Decision letter | Genomic DNA transposition induced by human PGBD5

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Genomic DNA transposition induced by human PGBD5

Decision letter

Affiliation details

Memorial Sloan Kettering Cancer Center, United States; Weill Cornell Medical College, United States; Harvard Medical School, United States; University of Utah School of Medicine, United States; Cornell University, United States
Michael R Botchan, Reviewing editor, University of California, Berkeley, United States

eLife posts the editorial decision letter and author response on a selection of the published articles (subject to the approval of the authors). An edited version of the letter sent to the authors after peer review is shown, indicating the substantive concerns or comments; minor concerns are not usually shown. Reviewers have the opportunity to discuss the decision before the letter is sent (see review process). Similarly, the author response typically shows only responses to the major concerns raised by the reviewers.

Thank you for submitting your work entitled “Genomic DNA transposition induced by human PGBD5” for peer review at eLife. Your submission has been evaluated by James Manley (Senior Editor), a Reviewing Editor, and two reviewers. One of the two reviewers, Harmit Malik, has agreed to share his identity.

The reviewers have discussed the reviews with one another and the Senior Editor has drafted this decision to help you prepare a revised submission.

In this well-performed study, the authors reveal the rather surprising conservation of catalytic activity of PGBD5, a piggyBac-derived domesticated transposase gene that is one of the oldest conserved domestication events in vertebrates. One of the reviewers commented that: “this is definitely a result of high importance in the field. Not only is it surprising but it opens the possibility of as yet unanticipated DNA transposition in vertebrates that is itself of high interest.” However, while the results are interesting, there are a number of questions that need to be addressed before the paper will be suitable for publication in eLife.

Essential revisions:

1) What and where are the sequences in the human genome that the authors indicate are “piggyBac transposon-like”? The authors imply that the human piggyBac transposons are not identifiable based on an evolutionary argument, but given the conservation of the TIRs of the Trichoplusia ni transposon, how were putative human piggyBac transposons attempted to be found? How similar are the terminal and sub-terminal inverted repeats in human DNA elements thought to be related to piggyBac elements relative to the Trichoplusia ni piggyBac elements?

2) PGBD5 is revealed to have a rather non-canonical catayltic triad of aspartate residues compared to the original well characterized piggyBacs. Rather surprisingly, even the dependence on these newly identified aspartates is not obligatory for catalytic activity. The authors (we think correctly) interpret this to imply a rather divergent piggyBac lineage gave rise to PGBD5 – however, there is no attempt to identify such lineages from sequence databases and use them to refine ideas about catalytic site conservation. The data presented is quite convincing about the lack of conservation of canonical aspartates, but rather sparse on the evolutionary history and conservation of PGBD5-like domains. This should not be a difficult task and we would ask you to include phylogenetic analysis and multiple alignments to augment the alanine scanning results presented.

3) The current title of the paper should be revised to indicate that the human PGBD5 protein is mobilizing the heterologous piggyBac transposon DNA element from Trichoplusia ni.

Other issues to address:

1) Given that conservation of the terminal inverted repeats in the Trichoplusia ni piggyBac transposon and the statement in the paper that there are human DNA sequences related to piggybac transposons in the human genome, have the author tried to see if PGBD5 can mobilize the human sequences?

2) The authors say that the catalytic DDD triad of residues in PGBD5 was not easy to find. In fact, a previous paper from the Weiner group claimed, using phylogenetic evidence, that the PGBD5 protein would be inactive. The alignment shown indicates a lack of acidic residues in common other PiggyBac transposases. Did the authors look at the paper from Susan Wessler to see if their catalytic residues coincide with their extensive phylogenetic predictions (The catalytic domain of all eukaryotic cut-and-paste transposase superfamilies. Yuan YW, Wessler SR. Proc Natl Acad Sci U S A. 2011 May 10;108(19):7884–9)?

3) Based on the mutagenesis performed in the paper, are the three D residues identified in the present work found in the protein sequences of any of the other related human PGBD1-4 proteins or in any of the primate-specific PiggyBac family members? The authors might indicate, on the supplemental figure showing the canonical catalytic residues for the insect PiggyBac transposases, where the three DDD residues found by the alanine mutagenesis shown in this paper.

4) The assays shown indicate that the human PGBD5 protein is less active than the cognate Trichoplusia ni transposase in mobilizing the piggyBac transposon. Can the authors give a better quantitation of these data and state that explicitly in the text? Based on the figure, it looks like ∼ 4–fold less active.

5) What is the biological consequence of the PGBD5 mediated transposition? We believe this is outside the scope of the study, but could be presented with additional information about expression patterns of this gene, for instance in mouse development.