1,721,031 research outputs found
The neglected giants: Uncovering the prevalence and functional groups of huge proteins in proteomes.
No full textAn often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for HPs are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusimicrobiota or Planctomycetota, have a higher tendency for encoding HPs, even more than the average eukaryote. To investigate if these macro-polypeptides represent "real" proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to non-ribosomomal peptide synthesis/polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology
All potential unreal huge proteins [Dataset]
No full textAn often-overlooked aspect of biology is formed by the outliers of the protein length distribution, specifically those proteins with more than 5000 amino acids, which we refer to as huge proteins (HPs). By examining UniprotKB, we discovered more than 41 000 HPs throughout the tree of life, with the majority found in eukaryotes. Notably, the phyla with the highest propensity for HPs are Apicomplexa and Fornicata. Moreover, we observed that certain bacteria, such as Elusimicrobiota or Planctomycetota, have a higher tendency for encoding HPs, even more than the average eukaryote. To investigate if these macro-polypeptides represent “real” proteins, we explored several indirect metrics. Additionally, orthology analyses reveals thousands of clusters of homologous sequences of HPs, revealing functional groups related to key cellular processes such as cytoskeleton organization and functioning as chaperones or as E3-ubiquitin ligases in eukaryotes. In the case of bacteria, the major clusters have functions related to non-ribosomomal peptide synthesis/polyketide synthesis, followed by pathogen-host attachment or recognition surface proteins. Further exploration of the annotations for each HPs supported the previously identified functional groups. These findings underscore the need for further investigation of the cellular and ecological roles of these HPs and their potential impact on biology and biotechnology.Peer reviewe
Domain composition and architecture of Huge proteins [Dataset]
No full text(A-C) Stacked bar distribution of PFAM domains, from A to C is bacteria, eukaryota and archaea, respectively. Each bar in the distribution is colored based on contribution from each phyla. Calculations were performed on a restricted subset limiting the maximum number of proteomes from each phylum to 50, as to not skew the distribution. Only the top 15 phyla in terms of contribution is shown, except for archaea. The distinct taxonomic pattern of each bar illustrates the differing contributions from each phyla. (D-F) Most common architectures of bacteria, eukaryotes and archaea, respectively. Sizes of the proteins are representative and not to scale.Peer reviewe
Close-up of the distribution of all the protein lengths up to 5000 aminoacids [Dataset]
No full textShowing the considerable number after the protein length average and before the 5000 threshold.
(TIFF)Peer reviewe
Protein features and localization [Dataset]
No full text(A) Scatter plot the Disorder percentage in relation to Protein Length. On the right is the same analysis, for Non-Huge proteins (less than 5000 aa’s). From top to bottom divided between Prokaryotes and Eukaryotes, respectively. Each subplot is followed by a histogram of disorder percentages. (B) Histogram of presence (red) or absence (blue) of signal peptides in relation to Protein Length. The y-axis is in logarithmic scale. (C) Density plot of the distribution of number of Transmembrane helices (TMHs) in relation to Protein Length, with corresponding rug-plot. Colored based on number of TMHs. The x-axis is in logarithmic scale.
(TIFF)Peer reviewe
Likelihood of Huge proteins Existence [Dataset]
No full text(A) Distribution of the proportion of the dataset for each Protein Existence level (Uniprot), either for Huge proteins (Blue) or Non-Huge proteins (Orange). (B) Inset of A, zoom of the first two levels. (C) Scatter plot comparing the number of huge proteins per proteome (top row, green, each green dot is a proteome) or Protein Length (bottom row, red, each dot is a protein) with the BUSCO Completeness score for each proteome. For archaea, bacteria and eukaryota, from left to right, respectively. (D) Box plot relating the Number of Huge proteins per Proteome with the Assembly level of the genomes. For archaea, bacteria and eukaryota, from left to right, respectively. Colored by Assembly level category.Peer reviewe
Protein length distribution across the three superkingdoms of life [Dataset]
No full text(A) Whole distribution for all proteins in Uniprot (Release 2023_01). (B) Inset of the Distribution, for protein lengths bigger than 5000 amino acids, by superkingdom. Relevant proteins are highlighted. (C) Plot of the relationship between the size of the proteome (number of proteins), at log scale, and the number of huge proteins. (D) Box plot showing the likelihood of a proteome to contain huge proteins, per phylum, in percentage (number of huge proteins divided by proteome size). Each dot is a single proteome. All plots but A are colored blue, red and green for archaea, bacteria and eukaryota, respectively.Peer reviewe
All Huge protein clusters [Dataset]
No full textAll clusters found colored by phyla, (A) Archaea, (B) Bacteria and (C) Eukaryotes.
(TIFF)Peer reviewe
Huge proteins clusters for each kingdom [Dataset]
No full textOnly the largest clusters are shown for A) bacteria (top 36) and B) eukaryotes (top 32). All clusters are shown for (C) archaea. Proteins inside the clusters are represented by dots colored by phyla. Total number of HPs in dataset is shown for each phyla.Peer reviewe
Distribution of Gene Ontology terms (GOterms), divided by superkingdom [Dataset]
No full text(A-C) corresponds to molecular function (MF), biological process (BP) and cellular component (CC), respectively. Each protein can contribute more than one GOterm to each category.
(TIFF)Peer reviewe
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