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UniProt release 2019_08

Published September 18, 2019

Headline

Magnetic personalities

Magnetotactic bacteria sense and align to the Earth’s magnetic field, swimming north in the Northern Hemisphere and south in the Southern in the presence of oxygen. This amazing ability to sense the Earth’s magnetic field is provided by small organelles, called magnetosomes, formed by iron nanocrystals of either magnetite (Fe3O4) or greigite (Fe3S4) surrounded by a phospholipid bilayer. Generally, magnetosomes form chains that align along the long axis of the cell using a dedicated actin-like cytoskeletal structure.


Source: Frank Mickoleit CC BY-SA 3.0

Magnetosome formation is a complex process, which includes invagination of the cell inner membrane to form vesicles, iron ion uptake, crystal biomineralization and magnetosome chain assembly. It involves a large number of proteins, encoded by genes clustered in an approximately 100 kb magnetosome island. Among all proteins involved in magnetosome formation, one of the single most important is MamB, a probable iron transporter with a role in both vesicle formation and biomineralization. MamB is stabilized by heterodimerization with MamM. Studies in genetically tractable Magnetospirillum magneticum (strain AMB-1) and Magnetospirillum gryphiswaldense (strain MSR) have pinpointed the function of many more proteins. For instance, MamA forms a scaffold to which other proteins attach on the organelle’s exterior. MamI aids in magnetite nucleation, while MamH is another probable iron transporter. MamN may control the pH of the magnetosome lumen. 4 redox-active multi-heme proteins are probably involved in correct iron oxidization (MamP, MamT, MamX and MamE), the latter is also a protease necessary for magnetosome protein maturation. There are proteins that positively regulate crystal size (including MamC, MamD MamG, MamF and those that negatively regulate crystal size (Mms36 and Mms48). Finally MamK is an actin-like protein involved in organelle positioning, along with MamJ.

The interest in magnetosomes goes far beyond the understanding of these fascinating bacteria. Magnetosomes may be instrumental for the improvement of magnetic nanoparticle biotechnologies. Purified bacterial magnetosomes represent magnetic nanoparticles with exceptionally well-defined characteristics, owing to the precise control that is exerted during all stages of biogenesis, and several unprecedented properties, such as high crystallinity, strong magnetization, and a uniform distribution of shape and size that cannot be replicated by synthesis using abiotic processes. In the biomedical field, promising results suggest that magnetosomes could be used in medical imaging, targeted drug delivery and tumor hyperthermia. In the context of wastewater treatment, it has been shown that heavy metal ions can be adsorbed onto magnetosome-producing microorganisms and then removed by magnetic separation. In addition, it may also help us learn more about the origin of life and the evolution of membrane-bound eukaryotic organelles.

As of this release nearly 70 magnetosome proteins have been annotated and can be retrieved using the term magnetosome.

UniProtKB news

Cross-references to DrugCentral

Cross-references have been added to DrugCentral, an online drug information resource providing information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action.

DrugCentral is available at http://drugcentral.org.

The format of the explicit links is:

Resource abbreviationDrugCentral
Resource identifierUniProtKB accession number

Example: P35372

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Example: P35372

DR   DrugCentral; P35372; -.

XML format

Example: P35372

<dbReference type="DrugCentral" id="P35372"/>

RDF format

Example: P35372

uniprot:P35372
  rdfs:seeAlso <http://purl.uniprot.org/drugcentral/P35372> .
<http://purl.uniprot.org/drugcentral/P35372>
  rdf:type up:Resource ;
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Cross-references to Pharos

Cross-references have been added to Pharos, a user interface to the knowledge-base for the Druggable Genome (DG), whose goal is to illuminate the uncharacterized and/or poorly annotated portion of the DG, focusing on three of the most commonly drug-targeted protein families: G-protein-coupled receptors (GPCRs), ion channels (ICs) and kinases.

Pharos is available at https://pharos.nih.gov.

The format of the explicit links is:

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DR   Pharos; Q7Z3E2; -.

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uniprot:Q7Z3E2
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Cross-references to MassIVE

Cross-references have been added to MassIVE, a community resource developed by the NIH-funded Center for Computational Mass Spectrometry to promote the global, free exchange of mass spectrometry data and provide a reusable aggregation of community-scale detection of peptides and proteins observations.

MassIVE is available at https://massive.ucsd.edu/.

The format of the explicit links is:

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Changes to the controlled vocabulary of human diseases

New diseases:

Changes in subcellular location controlled vocabulary

New subcellular locations:

Modified subcellular location:

UniRef news

Change of UniRef clustering method from CD-HIT to MMseqs2

We have switched the clustering program for UniRef90 and UniRef50 from CD-HIT to MMseqs2 (Steinegger M. and Soeding J., Nat. Commun. 9 (2018)).

The clustering algorithm remains “Greedy Incremental Clustering” with the same parameters (thanks to the MMseqs2 authors for making this available). UniRef100 was not affected.

UniProt XML news

Removal of whitespace characters in the XML amino acid sequence representations

The <sequence> elements of the UniProtKB, UniParc and UniRef XML representations formatted the amino acid sequence for historic reasons with spaces and newlines. These whitespace characters had to be removed before parsing with native XML tools. To avoid this complication we have removed all whitespace characters in the <sequence> elements, so that they contain only IUPAC amino acid codes.

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