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Sanejouand YH. Are Most Human-Specific Proteins Encoded by Long Noncoding RNAs? J Mol Evol 2024:10.1007/s00239-024-10174-z. [PMID: 38916610 DOI: 10.1007/s00239-024-10174-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/03/2024] [Indexed: 06/26/2024]
Abstract
By looking for a lack of homologs in a reference database of 27 well-annotated proteomes of primates and 52 well-annotated proteomes of other mammals, 170 putative human-specific proteins were identified. While most of them are deemed uncertain, 2 are known at the protein level and 23 at the transcript level, according to UniProt. Interestingly, 23 of these 25 proteins are found to be encoded or to have close homologs in an open reading frame of a long noncoding human RNA. However, half of them are predicted to be at least 80% globular, with a single structural domain, according to IUPred, and with at least 80% of ordered residues, according to flDPnn. Strikingly, there is a near-complete lack of structural knowledge about these proteins, with no tertiary structure presently available in the Protein Data Bank and a fair prediction for one of them in the AlphaFold Protein Structure Database. Moreover, knowledge about the function of these possibly key proteins remains scarce.
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Affiliation(s)
- Yves-Henri Sanejouand
- US2B, UMR 6286 of CNRS, Nantes University, 2 rue de la Houssinière, Nantes, 44322, Pays de la Loire, France.
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2
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Chen J, Li Q, Xia S, Arsala D, Sosa D, Wang D, Long M. The Rapid Evolution of De Novo Proteins in Structure and Complex. Genome Biol Evol 2024; 16:evae107. [PMID: 38753069 PMCID: PMC11149777 DOI: 10.1093/gbe/evae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2024] [Indexed: 06/06/2024] Open
Abstract
Recent studies in the rice genome-wide have established that de novo genes, evolving from noncoding sequences, enhance protein diversity through a stepwise process. However, the pattern and rate of their evolution in protein structure over time remain unclear. Here, we addressed these issues within a surprisingly short evolutionary timescale (<1 million years for 97% of Oryza de novo genes) with comparative approaches to gene duplicates. We found that de novo genes evolve faster than gene duplicates in the intrinsically disordered regions (such as random coils), secondary structure elements (such as α helix and β strand), hydrophobicity, and molecular recognition features. In de novo proteins, specifically, we observed an 8% to 14% decay in random coils and intrinsically disordered region lengths and a 2.3% to 6.5% increase in structured elements, hydrophobicity, and molecular recognition features, per million years on average. These patterns of structural evolution align with changes in amino acid composition over time as well. We also revealed higher positive charges but smaller molecular weights for de novo proteins than duplicates. Tertiary structure predictions showed that most de novo proteins, though not typically well folded on their own, readily form low-energy and compact complexes with other proteins facilitated by extensive residue contacts and conformational flexibility, suggesting a faster-binding scenario in de novo proteins to promote interaction. These analyses illuminate a rapid evolution of protein structure in de novo genes in rice genomes, originating from noncoding sequences, highlighting their quick transformation into active, protein complex-forming components within a remarkably short evolutionary timeframe.
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Affiliation(s)
- Jianhai Chen
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Qingrong Li
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Shengqian Xia
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Deanna Arsala
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Dylan Sosa
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
| | - Dong Wang
- Division of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093, USA
- Department of Cellular & Molecular Medicine, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Manyuan Long
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL 60637, USA
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Middendorf L, Eicholt LA. Random, de novo, and conserved proteins: How structure and disorder predictors perform differently. Proteins 2024; 92:757-767. [PMID: 38226524 DOI: 10.1002/prot.26652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/18/2023] [Accepted: 12/01/2023] [Indexed: 01/17/2024]
Abstract
Understanding the emergence and structural characteristics of de novo and random proteins is crucial for unraveling protein evolution and designing novel enzymes. However, experimental determination of their structures remains challenging. Recent advancements in protein structure prediction, particularly with AlphaFold2 (AF2), have expanded our knowledge of protein structures, but their applicability to de novo and random proteins is unclear. In this study, we investigate the structural predictions and confidence scores of AF2 and protein language model-based predictor ESMFold for de novo and conserved proteins from Drosophila and a dataset of comparable random proteins. We find that the structural predictions for de novo and random proteins differ significantly from conserved proteins. Interestingly, a positive correlation between disorder and confidence scores (pLDDT) is observed for de novo and random proteins, in contrast to the negative correlation observed for conserved proteins. Furthermore, the performance of structure predictors for de novo and random proteins is hampered by the lack of sequence identity. We also observe fluctuating median predicted disorder among different sequence length quartiles for random proteins, suggesting an influence of sequence length on disorder predictions. In conclusion, while structure predictors provide initial insights into the structural composition of de novo and random proteins, their accuracy and applicability to such proteins remain limited. Experimental determination of their structures is necessary for a comprehensive understanding. The positive correlation between disorder and pLDDT could imply a potential for conditional folding and transient binding interactions of de novo and random proteins.
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Affiliation(s)
- Lasse Middendorf
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Lars A Eicholt
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
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Aubel M, Buchel F, Heames B, Jones A, Honc O, Bornberg-Bauer E, Hlouchova K. High-throughput Selection of Human de novo-emerged sORFs with High Folding Potential. Genome Biol Evol 2024; 16:evae069. [PMID: 38597156 PMCID: PMC11024478 DOI: 10.1093/gbe/evae069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 03/11/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024] Open
Abstract
De novo genes emerge from previously noncoding stretches of the genome. Their encoded de novo proteins are generally expected to be similar to random sequences and, accordingly, with no stable tertiary fold and high predicted disorder. However, structural properties of de novo proteins and whether they differ during the stages of emergence and fixation have not been studied in depth and rely heavily on predictions. Here we generated a library of short human putative de novo proteins of varying lengths and ages and sorted the candidates according to their structural compactness and disorder propensity. Using Förster resonance energy transfer combined with Fluorescence-activated cell sorting, we were able to screen the library for most compact protein structures, as well as most elongated and flexible structures. We find that compact de novo proteins are on average slightly shorter and contain lower predicted disorder than less compact ones. The predicted structures for most and least compact de novo proteins correspond to expectations in that they contain more secondary structure content or higher disorder content, respectively. Our experiments indicate that older de novo proteins have higher compactness and structural propensity compared with young ones. We discuss possible evolutionary scenarios and their implications underlying the age-dependencies of compactness and structural content of putative de novo proteins.
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Affiliation(s)
- Margaux Aubel
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Filip Buchel
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Department of Biochemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Brennen Heames
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Alun Jones
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
| | - Ondrej Honc
- Imaging Methods Core Facility, BIOCEV, Prague, Czech Republic
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Muenster, Muenster, Germany
- Department of Protein Evolution, Max Planck-Institute for Biology Tuebingen, Tuebingen, Germany
| | - Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic
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Hlouchova K. Toxin rescue by a random sequence. Nat Ecol Evol 2023; 7:1963-1964. [PMID: 37945945 DOI: 10.1038/s41559-023-02252-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
- Klara Hlouchova
- Department of Cell Biology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.
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