ArticleJournal of proteome research2021
Functions of Essential Genes and a Scale-Free Protein Interaction Network Revealed by Structure-Based Function and Interaction Prediction for a Minimal Genome.
Article in Journal of proteome research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 26 citations in OpenAlex.
- Article
- Whole-proteome structure/function prediction in UropathogenicbioRxiv : the preprint server for biology · 2026Article
- Design biology and mind-body health.Journal, genetic engineering & biotechnology · 2025Review
- Improving the Annotations of JCVI-Syn3a Proteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Recent Progress of Protein Tertiary Structure Prediction.Molecules (Basel, Switzerland) · 2024Review
- Recent Advances in Deep Learning for Protein-Protein Interaction Analysis: A Comprehensive Review.Molecules (Basel, Switzerland) · 2023Review
- Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy.BMC bioinformatics · 2023Article
- Article
- I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.Nature protocols · 2022Review
- Toward the Complete Functional Characterization of a Minimal Bacterial Proteome.The journal of physical chemistry. B · 2022Article
- Article
- Bacterial genome reductions: Tools, applications, and challenges.Frontiers in genome editing · 2022Review
- Protein-protein interaction prediction with deep learning: A comprehensive review.Computational and structural biotechnology journal · 2022Review
- SynWiki: Functional annotation of the first artificial organism Mycoplasma mycoides JCVI-syn3A.Protein science : a publication of the Protein Society · 2022Article
- Investigation of nonsynonymous mutations in the spike protein of SARS-CoV-2 and its interaction with the ACE2 receptor by molecular docking and MM/GBSA approach.Computers in biology and medicine · 2021Article
- Toward the solution of the protein structure prediction problem.The Journal of biological chemistry · 2021Review
- Understanding Metabolic Flux Behaviour in Whole-Cell Model Output.Frontiers in molecular biosciences · 2021Article
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
When the JCVI-syn3.0 genome was designed and implemented in 2016 as the minimal genome of a free-living organism, approximately one-third of the 438 protein-coding genes had no known function. Subsequent refinement into JCVI-syn3A led to inclusion of 16 additional protein-coding genes, including several unknown functions, resulting in an improved growth phenotype. Here, we seek to unveil the biological roles and protein-protein interaction (PPI) networks for these poorly characterized proteins using state-of-the-art deep learning contact-assisted structure prediction, followed by structure-based annotation of functions and PPI predictions. Our pipeline is able to confidently assign functions for many previously unannotated proteins such as putative vitamin transporters, which suggest the importance of nutrient uptake even in a minimized genome. Remarkably, despite the artificial selection of genes in the minimal syn3 genome, our reconstructed PPI network still shows a power law distribution of node degrees typical of naturally evolved bacterial PPI networks. Making use of our framework for combined structure/function/interaction modeling, we are able to identify both fundamental aspects of network biology that are retained in a minimal proteome and additional essential functions not yet recognized among the poorly annotated components of the syn3.0 and syn3A proteomes.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.