Motivation: Many genomes have been completely sequenced. However, detecting and analyzing their protein-protein interactions by experimental methods such as co-immunoprecipitation, tandem affinity purification and Y2H is not as fast as genome sequencing. Therefore, a computational prediction method based on the known protein structural interactions will be useful to analyze large-scale protein-protein interaction rules within and among complete genomes.
Results: We confirmed that all the predicted protein family interactomes (the full set of protein family interactions within a proteome) of 146 species are scale-free networks, and they share a small core network comprising 36 protein families related to indispensable cellular functions. We found two fundamental differences among prokaryotic and eukaryotic interactomes: (1) eukarya had significantly more hub families than archaea and bacteria and (2) certain special hub families determined the topology of the eukaryotic interactomes. Our comparative analysis suggests that a very small number of expansive protein families led to the evolution of interactomes and seemed to have played a key role in species diversification.
Supplementary Information: http://interactomics.org.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1093/bioinformatics/bti512 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Proteomic Analyses in COVID-19-Associated Secondary Hemophagocytic Lymphohistiocytosis.
Crit Care Explor
February 2025
Center for Fundamental Immunology, Benaroya Research Institute, Seattle, WA.
Context: COVID-19 has been associated with features of a cytokine storm syndrome with some patients sharing features with the hyperinflammatory disorder, secondary hemophagocytic lymphohistiocytosis (sHLH).
Hypothesis: We hypothesized that proteins associated with sHLH from other causes will be associated with COVID-sHLH and that subjects with fatal COVID-sHLH would have defects in immune-related pathways.
Methods And Models: We identified two cohorts of adult patients presenting with COVID-19 at two tertiary care hospitals in Seattle, Washington in 2020 and 2021.
Upregulation of the MAP2K4 gene triggers endothelial-mesenchymal transition in COVID-19.
Mol Biol Rep
January 2025
Department of Molecular Biology and Genetics, Faculty of Art and Science, Tokat Gaziosmanpasa University, Tokat, 60200, Türkiye.
Background: SARS-CoV-2 infection is marked by an excessive inflammatory response, leading to elevated production of pro-inflammatory cytokines through activation of intracellular pathways like mitogen-activated protein kinase (MAPK). Viruses can use the MAPK signaling pathway to their advantage, but the relationship of this pathway to the severe SARS-CoV-2 period has not been fully elucidated. MAP2K4 is involved in the MAPK signaling pathway and affects cellular processes such as cell-cell junction, cell proliferation, differentiation and apoptosis.
View Article and Find Full Text PDFHistone methyltransferase KMT2A promotes pulmonary fibrogenesis via targeting pro-fibrotic factor PU.1 in fibroblasts.
Clin Transl Med
February 2025
Department of Pulmonary and Critical Care Medicine, The Affiliated Drum Tower Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China.
Background: Idiopathic pulmonary fibrosis (IPF) is a fibrotic disease driven by both environmental and genetic factors. Epigenetics refers to changes in gene expression or cellular phenotype that do not involve alterations to DNA sequence. KMT2A is a member of the SET family which catalyses H3K4 methylation.
View Article and Find Full Text PDFVersatile roles of disordered transcription factor effector domains in transcriptional regulation.
FEBS J
January 2025
Molecular Biology and Genetics Department, Ihsan Dogramaci Bilkent University, Ankara, Turkey.
Transcription, a crucial step in the regulation of gene expression, is tightly controlled and involves several essential processes, such as chromatin organization, recognition of the specific genomic sequences, DNA binding, and ultimately recruiting the transcriptional machinery to facilitate transcript synthesis. At the center of this regulation are transcription factors (TFs), which comprise at least one DNA-binding domain (DBD) and an effector domain (ED). Although the structure and function of DBDs have been well studied, our knowledge of the structure and function of effector domains is limited.
View Article and Find Full Text PDFIdentification of the CYPome associated with acetamiprid resistance based on the chromosome-level genome of Megalurothrips usitatus (Bagnall) (Thysanoptera: Thripidae).
Pest Manag Sci
January 2025
State Key Laboratory of Green Pesticide, College of Plant Protection, South China Agricultural University, Guangzhou, China.
Background: The bean flower thrips, Megalurothrips usitatus, poses a great threat to cowpea and other legume cultivars. Chemical insecticides have been applied to control M. usitatus, but have resulted in little profit because of the rapid evolution of insecticide resistance.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!