Quantitative Biology


Nylonase Genes and Proteins - Distribution, Conservation, and Possible Origins

Authors: S.T. Cordova, J.C. Sanford

Nylon comprises a family of man-made substances that were first manufactured in 1935. Nylonases are biological enzymes that can break down nylon oligomers. Although the most prominent nylonases are within the family of enzymes classified as 6-aminohexanoate hydrolases, some enzymes not formally classified as 6-aminohexanoate hydrolases also have the ability to breakdown nylons, and so can also be classified as nylonases. Organisms that encode a nylonase enzyme do not necessarily have the ability to actually survive on a nylon substrate as their sole carbon source. Among the first documented organisms that did have this ability was the soil bacterium Arthrobacter KI72. It has long been thought that nylonase genes and proteins were essentially absent from the biosphere prior to 1935. This belief led to the widespread assumption that any nylonase gene observed in the present must have emerged since 1935. Several authors developed hypothetical models of how a specific nylonase gene (the nylB gene found within Arthrobacter KI72), might have arisen very recently as a de novo gene. In this paper we show that the widely-held assumption that all nylonase genes must have evolved very recently is no longer credible. This is in light of the wide-spread distribution of diverse nylonases throughout the biosphere. Likewise, we show that the early speculations regarding the possible de novo origin of the nylB nylonase gene are no longer credible. Our review of the literature shows that a variety of nylonase-digesting bacteria have been found in extremely diverse natural environments – far removed from any synthetic nylon sources. In addition, we show there are over 1800 organisms with computationally predicted (provisional) 6-aminohexanoate hydrolase/nylonase genes in the NIH-funded UNIPROT database. These 1800 predicted nylonases are not yet experimentally confirmed to cleave nylons, but have significant homology to the experimentally confirmed nylonases. In addition to 6-aminohexanoate hydrolases, proteases like trypsin and certain lipases have been experimentally demonstrated to have nylonase activity. If we include all proteases and lipases that may have nylonase activity, the number of organisms with nylonase activity may exceed ten thousand. The widespread distribution of nylonases and their homologs strongly suggests that nylonases were already widespread prior to 1935. Lastly, we have carefully examined the claims that the nylB gene arose as a de novo gene very recently. The theories of Ohno (the frame shift hypothesis) and Okada (the gene duplication hypothesis), were speculative in nature, and yet were uncritically accepted. In light of new data, these early speculations no longer appear tenable.

Comments: 78 Pages.

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[v1] 2017-08-25 14:38:23

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