrane proteins, including 34 gene products involved in the uptake of iron. P. aeruginosa also has nearly 300 cytoplasmic membrane transport systems, where about two-thirds of which appear to be involved in the import of nutrients and other important molecules. Consistent with this is the finding that pseudomonas can metabolize a wide variety of carbon compounds. What is also interesting is that pseudomonas doesn't have many sugar transporters, where (echoing IC), it also lacks an intact glycolytic pathway. Apparently, these organisms are so good at metabolizing other carbon compounds that glycolysis has been lost by drift.

c. It is highly modular. The genome of pseudomonas is so large basically because it encodes a very large number of small gene families that each encode distinct functions. Standard evolutionary views would have expected such an increase in genomic size to be reflected as larger gene families and not a large number of distinct gene families.

d. It is highly complex. In keeping with the large genome, pseudomonas encode the largest number or regulatory factors among bacteria. As the researchers note, " There is an extraordinary number of putative two-component regulatory system proteins, with 55 sensors, 89 response regulators and 14 sensor-response regulator hybrids, far more than found in the other genomes analysed. Such systems permit organisms to respond to changes in their environment, and are often associated with global regulatory systems" What's more, the genome contains "468 genes containing motifs characteristic of transcriptional regulators or environmental sensors." This finding allowed the researchers to identify a pattern:

Similar computational analysis of regulatory motifs in 22 genomes indicates that as bacterial genome size increases, the proportion of the genome devoted to regulatory proteins increases as well. This trend appears most prominent in prototrophic bacteria that can survive in diverse environments. For example, motifs characteristic of regulatory proteins are found in 5.8% of E. coli genes and 5.3% of B. subtilis genes, but only in 3.0% of genes in M. tuberculosis, a highly specialized pathogen with a comparable genome size. Helicobacter pylori , another highly specialized bacterial pathogen with a much smaller genome, possesses even less regulatory potential (1.1% of genes).

One way to interpret this is that as bacteria evolve to become specialized (as most pathogens are), they lose genomic information and its consequent regulation. In other words, if you don't have to exist in an unpredictable environment, you don't need to tools for such existence.

e. It is redundant. Pseudomonas has 3 of the 4 known protein secretion systems. What's more, it possesses four separate chemotaxis systems. One is similar to that found in Salmonella, another resembles that from Rhodobacter, another resembles that from E. coli, and another from Myococcus. Such redundancy ties in to the versatile and robust essence of this organism.

Thus, while I would not argue that pseudomonas itself was designed, I think it represents a promising model to better characterize the state of the original life forms.

ID THINK