Gene-based inferences

Some years before our work started, the gene cluster from Streptomyces encoding the biosynthesis of the polyketide-based, polyenoyl chain of the lipomycins had been characterized by coworkers of a faculty colleague of ours, Professor Andreas Bechthold. Their analysis was in accordance with Zeeck s loci attributed to the methyl substituents. Gene-based inferences for the configuration of the side-chain stereocenters were not made at that time. Such inferences were made later, when our work was well underway. They came from Kitsche and Kalesse These workers compared ketoreductase amino acid sequences encoded by dozens of such gene clusters with the... 

Adjust for multiplicity of simultaneous inference on multiple genes based on the joint distribution of estimators. 

For proteins that are members of gene families, such as cytochrome P450, available structural models derived from X-ray crystallography and NMR data allow inference of the structure of newly discovered family members. The inference is based on the sequence variations derived from comparing the reference and new DNA sequences. While a high degree of computational power is needed, predictions based on this approach provide preliminary estimates of protein structure without a huge investment in expression, purification, and crystallization. A full structural elucidation requires several years for each protein, even if it can be crystallized. 

Newcomb, R.D. and Gleeson, D.M. (1998). Pheromone evolution within the genera Ctenopseustis and Planotortrix (Lepidoptera Tortricidae) inferred from a phylogeny based on cytochrome oxidase I gene variation. Biochemical Systematics and Ecology 26 473 184. 

The fact that there are four saline-based chromophores and the experimental evidence that they appear in at least two distinct but overlapping sets of three should be important in inferring the actual relationship between the genes and the chromophores. Comparing the genetic code for the common chromophores between the ultraviolet sensitive members of Arthropoda who are believed to lack a L-channel chromophore and the members of Mollusca and Chordata who do exhibit L-channel sensitivity should prove beneficial. Since most members of Chordata are known to be tetrachromatic, focusing on the presence or absence of the ultraviolet chromophore may not be as fruitful. Recent data has confirmed that the system architecture of the human system is tetrachromatic. Our vision in the ultraviolet is limited primarily by the absorption of our lens group. 

Despite their antiquity (perhaps 2.5 billion years old), the resurrected ancestral elongation factors are inferred for bacteria that lived long after the origin of life. Nevertheless, the notion that early life lived at high temperatures, in water, and at nearly neutral pH is consistent with available data. For example, a recent reconstruction of the phylogenetic tree of life based on 31 common gene families supports the notion that the last common ancestor lived at high temperatures.65... 

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