Whole-genome sequencing sheds light on adaptation of koala bears to their diet of eucalyptus leaves

The study reported in the Nature Genetics publication was primarily carried out in order to determine the entire koala genome by whole-genome sequencing (WGS). They found that the haploid genome spanned ~3.42 billion nucleotides, i.e. a diploid genome of ~3.42 gigabase pairs (Gbp). An incredible amount of information was gained by these authors in producing a complete and contiguous marsupial reference genome –– including centromeres.

CYP2C enzyme metabolism and substrate specificity of course could be the project for a future grant proposal. However, constructing 31 CYP2C cDNA expression vectors and inserting each of them into either bacteria or yeast in order to determine enzyme substrate specificity –– is no trivial experiment. However, I hope to see those results completed (by someone) within the next few years. πŸ™‚

From: ((Anonymous))
Sent: Thursday, October 04, 2018 4:19 PM


I’m suprised that the journal and the reviewers of this paper did not request proof that one or more of these koala CYP2C enzymes did indeed metabolize camphor or other various eucalyptus oils.
We did something like that with 36 sequence variants of POR (P450-oxidoreductase), tested for CYP1A2 and 2C19 activity. Took about a year, but certainly do-able in a small lab –– if you have a plate reader and a colorimetric assay. For anyone interested, the 2008 Pharmacogenet Genom paper is attached. Also, our 2011 review, on the entire topic, in Mol Cell Endocrinol is attached.

Along these same lines, just this minute I came across this article [abstract pasted below] –– describing a rapid procedure to measure the functional activity of 1,056 discovered single-nucleotide variants, just within the first 192 amino acids of the BRCA1 protein, measuring efficiency of double-strand DNA breaks. Therefore, ’31 CYP2C variants’, or ’36 POR variants’, would now be ‘small potatoes’ if one considers the latest advances in technology. πŸ™‚


Am J Hum Genet. 4 Oct 2018; 103: 498-508
A Multiplex Homology-Directed DNA Repair Assay Reveals the Impact of More Than 1,000 BRCA1 Missense Substitution Variants on Protein Function.

Starita LM1, Islam MM2, Banerjee T2, Adamovich AI2, Gullingsrud J3, Fields S4, Shendure J5, Parvin JD6.

Loss-of-function pathogenic variants in BRCA1 confer a predisposition to breast and ovarian cancer. Genetic testing for sequence changes in BRCA1 frequently reveals a missense variant for which the impact on cancer risk and on the molecular function of BRCA1 is unknown. Functional BRCA1 is required for the homology-directed repair (HDR) of double-strand DNA breaks, a critical activity for maintaining genome integrity and tumor suppression. Here, we describe a multiplex HDR reporter assay for concurrently measuring the effects of hundreds of variants of BRCA1 for their role in DNA repair. Using this assay, we characterized the effects of 1,056 amino acid substitutions in the first 192 residues of BRCA1. Benchmarking these results against variants with known effects on DNA repair function or on cancer predisposition, we demonstrate accurate discrimination of loss-of-function versus benign missense variants. We anticipate that this assay can be used to functionally characterize BRCA1 missense variants at scale, even before the variants are observed in results from genetic testing.

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