Testing the Hypothesis that the Nylonase NylB Protein Arose de novo via a Frameshift Mutation
In 1984, Susumu Ohno hypothesized that the nylon-degrading enzyme NylB arose de novo via a frameshift mutation within a hypothetical precursor protein (PR.C). However, the frameshift hypothesis was never actually tested, and there was no actual supporting biological evidence supporting the hypothesis. For decades, the frameshift hypothesis has been uncritically accepted as the correct explanation for the origin of NylB. In this paper we have surveyed the literature relevant to the frameshift
... o the frameshift hypothesis as well as the various alternative models that have been published regarding the origin of NylB. We have employed bioinformatic methods and leveraged databases not available when the frameshift hypothesis was first put forward. Results We searched multiple protein databases to determine the distribution of NylB and any possible homologs. We then determined the distribution of other known nylonases and their possible homologs. We also determined the distribution of Ohno's hypothetical PR.C. protein and any possible homologs. Lastly, we determined what protein families the various nylonases belong to. We found that the NylB protein is widely occurring, has thousands of homologs, and is found in diverse organisms and diverse habitats. It is not a new or unique protein. Likewise, we found that the other known nylonases are also widely occurring, have thousands of homologs, and are found in diverse organisms and diverse habitats. However, the hypothetical PR.C protein does not show up in any of the same databases, and there is no evidence of any homologs. Conserved domain searches showed that NylB is a member of the beta lactamase protein family -a highly conserved family of enzymes. Likewise, the other known nylonases belong to well-characterized enzyme families.Conclusions Our results very effectively falsify the NylB frameshift hypothesis, while they strongly support an alternative hypothesis by Yomo. Like NylB, none of the other nylonases that we examined were substantively new or unique. All had thousands of homologs, and they were found in diverse organisms and diverse habitats. Our findings not only falsify the NylB frameshift hypothesis, they also falsify the long-held assumption that all nylonases evolved after the invention of nylon in 1935. Sep;6(9):663-73. 28. Okamura K, Feuk L, Marques-Bonet T, Navarro A, Scherer SW. Frequent appearance of novel protein-coding sequences by frameshift translation. 2006 December;88(6):600-697. 29. Kiumarsi A, Parvinzadeh M. Enzymatic hydrolysis of nylon 6 fiber using lipolytic enzyme. A, et al. Xray Crystallographic analysis of the 6-aminohexanoate cyclic dimer hydrolase.