Figure 1.
Schematic of the ubiquitination pathway.
(1) A thiol ester bond between the E1-activating enzyme and ubiquitin is formed during ubiquitin activation. (2) The activated ubiquitin is then transferred to the E2-conjugating enzyme. (3) How ubiquitin is added onto a substrate varies according to the ubiquitin ligase (E3) category. (3A) RING-type E3 ligases function as a molecular scaffold that position the E2-conjugating enzyme with the substrate. (3B) HECT-type E3 ligases form an intermediary complex with ubiquitin leading to its transfer from the E2-conjugating enzyme to the substrate. (4A) Polyubiquitinated substrates may be targeted for cellular signaling or (4B) proteasomal degradation depending on the ubiquitin linkages (5). De-ubiquitinases (DUBs) recycle ubiquitin completing the cycle.
Figure 2.
Proteins encoded for the ubiquitin machinery within the genomes of four model eukaryotes and six medically important arthropod vectors.
Ten species are depicted at bottom, with model organisms colored gray (S. cerevisiae, H. sapiens, M. musculus and D. melanogaster) and arthropod vectors colored red (A. gambiae, A. aegypti, C. quinquefasciatus, P. humanus, R. prolixus and I. scapularis). The statistics shown are genome size in giga base pairs (Gb) and “all” referring to total number of predicted genes. “Ubi” refers to the total number of characterized (model organisms) or predicted (vectors) ubiquitin machinery proteins encoded within each genome, with “%U” the proportion of ubiquitin-related genes. Proteins were categorized into three major groups: Ubiquitin and ubiquitin-like proteins, E1-E3 enzymes, and de-ubiquitinases. For each genome, a breakdown within each major group depicts the composition of protein families (sub-groups).
Figure 3.
Composition of ubiquitin and ubiquitin-like proteins within the genomes of four model eukaryotes and six medically important arthropod vectors.
Using HMMER v.3.0, complete sets of proteins for all ten genomes were scanned for the presence of five Pfam domain models for ubiquitin and ubiquitin-like proteins: APG12 (PF04110), Atg8 (PF02991), ubiquitin (PF00240), Ufm1 (PF03671), and Urm1 (PF09138). Only protein matches to Pfam models with E-values <0.05 were selected for compilations.
Figure 4.
Composition of ubiquitin-activating enzymes (E1), ubiquitin conjugating enzymes (E2), and ubiquitin ligases (E3) within the genomes of four model eukaryotes and six medically important arthropod vectors.
Using HMMER v.3.0, complete sets of proteins for all ten genomes were scanned for the presence of two Pfam domain models for ubiquitin activating enzymes (E1): ThiF (PF00899) and UBACT (PF02134); one Pfam domain model for ubiquitin conjugating enzymes (E2): UQ-con (PF00179); and eight Pfam domain models for ubiquitin ligases (E3): zf-C3HC4 (PF00097), zf-Apc11 (PF12861), RINGv (PF12906), Rtf2 (PF04641), HECT (PF00632), Cullin (PF00888), U-box (PF04564), and F-box (PF00646). Only protein matches to Pfam models with E-values <0.05 were selected for compilations.
Figure 5.
Composition of de-ubiquitinases within the genomes of four model eukaryotes and six medically important arthropod vectors.
Using HMMER v.3.0, complete sets of proteins for all ten genomes were scanned for the presence of nine Pfam domain models for de-ubiquitinases: OTU (PF02338), Josephin (PF02099), JAB (PF01398), DUF862 (PF05903), WLM (PF08325), UCH (PF00443), Peptidase_C12 (PF01088), Peptidase_C48 (PF02902), and Peptidase_C54 (PF03416). Only protein matches to Pfam models with E-values <0.05 were selected for compilations.