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Medvedev KE, Schaeffer RD, Grishin NV. DrugDomain: The evolutionary context of drugs and small molecules bound to domains. Protein Sci 2024; 33:e5116. [PMID: 38979784 PMCID: PMC11231930 DOI: 10.1002/pro.5116] [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] [Received: 03/22/2024] [Revised: 06/27/2024] [Accepted: 06/29/2024] [Indexed: 07/10/2024]
Abstract
Interactions between proteins and small organic compounds play a crucial role in regulating protein functions. These interactions can modulate various aspects of protein behavior, including enzymatic activity, signaling cascades, and structural stability. By binding to specific sites on proteins, small organic compounds can induce conformational changes, alter protein-protein interactions, or directly affect catalytic activity. Therefore, many drugs available on the market today are small molecules (72% of all approved drugs in the last 5 years). Proteins are composed of one or more domains: evolutionary units that convey function or fitness either singly or in concert with others. Understanding which domain(s) of the target protein binds to a drug can lead to additional opportunities for discovering novel targets. The evolutionary classification of protein domains (ECOD) classifies domains into an evolutionary hierarchy that focuses on distant homology. Previously, no structure-based protein domain classification existed that included information about both the interaction between small molecules or drugs and the structural domains of a target protein. This data is especially important for multidomain proteins and large complexes. Here, we present the DrugDomain database that reports the interaction between ECOD of human target proteins and DrugBank molecules and drugs. The pilot version of DrugDomain describes the interaction of 5160 DrugBank molecules associated with 2573 human proteins. It describes domains for all experimentally determined structures of these proteins and incorporates AlphaFold models when such structures are unavailable. The DrugDomain database is available online: http://prodata.swmed.edu/DrugDomain/.
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Affiliation(s)
- Kirill E. Medvedev
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - R. Dustin Schaeffer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexasUSA
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2
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Padalko A, Nair G, Sousa FL. Fusion/fission protein family identification in Archaea. mSystems 2024; 9:e0094823. [PMID: 38700364 PMCID: PMC11237513 DOI: 10.1128/msystems.00948-23] [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] [Received: 09/05/2023] [Accepted: 04/02/2024] [Indexed: 05/05/2024] Open
Abstract
The majority of newly discovered archaeal lineages remain without a cultivated representative, but scarce experimental data from the cultivated organisms show that they harbor distinct functional repertoires. To unveil the ecological as well as evolutionary impact of Archaea from metagenomics, new computational methods need to be developed, followed by in-depth analysis. Among them is the genome-wide protein fusion screening performed here. Natural fusions and fissions of genes not only contribute to microbial evolution but also complicate the correct identification and functional annotation of sequences. The products of these processes can be defined as fusion (or composite) proteins, the ones consisting of two or more domains originally encoded by different genes and split proteins, and the ones originating from the separation of a gene in two (fission). Fusion identifications are required for proper phylogenetic reconstructions and metabolic pathway completeness assessments, while mappings between fused and unfused proteins can fill some of the existing gaps in metabolic models. In the archaeal genome-wide screening, more than 1,900 fusion/fission protein clusters were identified, belonging to both newly sequenced and well-studied lineages. These protein families are mainly associated with different types of metabolism, genetic, and cellular processes. Moreover, 162 of the identified fusion/fission protein families are archaeal specific, having no identified fused homolog within the bacterial domain. Our approach was validated by the identification of experimentally characterized fusion/fission cases. However, around 25% of the identified fusion/fission families lack functional annotations for both composite and split states, showing the need for experimental characterization in Archaea.IMPORTANCEGenome-wide fusion screening has never been performed in Archaea on a broad taxonomic scale. The overlay of multiple computational techniques allows the detection of a fine-grained set of predicted fusion/fission families, instead of rough estimations based on conserved domain annotations only. The exhaustive mapping of fused proteins to bacterial organisms allows us to capture fusion/fission families that are specific to archaeal biology, as well as to identify links between bacterial and archaeal lineages based on cooccurrence of taxonomically restricted proteins and their sequence features. Furthermore, the identification of poorly characterized lineage-specific fusion proteins opens up possibilities for future experimental and computational investigations. This approach enhances our understanding of Archaea in general and provides potential candidates for in-depth studies in the future.
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Affiliation(s)
- Anastasiia Padalko
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
- Vienna Doctoral School of Ecology and Evolution, University of Vienna, Vienna, Austria
| | - Govind Nair
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Filipa L. Sousa
- Genome Evolution and Ecology Group, Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
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3
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Tawfeeq C, Song J, Khaniya U, Madej T, Wang J, Youkharibache P, Abrol R. Towards a structural and functional analysis of the immunoglobulin-fold proteome. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2024; 138:135-178. [PMID: 38220423 DOI: 10.1016/bs.apcsb.2023.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The immunoglobulin fold (Ig fold) domain is a super-secondary structural motif consisting of a sandwich with two layers of β-sheets that is present in many proteins with very diverse biological functions covering a wide range of physiological processes. This domain presents a modular architecture built with β strands connected by variable length loops that has a highly conserved structural core of four β-strands and quite variable β-sheet extensions in the two sandwich layers that enable both divergent and convergent evolutionary mechanisms in the known Ig fold proteome. The central role of this Ig fold's structural plasticity in the evolutionary success of antibodies in our immune system is well established. Nature has also utilized this Ig fold in all domains of life in many different physiological contexts that go way beyond the immune system. Here we will present a structural and functional overview of the utilization of the Ig fold in different biological processes and in different cellular contexts to highlight some of the innumerable ways that this structural motif can interact in multidomain proteins to enable their diversity of functions. This includes shareable specific protein structure visualizations behind those functions that serve as starting points for further explorations of the biomolecular interactions spanning the Ig fold proteome. This overview also highlights how this Ig fold is being utilized through natural adaptation, engineering, and even building from scratch for a range of biotechnological applications.
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Affiliation(s)
- Caesar Tawfeeq
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States
| | - James Song
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Umesh Khaniya
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Thomas Madej
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Jiyao Wang
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Philippe Youkharibache
- Cancer Data Science Laboratory, National Cancer Institute, National Institutes of Health, Bethesda, United States.
| | - Ravinder Abrol
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, United States.
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4
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Garber ME, Frank V, Kazakov AE, Incha MR, Nava AA, Zhang H, Valencia LE, Keasling JD, Rajeev L, Mukhopadhyay A. REC protein family expansion by the emergence of a new signaling pathway. mBio 2023; 14:e0262223. [PMID: 37991384 PMCID: PMC10746176 DOI: 10.1128/mbio.02622-23] [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] [Received: 09/28/2023] [Accepted: 10/20/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE We explore when and why large classes of proteins expand into new sequence space. We used an unsupervised machine learning approach to observe the sequence landscape of REC domains of bacterial response regulator proteins. We find that within-gene recombination can switch effector domains and, consequently, change the regulatory context of the duplicated protein.
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Affiliation(s)
- Megan E. Garber
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Vered Frank
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Alexey E. Kazakov
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew R. Incha
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Alberto A. Nava
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
| | - Hanqiao Zhang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Luis E. Valencia
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
| | - Jay D. Keasling
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California, USA
- Department of Bioengineering, University of California, Berkeley, California, USA
- Center for Biosustainability, Danish Technical University, Lyngby, Denmark
- Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Lara Rajeev
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aindrila Mukhopadhyay
- Department of Comparative Biochemistry, University of California, Berkeley, California, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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5
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Nestor BJ, Bayer PE, Fernandez CGT, Edwards D, Finnegan PM. Approaches to increase the validity of gene family identification using manual homology search tools. Genetica 2023; 151:325-338. [PMID: 37817002 PMCID: PMC10692271 DOI: 10.1007/s10709-023-00196-8] [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] [Received: 06/07/2023] [Accepted: 10/01/2023] [Indexed: 10/12/2023]
Abstract
Identifying homologs is an important process in the analysis of genetic patterns underlying traits and evolutionary relationships among species. Analysis of gene families is often used to form and support hypotheses on genetic patterns such as gene presence, absence, or functional divergence which underlie traits examined in functional studies. These analyses often require precise identification of all members in a targeted gene family. Manual pipelines where homology search and orthology assignment tools are used separately are the most common approach for identifying small gene families where accurate identification of all members is important. The ability to curate sequences between steps in manual pipelines allows for simple and precise identification of all possible gene family members. However, the validity of such manual pipeline analyses is often decreased by inappropriate approaches to homology searches including too relaxed or stringent statistical thresholds, inappropriate query sequences, homology classification based on sequence similarity alone, and low-quality proteome or genome sequences. In this article, we propose several approaches to mitigate these issues and allow for precise identification of gene family members and support for hypotheses linking genetic patterns to functional traits.
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Affiliation(s)
- Benjamin J Nestor
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia.
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia.
| | - Philipp E Bayer
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Cassandria G Tay Fernandez
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - David Edwards
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
| | - Patrick M Finnegan
- School of Biological Sciences, University of Western Australia, Perth, WA, 6009, Australia
- Centre for Applied Bioinformatics, University of Western Australia, Perth, WA, 6009, Australia
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6
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Nguyen LAC, Mori M, Yasuda Y, Galipon J. Functional Consequences of Shifting Transcript Boundaries in Glucose Starvation. Mol Cell Biol 2023; 43:611-628. [PMID: 37937348 PMCID: PMC10761120 DOI: 10.1080/10985549.2023.2270406] [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: 07/11/2023] [Accepted: 10/10/2023] [Indexed: 11/09/2023] Open
Abstract
Glucose is a major source of carbon and essential for the survival of many organisms, ranging from yeast to human. A sudden 60-fold reduction of glucose in exponentially growing fission yeast induces transcriptome-wide changes in gene expression. This regulation is multilayered, and the boundaries of transcripts are known to vary, with functional consequences at the protein level. By combining direct RNA sequencing with 5'-CAGE and short-read sequencing, we accurately defined the 5'- and 3'-ends of transcripts that are both poly(A) tailed and 5'-capped in glucose starvation, followed by proteome analysis. Our results confirm previous experimentally validated loci with alternative isoforms and reveal several transcriptome-wide patterns. First, we show that sense-antisense gene pairs are more strongly anticorrelated when a time lag is taken into account. Second, we show that the glucose starvation response initially elicits a shortening of 3'-UTRs and poly(A) tails, followed by a shortening of the 5'-UTRs at later time points. These result in domain gains and losses in proteins involved in the stress response. Finally, the relatively poor overlap both between differentially expressed genes (DEGs), differential transcript usage events (DTUs), and differentially detected proteins (DDPs) highlight the need for further study on post-transcriptional regulation mechanisms in glucose starvation.
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Affiliation(s)
- Lan Anh Catherine Nguyen
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
| | - Masaru Mori
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Institute of Innovation for Future Society, Nagoya University, Aichi, Nagoya, Japan
| | - Yuji Yasuda
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Faculty of Environment and Information Studies, Keio University, Kanagawa, Fujisawa, Japan
| | - Josephine Galipon
- Institute for Advanced Biosciences, Keio University, Yamagata, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Kanagawa, Fujisawa, Japan
- Graduate School of Science and Engineering, Yamagata University, Yamagata, Yonezawa, Japan
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7
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Zheng L, Assane Hamidou A, Zhao X, Ouyang Z, Lin H, Li J, Zhang X, Luo K, Chen Y. Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis. iScience 2023; 26:107801. [PMID: 37954140 PMCID: PMC10638475 DOI: 10.1016/j.isci.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/29/2023] [Accepted: 08/29/2023] [Indexed: 11/14/2023] Open
Abstract
Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays a vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, and 2 MSODs) in cassava. Bioinformatics analyses provided insights into chromosomal location, phylogenetic relationships, gene structure, conserved motifs, and gene ontology annotations. MeSOD genes were classified into two groups through phylogenetic analysis, revealing evolutionary connections. Promoters of these genes harbored stress-related cis-elements. Duplication analysis indicated the functional significance of MeCSOD2/MeCSOD4 and MeMSOD1/MeMSOD2. Through qRT-PCR, MeCSOD2 responded to salt stress, MeMSOD2 to drought, and cassava bacterial blight. Silencing MeMSOD2 increased XpmCHN11 virulence, indicating MeMSOD2 is essential for cassava's defense against XpmCHN11 infection. These findings enhance our understanding of the SOD gene family's role in cassava and contribute to strategies for stress tolerance improvement.
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Affiliation(s)
- Linling Zheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Abdoulaye Assane Hamidou
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xuerui Zhao
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Zhiwei Ouyang
- HNU-ASU Joint International Tourism College, Hainan University, Haikou 570228, China
| | - Hongxin Lin
- Soil Fertilizer and Resources Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Junyi Li
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xiaofei Zhang
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Kai Luo
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
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8
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Gollapalli P, Rudrappa S, Kumar V, Santosh Kumar HS. Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery. J Mol Evol 2023; 91:598-615. [PMID: 37626222 DOI: 10.1007/s00239-023-10129-w] [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: 08/13/2022] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Genes duplicate, mutate, recombine, fuse or fission to produce new genes, or when genes are formed from de novo, novel functions arise during evolution. Researchers have tried to quantify the causes of these molecular diversification processes to know how these genes increase molecular complexity over a period of time, for instance protein domain organization. In contrast to global sequence similarity, protein domain architectures can capture key structural and functional characteristics, making them better proxies for describing functional equivalence. In Prokaryotes and eukaryotes it has proven that, domain designs are retained over significant evolutionary distances. Protein domain architectures are now being utilized to categorize and distinguish evolutionarily related proteins and find homologs among species that are evolutionarily distant from one another. Additionally, structural information stored in domain structures has accelerated homology identification and sequence search methods. Tools for functional protein annotation have been developed to discover, protein domain content, domain order, domain recurrence, and domain position as all these contribute to the prediction of protein functional accuracy. In this review, an attempt is made to summarise facts and speculations regarding the use of protein domain architecture and modularity to identify possible therapeutic targets among cellular activities based on the understanding their linked biological processes.
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Affiliation(s)
- Pavan Gollapalli
- Center for Bioinformatics and Biostatistics, Nitte (Deemed to be University), Mangalore, Karnataka, 575018, India
| | - Sushmitha Rudrappa
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka, 577451, India
| | - Vadlapudi Kumar
- Department of Biochemistry, Davangere University, Shivagangothri, Davangere, Karnataka, 577007, India
| | - Hulikal Shivashankara Santosh Kumar
- Department of Biotechnology and Bioinformatics, Jnana Sahyadri Campus, Kuvempu University, Shankaraghatta, Shivamogga, Karnataka, 577451, India.
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9
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Zhang J, Schaeffer RD, Durham J, Cong Q, Grishin NV. DPAM: A domain parser for AlphaFold models. Protein Sci 2023; 32:e4548. [PMID: 36539305 PMCID: PMC9850437 DOI: 10.1002/pro.4548] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/06/2022] [Accepted: 12/13/2022] [Indexed: 01/20/2023]
Abstract
The recent breakthroughs in structure prediction, where methods such as AlphaFold demonstrated near-atomic accuracy, herald a paradigm shift in structural biology. The 200 million high-accuracy models released in the AlphaFold Database are expected to guide protein science in the coming decades. Partitioning these AlphaFold models into domains and assigning them to an evolutionary hierarchy provide an efficient way to gain functional insights into proteins. However, classifying such a large number of predicted structures challenges the infrastructure of current structure classifications, including our Evolutionary Classification of protein Domains (ECOD). Better computational tools are urgently needed to parse and classify domains from AlphaFold models automatically. Here we present a Domain Parser for AlphaFold Models (DPAM) that can automatically recognize globular domains from these models based on inter-residue distances in 3D structures, predicted aligned errors, and ECOD domains found by sequence (HHsuite) and structural (Dali) similarity searches. Based on a benchmark of 18,759 AlphaFold models, we demonstrate that DPAM can recognize 98.8% of domains and assign correct boundaries for 87.5%, significantly outperforming structure-based domain parsers and homology-based domain assignment using ECOD domains found by HHsuite or Dali. Application of DPAM to the massive AlphaFold models will enable efficient classification of domains, providing evolutionary contexts and facilitating functional studies.
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Affiliation(s)
- Jing Zhang
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - R. Dustin Schaeffer
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Jesse Durham
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Qian Cong
- Eugene McDermott Center for Human Growth and DevelopmentUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Harold C. Simmons Comprehensive Cancer CenterUniversity of Texas Southwestern Medical CenterDallasTexasUSA
| | - Nick V. Grishin
- Department of BiophysicsUniversity of Texas Southwestern Medical CenterDallasTexasUSA
- Department of BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexasUSA
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10
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Kress A, Poch O, Lecompte O, Thompson JD. Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events. FRONTIERS IN BIOINFORMATICS 2023; 3:1178926. [PMID: 37151482 PMCID: PMC10158824 DOI: 10.3389/fbinf.2023.1178926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/05/2023] [Indexed: 05/09/2023] Open
Abstract
Protein annotation errors can have significant consequences in a wide range of fields, ranging from protein structure and function prediction to biomedical research, drug discovery, and biotechnology. By comparing the domains of different proteins, scientists can identify common domains, classify proteins based on their domain architecture, and highlight proteins that have evolved differently in one or more species or clades. However, genome-wide identification of different protein domain architectures involves a complex error-prone pipeline that includes genome sequencing, prediction of gene exon/intron structures, and inference of protein sequences and domain annotations. Here we developed an automated fact-checking approach to distinguish true domain loss/gain events from false events caused by errors that occur during the annotation process. Using genome-wide ortholog sets and taking advantage of the high-quality human and Saccharomyces cerevisiae genome annotations, we analyzed the domain gain and loss events in the predicted proteomes of 9 non-human primates (NHP) and 20 non-S. cerevisiae fungi (NSF) as annotated in the Uniprot and Interpro databases. Our approach allowed us to quantify the impact of errors on estimates of protein domain gains and losses, and we show that domain losses are over-estimated ten-fold and three-fold in the NHP and NSF proteins respectively. This is in line with previous studies of gene-level losses, where issues with genome sequencing or gene annotation led to genes being falsely inferred as absent. In addition, we show that insistent protein domain annotations are a major factor contributing to the false events. For the first time, to our knowledge, we show that domain gains are also over-estimated by three-fold and two-fold respectively in NHP and NSF proteins. Based on our more accurate estimates, we infer that true domain losses and gains in NHP with respect to humans are observed at similar rates, while domain gains in the more divergent NSF are observed twice as frequently as domain losses with respect to S. cerevisiae. This study highlights the need to critically examine the scientific validity of protein annotations, and represents a significant step toward scalable computational fact-checking methods that may 1 day mitigate the propagation of wrong information in protein databases.
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11
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Cui X, Xue Y, McCormack C, Garces A, Rachman TW, Yi Y, Stolzer M, Durand D. Simulating domain architecture evolution. Bioinformatics 2022; 38:i134-i142. [PMID: 35758772 PMCID: PMC9236583 DOI: 10.1093/bioinformatics/btac242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Motivation Simulation is an essential technique for generating biomolecular data with a ‘known’ history for use in validating phylogenetic inference and other evolutionary methods. On longer time scales, simulation supports investigations of equilibrium behavior and provides a formal framework for testing competing evolutionary hypotheses. Twenty years of molecular evolution research have produced a rich repertoire of simulation methods. However, current models do not capture the stringent constraints acting on the domain insertions, duplications, and deletions by which multidomain architectures evolve. Although these processes have the potential to generate any combination of domains, only a tiny fraction of possible domain combinations are observed in nature. Modeling these stringent constraints on domain order and co-occurrence is a fundamental challenge in domain architecture simulation that does not arise with sequence and gene family simulation. Results Here, we introduce a stochastic model of domain architecture evolution to simulate evolutionary trajectories that reflect the constraints on domain order and co-occurrence observed in nature. This framework is implemented in a novel domain architecture simulator, DomArchov, using the Metropolis–Hastings algorithm with data-driven transition probabilities. The use of a data-driven event module enables quick and easy redeployment of the simulator for use in different taxonomic and protein function contexts. Using empirical evaluation with metazoan datasets, we demonstrate that domain architectures simulated by DomArchov recapitulate properties of genuine domain architectures that reflect the constraints on domain order and adjacency seen in nature. This work expands the realm of evolutionary processes that are amenable to simulation. Availability and implementation DomArchov is written in Python 3 and is available at http://www.cs.cmu.edu/~durand/DomArchov. The data underlying this article are available via the same link. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaoyue Cui
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Yifan Xue
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Collin McCormack
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alejandro Garces
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Thomas W Rachman
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Yang Yi
- Computational Biology, Carnegie Mellon University, Pittsburgh, PA 15213, USA.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Maureen Stolzer
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Dannie Durand
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA 15213, USA
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12
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Rivera AM, Swanson WJ. The Importance of Gene Duplication and Domain Repeat Expansion for the Function and Evolution of Fertilization Proteins. Front Cell Dev Biol 2022; 10:827454. [PMID: 35155436 PMCID: PMC8830517 DOI: 10.3389/fcell.2022.827454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/12/2022] [Indexed: 11/13/2022] Open
Abstract
The process of gene duplication followed by gene loss or evolution of new functions has been studied extensively, yet the role gene duplication plays in the function and evolution of fertilization proteins is underappreciated. Gene duplication is observed in many fertilization protein families including Izumo, DCST, ZP, and the TFP superfamily. Molecules mediating fertilization are part of larger gene families expressed in a variety of tissues, but gene duplication followed by structural modifications has often facilitated their cooption into a fertilization function. Repeat expansions of functional domains within a gene also provide opportunities for the evolution of novel fertilization protein. ZP proteins with domain repeat expansions are linked to species-specificity in fertilization and TFP proteins that experienced domain duplications were coopted into a novel sperm function. This review outlines the importance of gene duplications and repeat domain expansions in the evolution of fertilization proteins.
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Affiliation(s)
- Alberto M. Rivera
- Department of Genome Sciences, University of Washington, Seattle, WA, United States
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13
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Pérez de la Lastra JM, Baca-González V, González-Acosta S, Asensio-Calavia P, Otazo-Pérez A, Morales-delaNuez A. Antibodies targeting enzyme inhibition as potential tools for research and drug development. Biomol Concepts 2021; 12:215-232. [PMID: 35104929 DOI: 10.1515/bmc-2021-0021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 12/31/2021] [Indexed: 12/29/2022] Open
Abstract
Antibodies have transformed biomedical research and are now being used for different experimental applications. Generally, the interaction of enzymes with their specific antibodies can lead to a reduction in their enzymatic activity. The effect of the antibody is dependent on its narrow i.e. the regions of the enzyme to which it is directed. The mechanism of this inhibition is rarely a direct combination of the antibodies with the catalytic site, but is rather due to steric hindrance, barring the substrate access to the active site. In several systems, however, the interaction with the antibody induces conformational changes on the enzyme that can either inhibit or enhance its catalytic activity. The extent of enzyme inhibition or enhancement is, therefore, a reflection of the nature and distribution of the various antigenic determinants on the enzyme molecule. Currently, the mode of action of many enzymes has been elucidated at the molecular level. We here review the molecular mechanisms and recent trends by which antibodies inhibit the catalytic activity of enzymes and provide examples of how specific antibodies can be useful for the neutralization of biologically active molecules.
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Affiliation(s)
- José Manuel Pérez de la Lastra
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
| | - Victoria Baca-González
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Sergio González-Acosta
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
| | - Patricia Asensio-Calavia
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Andrea Otazo-Pérez
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain.,Escuela Doctorado y Estudios de Posgrado. Universidad de La Laguna (ULL). C/ Pedro Zerolo, s/n. 38200. San Cristóbal de La Laguna. S/C de Tenerife, Spain
| | - Antonio Morales-delaNuez
- Biotechnology of macromolecules. Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), San Cristóbal de la Laguna, Tenerife, Spain
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14
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Structural dynamics in the evolution of a bilobed protein scaffold. Proc Natl Acad Sci U S A 2021; 118:2026165118. [PMID: 34845009 PMCID: PMC8694067 DOI: 10.1073/pnas.2026165118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2021] [Indexed: 11/18/2022] Open
Abstract
Proteins conduct numerous complex biological functions by use of tailored structural dynamics. The molecular details of how these emerged from ancestral peptides remains mysterious. How does nature utilize the same repertoire of folds to diversify function? To shed light on this, we analyzed bilobed proteins with a common structural core, which is spread throughout the tree of life and is involved in diverse biological functions such as transcription, enzymatic catalysis, membrane transport, and signaling. We show here that the structural dynamics of the structural core differentiate predominantly via terminal additions during a long-period evolution. This diversifies substrate specificity and, ultimately, biological function. Novel biophysical tools allow the structural dynamics of proteins and the regulation of such dynamics by binding partners to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remain poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the periplasmic-binding protein–like II domain family, have undergone divergent evolution, leading to adaptation of their structural dynamics. We performed a structural analysis on ∼600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Förster resonance energy transfer and Hydrogen–Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enable distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extracytoplasmic transport-related proteins. Structural embellishments of the core created interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately altered substrate specificity. Our findings reveal an as-yet-unrecognized mechanism for the emergence of functional promiscuity during long periods of evolution and are applicable to a large number of domain architectures.
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15
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Liang B, Su J. Advances in aquatic animal RIG-I-like receptors. FISH AND SHELLFISH IMMUNOLOGY REPORTS 2021; 2:100012. [DOI: 10.1016/j.fsirep.2021.100012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/29/2021] [Accepted: 05/16/2021] [Indexed: 01/12/2023] Open
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16
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Matveevsky S, Grishaeva T. Heterogeneity in conservation of multifunctional partner enzymes with meiotic importance, CDK2 kinase and BRCA1 ubiquitin ligase. PeerJ 2021; 9:e12231. [PMID: 34692254 PMCID: PMC8483008 DOI: 10.7717/peerj.12231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/09/2021] [Indexed: 12/04/2022] Open
Abstract
The evolution of proteins can be accompanied by changes not only to their amino acid sequences, but also their structural and spatial molecular organization. Comparison of the protein conservation within different taxonomic groups (multifunctional, or highly specific) allows to clarify their specificity and the direction of evolution. Two multifunctional enzymes, cyclin-dependent kinase 2 (CDK2) and BRCA1 ubiquitin ligase, that are partners in some mitotic and meiotic processes were investigated in the present work. Two research methods, bioinformatics and immunocytochemical, were combined to examine the conservation levels of the two enzymes. It has been established that CDK2 is a highly conserved protein in different taxonomic lineages of the eukaryotic tree. Immunocytochemically, a conserved CDK2 pattern was revealed in the meiotic autosomes of five rodent species and partially in domestic turkey and clawed frog. Nevertheless, variable CDK2 distribution was detected at the unsynapsed segments of the rodent X chromosomes. BRCA1 was shown to be highly conserved only within certain mammalian taxa. It was also noted that in those rodent nuclei, where BRCA1 specifically binds to antigens, asynaptic regions of sex chromosomes were positive. BRCA1 staining was not always accompanied by specific binding, and a high nonspecificity in the nucleoplasm was observed. Thus, the studies revealed different conservation of the two enzymes at the level of protein structure as well as at the level of chromosome behavior. This suggests variable rates of evolution due to both size and configuration of the protein molecules and their multifunctionality.
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Affiliation(s)
- Sergey Matveevsky
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Tatiana Grishaeva
- Laboratory of Cytogenetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
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17
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Genome-wide analysis of RING-type E3 ligase family identifies potential candidates regulating high amylose starch biosynthesis in wheat (Triticum aestivum L.). Sci Rep 2021; 11:11461. [PMID: 34075092 PMCID: PMC8169666 DOI: 10.1038/s41598-021-90685-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 05/10/2021] [Indexed: 12/02/2022] Open
Abstract
In ubiquitin-mediated post-translational modifications, RING finger families are emerged as important E3 ligases in regulating biological processes. Amylose and amylopectin are two major constituents of starch in wheat seed endosperm. Studies have been found the beneficial effects of high amylose or resistant starch on health. The ubiquitin-mediated post-translational regulation of key enzymes for amylose/amylopectin biosynthesis (GBSSI and SBEII) is still unknown. In this study, the genome-wide analysis identified 1272 RING domains in 1255 proteins in wheat, which is not reported earlier. The identified RING domains classified into four groups—RING-H2, RING-HC, RING-v, RING-G, based on the amino acid residues (Cys, His) at metal ligand positions and the number of residues between them with the predominance of RING-H2 type. A total of 1238 RING protein genes were found to be distributed across all 21 wheat chromosomes. Among them, 1080 RING protein genes were identified to show whole genome/segmental duplication within the hexaploid wheat genome. In silico expression analysis using transcriptome data revealed 698 RING protein genes, having a possible role in seed development. Based on differential gene expression and correlation analysis of 36 RING protein genes in diverse (high and low) amylose mutants and parent, 10 potential RING protein genes found to be involved in high amylose biosynthesis and significantly associated with two starch biosynthesis genes; GBSSI and SBEIIa. Characterization of mutant lines using next-generation sequencing method identified unique mutations in 698 RING protein genes. This study signifies the putative role of RING-type E3 ligases in amylose biosynthesis and this information will be helpful for further functional validation and its role in other biological processes in wheat.
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18
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Mix and match: Patchwork domain evolution of the land plant-specific Ca2+-permeable mechanosensitive channel MCA. PLoS One 2021; 16:e0249735. [PMID: 33857196 PMCID: PMC8049495 DOI: 10.1371/journal.pone.0249735] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 03/23/2021] [Indexed: 11/19/2022] Open
Abstract
Multidomain proteins can have a complex evolutionary history that may involve de novo domain evolution, recruitment and / or recombination of existing domains and domain losses. Here, the domain evolution of the plant-specific Ca2+-permeable mechanosensitive channel protein, MID1-COMPLEMENTING ACTIVITY (MCA), was investigated. MCA, a multidomain protein, possesses a Ca2+-influx-MCAfunc domain and a PLAC8 domain. Profile Hidden Markov Models (HMMs) of domains were assessed in 25 viridiplantae proteomes. While PLAC8 was detected in plants, animals, and fungi, MCAfunc was found in streptophytes but not in chlorophytes. Full MCA proteins were only found in embryophytes. We identified the MCAfunc domain in all streptophytes including charophytes where it appeared in E3 ubiquitin ligase-like proteins. Our Maximum Likelihood (ML) analyses suggested that the MCAfunc domain evolved early in the history of streptophytes. The PLAC8 domain showed similarity to Plant Cadmium Resistance (PCR) genes, and the coupling of MCAfunc and PLAC8 seemed to represent a single evolutionary event. This combination is unique in MCA, and does not exist in other plant mechanosensitive channels. Within angiosperms, gene duplications increased the number of MCAs. Considering their role in mechanosensing in roots, MCA might be instrumental for the rise of land plants. This study provides a textbook example of de novo domain emergence, recombination, duplication, and losses, leading to the convergence of function of proteins in plants.
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James JE, Willis SM, Nelson PG, Weibel C, Kosinski LJ, Masel J. Universal and taxon-specific trends in protein sequences as a function of age. eLife 2021; 10:e57347. [PMID: 33416492 PMCID: PMC7819706 DOI: 10.7554/elife.57347] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 01/05/2021] [Indexed: 01/12/2023] Open
Abstract
Extant protein-coding sequences span a huge range of ages, from those that emerged only recently to those present in the last universal common ancestor. Because evolution has had less time to act on young sequences, there might be 'phylostratigraphy' trends in any properties that evolve slowly with age. A long-term reduction in hydrophobicity and hydrophobic clustering was found in previous, taxonomically restricted studies. Here we perform integrated phylostratigraphy across 435 fully sequenced species, using sensitive HMM methods to detect protein domain homology. We find that the reduction in hydrophobic clustering is universal across lineages. However, only young animal domains have a tendency to have higher structural disorder. Among ancient domains, trends in amino acid composition reflect the order of recruitment into the genetic code, suggesting that the composition of the contemporary descendants of ancient sequences reflects amino acid availability during the earliest stages of life, when these sequences first emerged.
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Affiliation(s)
- Jennifer E James
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
| | - Sara M Willis
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
| | - Paul G Nelson
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
| | - Catherine Weibel
- Department of Physics, University of ArizonaTucsonUnited States
- Department of Mathematics, University of ArizonaTucsonUnited States
| | - Luke J Kosinski
- Department of Molecular and Cellular Biology, University of ArizonaTucsonUnited States
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of ArizonaTucsonUnited States
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20
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Wang Y, Wang B, Liu M, Jiang K, Wang M, Wang L. Characterization and function analysis of a Kazal-type serine proteinase inhibitor in the red claw crayfish Cherax quadricarinatus. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2021; 114:103871. [PMID: 32946920 DOI: 10.1016/j.dci.2020.103871] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 09/11/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
Kazal-type serine proteinase inhibitors (KPIs) function in physiological and immunological processes requiring proteinase action. In the present study, the first Cherax quadricarinatus KPI gene (designated CqKPI) was identified and characterized. The open reading frame of CqKPI contains 405 nucleotides and encodes a protein of 134 amino acids. CqKPI has two Kazal domains comprising 44 amino acid residues with the conserved amino acid sequence C-X3-C-X7-C-X6-Y-X3-C-X6-C-X12-C. Each Kazal domain has six conserved cysteine residues, which can form a structural conformation of three pairs of disulfide bonds stabilizing the Kazal domain. CqKPI exhibited high similarity with previously identified KPIs from crayfish hemocytes. The results of tissue distribution showed that CqKPI had the highest expression level in hemocytes, and this was in agreement with phylogenic relationships. Recombinant CqKPI (rCqKPI) was heterologously expressed in Escherichia coli and purified for further study. The proteinase inhibition assays suggested that rCqKPI could potently inhibit elastase and weakly inhibit trypsin, subtilisin A, and proteinase K, but not α-chymotrypsin. It can firmly bind to Bacillus hwajinpoensis, Staphylococcus aureus, and Vibrio parahaemolyticus, with weak binding to Candida albicans. In addition, CqKPI inhibited bacterial secretory proteinase activity and inhibited the growth of B. hwajinpoensis and C. albicans. These data suggest that CqKPI might be involved in anti-bacterial immunity, acting as an inhibitor of the proteinase cascade in the resistance to invasion of pathogens.
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Affiliation(s)
- Yan Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Baojie Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mei Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Keyong Jiang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Mengqiang Wang
- MOE Key Laboratory of Marine Genetics and Breeding, Ocean University of China, Qingdao, 266003, China; The Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, SANYA Oceanographic Institution of the Ocean University of China, Sanya, 572024, China; Center for Marine Molecular Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 266237, China.
| | - Lei Wang
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, National Laboratory for Marine Science and Technology, Qingdao, 266237, China; CAS Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266400, China.
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21
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Phylogeny and Structure of Fatty Acid Photodecarboxylases and Glucose-Methanol-Choline Oxidoreductases. Catalysts 2020. [DOI: 10.3390/catal10091072] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glucose-methanol-choline (GMC) oxidoreductases are a large and diverse family of flavin-binding enzymes found in all kingdoms of life. Recently, a new related family of proteins has been discovered in algae named fatty acid photodecarboxylases (FAPs). These enzymes use the energy of light to convert fatty acids to the corresponding Cn-1 alkanes or alkenes, and hold great potential for biotechnological application. In this work, we aimed at uncovering the natural diversity of FAPs and their relations with other GMC oxidoreductases. We reviewed the available GMC structures, assembled a large dataset of GMC sequences, and found that one active site amino acid, a histidine, is extremely well conserved among the GMC proteins but not among FAPs, where it is replaced with alanine. Using this criterion, we found several new potential FAP genes, both in genomic and metagenomic databases, and showed that related bacterial, archaeal and fungal genes are unlikely to be FAPs. We also identified several uncharacterized clusters of GMC-like proteins as well as subfamilies of proteins that lack the conserved histidine but are not FAPs. Finally, the analysis of the collected dataset of potential photodecarboxylase sequences revealed the key active site residues that are strictly conserved, whereas other residues in the vicinity of the flavin adenine dinucleotide (FAD) cofactor and in the fatty acid-binding pocket are more variable. The identified variants may have different FAP activity and selectivity and consequently may prove useful for new biotechnological applications, thereby fostering the transition from a fossil carbon-based economy to a bio-economy by enabling the sustainable production of hydrocarbon fuels.
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22
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Xiao X, Xue GF, Stamatovic B, Qiu WR. Using Cellular Automata to Simulate Domain Evolution in Proteins. Front Genet 2020; 11:515. [PMID: 32582278 PMCID: PMC7296063 DOI: 10.3389/fgene.2020.00515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 04/28/2020] [Indexed: 11/26/2022] Open
Abstract
Proteins play primary roles in important biological processes such as catalysis, physiological functions, and immune system functions. Thus, the research on how proteins evolved has been a nuclear question in the field of evolutionary biology. General models of protein evolution help to determine the baseline expectations for evolution of sequences, and these models have been extensively useful in sequence analysis as well as for the computer simulation of artificial sequence data sets. We have developed a new method of simulating multi-domain protein evolution, including fusions of domains, insertion, and deletion. It has been observed via the simulation test that the success rates achieved by the proposed predictor are remarkably high. For the convenience of the most experimental scientists, a user-friendly web server has been established at http://jci-bioinfo.cn/domainevo, by which users can easily get their desired results without having to go through the detailed mathematics. Through the simulation results of this website, users can predict the evolution trend of the protein domain architecture.
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Affiliation(s)
- Xuan Xiao
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Guang-Fu Xue
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
| | - Biljana Stamatovic
- Faculty of Information Systems and Technologies, University of Donja Gorica, Podgorica, Montenegro
| | - Wang-Ren Qiu
- Computer Department, Jing-De-Zhen Ceramic Institute, Jingdezhen, China
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23
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Zhang W, Chen Z, Kang Y, Fan Y, Liu Y, Yang X, Shi M, Yao K, Qin S. Genome-wide analysis of lectin receptor-like kinases family from potato ( Solanum tuberosum L.). PeerJ 2020; 8:e9310. [PMID: 32566405 PMCID: PMC7293193 DOI: 10.7717/peerj.9310] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/17/2020] [Indexed: 12/29/2022] Open
Abstract
Lectin receptor-like kinases (LecRLKs) are involved in responses to diverse environmental stresses and pathogenic microbes. A comprehensive acknowledgment of the family members in potato (Solanum tuberosum) genome is largely limited until now. In total, 113 potato LecRLKs (StLecRLKs) were first identified, including 85 G-type, 26 L-type and 2 C-type members. Based on phylogenetic analysis, StLecRLKs were sub-grouped into seven clades, including C-type, L-type, G-I, G-II, G-III G-IV and G-V. Chromosomal distribution and gene duplication analysis revealed the expansion of StLecRLKs occurred majorly through tandem duplication although the whole-genome duplication (WGD)/segmental duplication events were found. Cis-elements in the StLecRLKs promoter region responded mainly to signals of defense and stress, phytohormone, biotic or abiotic stress. Moreover, expressional investigations indicated that the family members of the clades L-type, G-I, G-IV and G-V were responsive to both bacterial and fungal infection. Based on qRT-PCR analysis, the expressions of PGSC0003DMP400055136 and PGSC0003DMP400067047 were strongly induced in all treatments by both Fusarium sulphureum (Fs) and Phytophthora infestans (Pi) inoculation. The present study provides valuable information for LecRLKs gene family in potato genome, and establishes a foundation for further research into the functional analysis.
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Affiliation(s)
- Weina Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Zhongjian Chen
- Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yichen Kang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yanling Fan
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Yuhui Liu
- Gansu Key Laboratory of Crop Improvement and Germplasm Enhancement, Gansu Agricultural University, Lanzhou, China
| | - Xinyu Yang
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Mingfu Shi
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Kai Yao
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
| | - Shuhao Qin
- College of Horticulture, Gansu Agricultural University, Lanzhou, China
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24
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Genome-Wide Identification, Characterization, and Expression Analysis of the Grapevine Superoxide Dismutase (SOD) Family. Int J Genomics 2019; 2019:7350414. [PMID: 30923713 PMCID: PMC6409070 DOI: 10.1155/2019/7350414] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 12/01/2018] [Accepted: 12/20/2018] [Indexed: 01/23/2023] Open
Abstract
Superoxide dismutase (SOD) is an essential enzyme of the plant antioxidant system that responds to oxidative damage caused by adverse conditions. However, little is known about the SOD gene family in Vitis vinifera (Vv). In the present study, ten SOD genes, including 6 copper/zinc SODs, 2 iron SODs, and 2 manganese SODs, were identified in the grapevine genome where they were unevenly distributed on 12 chromosomes. Ten VvSOD genes were divided into three main groups based on phylogenetic analysis, subcellular localization, and the distribution of conserved protein motifs. Additionally, many cis-elements related to different stresses were found in the promoters of the 10 VvSOD genes. Syntenic analysis revealed that VvMSD1 and VvMSD2 were derived from segmental duplication, and VvCSD4 and VvCSD5 belong to a pair of tandemly duplicated genes. Gene expression analysis based on microarray data showed that the 10 VvSOD genes were expressed in all the tested tissues. Interestingly, the segmentally duplicated gene pair (VvMSD1 and VvMSD2) exhibited differential expression patterns in various organs. In contrast, the tandemly duplicated gene pair (VvCSD4 and VvCSD5) displayed similar expression patterns in the tested organs. Our results provide a basis for further functional research on the SOD gene family in grapevine.
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Abstract
This chapter reviews current research on how protein domain architectures evolve. We begin by summarizing work on the phylogenetic distribution of proteins, as this will directly impact which domain architectures can be formed in different species. Studies relating domain family size to occurrence have shown that they generally follow power law distributions, both within genomes and larger evolutionary groups. These findings were subsequently extended to multi-domain architectures. Genome evolution models that have been suggested to explain the shape of these distributions are reviewed, as well as evidence for selective pressure to expand certain domain families more than others. Each domain has an intrinsic combinatorial propensity, and the effects of this have been studied using measures of domain versatility or promiscuity. Next, we study the principles of protein domain architecture evolution and how these have been inferred from distributions of extant domain arrangements. Following this, we review inferences of ancestral domain architecture and the conclusions concerning domain architecture evolution mechanisms that can be drawn from these. Finally, we examine whether all known cases of a given domain architecture can be assumed to have a single common origin (monophyly) or have evolved convergently (polyphyly). We end by a discussion of some available tools for computational analysis or exploitation of protein domain architectures and their evolution.
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Diepeveen ET, Gehrmann T, Pourquié V, Abeel T, Laan L. Patterns of Conservation and Diversification in the Fungal Polarization Network. Genome Biol Evol 2018; 10:1765-1782. [PMID: 29931311 PMCID: PMC6054225 DOI: 10.1093/gbe/evy121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2018] [Indexed: 12/12/2022] Open
Abstract
The combined actions of proteins in networks underlie all fundamental cellular functions. Deeper insights into the dynamics of network composition across species and their functional consequences are crucial to fully understand protein network evolution. Large-scale comparative studies with high phylogenetic resolution are now feasible through the recent rise in available genomic data sets of both model and nonmodel species. Here, we focus on the polarity network, which is universally essential for cell proliferation and studied in great detail in the model organism, Saccharomyces cerevisiae. We examine 42 proteins, directly related to cell polarization, across 298 fungal strains/species to determine the composition of the network and patterns of conservation and diversification. We observe strong protein conservation for a group of 23 core proteins: >95% of all examined strains/species possess at least 14 of these core proteins, albeit in varying compositions, and non of the individual core proteins is 100% conserved. We find high levels of variation in prevalence and sequence identity in the remaining 19 proteins, resulting in distinct lineage-specific compositions of the network in the majority of strains/species. We show that the observed diversification in network composition correlates with lineage, lifestyle, and genetic distance. Yeast, filamentous and basal unicellular fungi, form distinctive groups based on these analyses, with substantial differences to their polarization network. Our study shows that the fungal polarization network is highly dynamic, even between closely related species, and that functional conservation appears to be achieved by varying the specific components of the fungal polarization repertoire.
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Affiliation(s)
- Eveline T Diepeveen
- Department of Bionanoscience, Faculty of Applied Sciences, Kavli Institute of NanoScience, Delft University of Technology, The Netherlands
| | - Thies Gehrmann
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Intelligent Systems, Delft University of Technology, The Netherlands
- Department of Molecular Epidemiology, Leiden Computational Biology Center, Leiden University Medical Centre, The Netherlands
| | - Valérie Pourquié
- Department of Bionanoscience, Faculty of Applied Sciences, Kavli Institute of NanoScience, Delft University of Technology, The Netherlands
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Intelligent Systems, Delft University of Technology, The Netherlands
| | - Thomas Abeel
- Delft Bioinformatics Lab, Faculty of Electrical Engineering, Mathematics and Computer Science, Intelligent Systems, Delft University of Technology, The Netherlands
- Genome Sequencing and Analysis Program, Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts
| | - Liedewij Laan
- Department of Bionanoscience, Faculty of Applied Sciences, Kavli Institute of NanoScience, Delft University of Technology, The Netherlands
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Klasberg S, Bitard-Feildel T, Callebaut I, Bornberg-Bauer E. Origins and structural properties of novel and de novo protein domains during insect evolution. FEBS J 2018; 285:2605-2625. [PMID: 29802682 DOI: 10.1111/febs.14504] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 04/12/2018] [Accepted: 05/11/2018] [Indexed: 12/11/2022]
Abstract
Over long time scales, protein evolution is characterized by modular rearrangements of protein domains. Such rearrangements are mainly caused by gene duplication, fusion and terminal losses. To better understand domain emergence mechanisms we investigated 32 insect genomes covering a speciation gradient ranging from ~ 2 to ~ 390 mya. We use established domain models and foldable domains delineated by hydrophobic cluster analysis (HCA), which does not require homologous sequences, to also identify domains which have likely arisen de novo, that is, from previously noncoding DNA. Our results indicate that most novel domains emerge terminally as they originate from ORF extensions while fewer arise in middle arrangements, resulting from exonization of intronic or intergenic regions. Many novel domains rapidly migrate between terminal or middle positions and single- and multidomain arrangements. Young domains, such as most HCA-defined domains, are under strong selection pressure as they show signals of purifying selection. De novo domains, linked to ancient domains or defined by HCA, have higher degrees of intrinsic disorder and disorder-to-order transition upon binding than ancient domains. However, the corresponding DNA sequences of the novel domains of de novo origins could only rarely be found in sister genomes. We conclude that novel domains are often recruited by other proteins and undergo important structural modifications shortly after their emergence, but evolve too fast to be characterized by cross-species comparisons alone.
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Affiliation(s)
- Steffen Klasberg
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Germany
| | - Tristan Bitard-Feildel
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), Paris, France
| | - Isabelle Callebaut
- Sorbonne Université, Muséum National d'Histoire Naturelle, UMR CNRS 7590, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie, IMPMC, Paris, France
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University Muenster, Germany
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28
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Shapiro JA. Living Organisms Author Their Read-Write Genomes in Evolution. BIOLOGY 2017; 6:E42. [PMID: 29211049 PMCID: PMC5745447 DOI: 10.3390/biology6040042] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/28/2017] [Indexed: 12/18/2022]
Abstract
Evolutionary variations generating phenotypic adaptations and novel taxa resulted from complex cellular activities altering genome content and expression: (i) Symbiogenetic cell mergers producing the mitochondrion-bearing ancestor of eukaryotes and chloroplast-bearing ancestors of photosynthetic eukaryotes; (ii) interspecific hybridizations and genome doublings generating new species and adaptive radiations of higher plants and animals; and, (iii) interspecific horizontal DNA transfer encoding virtually all of the cellular functions between organisms and their viruses in all domains of life. Consequently, assuming that evolutionary processes occur in isolated genomes of individual species has become an unrealistic abstraction. Adaptive variations also involved natural genetic engineering of mobile DNA elements to rewire regulatory networks. In the most highly evolved organisms, biological complexity scales with "non-coding" DNA content more closely than with protein-coding capacity. Coincidentally, we have learned how so-called "non-coding" RNAs that are rich in repetitive mobile DNA sequences are key regulators of complex phenotypes. Both biotic and abiotic ecological challenges serve as triggers for episodes of elevated genome change. The intersections of cell activities, biosphere interactions, horizontal DNA transfers, and non-random Read-Write genome modifications by natural genetic engineering provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations.
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Affiliation(s)
- James A Shapiro
- Department of Biochemistry and Molecular Biology, University of Chicago GCIS W123B, 979 E. 57th Street, Chicago, IL 60637, USA.
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29
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Zhong Y, Cheng ZMM. A unique RPW8-encoding class of genes that originated in early land plants and evolved through domain fission, fusion, and duplication. Sci Rep 2016; 6:32923. [PMID: 27678195 PMCID: PMC5039405 DOI: 10.1038/srep32923] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Accepted: 08/16/2016] [Indexed: 01/17/2023] Open
Abstract
Duplication, lateral gene transfer, domain fusion/fission and de novo domain creation play a key role in formation of initial common ancestral protein. Abundant protein diversities are produced by domain rearrangements, including fusions, fissions, duplications, and terminal domain losses. In this report, we explored the origin of the RPW8 domain and examined the domain rearrangements that have driven the evolution of RPW8-encoding genes in land plants. The RPW8 domain first emerged in the early land plant, Physcomitrella patens, and it likely originated de novo from a non-coding sequence or domain divergence after duplication. It was then incorporated into the NBS-LRR protein to create a main sub-class of RPW8-encoding genes, the RPW8-NBS-encoding genes. They evolved by a series of genetic events of domain fissions, fusions, and duplications. Many species-specific duplication events and tandemly duplicated clusters clearly demonstrated that species-specific and tandem duplications played important roles in expansion of RPW8-encoding genes, especially in gymnosperms and species of the Rosaceae. RPW8 domains with greater Ka/Ks values than those of the NBS domains indicated that they evolved faster than the NBS domains in RPW8-NBSs.
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Affiliation(s)
- Yan Zhong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zong-Ming Max Cheng
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.,Department of Plant Science, University of Tennessee, Knoxville, 37996, USA
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30
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Henry CS, Lerma-Ortiz C, Gerdes SY, Mullen JD, Colasanti R, Zhukov A, Frelin O, Thiaville JJ, Zallot R, Niehaus TD, Hasnain G, Conrad N, Hanson AD, de Crécy-Lagard V. Systematic identification and analysis of frequent gene fusion events in metabolic pathways. BMC Genomics 2016; 17:473. [PMID: 27342196 PMCID: PMC4921024 DOI: 10.1186/s12864-016-2782-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 05/26/2016] [Indexed: 11/19/2022] Open
Abstract
Background Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. Results Here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These sets were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database at http://modelseed.org/projects/fusions/. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. Conclusions Customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2782-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA. .,Computation Institute, The University of Chicago, Chicago, IL, 60637, USA.
| | - Claudia Lerma-Ortiz
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Svetlana Y Gerdes
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA.,Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jeffrey D Mullen
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Aleksey Zhukov
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Océane Frelin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Jennifer J Thiaville
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Rémi Zallot
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ghulam Hasnain
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Neal Conrad
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, 60439, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Valérie de Crécy-Lagard
- Microbiology and Cell Science Department, University of Florida, Gainesville, FL, 32611, USA.
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31
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Lees JG, Dawson NL, Sillitoe I, Orengo CA. Functional innovation from changes in protein domains and their combinations. Curr Opin Struct Biol 2016; 38:44-52. [DOI: 10.1016/j.sbi.2016.05.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 05/17/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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32
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Reddy BL, Saier MH. Properties and Phylogeny of 76 Families of Bacterial and Eukaryotic Organellar Outer Membrane Pore-Forming Proteins. PLoS One 2016; 11:e0152733. [PMID: 27064789 PMCID: PMC4827864 DOI: 10.1371/journal.pone.0152733] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/18/2016] [Indexed: 12/11/2022] Open
Abstract
We here report statistical analyses of 76 families of integral outer membrane pore-forming proteins (OMPPs) found in bacteria and eukaryotic organelles. 47 of these families fall into one superfamily (SFI) which segregate into fifteen phylogenetic clusters. Families with members of the same protein size, topology and substrate specificities often cluster together. Virtually all OMPP families include only proteins that form transmembrane pores. Nine such families, all of which cluster together in the SFI phylogenetic tree, contain both α- and β-structures, are multi domain, multi subunit systems, and transport macromolecules. Most other SFI OMPPs transport small molecules. SFII and SFV homologues derive from Actinobacteria while SFIII and SFIV proteins derive from chloroplasts. Three families of actinobacterial OMPPs and two families of eukaryotic OMPPs apparently consist primarily of α-helices (α-TMSs). Of the 71 families of (putative) β-barrel OMPPs, only twenty could not be assigned to a superfamily, and these derived primarily from Actinobacteria (1), chloroplasts (1), spirochaetes (8), and proteobacteria (10). Proteins were identified in which two or three full length OMPPs are fused together. Family characteristic are described and evidence agrees with a previous proposal suggesting that many arose by adjacent β-hairpin structural unit duplications.
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Affiliation(s)
- Bhaskara L. Reddy
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California, United States of America
- * E-mail:
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33
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Hsu CH, Chiang AWT, Hwang MJ, Liao BY. Proteins with Highly Evolvable Domain Architectures Are Nonessential but Highly Retained. Mol Biol Evol 2016; 33:1219-30. [DOI: 10.1093/molbev/msw006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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34
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Kammerer R, Herse F, Zimmermann W. Convergent Evolution Within CEA Gene Families in Mammals: Hints for Species-Specific Selection Pressures. Evol Biol 2016. [DOI: 10.1007/978-3-319-41324-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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35
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Brinkmann K, Winterhoff M, Önel SF, Schultz J, Faix J, Bogdan S. WHAMY is a novel actin polymerase promoting myoblast fusion, macrophage cell motility and sensory organ development in Drosophila. J Cell Sci 2015; 129:604-20. [PMID: 26675239 DOI: 10.1242/jcs.179325] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/09/2015] [Indexed: 01/06/2023] Open
Abstract
Wiskott-Aldrich syndrome proteins (WASPs) are nucleation-promoting factors (NPF) that differentially control the Arp2/3 complex. In Drosophila, three different family members, SCAR (also known as WAVE), WASP and WASH (also known as CG13176), have been analyzed so far. Here, we characterized WHAMY, the fourth Drosophila WASP family member. whamy originated from a wasp gene duplication and underwent a sub-neofunctionalization. Unlike WASP, we found that WHAMY specifically interacted with activated Rac1 through its two CRIB domains, which were sufficient for targeting WHAMY to lamellipodial and filopodial tips. Biochemical analyses showed that WHAMY promoted exceptionally fast actin filament elongation, although it did not activate the Arp2/3 complex. Loss- and gain-of-function studies revealed an important function of WHAMY in membrane protrusions and cell migration in macrophages. Genetic data further implied synergistic functions between WHAMY and WASP during morphogenesis. Double mutants were late-embryonic lethal and showed severe defects in myoblast fusion. Trans-heterozygous mutant animals showed strongly increased defects in sensory cell fate specification. Thus, WHAMY is a novel actin polymerase with an initial partitioning of ancestral WASP functions in development and subsequent acquisition of a new function in cell motility during evolution.
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Affiliation(s)
- Klaus Brinkmann
- Institut für Neurobiologie, Universität Münster, Badestr. 9, Münster 48149, Germany
| | - Moritz Winterhoff
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, Hannover 30625, Germany
| | - Susanne-Filiz Önel
- Fachbereich Biologie, Entwicklungsbiologie, Philipps-Universität Marburg, Karl-von-Frisch Str. 8, Marburg 35043, Germany
| | - Jörg Schultz
- Center for Computational and Theoretical Biology, Campus Nord and Bioinformatik, Biozentrum, Am Hubland, Universität Würzburg, Würzburg 97074, Germany
| | - Jan Faix
- Institut für Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg Strasse 1, Hannover 30625, Germany
| | - Sven Bogdan
- Institut für Neurobiologie, Universität Münster, Badestr. 9, Münster 48149, Germany
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36
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Das S, Dawson NL, Orengo CA. Diversity in protein domain superfamilies. Curr Opin Genet Dev 2015; 35:40-9. [PMID: 26451979 PMCID: PMC4686048 DOI: 10.1016/j.gde.2015.09.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 09/07/2015] [Accepted: 09/08/2015] [Indexed: 01/25/2023]
Abstract
Whilst ∼93% of domain superfamilies appear to be relatively structurally and functionally conserved based on the available data from the CATH-Gene3D domain classification resource, the remainder are much more diverse. In this review, we consider how domains in some of the most ubiquitous and promiscuous superfamilies have evolved, in particular the plasticity in their functional sites and surfaces which expands the repertoire of molecules they interact with and actions performed on them. To what extent can we identify a core function for these superfamilies which would allow us to develop a ‘domain grammar of function’ whereby a protein's biological role can be proposed from its constituent domains? Clearly the first step is to understand the extent to which these components vary and how changes in their molecular make-up modifies function.
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Affiliation(s)
- Sayoni Das
- Institute of Structural and Molecular Biology, UCL, 627 Darwin Building, Gower Street, WC1E 6BT, UK
| | - Natalie L Dawson
- Institute of Structural and Molecular Biology, UCL, 627 Darwin Building, Gower Street, WC1E 6BT, UK
| | - Christine A Orengo
- Institute of Structural and Molecular Biology, UCL, 627 Darwin Building, Gower Street, WC1E 6BT, UK.
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37
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Ero-Tolliver IA, Hudson BG, Bhave G. The Ancient Immunoglobulin Domains of Peroxidasin Are Required to Form Sulfilimine Cross-links in Collagen IV. J Biol Chem 2015; 290:21741-8. [PMID: 26178375 PMCID: PMC4571896 DOI: 10.1074/jbc.m115.673996] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2015] [Revised: 07/13/2015] [Indexed: 02/02/2023] Open
Abstract
The collagen IV sulfilimine cross-link and its catalyzing enzyme, peroxidasin, represent a dyad critical for tissue development, which is conserved throughout the animal kingdom. Peroxidasin forms novel sulfilimine bonds between opposing methionine and hydroxylysine residues to structurally reinforce the collagen IV scaffold, a function critical for basement membrane and tissue integrity. However, the molecular mechanism underlying cross-link formation remains unclear. In this work, we demonstrate that the catalytic domain of peroxidasin and its immunoglobulin (Ig) domains are required for efficient sulfilimine bond formation. Thus, these molecular features underlie the evolutionarily conserved function of peroxidasin in tissue development and integrity and distinguish peroxidasin from other peroxidases, such as myeloperoxidase (MPO) and eosinophil peroxidase (EPO).
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Affiliation(s)
- Isi A Ero-Tolliver
- From the Division of Nephrology and Hypertension and Department of Medicine, Center for Matrix Biology
| | - Billy G Hudson
- From the Division of Nephrology and Hypertension and Department of Medicine, Center for Matrix Biology, Departments of Biochemistry and Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232
| | - Gautam Bhave
- From the Division of Nephrology and Hypertension and Department of Medicine, Center for Matrix Biology,
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38
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Behura SK. Insect phylogenomics. INSECT MOLECULAR BIOLOGY 2015; 24:403-11. [PMID: 25963452 PMCID: PMC4503476 DOI: 10.1111/imb.12174] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 03/10/2015] [Accepted: 04/04/2015] [Indexed: 05/08/2023]
Abstract
Phylogenomics, the integration of phylogenetics with genome data, has emerged as a powerful approach to study the evolution and systematics of species. Recently, several studies employing phylogenomic tools have provided better insights into insect evolution. Next-generation sequencing methods are now increasingly used by entomologists to generate genomic and transcript sequences of various insect species and strains. These data provide opportunities for comparative genomics and large-scale multigene phylogenies of diverse lineages of insects. Phy-logenomic investigations help us to better understand systematic and evolutionary relationships of insect species that play important roles as herbivores, predators, detritivores, pollinators and disease vectors. It is important that we critically assess the prospects and limitations of phylogenomic methods. In this review, I describe the current status, outline the major challenges and remark on potential future applications of phylogenomic tools in studying insect systematics and evolution.
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Affiliation(s)
- S K Behura
- Eck Institute for Global Health and Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
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39
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Guo P, Yoshimura A, Ishikawa N, Yamaguchi T, Guo Y, Tsukaya H. Comparative analysis of the RTFL peptide family on the control of plant organogenesis. JOURNAL OF PLANT RESEARCH 2015; 128:497-510. [PMID: 25701405 PMCID: PMC4408365 DOI: 10.1007/s10265-015-0703-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 12/25/2014] [Indexed: 05/22/2023]
Abstract
Plant peptides play important roles in various aspects of plant growth and development. The RTFL/DVL family includes small peptides that are widely conserved among land plants. Overexpression of six RTFL genes in Arabidopsis was suggestive of their functions as negative regulators of cell proliferation and as positional cues along the longitudinal axis of the plant body . At this time, few reports are available on RTFL paralogs in other species and the evolutionary relationship of RTFL members among land plants remains unclear. In this study, we compared and analyzed whole amino acid sequences of 188 RTFL members from 22 species among land plants and identified 73 motifs. All RTFL members could be grouped into four clades, and each clade exhibited specific motif patterns, indicative of unique evolutionary traits in the RTFL family. In agreement with this hypothesis, we analyzed two RTFL members from Oryza sativa and Arabidopsis by overexpressing them in Arabidopsis, revealing similar phenotypes suggestive of a conserved function of the RTFL family between eudicots and monocots, as well as different phenotypes and unique functions.
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Affiliation(s)
- Pin Guo
- College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
| | - Asami Yoshimura
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
| | - Naoko Ishikawa
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
- Present Address: Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Tokyo, 153-8902 Japan
| | - Takahiro Yamaguchi
- Acel, Inc. SIC1 1201, 5-4-21 Nishihashimoto, Midori-ku, Sagamihara, Kanagawa Japan
| | - Youhao Guo
- College of Life Science, Wuhan University, Wuhan, 430072 Hubei China
| | - Hirokazu Tsukaya
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo, 113-0033 Japan
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40
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Hoxha E, Campion SR. Structure-critical distribution of aromatic residues in the fibronectin type III protein family. Protein J 2014; 33:165-73. [PMID: 24563228 DOI: 10.1007/s10930-014-9549-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Over a thousand individual Fibronectin type III (FnIII) domain sequences, extracted from more than 60 different FnIII-dependent protein super-structures, were downloaded from curated database resources. Three regions of extreme sequence conservation within the well-characterized FnIII β-sandwich structure were respectively defined by near absolute conservation of a tryptophan (Trp) in β-strand-B, tyrosines (Tyr) in both β-strand-C and β-strand-F, and a leucine (Leu) residue in the unstructured region immediately preceding β-strand-F. Employing these four conserved landmarks, the entire FnIII sequence dataset was vertically registered to align the three conserved regions, and the cumulative distribution of all other amino acid functionality was determined and plotted relative to these landmark residues. Conserved aromatic sites were each found to be flanked by aliphatic residues that assure localization of these sites to the inaccessible hydrophobic interface between major sheet structures. Mapping the location of conserved aromatic sites in numerous PDB structures demonstrated the consistent pair-wise co-localization of the indole side-chain of the conserved strand-B Trp site to within 0.35 nm of the phenolic side-chain of the strand-C Tyr site located 8-14 amino acids distal. Likewise, the side-chain of the strand-F Tyr site co-localized to within 0.45 nm of the aliphatic side-chain of the conserved Leu that uniformly precedes it by six residues. While classic hydropathy-based theories would deem the "burying" of Tyr and Trp side-chains and/or their association with hydrophobic FnIII core residues thermodynamically unnecessary, alternative contributions of conserved Trp and Tyr residues, and particularly the role of the absolutely conserved tyrosine phenolic -OH in native FnIII structure-function are considered. A more global role for conserved FnIII aromaticity is also discussed in light of the aromatic conservation observed in other well-established protein families.
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Affiliation(s)
- Ema Hoxha
- Department of Science and Mathematics, Alvernia University, Reading, PA, 19607, USA
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Sonnhammer ELL, Gabaldón T, Sousa da Silva AW, Martin M, Robinson-Rechavi M, Boeckmann B, Thomas PD, Dessimoz C. Big data and other challenges in the quest for orthologs. Bioinformatics 2014; 30:2993-8. [PMID: 25064571 PMCID: PMC4201156 DOI: 10.1093/bioinformatics/btu492] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/25/2014] [Accepted: 07/16/2014] [Indexed: 01/29/2023] Open
Abstract
UNLABELLED Given the rapid increase of species with a sequenced genome, the need to identify orthologous genes between them has emerged as a central bioinformatics task. Many different methods exist for orthology detection, which makes it difficult to decide which one to choose for a particular application. Here, we review the latest developments and issues in the orthology field, and summarize the most recent results reported at the third 'Quest for Orthologs' meeting. We focus on community efforts such as the adoption of reference proteomes, standard file formats and benchmarking. Progress in these areas is good, and they are already beneficial to both orthology consumers and providers. However, a major current issue is that the massive increase in complete proteomes poses computational challenges to many of the ortholog database providers, as most orthology inference algorithms scale at least quadratically with the number of proteomes. The Quest for Orthologs consortium is an open community with a number of working groups that join efforts to enhance various aspects of orthology analysis, such as defining standard formats and datasets, documenting community resources and benchmarking. AVAILABILITY AND IMPLEMENTATION All such materials are available at http://questfororthologs.org.
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Affiliation(s)
- Erik L L Sonnhammer
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
| | - Toni Gabaldón
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
| | - Alan W Sousa da Silva
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Maria Martin
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Marc Robinson-Rechavi
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
| | - Brigitte Boeckmann
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Paul D Thomas
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK
| | - Christophe Dessimoz
- Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London WC1E 6BT, UK Stockholm Bioinformatics Center, Science for Life Laboratory, Box 1031, SE-17121 Solna, Sweden, Swedish eScience Research Center, Stockholm, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden, Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain, Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain, Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain, EMBL-European Bioinformatics Institute, Hinxton CB10 1SD, UK, Department of Ecology and Evolution, University of Lausanne, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, SwissProt, Swiss Institute of Bioinformatics, 1211 Geneva, Switzerland, Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, CA 90089, USA and Department of Genetics, Evolution and Environment, and Department of Computer Science, University College London, Gower St, London
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Ye F, Cheng Q, Shen J, Zhou C, Chen H. Mismatch repair gene MLH3 Pro844Leu and Thr942Ile polymorphisms and the susceptibility to cervical carcinoma and HPV infection: a case-control study in a Chinese population. PLoS One 2014; 9:e96224. [PMID: 24759751 PMCID: PMC3997526 DOI: 10.1371/journal.pone.0096224] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 04/03/2014] [Indexed: 01/09/2023] Open
Abstract
To investigate the association between MLH3 Pro844Leu, Thr942Ile polymorphisms and potential linkage with the risk of cervical carcinoma and potential effect on protein function, we carried out a case-control study with 400 cervical squamous cell carcinoma, 400 CIN3 and 1200 normal controls in a Chinese population. The results showed that there was an increased risk of cervical carcinoma and CIN3 associated with the genotype 844CT [OR 2.17 (1.61–2.94); P<0.001; OR 1.49 (1.08–2.07), P 0.017, respectively] and a decreased risk with the 942CT genotype [OR 0.56 (0.38–0.82); P<0.001; OR 0.37 (0.24–0.58), P<0.001, respectively]. Most 844CT genotypes were linkage CT(844)-CC(942), which increased the risk of cervical carcinoma and CIN3 [77/83, OR 2.04 (1.48–2.80), P<0.001; 55/61, OR 1.46 (1.03–2.06), P 0.035, respectively]. Most 942CT were linkage CC(844)-CT(942), which decreased the risk of cervical carcinoma [29/35, OR 0.60 (0.40–0.91); P 0.017; 18/24, OR 0.33 (0.20–0.55), P<0.001, respectively]. In some grouping, the 844CT and 942CT were further enriched; especially HR-HPV-positive subjects both in the CIN3 and the cervical carcinoma, the 844CT had greater enrichment. These results included that CT(844)-CC(942) was associated with a high risk of cervical carcinoma and CIN3, and the CC(844)-CT(942) decreased the risk. The 844CT had a higher level of enrichment in HR-HPV positive individuals, which is probably related to HR-HPV susceptibility. There was no significant difference of the MLH3 mRNA expression and these two amino acid substitutions did not impact on the protein function.
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Affiliation(s)
- Feng Ye
- Women’s Reproductive Health Key Laboratory of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qi Cheng
- Women’s Reproductive Health Key Laboratory of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jiajie Shen
- Women’s Reproductive Health Key Laboratory of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Caiyun Zhou
- Department of Pathology, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Huaizeng Chen
- Women’s Reproductive Health Key Laboratory of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- * E-mail:
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Global patterns of protein domain gain and loss in superkingdoms. PLoS Comput Biol 2014; 10:e1003452. [PMID: 24499935 PMCID: PMC3907288 DOI: 10.1371/journal.pcbi.1003452] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/03/2013] [Indexed: 12/21/2022] Open
Abstract
Domains are modules within proteins that can fold and function independently and are evolutionarily conserved. Here we compared the usage and distribution of protein domain families in the free-living proteomes of Archaea, Bacteria and Eukarya and reconstructed species phylogenies while tracing the history of domain emergence and loss in proteomes. We show that both gains and losses of domains occurred frequently during proteome evolution. The rate of domain discovery increased approximately linearly in evolutionary time. Remarkably, gains generally outnumbered losses and the gain-to-loss ratios were much higher in akaryotes compared to eukaryotes. Functional annotations of domain families revealed that both Archaea and Bacteria gained and lost metabolic capabilities during the course of evolution while Eukarya acquired a number of diverse molecular functions including those involved in extracellular processes, immunological mechanisms, and cell regulation. Results also highlighted significant contemporary sharing of informational enzymes between Archaea and Eukarya and metabolic enzymes between Bacteria and Eukarya. Finally, the analysis provided useful insights into the evolution of species. The archaeal superkingdom appeared first in evolution by gradual loss of ancestral domains, bacterial lineages were the first to gain superkingdom-specific domains, and eukaryotes (likely) originated when an expanding proto-eukaryotic stem lineage gained organelles through endosymbiosis of already diversified bacterial lineages. The evolutionary dynamics of domain families in proteomes and the increasing number of domain gains is predicted to redefine the persistence strategies of organisms in superkingdoms, influence the make up of molecular functions, and enhance organismal complexity by the generation of new domain architectures. This dynamics highlights ongoing secondary evolutionary adaptations in akaryotic microbes, especially Archaea.
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Identification and expression analysis of diapause hormone and pheromone biosynthesis activating neuropeptide (DH-PBAN) in the legume pod borer, Maruca vitrata Fabricius. PLoS One 2014; 9:e84916. [PMID: 24409312 PMCID: PMC3883689 DOI: 10.1371/journal.pone.0084916] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 11/27/2013] [Indexed: 11/29/2022] Open
Abstract
Neuropeptides play essential roles in a variety of physiological responses that contribute to the development and reproduction of insects. Both the diapause hormone (DH) and pheromone biosynthesis activating neuropeptide (PBAN) belong to the PBAN/pyrokinin neuropeptide family, which has a conserved pentapeptide motif FXPRL at the C-terminus. We identified the full-length cDNA encoding DH-PBAN in Maruca vitrata, a major lepidopteran pest of leguminous crops. The open reading frame of Marvi-DH-PBAN is 591 bp in length, encoding 197 amino acids, from which five putative neuropeptides [DH, PBAN, α-subesophageal ganglion neuropeptide (SGNP), β-SGNP and γ-SGNP] are derived. Marvi-DH-PBAN was highly similar (83%) to DH-PBAN of Omphisa fuscidentalis (Lepidoptera: Crambidae), but possesses a unique C-terminal FNPRL motif, where asparagine has replaced a serine residue present in other lepidopteran PBAN peptides. The genomic DNA sequence of Marvi-DH-PBAN is 6,231 bp in size and is composed of six exons. Phylogenetic analysis has revealed that the Marvi-DH-PBAN protein sequence is closest to its homolog in Crambidae, but distant from Diptera, Coleoptera and Hymenoptera DH-PBAN, which agrees with the current taxonomy. DH-PBAN transcripts were present in the head and thoracic complex, but absent in the abdomen of M. vitrata. Real-time quantitative PCR assays have demonstrated a relatively higher expression of Marvi-DH-PBAN mRNA in the latter half of the pupal stages and in adults. These findings represent a significant step forward in our understanding of the DH-PBAN gene architecture and phylogeny, and raise the possibility of using Marvi-DH-PBAN to manage M. vitrata populations through molecular techniques.
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Fuxe K, Borroto-Escuela DO, Romero-Fernandez W, Palkovits M, Tarakanov AO, Ciruela F, Agnati LF. Moonlighting proteins and protein-protein interactions as neurotherapeutic targets in the G protein-coupled receptor field. Neuropsychopharmacology 2014; 39:131-55. [PMID: 24105074 PMCID: PMC3857668 DOI: 10.1038/npp.2013.242] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 07/04/2013] [Accepted: 07/05/2013] [Indexed: 12/28/2022]
Abstract
There is serious interest in understanding the dynamics of the receptor-receptor and receptor-protein interactions in space and time and their integration in GPCR heteroreceptor complexes of the CNS. Moonlighting proteins are special multifunctional proteins because they perform multiple autonomous, often unrelated, functions without partitioning into different protein domains. Moonlighting through receptor oligomerization can be operationally defined as an allosteric receptor-receptor interaction, which leads to novel functions of at least one receptor protomer. GPCR-mediated signaling is a more complicated process than previously described as every GPCR and GPCR heteroreceptor complex requires a set of G protein interacting proteins, which interacts with the receptor in an orchestrated spatio-temporal fashion. GPCR heteroreceptor complexes with allosteric receptor-receptor interactions operating through the receptor interface have become major integrative centers at the molecular level and their receptor protomers act as moonlighting proteins. The GPCR heteroreceptor complexes in the CNS have become exciting new targets for neurotherapeutics in Parkinson's disease, schizophrenia, drug addiction, and anxiety and depression opening a new field in neuropsychopharmacology.
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Affiliation(s)
- Kjell Fuxe
- Department of Neuroscience, Karolinska Institutet,, Stockholm, Sweden
| | | | | | - Miklós Palkovits
- Department of Anatomy, Histology and Embryology, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - Alexander O Tarakanov
- Russian Academy of Sciences, St. Petersburg Institute for Informatics and Automation, Saint Petersburg, Russia
| | - Francisco Ciruela
- Facultat de Medicina, Departament de Patologia i Terapèutica Experimental IDIBELL-Universitat de Barcelona, L'Hospitalet de Llobregat, Unitat de Farmacologia, Barcelona, Spain
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Hammond B, Kough J, Herouet-Guicheney C, Jez JM. Toxicological evaluation of proteins introduced into food crops. Crit Rev Toxicol 2013; 43 Suppl 2:25-42. [PMID: 24164515 PMCID: PMC3835160 DOI: 10.3109/10408444.2013.842956] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2013] [Revised: 09/04/2013] [Accepted: 09/06/2013] [Indexed: 11/13/2022]
Abstract
This manuscript focuses on the toxicological evaluation of proteins introduced into GM crops to impart desired traits. In many cases, introduced proteins can be shown to have a history of safe use. Where modifications have been made to proteins, experience has shown that it is highly unlikely that modification of amino acid sequences can make a non-toxic protein toxic. Moreover, if the modified protein still retains its biological function, and this function is found in related proteins that have a history of safe use (HOSU) in food, and the exposure level is similar to functionally related proteins, then the modified protein could also be considered to be "as-safe-as" those that have a HOSU. Within nature, there can be considerable evolutionary changes in the amino acid sequence of proteins within the same family, yet these proteins share the same biological function. In general, food crops such as maize, soy, rice, canola etc. are subjected to a variety of processing conditions to generate different food products. Processing conditions such as cooking, modification of pH conditions, and mechanical shearing can often denature proteins in these crops resulting in a loss of functional activity. These same processing conditions can also markedly lower human dietary exposure to (functionally active) proteins. Safety testing of an introduced protein could be indicated if its biological function was not adequately characterized and/or it was shown to be structurally/functionally related to proteins that are known to be toxic to mammals.
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Affiliation(s)
| | - John Kough
- Office of Pesticide Programs, Microbial Pesticides Branch, US Environmental Protection AgencyWashington, DCUSA
| | | | - Joseph M. Jez
- Department of Biology, Washington University in St. LouisSt. Louis, MOUSA
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Hleap JS, Susko E, Blouin C. Defining structural and evolutionary modules in proteins: a community detection approach to explore sub-domain architecture. BMC STRUCTURAL BIOLOGY 2013; 13:20. [PMID: 24131821 PMCID: PMC4016585 DOI: 10.1186/1472-6807-13-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 10/11/2013] [Indexed: 12/23/2022]
Abstract
Background Assessing protein modularity is important to understand protein evolution. Still the question of the existence of a sub-domain modular architecture remains. We propose a graph-theory approach with significance and power testing to identify modules in protein structures. In the first step, clusters are determined by optimizing the partition that maximizes the modularity score. Second, each cluster is tested for significance. Significant clusters are referred to as modules. Evolutionary modules are identified by analyzing homologous structures. Dynamic modules are inferred from sets of snapshots of molecular simulations. We present here a methodology to identify sub-domain architecture robustly, biologically meaningful, and statistically supported. Results The robustness of this new method is tested using simulated data with known modularity. Modules are correctly identified even when there is a low correlation between landmarks within a module. We also analyzed the evolutionary modularity of a data set of α-amylase catalytic domain homologs, and the dynamic modularity of the Niemann-Pick C1 (NPC1) protein N-terminal domain. The α-amylase contains an (α/β)8 barrel (TIM barrel) with the polysaccharides cleavage site and a calcium-binding domain. In this data set we identified four robust evolutionary modules, one of which forms the minimal functional TIM barrel topology. The NPC1 protein is involved in the intracellular lipid metabolism coordinating sterol trafficking. NPC1 N-terminus is the first luminal domain which binds to cholesterol and its oxygenated derivatives. Our inferred dynamic modules in the protein NPC1 are also shown to match functional components of the protein related to the NPC1 disease. Conclusions A domain compartmentalization can be found and described in correlation space. To our knowledge, there is no other method attempting to identify sub-domain architecture from the correlation among residues. Most attempts made focus on sequence motifs of protein-protein interactions, binding sites, or sequence conservancy. We were able to describe functional/structural sub-domain architecture related to key residues for starch cleavage, calcium, and chloride binding sites in the α-amylase, and sterol opening-defining modules and disease-related residues in the NPC1. We also described the evolutionary sub-domain architecture of the α-amylase catalytic domain, identifying the already reported minimum functional TIM barrel.
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Affiliation(s)
- Jose Sergio Hleap
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, B3H 4R2, Canada.
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Model the evolution of protein interaction network assisted with protein age. J Theor Biol 2013; 333:10-7. [DOI: 10.1016/j.jtbi.2013.05.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2013] [Revised: 04/24/2013] [Accepted: 05/07/2013] [Indexed: 11/21/2022]
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Tarakanov AO, Fuxe KG. Integrin triplets of marine sponges in the murine and human MHCI-CD8 interface and in the interface of human neural receptor heteromers and subunits. SPRINGERPLUS 2013; 2:128. [PMID: 23556147 PMCID: PMC3612178 DOI: 10.1186/2193-1801-2-128] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Accepted: 03/11/2013] [Indexed: 11/10/2022]
Abstract
Based on our theory, main triplets of amino acid residues have been discovered in cell-adhesion receptors (integrins) of marine sponges, which participate as homologies in the interface between two major immune molecules, MHC class I (MHCI) and CD8αβ. They appear as homologies also in several human neural receptor heteromers and subunits. The obtained results probably mean that neural and immune receptors also utilize these structural integrin triplets to form heteromers and ion channels, which are required for a tuned and integrated intracellular and intercellular communication and a communication between cells and the extracellular matrix with an origin in sponges, the oldest multicellular animals.
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Affiliation(s)
- Alexander O Tarakanov
- Russian Academy of Sciences, St. Petersburg Institute for Informatics and Automation, Saint Petersburg, Russia
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Toll-Riera M, Albà MM. Emergence of novel domains in proteins. BMC Evol Biol 2013; 13:47. [PMID: 23425224 PMCID: PMC3599535 DOI: 10.1186/1471-2148-13-47] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/31/2013] [Indexed: 12/31/2022] Open
Abstract
Background Proteins are composed of a combination of discrete, well-defined, sequence domains, associated with specific functions that have arisen at different times during evolutionary history. The emergence of novel domains is related to protein functional diversification and adaptation. But currently little is known about how novel domains arise and how they subsequently evolve. Results To gain insights into the impact of recently emerged domains in protein evolution we have identified all human young protein domains that have emerged in approximately the past 550 million years. We have classified them into vertebrate-specific and mammalian-specific groups, and compared them to older domains. We have found 426 different annotated young domains, totalling 995 domain occurrences, which represent about 12.3% of all human domains. We have observed that 61.3% of them arose in newly formed genes, while the remaining 38.7% are found combined with older domains, and have very likely emerged in the context of a previously existing protein. Young domains are preferentially located at the N-terminus of the protein, indicating that, at least in vertebrates, novel functional sequences often emerge there. Furthermore, young domains show significantly higher non-synonymous to synonymous substitution rates than older domains using human and mouse orthologous sequence comparisons. This is also true when we compare young and old domains located in the same protein, suggesting that recently arisen domains tend to evolve in a less constrained manner than older domains. Conclusions We conclude that proteins tend to gain domains over time, becoming progressively longer. We show that many proteins are made of domains of different age, and that the fastest evolving parts correspond to the domains that have been acquired more recently.
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Affiliation(s)
- Macarena Toll-Riera
- Evolutionary Genomics Group, Research Programme on Biomedical Informatics (GRIB) - Hospital del Mar Research Institute (IMIM), Universitat Pompeu Fabra (UPF), Barcelona, Spain
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