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UniProt release 2017_02

Published February 15, 2017

Headline

Freshwater fish see red

Vision relies on specialized neurons found in the retina, called photoreceptor cells. Vertebrate photoreceptor cells contain visual pigments consisting of a G-protein-coupled receptor, called opsin, and a covalently bound chromophore derived from vitamin A, most commonly 11-cis retinal (a derivative of vitamin A1). Light-induced isomerization of 11-cis retinal to all-trans triggers a conformational change leading to G-protein activation, release of all-trans retinal and activation of the phototransduction cascade.

Typical rod photopigments have a maximum light absorbance of around 500 nm. However, at the end of the 19th century, Köttgen and Abelsdorff observed that the rod pigments in certain freshwater fish were “red-shifted” towards 20-30 nm longer wavelengths than those of marine fish and terrestrial animals. This difference is due to a change in chromophore. Instead of 11-cis retinal, freshwater vertebrates use 11-cis 3,4-didehydroretinal, a derivative of vitamin A2, whose only difference with vitamin A1 is an additional conjugated double bond within its beta-ionone ring. What is the evolutionary advantage of this modification? Fresh water, in lakes or streams, is often murky. As a result, the light environment is shifted to the red and infrared end of the spectrum. Switching light absorbance seems to be the appropriate response to optimize vision in this specific aquatic milieu.

The chromophore switch is not only specific for certain species, it can also be regulated during life. For example, many amphibians use 11-cis 3,4-didehydroretinal during the tadpole stage, that they spend in ponds. Upon metamorphosis, they switch to 11-cis retinal which provides clear vision to the terrestrial adult they have become. Conversely, salmon live happily with 11-cis retinal in the open ocean. During spawning migration, however, 11-cis retinal is progressively replaced by 11-cis 3,4-didehydroretinal, possibly through the action of thyroid hormones. In zebrafish also, the switch to vitamin A2-based chromophores can be induced by thyroid hormone treatment. Maybe the most striking example of differential usage of visual chromophores is provided by the American bullfrog. This voracious predator spends a large part of its life floating or swimming at the surface of the water, looking for aquatic, as well as aerial prey, with its eyes just above the waterline. Its dorsal retina, steered towards water, contains 11-cis 3,4-didehydroretinal, while its ventral retina uses 11-cis retinal.

While much of this knowledge on vitamins A1 and A2 was acquired long ago, the identity of the dehydrogenase catalyzing the switch between both forms remained elusive until December 2015, when Enright et al. published the identification of the enzyme. The authors compared the expression profile of zebrafish retinal pigment epithelium (RPE) of thyroid hormone-treated versus control animals. The most highly up-regulated transcript was that encoding cyp27c1, a cytochrome P450 family member. cyp27c1 was also strongly expressed in dorsal, but not ventral bullfrog RPE, correlating with the distribution of vitamin A2. In vitro, purified cyp27c1 was able to very efficiently catalyze the conversion of vitamin A1 to vitamin A2. In vivo, cyp27c1 knockout zebrafish survive to adulthood without overt developmental abnormalities. However, upon treatment with thyroid hormone, the mutant fish eyes fail to produce any vitamin A2 and their photoreceptors do not undergo a red-shift in sensitivity. Thus, the expression of a single enzyme, cyp27c1, mediates the dynamic spectral tuning of the entire visual system by controlling the balance of vitamin A1 and A2 in the eye.

Obviously, humans are not adapted for aquatic vision. However, they do produce vitamin A2, as has been documented in keratinocytes, and they express CYP27C1 in liver, kidney and pancreas”:https://www.ncbi.nlm.nih.gov/pubmed/16360114. The human enzyme catalyzes the same reaction as fish and amphibian orthologs, but the physiological relevance of this observation is not clear at present.

Zebrafish and bullfrog CYP27C1 entries have been annotated in UniProtKB/Swiss-Prot. The preliminary sequence of American bullfrog CYP27C1 was kindly provided by Professor Corbo and Dr. Enright and we would like to thank them sincerely. The human ortholog has been updated. All 3 entries are publicly available as of this release.

Cross-references to Araport

Cross-references have been added to the Arabidopsis Information Portal Araport, an open-access online community resource for Arabidopsis research.

Araport is available at https://www.araport.org/.

The format of the explicit links is:

Resource abbreviation Araport
Resource identifier AGI locus code

Example: Q43125

Show all entries having a cross-reference to Araport.

Text format

Example: Q43125

DR   Araport; AT4G08920; -.

XML format

Example: Q43125

<dbReference type="Araport" id="AT4G08920"/>

RDF format

Example: Q43125

uniprot:Q43125
  rdfs:seeAlso <http://purl.uniprot.org/araport/AT4G08920> .
<http://purl.uniprot.org/araport/AT4G08920> 
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/Araport> .

Cross-references to IMGT/GENE-DB

Cross-references have been added to IMGT/GENE-DB, the genome database of the international Immunogenetics information system (IMGT) for genes encoding immunoglobulins and T-cell receptors.

IMGT/GENE-DB is available at http://www.imgt.org/genedb/.

The format of the explicit links is:

Resource abbreviation IMGT/GENE-DB in entry view, IMGT_GENE-DB in source formats
Resource identifier Gene name

Example: P01871

Show all entries having a cross-reference to IMGT/GENE-DB.

Text format

Example: P01871

DR   IMGT_GENE-DB; IGHM; -.

XML format

Example: P01871

<dbReference type="IMGT_GENE-DB" id="IGHM"/>

RDF format

Example: P01871

uniprot:P01871
  rdfs:seeAlso <http://purl.uniprot.org/imgt_gene-db/IGHM> .
<http://purl.uniprot.org/imgt_gene-db/IGHM> 
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/IMGT_GENE-DB> .
 

Change of the cross-references to TAIR

We have modified our cross-references to the TAIR database, and now use the TAIR accession number as the primary resource identifier, while continuing to show the TAIR locus name in an additional field.

Text format

Example: Q9ZVI3

Previous format:

DR   TAIR; AT2G38610; -.

New format:

DR   TAIR; locus:2064097; AT2G38610.

XML format

Example: Q9ZVI3

Previous format:

<dbReference type="TAIR" id="AT2G38610"/>

New format:

<dbReference type="TAIR" id="locus:2064097">
  <property type="gene designation" value="AT2G38610"/>
</dbReference>

This change does not affect the XSD, but may nevertheless require code changes.

RDF format

Example: Q9ZVI3

Previous format:

uniprot:Q9ZVI3
  rdfs:seeAlso <http://purl.uniprot.org/tair/AT2G38610> .
<http://purl.uniprot.org/tair/AT2G38610>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/TAIR> .

New format:

uniprot:Q9ZVI3
  rdfs:seeAlso <http://purl.uniprot.org/tair/locus:2064097> .
<http://purl.uniprot.org/tair/locus:2064097>
  rdf:type up:Resource ;
  up:database <http://purl.uniprot.org/database/TAIR> .
  rdfs:comment "AT2G38610" .

Removal of sequence similarity annotations for domains

Sequence similarity annotations were mainly used to describe two types of information:

  1. A family to which the protein belongs, worded as:
    Belongs to FamilyName.
  2. A structural domain that the protein contains, worded as:
    Contains NumberOfOccurence DomainName.

The domains that a protein contains are also annotated in ‘Domain’, ‘Zinc finger’, ‘Repeat’, ‘Calcium binding’ or ‘DNA binding’ annotations, which describe a domain’s name and sequence coordinates. The ‘Sequence similarity’ annotations of type 2, however, described only a domain’s name and number of occurences. We have therefore removed these less detailed annotations.

Changes to the controlled vocabulary of human diseases

New diseases:

Modified diseases:

Deleted diseases

  • Thyroxine-binding globulin deficiency

Changes to the controlled vocabulary for PTMs

New term for the feature key ‘Modified residue’ (‘MOD_RES’ in the flat file):

  • N,N,N-trimethylmethionine