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. 2015 Jan;43(Database issue):D328-34.
doi: 10.1093/nar/gku1125. Epub 2014 Nov 11.

MiCroKiTS 4.0: A Database of Midbody, Centrosome, Kinetochore, Telomere and Spindle

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Free PMC article

MiCroKiTS 4.0: A Database of Midbody, Centrosome, Kinetochore, Telomere and Spindle

Zhengnan Huang et al. Nucleic Acids Res. .
Free PMC article

Abstract

We reported an updated database of MiCroKiTS 4.0 (http://microkit.biocuckoo.org) for proteins temporally and spatially localized in distinct subcellular positions including midbody, centrosome, kinetochore, telomere and mitotic spindle during cell division/mitosis. The database was updated from our previously developed database of MiCroKit 3.0, which contained 1489 proteins mostly forming super-complexes at midbody, centrosome and kinetochore from seven eukaryotes. Since the telomere and spindle apparatus are critical for cell division, the proteins localized at the two positions were also integrated. From the scientific literature, we curated 1872 experimentally identified proteins which at least locate in one of the five positions from eight species. Then the ortholog detection was performed to identify potential MiCroKiTS proteins from 144 eukaryotic organisms, which contains 66, 45 and 33 species of animals, fungi and plants, respectively. In total, 87,983 unique proteins with corresponding localization information were integrated into the database. The primary references of experimentally identified localizations were provided and the fluorescence microscope figures for the localizations of human proteins were shown. The orthologous relations between predicted and experimental localizations were also present. Taken together, we anticipate the database can serve as a useful resource for further analyzing the molecular mechanisms during cell division.

Figures

Figure 1.
Figure 1.
The schematic diagram for the five subcellular positions including midbody/cleavage furrow/bud neck/phragmoplast, centrosome/spindle pole body, kinetochore/centromere, telomere and spindle apparatus in eukaryotic cells.
Figure 2.
Figure 2.
The search options of MiCroKiTS database. (A) The database can be directly queried with one or multiple keywords. (B) The ‘Advanced search’ option allows users to submit a combination of two terms for searching. (C) The database could be searched to retrieve a list of proteins through submitting a list of keywords such as UniProt accessions. (D) The database can be queried with a protein sequence in FASTA format to find identical or homologous proteins. (E) The protein list derived from the search options. (F) The details of the MiCroKiTS protein Aurora kinase B in H. sapiens, while the fluorescence microscope figure for the localizations can also be visualized.
Figure 3.
Figure 3.
The MiCroKiTS database can be browsed by either localizations or by species. (A) Browse by single localization. (B) The distribution of centrosomal proteins in different organisms. (C) The list of centrosomal proteins in H. sapiens. (D) The proteins with multiple localizations can also be browsed. (E) For example, the distribution of proteins located at centrosome, kinetochore and midbody among different organisms can be shown. (F) The list of proteins located in all of the three positions in H. sapiens. (G) Browse by species. (H) The distribution of human MiCroKiTS proteins in different subcellular positions. (I) The list of midbody proteins in H. sapiens.
Figure 4.
Figure 4.
The heatmap about the distribution of MiCroKiTS proteins in the MiCroKiTS 4.0 database for different localizations among 144 eukaryotic species from different kingdoms. The upper part was the results for the 66 animals, and the lower section was the results for the 33 plants and 45 fungi.

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