The Nature of Protein Domain Evolution: Shaping the Interaction Network

Understanding the origins of animal multicellularity is a fundamental biological question. Recent genome data have unravelled the role that co-option of pre-existing genes played in the origin of animals. However, there were also some important genetic novelties at the onset of Metazoa. To have a clear understanding of the specific genetic innovations and how they appeared, we need the broadest taxon sampling possible, especially among early-branching animals and their unicellular relatives. Here, we take advantage of single-cell genomics to expand our understanding of the genomic diversity of choanoflagellates, the sister-group to animals. With these genomes, we have performed an updated and taxon-rich reconstruction of protein evolution from the Last Eukaryotic Common Ancestor (LECA) to animals. Our novel data re-defines the origin of some genes previously thought to be metazoan-specific, like the POU transcription factor, which we show appeared earlier in evolution. Moreover, our data indicate that the acquisition of new genes at the stem of Metazoa was mainly driven by duplications and protein domain rearrangement processes at the stem of Metazoa. Furthermore, our analysis allowed us to reveal protein domains that are essential to the maintenance of animal multicellularity. Our analyses also demonstrate the utility of single-cell genomics from uncultured taxa to address evolutionary questions. This article is part of a discussion meeting issue ‘Single cell ecology’.

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Potential Pathogenic Genes Prioritization Based on Protein Domain Interaction Network Analysis

IEEE/ACM Transactions on Computational Biology and Bioinformatics ◽

10.1109/tcbb.2020.2983894 ◽

2020 ◽

pp. 1-1 ◽

Cited By ~ 3

Author(s):

Wenyan Wang ◽

Yuming Zhou ◽

Mu-tian Cheng ◽

Yan Wang ◽

Chun-hou Zheng ◽

...

Keyword(s):

Network Analysis ◽

Interaction Network ◽

Protein Domain ◽

Domain Interaction ◽

Pathogenic Genes

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Gene Content Evolution in the Arthropods

10.1101/382945 ◽

2018 ◽

Cited By ~ 8

Author(s):

Gregg W.C. Thomas ◽

Elias Dohmen ◽

Daniel S.T. Hughes ◽

Shwetha C. Murali ◽

Monica Poelchau ◽

...

Keyword(s):

Dna Methylation ◽

Large Scale ◽

Gene Families ◽

Protein Domain ◽

Whole Genome ◽

Genome Sequences ◽

Arthropod Evolution ◽

Animal Diversity ◽

Physiological Adaptations ◽

Protein Domain Evolution

AbstractBackgroundArthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods.ResultsUsing 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality and chemoperception.ConclusionsThese analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

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Method for Essential Protein Prediction Based on a Novel Weighted Protein-Domain Interaction Network

Frontiers in Genetics ◽

10.3389/fgene.2021.645932 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zixuan Meng ◽

Linai Kuang ◽

Zhiping Chen ◽

Zhen Zhang ◽

Yihong Tan ◽

...

Keyword(s):

Protein Identification ◽

Computational Models ◽

Predictive Accuracy ◽

Interaction Network ◽

Protein Domain ◽

Biological Information ◽

Ppi Network ◽

Domain Interaction ◽

Topological Features ◽

Ppi Networks

In recent years a number of calculative models based on protein-protein interaction (PPI) networks have been proposed successively. However, due to false positives, false negatives, and the incompleteness of PPI networks, there are still many challenges affecting the design of computational models with satisfactory predictive accuracy when inferring key proteins. This study proposes a prediction model called WPDINM for detecting key proteins based on a novel weighted protein-domain interaction (PDI) network. In WPDINM, a weighted PPI network is constructed first by combining the gene expression data of proteins with topological information extracted from the original PPI network. Simultaneously, a weighted domain-domain interaction (DDI) network is constructed based on the original PDI network. Next, through integrating the newly obtained weighted PPI network and weighted DDI network with the original PDI network, a weighted PDI network is further constructed. Then, based on topological features and biological information, including the subcellular localization and orthologous information of proteins, a novel PageRank-based iterative algorithm is designed and implemented on the newly constructed weighted PDI network to estimate the criticality of proteins. Finally, to assess the prediction performance of WPDINM, we compared it with 12 kinds of competitive measures. Experimental results show that WPDINM can achieve a predictive accuracy rate of 90.19, 81.96, 70.72, 62.04, 55.83, and 51.13% in the top 1%, top 5%, top 10%, top 15%, top 20%, and top 25% separately, which exceeds the prediction accuracy achieved by traditional state-of-the-art competing measures. Owing to the satisfactory identification effect, the WPDINM measure may contribute to the further development of key protein identification.

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The Redox Proteome of Thiol Proteins in the Rice Blast Fungus Magnaporthe oryzae

Frontiers in Microbiology ◽

10.3389/fmicb.2021.648894 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xinrong Zhang ◽

Zhenhua Zhang ◽

Xiao-Lin Chen

Keyword(s):

Magnaporthe Oryzae ◽

Fungal Growth ◽

Interaction Network ◽

Pathogenic Fungi ◽

Protein Domain ◽

Post Translational Modification ◽

Cellular Functions ◽

Protein Protein Interaction ◽

Network Analyses ◽

Wide Range

Redox modification, a post-translational modification, has been demonstrated to be significant for many physiological pathways and biological processes in both eukaryotes and prokaryotes. However, little is known about the global profile of protein redox modification in fungi. To explore the roles of redox modification in the plant pathogenic fungi, a global thiol proteome survey was performed in the model fungal pathogen Magnaporthe oryzae. A total of 3713 redox modification sites from 1899 proteins were identified through a mix sample containing mycelia with or without oxidative stress, conidia, appressoria, and invasive hyphae of M. oryzae. The identified thiol-modified proteins were performed with protein domain, subcellular localization, functional classification, metabolic pathways, and protein–protein interaction network analyses, indicating that redox modification is associated with a wide range of biological and cellular functions. These results suggested that redox modification plays important roles in fungal growth, conidium formation, appressorium formation, as well as invasive growth. Interestingly, a large number of pathogenesis-related proteins were redox modification targets, suggesting the significant roles of redox modification in pathogenicity of M. oryzae. This work provides a global insight into the redox proteome of the pathogenic fungi, which built a groundwork and valuable resource for future studies of redox modification in fungi.

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Topology and weights in a protein domain interaction network – a novel way to predict protein interactions

BMC Genomics ◽

10.1186/1471-2164-7-122 ◽

2006 ◽

Vol 7 (1) ◽

Cited By ~ 20

Author(s):

Stefan Wuchty

Keyword(s):

Protein Interactions ◽

Interaction Network ◽

Protein Domain ◽

Domain Interaction

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The deep(er) roots of Eukaryotes and Akaryotes

F1000Research ◽

10.12688/f1000research.22338.1 ◽

2020 ◽

Vol 9 ◽

pp. 112

Author(s):

Ajith Harish ◽

David Morrison

Keyword(s):

Phylogenetic Signal ◽

Protein Domains ◽

Protein Domain ◽

Root Node ◽

Molecular Features ◽

Phylogenetic Reconstructions ◽

Universal Common Ancestor ◽

Evolutionary Relatedness ◽

Protein Domain Evolution ◽

Phylogenetic Character

Background: Locating the root node of the “tree of life” (ToL) is one of the hardest problems in phylogenetics. The root-node or the universal common ancestor (UCA) divides descendants into organismal domains. Two notable variants of the two-domains ToL (2D-ToL) have gained support recently. One 2D-ToL posits that eukaryotes (organisms with nuclei) and akaryotes (organisms without nuclei) are sister clades that diverged from the UCA and that Asgard archaea are sister to other archaea, whereas the other proposes that eukaryotes emerged within archaea and places Asgard archaea sister to eukaryotes. Williams et al. (Nature Ecol. Evol. 4: 138–147; 2020) re-evaluated the data and methods that support the competing two-domains proposals and concluded that eukaryotes are the closest relatives of Asgard archaea. Critique: We argue that important aspects of estimating evolutionary relatedness and assessing phylogenetic signal in empirical data were overlooked. We focus on phylogenetic character reconstructions necessary to describe the UCA or its closest descendants in the absence of reliable fossils. It is well known that different character types present different perspectives on evolutionary history that relate to different phylogenetic depths. Which 2D-ToL is better supported depends on which kind of molecular features – protein-domains or their component amino acids – are better for resolving common ancestors at the roots of clades. In practice, this involves reconstructing character compositions of the ancestral nodes all the way back to the UCA. We believe the criticisms of 2D-ToL focus on superficial aspects of the data and reflects common misunderstandings of phylogenetic reconstructions using protein domains (folds). Clarifications: Models of protein domain evolution support more reliable phylogenetic reconstructions. In contrast, even the best available amino acid substitution models fail to resolve the archaeal radiation, despite employing thousands of genes. Therefore, the primary domains Eukaryotes and Akaryotes are better supported in a 2D-ToL.

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