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UniProt release 2016_04

Published April 13, 2016

Headline

Small changes, big effects

Our brain has the ability to reorganize itself by forming new neural connections throughout life. This plasticity allows neurons to adjust their activities in response to new situations, to changes in their environment, and to compensate for injury and disease. Plasticity is not only due to the creation/destruction of neuronal connections, but also to the modulation of synaptic strength depending upon its activity, a process called ‘short-term synaptic plasticity’ (STP). There are 2 types of STP, with opposite effects, known as ‘depression’ and ‘facilitation’. When neurons receive excitatory input, they generate strong electrical impulses (called spikes) which cause a release of neurotransmitters at the synaptic connections with other neurons. The neurotransmitters stimulate receptors on the postsynaptic neuron and trigger downstream electrical impulses. Action potential activity leads to the depletion of neurotransmitters consumed during the synaptic signaling process at the axon terminal of a presynaptic neuron, causing ‘depression’. It also induces an influx of calcium into the axon terminal. The calcium accumulation increases neurotransmitter release by the next presynaptic spike, facilitating synaptic transmission and temporarily potentiating the synapse (‘facilitation’).

Facilitation is important for the proper function of mammalian brains. It may form the basis of short-term working memory. In the hippocampus, it has been proposed to play a role in the acquisition of spatial information. In the auditory pathway, it allows the maintenance of linear transmission of rate-coded sound intensity.

Although synaptic facilitation was observed more than 70 years ago, the underlying mechanism is not yet fully elucidated. However, a major breakthrough was recently achieved and published in January in Nature. In their article, Jackman et al. identified a synaptotagmin-7 (SYT7) requirement for facilitation to occur in most central synapses. SYT7 is a calcium- and phospholipid-binding protein involved in the exocytosis of many secretory and synaptic vesicles. In SYT7-knockout mice, facilitation was eliminated at all synapses (except for mossy fiber synapses), although calcium influx was not affected by the mutation.

To rule out an indirect effect of SYT7 knockout, the authors tried to rescue facilitation through viral expression of SYT7 in hippocampal CA3 pyramidal cells. To do so, they used an adeno-associated virus that drove bicistronic expression of both channelrhodopsin-2 and SYT7. Channelrhodopsins are unicellular green algae proteins that serve as sensory photoreceptors. When expressed in the experimental setting established by Jackman et al., they enabled light to control electrical excitability only in the fibers expressing SYT7. The result was clear-cut: facilitation was restored. The identification of a protein required for synaptic facilitation may pave the way for future investigations on the functional role of this process.

As of this release, SYT7 proteins have been updated in UniProtKB/Swiss-Prot and are publicly available.

UniProtKB news

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

Deleted diseases

  • Inclusion body myopathy 2

UniProt service news

New UniProt JAPI

We have developed a new version of the UniProt JAPI. The legacy UniProt JAPI will be retired as of Wednesday, April 13th 2016. If you have any questions or concerns, please feel free to contact us at help@uniprot.org.

UniProt RDF news

Change of the UniProt RDF files distribution

The UniProt RDF distribution has been available on the UniProt FTP site since 2008 with data split into one file per dataset. Over time the size of the largest files has grown to over 80 Gigabytes. These large files are difficult to download and they also limit the maximum rate at which the data can be loaded into many RDF stores. We have therefore split the files of the three biggest datasets into sets of smaller files:

  • The UniProtKB dataset is split based on taxonomy and whether entries are active or not. The resulting files contain at most 1 million active or 10 million obsolete entries.
  • The UniRef dataset is split into files that contain at most 1 million entries.
  • The UniParc dataset is split into files of approximately 1 Gigabyte in size.

We also reduced the data redundancy between the datasets to further decrease the total data volume:

  • The UniProtKB dataset has always been fully normalized with respect to the taxonomy dataset and it is now also normalized with respect to the keywords, GO and citations datasets. The total number of unique triples across these datasets remains the same, but it means that if you have so far only loaded the UniProtKB and taxonomy RDF files into your RDF store, you must now also load the keywords.rdf.xz, go.owl.xz and citations.rdf.xz files in order to have the same data.
  • The UniRef dataset has been normalized with respect to the UniProtKB and UniParc datasets. It now only describes the UniRef cluster memberships. The sequence and entry information of UniProtKB and UniParc member entries is no longer repeated in the UniRef RDF files.