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Opinion Article
Revised

Changing the name of the NBPF/DUF1220 domain to the Olduvai domain

[version 2; peer review: 3 approved]
Previously titled: A proposal to change the name of the NBPF/DUF1220 domain to the Olduvai domain
PUBLISHED 17 Jul 2018
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OPEN PEER REVIEW
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Abstract

We are jointly proposing a new name for a protein domain of approximately 65 amino acids that has been previously termed NBPF or DUF1220. Our two labs independently reported the initial studies of this domain, which is encoded almost entirely within a single gene family. The name Neuroblastoma Breakpoint Family (NBPF) was applied to this gene family when the first identified member of the family was found to be interrupted in an individual with neuroblastoma.
Prior to this discovery, the Pfam database had termed the domain DUF1220, denoting it as one of many protein domains of unknown function. It has been Pfam’s intention to use “DUF” nomenclature to serve only as a temporary placeholder until more appropriate names are proposed based on research findings.
We believe that additional studies of this domain, primarily from our laboratories over the past 10 years, have resulted in furthering our understanding of these sequences to the point where proposing a new name for this domain is warranted. Because of considerable data linking the domain to human-specific evolution, brain expansion and cognition, we believe a name reflecting these findings would be appropriate. With this in mind, we have chosen to name the domain (and the repeat that encodes it) Olduvai. The gene family will remain as NBPF for now. The primary domain subtypes will retain their previously assigned names (e.g. CON1-3; HLS1-3), and the three-domain block that expanded dramatically in the human lineage will be termed the Olduvai triplet.
The new name refers to Olduvai Gorge, which is a site in East Africa that has been the source of major anthropological discoveries in the early-mid 1900’s. We also chose the name as a tribute to the scientists who made important contributions to the early studies of human origins and our African genesis.

Keywords

DUF1220, NBPF, protein domain, human brain evolution, copy number, gene duplication, genome evolution, Olduvai Gorge

Revised Amendments from Version 1

We appreciate the helpful comments of reviewers and have modified our original paper to address specific reviewer suggestions. Specifically we have:
1. Altered the title to now read “Changing the name of the NBPF/DUF1220 domain to the Olduvai domain”.
2. After “propose that, for now, the gene family name should remain NBPF.” we added the following sentence: “It is also worth noting that there is an Olduvai domain that is separate from those encoded by NBPF genes: a single, likely ancestral, copy of the domain is found within the PDE4DIP/myomegalin gene.”
3. Changed PFAM to Pfam
4. (after “our African genesis”.) we added the following sentence. “While we are aware that naming a protein domain after a geographic location is unusual, we believe the name Olduvai is more than a place. Rather it has also come to be thought of as a symbol of the efforts of our species to understand itself.”
5. Added the name Mark Johnston to the Acknowledgments.

To read any peer review reports and author responses for this article, follow the "read" links in the Open Peer Review table.

Protein domains are portable units within proteins that can serve important biological functions. They have been implicated in a broad range of key biological phenomena, including development, disease and evolution1,2. Here we jointly propose a new name for a protein domain of approximately 65 amino acids that has been previously termed NBPF3 or DUF12204. Our two labs independently reported the initial studies of this domain, which is encoded almost entirely within a single gene family. The name Neuroblastoma Breakpoint Family (NBPF) was applied to this gene family when the first identified member of the family was found to be interrupted in an individual with neuroblastoma3,5. Prior to this discovery, the Pfam database had termed the domain DUF1220, denoting it as one of many protein domains of unknown function6. It has been Pfam’s intention to use “DUF” nomenclature to serve only as a temporary placeholder until more appropriate names are proposed based on research findings. We believe that additional studies of this domain, primarily from our laboratories over the past 10 years, have resulted in furthering our understanding of these sequences to the point where proposing a new name for this domain is warranted.

Key findings relevant to assigning a name to the domain are as follows:

  • 1. The domain has been repeatedly linked with human-specific evolution. The haploid human genome is estimated to encode approximately 300 copies of the NBPF/DUF1220 domain, while the copy number for other species is substantially lower: great apes 90–120, monkeys 30–40, and all other mammalian species 1–97,8. The increase in humans (at least 165 additional human copies) represents the largest human lineage-specific copy number increase of any coding region in the genome. These findings, involving the copy number of a protein coding domain, provide strong support for an involvement in human-specific evolution.

  • 2. The domain has been linked with human brain evolution and cognitive function. Over the past 10 years we have published several papers on NBPF/DUF1220 protein domains and the NBPF gene family. These have implicated the copy number of the domain in human brain evolution7,911, brain size-related phenotypes7,911, brain disorders (autism/schizophrenia/micro- and macrocephaly)9,1214, and measures of cognitive function13,15. Also, our finding of a robust linear association between NBPF/DUF1220 copy number and brain size across primate species was confirmed by an independent study16.

Given the above research findings, a new name for this protein domain that is related to human-specific evolution would be appropriate. We believe a name that would do this is “Olduvai” (ohl’-du-vi) (when necessary it can be abbreviated as “ODV”). This name refers to Olduvai Gorge, which is located in the rift valley of Eastern Africa. Olduvai has been the site of key paleoanthropological discoveries related to human origins and has been called “the Cradle of Mankind”, and “the Grand Canyon of Human Evolution”17. Deposits at the gorge are estimated to cover a time span from 2.1 million to 15,000 years ago, and the fossil remains that have been identified there are thought to represent more than 60 hominins (members of the human lineage). These findings are believed to constitute the most continuous known record of human evolution over the past 2 million years, and the longest known archaeological record of the development of stone-tool industries. Olduvai Gorge was designated part of a UNESCO World Heritage site in 197918. Just as the protein domain appears to be important to human-specific evolution, so too, Olduvai Gorge has provided key insights into human’s evolutionary origin. We believe both are central to the story of what made us human.

Finally, we have also chosen this name because it reflects an appreciation for the important contributions of the scientists who made major anthropological discoveries in Africa in the early/mid-20th century that stimulated further research into human origins and our African genesis. While we are aware that naming a protein domain after a geographic location is unusual, we believe the name Olduvai is more than a place. Rather it has also come to be thought of as a symbol of the efforts of our species to understand itself.

While we believe that the domain and repeat should now be called “Olduvai”, we also propose that, for now, the gene family name should remain NBPF. It is also worth noting that there is an Olduvai domain that is separate from those encoded by NBPF genes: a single, likely ancestral, copy of the domain is found within the PDE4DIP/myomegalin gene. In summary, the NBPF domain and DUF1220 domain will be termed the Olduvai domain, and the NBPF repeat and DUF1220 repeat will be termed the Olduvai repeat. The primary gene family that encodes these sequences will continue to be called NBPF, and the primary domain subtypes will retain established nomenclature (CON1-3, HLS1-3)8. The three-domain block, composed of HLS1, HLS2 and HLS3 subtypes, that is tandemly repeated within several human NBPF genes and responsible for the great majority of additional human copies of the domain, will be called the Olduvai triplet.

The Olduvai domain hyper-amplification in the human lineage was one of the most extreme and rapid copy number expansions in the human genome, and we look forward to additional studies that may provide further insights into the role this protein domain family plays in human disease and evolution.

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VERSION 2 PUBLISHED 28 Dec 2017
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Sikela JM and van Roy F. Changing the name of the NBPF/DUF1220 domain to the Olduvai domain [version 2; peer review: 3 approved]. F1000Research 2018, 6:2185 (https://doi.org/10.12688/f1000research.13586.2)
NOTE: If applicable, it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Open Peer Review

Current Reviewer Status: ?
Key to Reviewer Statuses VIEW
ApprovedThe paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approvedFundamental flaws in the paper seriously undermine the findings and conclusions
Version 2
VERSION 2
PUBLISHED 17 Jul 2018
Revised
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Reviewer Report 25 Jul 2018
Christian J.A. Sigrist, Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland 
Approved
VIEWS 7
The authors have taken into account the reviewers remarks. I hope that this paper will encourage the NBPF and myomegalin ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Sigrist CJA. Reviewer Report For: Changing the name of the NBPF/DUF1220 domain to the Olduvai domain [version 2; peer review: 3 approved]. F1000Research 2018, 6:2185 (https://doi.org/10.5256/f1000research.16945.r36115)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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8
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Reviewer Report 17 Jul 2018
Alex Bateman, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK 
Approved
VIEWS 8
I approve the new ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Bateman A. Reviewer Report For: Changing the name of the NBPF/DUF1220 domain to the Olduvai domain [version 2; peer review: 3 approved]. F1000Research 2018, 6:2185 (https://doi.org/10.5256/f1000research.16945.r36117)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
Version 1
VERSION 1
PUBLISHED 28 Dec 2017
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Reviewer Report 18 Jan 2018
Elspeth A. Bruford, HUGO Gene Nomenclature Committee (HGNC), European Bioinformatics Institute (EMBL-EBI), Hinxton, UK 
Approved
VIEWS 16
This brief opinion article describes the authors' proposal to rename a domain found in a discrete group of proteins, which was originally named DUF1220 (domain of unknown function 1220) and subsequently reassigned as NBPF. The NBPF nomenclature referenced the fact ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Bruford EA. Reviewer Report For: Changing the name of the NBPF/DUF1220 domain to the Olduvai domain [version 2; peer review: 3 approved]. F1000Research 2018, 6:2185 (https://doi.org/10.5256/f1000research.14757.r29429)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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18
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Reviewer Report 17 Jan 2018
Christian J.A. Sigrist, Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland 
Approved with Reservations
VIEWS 18
This paper proposes to change the name of a protein domain from NBPF (Neuroblastoma Breakpoint Family) to Olduvai, arguing that this new name illustrates the fact that the domain copy number has been linked with human evolution. Although, it is ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Sigrist CJA. Reviewer Report For: Changing the name of the NBPF/DUF1220 domain to the Olduvai domain [version 2; peer review: 3 approved]. F1000Research 2018, 6:2185 (https://doi.org/10.5256/f1000research.14757.r29374)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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41
Cite
Reviewer Report 02 Jan 2018
Alex Bateman, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge, UK 
Approved
VIEWS 41
This manuscript describes a straightforward proposal to rename the NBPF/DUF1220 domain to the Olduvai domain. This is welcome because the domain has been referred to by two different names in the past.  The authors are the major players in the ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Bateman A. Reviewer Report For: Changing the name of the NBPF/DUF1220 domain to the Olduvai domain [version 2; peer review: 3 approved]. F1000Research 2018, 6:2185 (https://doi.org/10.5256/f1000research.14757.r29376)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.

Comments on this article Comments (0)

Version 2
VERSION 2 PUBLISHED 28 Dec 2017
Comment
Alongside their report, reviewers assign a status to the article:
Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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