Table of contents

Change of molecule type in the DR EMBL line
New comment line (CC) topic DISRUPTION PHENOTYPE
Change of the comment line (CC) topic INTERACTION
Introduction of the new event types 'Protein splicing' and 'Miscellaneous' in the comment line (CC) topic ALTERNATIVE PRODUCTS

Not before: 13-Jan-2008

Following changes in the the EMBL nucleotide sequence database, the term pre-RNA will be replaced by Transcribed_RNA as a valid value for the quarternary qualifier (MOLECULE_TYPE) of cross-references to EMBL.

The format of the DR EMBL line is:

DR   EMBL; ACCESSION_NUMBER; PROTEIN_ID; STATUS_IDENTIFIER; MOLECULE_TYPE.

The controlled vocabulary of the MOLECULE_TYPE will then consist of:

• Genomic_DNA
• Genomic_RNA
• mRNA
• Transcribed_RNA
• Viral_cRNA
• Unassigned_DNA
• Unassigned_RNA
• Other_DNA
• Other_RNA
• -

Not before: 13-Jan-2008

We are going to introduce the new CC line topic DISRUPTION PHENOTYPE to describe the effects caused by the disruption of the gene coding for a protein. Note that we only describe effects caused by the complete absence of a gene and thus of a protein in vivo (null mutants caused by random or target deletions, insertions of a transposable element etc.) To avoid description of phenotypes due to partial or dominant negative mutants, missense mutations will not be described in this topic, but in FT MUTAGEN instead. Defects caused by transient inactivation by methods such as RNA interference or blockage by antibodies will also not be described in this topic due to the difficulty of interpreting results.

The format of the new topic is free text.

Examples:

CC   -!- DISRUPTION PHENOTYPE: Death occurs by the end of preimplantation
CC       development. Embryos exhibit a dramatic reduction in the total cell
CC       number, a high mitotic index, and the presence of abnormal mitotic
CC       figures.

CC   -!- DISRUPTION PHENOTYPE: Developmental arrest of the embryos at the
CC       globular stage.

CC   -!- DISRUPTION PHENOTYPE: Impaired B-cell development which fails to
CC       progress past the progenitor stage.

Not before: 03-Feb-2009

The CC line topic INTERACTION conveys information about binary protein-protein interactions. A description of its current format is available in the UniProtKB User Manual. Currently, all interaction data is automatically derived from the IntAct database. In the future, we will start to add manually curated binary protein-protein interactions to this topic (these are currently described in the CC line topic SUBUNIT). In order to represent isoform- and chain-specific interactions (e.g. for viral polyproteins) and to add interactor-specific comments (e.g. PTMs and binding regions), we are going to modify the format of the INTERACTION lines. Each binary interaction will be represented by a block of 3 to 4 lines:

• The first line of a block indicates the experimental evidence for the interaction and the data source (literature reference or By similarity and/or cross-reference to the database from which the data was derived).
• The next line is an optional comment about the interaction.
• The last two lines give details on the interacting proteins: the Protein1= line represents the currently displayed entry, the Protein2= line the other interacting protein. If Protein2 is from a different species than Protein1, its species or taxonomic range is indicated.

Note: Variable values are represented in italics. Perl-style multipliers indicate whether a pattern (as delimited by parentheses) is optional (?), may occur 0 or more times (*), or 1 or more times (+). Alternative values are separated by a pipe symbol (|). Special characters are escaped by a backslash (\).

 CC   -!- INTERACTION:
(CC       Interact=status( \(source|By similarity\))?;( Xref=xref;)?
(CC         Comment=free_text;)?
 CC         Protein1=name [id(:subid)?];( Note=free_text;)?
 CC         Protein2=name [id(:subid)?];( Organism=organism;)?( Note=free_text;)?)+

• status = Yes | No | Uncertain
  Displays the experimental evidence for the interaction:
  • Yes if there is experimental evidence that the two proteins (or their homologues) interact in a physiological context.
  • No if there is experimental evidence that the two proteins (or their homologues) do not interact under the experimental conditions described in the cited publication.
  • Uncertain if the experimental evidence for the interaction between the two proteins (or their homologues) is not considered to reliably reflect an interaction in a physiological context (e.g. results from not further validated yeast-two-hybrid or in-vitro experiments).
• db_xref = db:db_id(, db:db_id)*
  List of database cross-references, each consisting of database name and unique database identifier.
• source: A db_xref with db = PubMed
  Literature sources for the interaction.
• xref: A db_xref with db = IntAct
  Database entries from which the interaction was imported (currently only IntAct).
• name: Biologically meaningful label or name for the protein.
  Displays the gene name (as shown in the GN line field Name= or OrderedLocusNames= or ORFNames=) or a dash '-' if the gene name is unknown.
  If the protein contains multiple chains (e.g. a viral polyprotein), the chain name (from the FT line) is displayed instead and the identifier which follows in square brackets must contain the FTId of the chain.
• id: UniProt accession number or isoform identifier (IsoId= field).
• subid: UniProt feature identifier (FTId= field).
• organism: Indicates that the interacting proteins originate from different species. The value of this field is one of the following:
  • tax_name [NCBI_TaxID:tax_id]: Scientific name and NCBI taxonomy database identifier of (group of) species of Protein2. In a host-virus protein interaction, this refers to the range of species of Protein2. An entry from a representative virus strain/isolate is displayed in Protein2.
  • Host: In a virus-host protein interaction, this refers to the range of species of Protein2 which corresponds to the OH line of Protein1. An entry from a representative host is displayed in Protein2.
• free_text: Free text.
  • Comment= contains additional information concerning the interaction (like subcellular location).
  • Note= contains additional information concerning the interacting protein (like PTM status, binding domains).

Examples:

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:11533489);
CC         Comment=HDAC3 mediates the deacetylation of RELA.
CC         Protein1=RELA [Q04206];
CC         Protein2=HDAC3 [O15379];

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:10837489);
CC         Protein1=MCL1 [Q07820-1];
CC         Protein2=BAK1 [Q16611];
CC       Interact=Yes (PubMed:15901672, 17097560); Xref=IntAct:EBI-1003422,EBI-519866;
CC         Protein1=MCL1 [Q07820];
CC         Protein2=BAK1 [Q16611];

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:11418237); Xref=IntAct:EBI-375446,EBI-389883;
CC         Protein1=ABI1 [Q8IZP0];
CC         Protein2=NCK1 [P16333]; Note=SH3 1 domain;
CC       Interact=No (PubMed:12681507);
CC         Protein1=ABI1 [Q8IZP0-6];
CC         Protein2=NCK1 [P16333];
CC       Interact=Yes (By similarity);
CC         Protein1=ABI1 [Q8IZP0]; Note=N-terminus;
CC         Protein2=WASF1 [Q92558];

CC   -!- INTERACTION:
CC       Interact=Yes (By similarity);
CC         Protein1=C1QR1 [Q9NPY3];
CC         Protein2=Core protein p21 [P27955:PRO_0000037583)]; Organism=Hepatitis C virus [NCBI_TaxID=11103]; Note=See also other virus strains;

CC   -!- INTERACTION:
CC       Interact=Yes (By similarity);
CC         Protein1=Core protein p21 [P27955:PRO_0000037583];
CC         Protein2=C1QR1 [Q9NPY3]; Organism=Host; Note=See also other hosts;

CC   -!- INTERACTION:
CC       Interact=Yes (PubMed:16470652); Xref=IntAct:EBI-907934,EBI-907894;
CC         Protein1=CNP [P06623];
CC         Protein2=CABP1 [Q9NZU7]; Organism=Homo sapiens [NCBI_TaxID=9606];

CC   -!- INTERACTION:
CC       Interact=Uncertain (PubMed:15231747);
CC          Protein1=NOB1 [Q9ULX3];
CC          Protein2=UPF2 [Q9HAU5];

Not before: 03-Feb-2009

The comment line topic ALTERNATIVE PRODUCTS, together with the feature key VAR_SEQ, describes alternative protein sequences (isoforms) that are the result of alternative splicing, alternative initiation, alternative promoter usage and ribosomal frameshifting events.

We are going to broaden this topic with the new event type Protein splicing to describe protein sequences that arise by intein processing events. Note that other protein maturation events, such as the hedgehog protein processing or other types of cleavages, will not be described by this event.

We will also introduce the general event type Miscellaneous to describe uncommon molecular mechanisms, such as ribosome shunt, ribosome skipping (PMID:12522142) or ribosome termination-reinitiation (PMID:18056426) events.

Example with intein:

Current format:

FT   INIT_MET      1      1       Removed.
FT   CHAIN         2    283       Vacuolar ATP synthase catalytic subunit
FT                                A, 1st part.
FT                                /FTId=PRO_0000002458.
FT   CHAIN       284    737       Endonuclease PI-SceI.
FT                                /FTId=PRO_0000002459.
FT   CHAIN       738   1071       Vacuolar ATP synthase catalytic subunit
FT                                A, 2nd part.
FT                                /FTId=PRO_0000002460.

New format:

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Protein splicing; Named isoforms=3;
CC         Comment=This protein undergoes a protein self splicing that
CC         involves a post-translational excision of the intervening region
CC         (intein) followed by peptide ligation;
CC       Name=Intein-containing vacuolar ATP synthase catalytic subunit A;
CC         IsoId=P17255-1; Sequence=Displayed;
CC         Note=Unprocessed;
CC       Name=Vacuolar ATP synthase catalytic subunit A;
CC         IsoId=P17255-2; Sequence=VSP_000002;
CC         Note=Mature;
CC       Name=Endonuclease PI-SceI;
CC         IsoId=P17255-3; Sequence=VSP_000001, VSP_000003;
CC         Note=Intein;
..
FT   INIT_MET      1      1       Removed.
FT   CHAIN         2    737       Intein-containing vacuolar ATP synthase
FT                                catalytic subunit A.
FT   REGION      284    737       Endonuclease PI-SceI.
FT   VAR_SEQ       2    283       Missing (in isoform Endonuclease PI-SceI).
FT                                /FTId=VSP_000001.
FT   VAR_SEQ     284    737       Missing (in isoform Vacuolar ATP synthase
FT                                catalytic subunit A).
FT                                /FTId=VSP_000002.
FT   VAR_SEQ     738   1071       Missing (in isoform Endonuclease PI-SceI).
FT                                /FTId=VSP_000003.

Example for ribosomal termination-reinitiation:

Current format:

CC   -!- MISCELLANEOUS: Translated by a ribosomal termination-reinitiation
CC       process from the bicistronic mRNA encoding for VP1 and VP2.

New format:

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative initiation, Miscellaneous; Named isoforms=3;
CC       Name=Protein VP2; Synonyms=VP2;
CC         IsoId=Q672H9-1; Sequence=Displayed;
CC         Note=Produced by ribosomal termination-reinitiation at the end
CC         of VP1 ORF;
CC       Name=Uncharacterized protein VP3;
CC         IsoId=Q672I0-1; Sequence=External;
CC         Note=Produced by alternative initiation from the subgenomic RNA;
CC       Name=Subgenomic capsid protein; Synonyms=VP1;
CC         IsoId=Q672I1-2; Sequence=External;
CC         Note=Produced from the subgenomic RNA;