Tuesday, July 3, 2018

New guidelines to help with protein naming


Why is consistent protein naming important?

For many proteins, a variety of different names are used across the scientific literature and public biological databases which makes effective organization and exchange of biological information a difficult task. Consistent protein nomenclature is indispensable for communication, literature searching and retrieval of database records.

New protein nomenclature guidelines

To address this issue and provide some help in protein naming, a set of protein nomenclature guidelines have been produced jointly by the European Bioinformatics Institute (EMBL-EBI), the National Center for Biotechnology Information (NCBI), the Protein Information Resource (PIR) and the Swiss Institute for Bioinformatics (SIB). UniProt has been heavily involved in this work along with other groups from the four institutes. These efforts have built on existing guidelines which were already in use by groups such as UniProt and RefSeq, expanding and consolidating them into a single shared document which provides a comprehensive set of recommendations.

What makes a good protein name?

A good protein name is one which is unique, unambiguous, can be attributed to orthologs from other species and follows official gene nomenclature where applicable. The guidelines help to achieve this goal by covering all aspects of protein naming from advice on expert sources of protein names and how to name novel proteins of unknown function to more detailed advice such as terms to avoid in a protein name and acceptable abbreviations.

Who are the guidelines intended for?

The guidelines are intended for use by anyone who wants to name a protein. Groups who will find these guidelines helpful include:

  • Biocurators who want to assign a protein name as part of a database record
  • Bioinformaticians who intend to assign protein names as part of gene annotation pipelines prior to submission to public archives
  • Researchers who isolate a new protein and want to name it prior to publication

Where are the guidelines?

The guidelines can be found on the UniProt website at http://www.uniprot.org/docs/International_Protein_Nomenclature_Guidelines.pdf and on the NCBI website at https://www.ncbi.nlm.nih.gov/genome/doc/internatprot_nomenguide/.

Can I give feedback?

We welcome feedback on these guidelines and are happy to receive any comments at help@uniprot.org which we will share with the other groups involved in producing the document and use to improve the guidelines in future updates.

Wednesday, May 9, 2018

Learning from our closest living relatives


In the March 2018 release, UniProt added the proteins of 10 new primate species to our collection of complete proteomes; the set of proteins believed to be expressed by an organism and typically obtained from the translation of a fully sequenced, annotated genome. As of release 2018_04 the total number of primate complete proteomes in UniProtKB stands at 24, a set which of course includes that of human. So why is this important?



Studying non-human primates enables scientists to understand the evolution of genomic change and how this has impacted on protein expression patterns. Comparisons across proteome sets allow us to understand which proteins are shared by all primates, and which are species specific, and how changes in protein expression patterns have affected our evolutionary development.
For example, multiple copies of a domain of unknown function, the recently renamed Olduvai domain (IPR010630), are found in neuroblastoma breakpoint family (NBPF) proteins. The copy number is highest in humans, lower in African great apes and further reduced in Orangutan and Old World monkeys. It has been speculated that this may be directly related to the size of the primate’s brain, more specifically to the volume of the neocortex, and links between domain copy number and both cognitive function and the severity of autism have been identified.
Another study looked at why gene duplication has led to a marked expansion of HLA proteins in macaque monkeys in comparison to other primates. The HLA cell-surface proteins are responsible for the regulation of the immune system, so does this mean that this genus of monkeys is more resistant to infection than other closely related species?



Primate proteomes are also studied as models of human disease. Non-human primates appear to be resistant to developing Alzheimer’s disease, despite depositing misfolded protein in the brain as they age. Aged brains from gorillas, orangutans, chimpanzees, green monkeys, baboons, guenons, mangabeys, squirrel monkeys, marmosets, tamarins, and lemurs have all been examined but Aβ plaques and neurofibrillary (tau) tangles have not been identified, nor do any of these species develop the behavioural and pathologic changes associated with the disease. Studying why Alzheimer’s disease fails to develop in species that are closely related to humans could help us to identify new therapeutic targets and treatments for this condition.


How do I find this these data?



To find the full list of primate proteomes, click on the ‘Proteomes’ button on the UniProt website Home Page, then search for ‘Primates’.

The proteomes portal provides two types of proteomes:


References 

Demuth J. P., et al (2006). The evolution of mammalian gene families. PLoS One 1:e85. 10.1371/journal.pone.0000085
Hahn, MW. Et al. (2007)  Accelerated Rate of Gene Gain and Loss in Primates Genetics. 177(3): 1941–1949. doi:  10.1534/genetics.107.080077
Sikela, JM, van Roy, F. (2018) A proposal to change the name of the NBPF/DUF1220 domain to the Olduvai domain https://f1000research.com/articles/6-2185/v1
Walker LC, Jucker M. The Exceptional Vulnerability of Humans to Alzheimer's Disease. Trends Mol Med. 2017 23(6) 534-545. doi:10.1016/j.molmed.2017.04.001. PMID: 28483344.
Sikela, J. M., & Searles Quick, V. B. (2018). Genomic trade-offs: are autism and schizophrenia the steep price of the human brain? Human Genetics, 137(1), 1–13. https://doi.org/10.1007/s00439-017-1865-9