1
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Godbole SS, Dokholyan NV. Allosteric regulation of kinase activity in living cells. eLife 2023; 12:RP90574. [PMID: 37943025 PMCID: PMC10635643 DOI: 10.7554/elife.90574] [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] [Indexed: 11/10/2023] Open
Abstract
The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities, making it difficult to specifically target one kinase, and allosteric control allows specific regulation and study of kinase function without directly targeting the active site. Allosteric sites are distal to the active site but coupled via a dynamic network of inter-atomic interactions between residues in the protein. Establishing an allosteric control over a kinase requires understanding the allosteric wiring of the protein. Computational techniques offer effective and inexpensive mapping of the allosteric sites on a protein. Here, we discuss the methods to map and regulate allosteric communications in proteins, and strategies to establish control over kinase functions in live cells and organisms. Protein molecules, or 'sensors,' are engineered to function as tools to control allosteric activity of the protein as these sensors have high spatiotemporal resolution and help in understanding cell phenotypes after immediate activation or inactivation of a kinase. Traditional methods used to study protein functions, such as knockout, knockdown, or mutation, cannot offer a sufficiently high spatiotemporal resolution. We discuss the modern repertoire of tools to regulate protein kinases as we enter a new era in deciphering cellular signaling and developing novel approaches to treat diseases associated with signal dysregulation.
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Affiliation(s)
| | - Nikolay V Dokholyan
- Department of Pharmacology, Penn State College of MedicineHersheyUnited States
- Department of Biomedical Engineering, Penn State University, University ParkHersheyUnited States
- Department of Engineering Science and Mechanics, Penn State University, University ParkHersheyUnited States
- Department of Biochemistry & Molecular Biology, Penn State College of MedicineHersheyUnited States
- Department of Chemistry, Penn State University, University ParkHersheyUnited States
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2
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Bastin BR, Meha SM, Khindurangala L, Schneider SQ. Cooption of regulatory modules for tektin paralogs during ciliary band formation in a marine annelid larva. Dev Biol 2023; 503:95-110. [PMID: 37557946 DOI: 10.1016/j.ydbio.2023.07.006] [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: 04/20/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
Tektins are a highly conserved family of coiled-coil domain containing proteins known to play a role in structure, stability and function of cilia and flagella. Tektin proteins are thought to form filaments which run the length of the axoneme along the inner surface of the A tubule of each microtubule doublet. Phylogenetic analyses suggest that the tektin family arose via duplications from a single tektin gene in a unicellular organism giving rise to four and five tektin genes in bilaterians and in spiralians, respectively. Although tektins are found in most metazoans, little is known about their expression and function outside of a handful of model species. Here we present the first comprehensive study of tektin family gene expression in any animal system, in the spiralian annelid Platynereis dumerilii. This indirect developing species retains a full ancient spiralian complement of five tektin genes. We show that all five tektins are expressed almost exclusively in known ciliary structures following the expression of the motile cilia master regulator foxJ1. The three older bilaterian tektin-1, tektin-2, and tektin-4 genes, show a high degree of spatial and temporal co-regulation, while the spiralian specific tektin-3/5A and tektin-3/5B show a delay in onset of expression in every ciliary structure. In addition, tektin-3/5B transcripts show a restricted subcellular localization to the most apical region near the multiciliary arrays. The exact recapitulation of the sequence of expression and localization of the five tektins at different times during larval development indicates the cooption of a fixed regulatory and cellular program during the formation of each ciliary band and multiciliated cell type in this spiralian.
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Affiliation(s)
- Benjamin R Bastin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
| | - Steffanie M Meha
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
| | - Lalith Khindurangala
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA.
| | - Stephan Q Schneider
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA; Institute of Cellular and Organismic Biology, Academia Sinica, Taipei, Taiwan.
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3
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Godbole S, Dokholyan NV. Allosteric regulation of kinase activity in living cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.19.549709. [PMID: 37503033 PMCID: PMC10370130 DOI: 10.1101/2023.07.19.549709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The dysregulation of protein kinases is associated with multiple diseases due to the kinases' involvement in a variety of cell signaling pathways. Manipulating protein kinase function, by controlling the active site, is a promising therapeutic and investigative strategy to mitigate and study diseases. Kinase active sites share structural similarities making it difficult to specifically target one kinase, allosteric control allows specific regulation and study of kinase function without directly targeting the active site. Allosteric sites are distal to the active site but coupled via a dynamic network of inter-atomic interactions between residues in the protein. Establishing an allosteric control over a kinase requires understanding the allosteric wiring of the protein. Computational techniques offer effective and inexpensive mapping of the allosteric sites on a protein. Here, we discuss methods to map and regulate allosteric communications in proteins, and strategies to establish control over kinase functions in live cells and organisms. Protein molecules, or "sensors" are engineered to function as tools to control allosteric activity of the protein as these sensors have high spatiotemporal resolution and help in understanding cell phenotypes after immediate activation or inactivation of a kinase. Traditional methods used to study protein functions, such as knockout, knockdown, or mutation, cannot offer a sufficiently high spatiotemporal resolution. We discuss the modern repertoire of tools to regulate protein kinases as we enter a new era in deciphering cellular signaling and developing novel approaches to treat diseases associated with signal dysregulation.
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Affiliation(s)
- Shivani Godbole
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Biomedical Engineering, Penn State University, University Park, PA 16802, USA
- Department of Engineering Science and Mechanics, Penn State University, University Park, PA 16802, USA
- Department of Biochemistry & Molecular Biology, Penn State College of Medicine, Hershey, PA 17033-0850, USA
- Department of Chemistry, Penn State University, University Park, PA 16802, USA
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4
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Li S, Jing T, Zhu F, Chen Y, Yao X, Tang X, Zuo C, Liu M, Xie Y, Jiang Y, Wang Y, Li D, Li L, Gao S, Chen D, Zhao H, Ma W. Genetic Analysis of Orf Virus (ORFV) Strains Isolated from Goats in China: Insights into Epidemiological Characteristics and Evolutionary Patterns. Virus Res 2023; 334:199160. [PMID: 37402415 PMCID: PMC10410590 DOI: 10.1016/j.virusres.2023.199160] [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: 03/08/2023] [Revised: 06/14/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023]
Abstract
Contagious ecthyma (CE) is an acute infectious zoonosis caused by orf virus (ORFV) that mainly infects sheep and goats and causes obvious lesions and low market value of livestock, resulting in huge economic losses for farmers. In this study, two strains of ORFV were isolated from Shaanxi Province and Yunnan Province in China, named FX and LX. The two ORFVs were located in the major clades of domestic strains respectively, and exhibited distinct sequence homology. We analyzed the genetic data of core genes (B2L, F1L, VIR, ORF109) and variable genes (GIF, ORF125 and vIL-10) of ORFV to investigate its epidemiological and evolutionary characteristics. The sequences from 2007 to 2018 constituted the majority of the viral population, predominantly concentrated in India and China. Most genes were clustered into SA00-like type and IA82-like type, and the hotspots in East and South Asia were identified in the ORFV transmission trajectories. For these genes, VIR had the highest substitution rate of 4.85 × 10-4, both VIR and vIL-10 suffered the positive selection pressure during ORFV evolution. Many motifs associated with viral survival were distributed among ORFVs. In addition, some possible viral epitopes have been predicted, which still require validation in vivo and in vitro. This work gives more insight into the prevalence and phylogenetic relationships of existing orf viruses and facilitate better vaccine design.
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Affiliation(s)
- Shaofei Li
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Tian Jing
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Fang Zhu
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yiming Chen
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Xiaoting Yao
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Xidian Tang
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Chenxiang Zuo
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Mingjie Liu
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yanfei Xie
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yuecai Jiang
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Yunpeng Wang
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Dengliang Li
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Lulu Li
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China
| | - Shikong Gao
- Shenmu Animal Husbandry Development Center, Shenmu, Shaanxi Province 719399, China
| | - Dekun Chen
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China.
| | - Huiying Zhao
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China.
| | - Wentao Ma
- Veterinary Immunology Laboratory, College of Veterinary Medicine, Northwest Agriculture and Forestry University, Yangling, Shaanxi Province 712100, China.
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Wilde V, Canard B, Ferron F. Viral Instant Mutation Viewer: A Tool to Speed Up the Identification and Analysis of New SARS-CoV-2 Emerging Variants and Beyond. Viruses 2023; 15:1628. [PMID: 37631971 PMCID: PMC10458308 DOI: 10.3390/v15081628] [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: 06/30/2023] [Revised: 07/19/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Abstract
The appearance of genetic variants impacts vaccination efficiency and therapeutic options, generating a need to map and relate mutations observed in the proteome and the genome. We develop an user-friendly web service software (Viral Instant Mutation Viewer or VIMVer) which allows a direct identification of mutations in the genome and its counterpart in the viral proteome. Since its emergence in 2019, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the COVID-19 pandemic, has generated an overwhelming amount of data while becoming one of the most studied viruses of the Nidovirales order. We originally developed this tool during the COVID pandemic; thus, for any SARS-CoV-2 nucleotide sequence, the web service gives a fast identification, mapping, and display of new mutations simultaneously at the nucleotide and amino acid level in comparison to a reference sequence (Wuhan-1). Furthermore, the lineage or the relative position to the known lineage of the variant of interest is available on the link to Phylogenetic Assignment of Named Global Outbreak LINeages (PANGOLIN COVID-19). The workflow presented here is available online. The source code is released under public license and can be easily adapted for further development to other viruses.
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Affiliation(s)
- Vincent Wilde
- Architecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, France; (V.W.); (B.C.)
- Marseille and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France
| | - Bruno Canard
- Architecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, France; (V.W.); (B.C.)
- Marseille and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - François Ferron
- Architecture et Fonction des Macromolécules Biologiques, CNRS-UMR 7257, Polytech Case 925, 13009 Marseille, France; (V.W.); (B.C.)
- Marseille and Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), Aix-Marseille Université, AFMB UMR 7257, 13288 Marseille, France
- European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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6
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Czernecki D, Nourisson A, Legrand P, Delarue M. Reclassification of family A DNA polymerases reveals novel functional subfamilies and distinctive structural features. Nucleic Acids Res 2023; 51:4488-4507. [PMID: 37070157 PMCID: PMC10201439 DOI: 10.1093/nar/gkad242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 03/07/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Family A DNA polymerases (PolAs) form an important and well-studied class of extant polymerases participating in DNA replication and repair. Nonetheless, despite the characterization of multiple subfamilies in independent, dedicated works, their comprehensive classification thus far is missing. We therefore re-examine all presently available PolA sequences, converting their pairwise similarities into positions in Euclidean space, separating them into 19 major clusters. While 11 of them correspond to known subfamilies, eight had not been characterized before. For every group, we compile their general characteristics, examine their phylogenetic relationships and perform conservation analysis in the essential sequence motifs. While most subfamilies are linked to a particular domain of life (including phages), one subfamily appears in Bacteria, Archaea and Eukaryota. We also show that two new bacterial subfamilies contain functional enzymes. We use AlphaFold2 to generate high-confidence prediction models for all clusters lacking an experimentally determined structure. We identify new, conserved features involving structural alterations, ordered insertions and an apparent structural incorporation of a uracil-DNA glycosylase (UDG) domain. Finally, genetic and structural analyses of a subset of T7-like phages indicate a splitting of the 3'-5' exo and pol domains into two separate genes, observed in PolAs for the first time.
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Affiliation(s)
- Dariusz Czernecki
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Antonin Nourisson
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Sorbonne Université, Collège Doctoral, ED 515, 75005 Paris, France
| | - Pierre Legrand
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
- Synchrotron SOLEIL, L’Orme des Merisiers, 91190 Saint-Aubin, France
| | - Marc Delarue
- Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unit of Architecture and Dynamics of Biological Macromolecules, 75015 Paris, France
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7
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Zheng C, Chen X, Zhang T, Sahinidis NV, Siirola JJ. Learning process patterns via multiple sequence alignment. Comput Chem Eng 2022. [DOI: 10.1016/j.compchemeng.2022.107676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Shen C, Zaharias P, Warnow T. MAGUS+eHMMs: improved multiple sequence alignment accuracy for fragmentary sequences. Bioinformatics 2021; 38:918-924. [PMID: 34791036 PMCID: PMC8796358 DOI: 10.1093/bioinformatics/btab788] [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: 06/28/2021] [Revised: 10/14/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY Multiple sequence alignment is an initial step in many bioinformatics pipelines, including phylogeny estimation, protein structure prediction and taxonomic identification of reads produced in amplicon or metagenomic datasets, etc. Yet, alignment estimation is challenging on datasets that exhibit substantial sequence length heterogeneity, and especially when the datasets have fragmentary sequences as a result of including reads or contigs generated by next-generation sequencing technologies. Here, we examine techniques that have been developed to improve alignment estimation when datasets contain substantial numbers of fragmentary sequences. We find that MAGUS, a recently developed MSA method, is fairly robust to fragmentary sequences under many conditions, and that using a two-stage approach where MAGUS is used to align selected 'backbone sequences' and the remaining sequences are added into the alignment using ensembles of Hidden Markov Models further improves alignment accuracy. The combination of MAGUS with the ensemble of eHMMs (i.e. MAGUS+eHMMs) clearly improves on UPP, the previous leading method for aligning datasets with high levels of fragmentation. AVAILABILITY AND IMPLEMENTATION UPP is available on https://github.com/smirarab/sepp, and MAGUS is available on https://github.com/vlasmirnov/MAGUS. MAGUS+eHMMs can be performed by running MAGUS to obtain the backbone alignment, and then using the backbone alignment as an input to UPP. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Chengze Shen
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Paul Zaharias
- Department of Computer Science, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
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Tizei PAG, Harris E, Withanage S, Renders M, Pinheiro VB. A novel framework for engineering protein loops exploring length and compositional variation. Sci Rep 2021; 11:9134. [PMID: 33911147 PMCID: PMC8080606 DOI: 10.1038/s41598-021-88708-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/12/2021] [Indexed: 02/02/2023] Open
Abstract
Insertions and deletions (indels) are known to affect function, biophysical properties and substrate specificity of enzymes, and they play a central role in evolution. Despite such clear significance, this class of mutation remains an underexploited tool in protein engineering with few available platforms capable of systematically generating and analysing libraries of varying sequence composition and length. We present a novel DNA assembly platform (InDel assembly), based on cycles of endonuclease restriction digestion and ligation of standardised dsDNA building blocks, that can generate libraries exploring both composition and sequence length variation. In addition, we developed a framework to analyse the output of selection from InDel-generated libraries, combining next generation sequencing and alignment-free strategies for sequence analysis. We demonstrate the approach by engineering the well-characterized TEM-1 β-lactamase Ω-loop, involved in substrate specificity, identifying multiple novel extended spectrum β-lactamases with loops of modified length and composition-areas of the sequence space not previously explored. Together, the InDel assembly and analysis platforms provide an efficient route to engineer protein loops or linkers where sequence length and composition are both essential functional parameters.
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Affiliation(s)
- Pedro A. G. Tizei
- grid.83440.3b0000000121901201Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK
| | - Emma Harris
- grid.4464.20000 0001 2161 2573Department of Biological Sciences, University of London, Malet Street, Birkbeck, WC1E 7HX UK
| | - Shamal Withanage
- grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Marleen Renders
- grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
| | - Vitor B. Pinheiro
- grid.83440.3b0000000121901201Department of Structural and Molecular Biology, University College London, Gower Street, London, WC1E 6BT UK ,grid.4464.20000 0001 2161 2573Department of Biological Sciences, University of London, Malet Street, Birkbeck, WC1E 7HX UK ,grid.415751.3KU Leuven, Rega Institute for Medical Research, Medicinal Chemistry, Herestraat 49, Box 1041, 3000 Leuven, Belgium
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Repecka D, Jauniskis V, Karpus L, Rembeza E, Rokaitis I, Zrimec J, Poviloniene S, Laurynenas A, Viknander S, Abuajwa W, Savolainen O, Meskys R, Engqvist MKM, Zelezniak A. Expanding functional protein sequence spaces using generative adversarial networks. NAT MACH INTELL 2021. [DOI: 10.1038/s42256-021-00310-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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11
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Bradley D, Viéitez C, Rajeeve V, Selkrig J, Cutillas PR, Beltrao P. Sequence and Structure-Based Analysis of Specificity Determinants in Eukaryotic Protein Kinases. Cell Rep 2021; 34:108602. [PMID: 33440154 PMCID: PMC7809594 DOI: 10.1016/j.celrep.2020.108602] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 11/03/2020] [Accepted: 12/14/2020] [Indexed: 01/04/2023] Open
Abstract
Protein kinases lie at the heart of cell-signaling processes and are often mutated in disease. Kinase target recognition at the active site is in part determined by a few amino acids around the phosphoacceptor residue. However, relatively little is known about how most preferences are encoded in the kinase sequence or how these preferences evolved. Here, we used alignment-based approaches to predict 30 specificity-determining residues (SDRs) for 16 preferences. These were studied with structural models and were validated by activity assays of mutant kinases. Cancer mutation data revealed that kinase SDRs are mutated more frequently than catalytic residues. We have observed that, throughout evolution, kinase specificity has been strongly conserved across orthologs but can diverge after gene duplication, as illustrated by the G protein-coupled receptor kinase family. The identified SDRs can be used to predict kinase specificity from sequence and aid in the interpretation of evolutionary or disease-related genomic variants.
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Affiliation(s)
- David Bradley
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK
| | - Cristina Viéitez
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK; European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Vinothini Rajeeve
- Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Joel Selkrig
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Pedro R Cutillas
- Integrative Cell Signalling & Proteomics, Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
| | - Pedro Beltrao
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge CB10 1SD, UK.
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12
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Computational Evolutionary Biology. Adv Bioinformatics 2021. [DOI: 10.1007/978-981-33-6191-1_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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13
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Carpentier M, Chomilier J. Protein multiple alignments: sequence-based versus structure-based programs. Bioinformatics 2020; 35:3970-3980. [PMID: 30942864 DOI: 10.1093/bioinformatics/btz236] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 03/05/2019] [Accepted: 04/02/2019] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Multiple sequence alignment programs have proved to be very useful and have already been evaluated in the literature yet not alignment programs based on structure or both sequence and structure. In the present article we wish to evaluate the added value provided through considering structures. RESULTS We compared the multiple alignments resulting from 25 programs either based on sequence, structure or both, to reference alignments deposited in five databases (BALIBASE 2 and 3, HOMSTRAD, OXBENCH and SISYPHUS). On the whole, the structure-based methods compute more reliable alignments than the sequence-based ones, and even than the sequence+structure-based programs whatever the databases. Two programs lead, MAMMOTH and MATRAS, nevertheless the performances of MUSTANG, MATT, 3DCOMB, TCOFFEE+TM_ALIGN and TCOFFEE+SAP are better for some alignments. The advantage of structure-based methods increases at low levels of sequence identity, or for residues in regular secondary structures or buried ones. Concerning gap management, sequence-based programs set less gaps than structure-based programs. Concerning the databases, the alignments of the manually built databases are more challenging for the programs. AVAILABILITY AND IMPLEMENTATION All data and results presented in this study are available at: http://wwwabi.snv.jussieu.fr/people/mathilde/download/AliMulComp/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mathilde Carpentier
- Institut Systématique Evolution Biodiversité (ISYEB), Sorbonne Université, MNHN, CNRS, EPHE, Paris, France
| | - Jacques Chomilier
- Sorbonne Université, MNHN, CNRS, IRD, Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), BiBiP, Paris, France
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14
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Matar J, Khoury HE, Charr JC, Guyeux C, Chrétien S. SpCLUST: Towards a fast and reliable clustering for potentially divergent biological sequences. Comput Biol Med 2019; 114:103439. [PMID: 31550555 DOI: 10.1016/j.compbiomed.2019.103439] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/05/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022]
Abstract
This paper presents SpCLUST, a new C++ package that takes a list of sequences as input, aligns them with MUSCLE, computes their similarity matrix in parallel and then performs the clustering. SpCLUST extends a previously released software by integrating additional scoring matrices which enables it to cover the clustering of amino-acid sequences. The similarity matrix is now computed in parallel according to the master/slave distributed architecture, using MPI. Performance analysis, realized on two real datasets of 100 nucleotide sequences and 1049 amino-acids ones, show that the resulting library substantially outperforms the original Python package. The proposed package was also intensively evaluated on simulated and real genomic and protein data sets. The clustering results were compared to the most known traditional tools, such as UCLUST, CD-HIT and DNACLUST. The comparison showed that SpCLUST outperforms the other tools when clustering divergent sequences, and contrary to the others, it does not require any user intervention or prior knowledge about the input sequences.
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Affiliation(s)
- Johny Matar
- Université de Bourgogne Franche-Comté, UMR 6174 CNRS, 16 route de Gray, Besançon, France; LaRRIS, Faculty of Science, Lebanese University, Fanar, Lebanon
| | | | - Jean-Claude Charr
- Université de Bourgogne Franche-Comté, UMR 6174 CNRS, 16 route de Gray, Besançon, France.
| | - Christophe Guyeux
- Université de Bourgogne Franche-Comté, UMR 6174 CNRS, 16 route de Gray, Besançon, France
| | - Stéphane Chrétien
- National Physical Laboratory, Hampton Road, Teddington, United Kingdom
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15
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Matsui M, Iwasaki W. Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction. Syst Biol 2019; 69:265-279. [DOI: 10.1093/sysbio/syz049] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 07/09/2019] [Accepted: 07/20/2019] [Indexed: 11/12/2022] Open
Abstract
Abstract
A protein superfamily contains distantly related proteins that have acquired diverse biological functions through a long evolutionary history. Phylogenetic analysis of the early evolution of protein superfamilies is a key challenge because existing phylogenetic methods show poor performance when protein sequences are too diverged to construct an informative multiple sequence alignment (MSA). Here, we propose the Graph Splitting (GS) method, which rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach. Evolutionary simulation showed that the GS method can accurately reconstruct phylogenetic trees and be robust to major problems in phylogenetic estimation, such as biased taxon sampling, heterogeneous evolutionary rates, and long-branch attraction when sequences are substantially diverge. Its application to an empirical data set of the triosephosphate isomerase (TIM)-barrel superfamily suggests rapid evolution of protein-mediated pyrimidine biosynthesis, likely taking place after the RNA world. Furthermore, the GS method can also substantially improve performance of widely used MSA methods by providing accurate guide trees.
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Affiliation(s)
- Motomu Matsui
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Wataru Iwasaki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8568, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8564, Japan
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16
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Alazem O, Abramyan J. Reptile enamel matrix proteins: Selection, divergence, and functional constraint. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:136-148. [PMID: 31045323 DOI: 10.1002/jez.b.22857] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 02/24/2019] [Accepted: 04/01/2019] [Indexed: 12/14/2022]
Abstract
The three major enamel matrix proteins (EMPs): amelogenin (AMEL), ameloblastin (AMBN), and enamelin (ENAM), are intrinsically linked to tooth development in tetrapods. However, reptiles and mammals exhibit significant differences in dental patterning and development, potentially affecting how EMPs evolve in each group. In most reptiles, teeth are replaced continuously throughout life, while mammals have reduced replacement to only one or two generations. Reptiles also form structurally simple, aprismatic enamel while mammalian enamel is composed of highly organized hydroxyapatite prisms. These differences, combined with reported low sequence homology in reptiles, led us to predict that reptiles may experience lower selection pressure on their EMPs as compared with mammals. However, we found that like mammals, reptile EMPs are under moderate purifying selection, with some differences evident between AMEL, AMBN, and ENAM. We also demonstrate that sequence homology in reptile EMPs is closely associated with divergence times, with more recently diverged lineages exhibiting high homology, along with strong phylogenetic signal. Lastly, despite sequence divergence, none of the reptile species in our study exhibited mutations consistent with diseases that cause degeneration of enamel (e.g. amelogenesis imperfecta). Despite short tooth retention time and simplicity in enamel structure, reptile EMPs still exhibit purifying selection required to form durable enamel.
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Affiliation(s)
- Omar Alazem
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, Michigan
| | - John Abramyan
- Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, Michigan
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17
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Bastin BR, Schneider SQ. Taxon-specific expansion and loss of tektins inform metazoan ciliary diversity. BMC Evol Biol 2019; 19:40. [PMID: 30704394 PMCID: PMC6357514 DOI: 10.1186/s12862-019-1360-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 01/14/2019] [Indexed: 11/15/2022] Open
Abstract
Background Cilia and flagella are complex cellular structures thought to have first evolved in a last ciliated eukaryotic ancestor due to the conserved 9 + 2 microtubule doublet structure of the axoneme and associated proteins. The Tektin family of coiled-coil domain containing proteins was previously identified in cilia of organisms as diverse as green algae and sea urchin. While studies have shown that some Tektins are necessary for ciliary function, there has been no comprehensive phylogenetic survey of tektin genes. To fill this gap, we sampled tektin sequences broadly among metazoan and unicellular lineages in order to determine how the tektin gene complements evolved in over 100 different extant species. Results Using Bayesian and Maximum Likelihood analyses, we have ascertained with high confidence that all metazoan tektins arose from a single ancestral tektin gene in the last common ancestor of metazoans and choanoflagellates. Gene duplications gave rise to two tektin genes in the metazoan ancestor, and a subsequent expansion to three and four tektin genes in early bilaterian ancestors. While all four tektin genes remained highly conserved in most deuterostome and spiralian species surveyed, most tektin genes in ecdysozoans are highly derived with extensive gene loss in several lineages including nematodes and some crustaceans. In addition, while tektin-1, − 2, and − 4 have remained as single copy genes in most lineages, tektin-3/5 has been duplicated independently several times, notably at the base of the spiralian, vertebrate and hymenopteran (Ecdysozoa) clades. Conclusions We provide a solid description of tektin evolution supporting one, two, three, and four ancestral tektin genes in a holozoan, metazoan, bilaterian, and nephrozoan ancestor, respectively. The isolated presence of tektin in a cryptophyte and a chlorophyte branch invokes events of horizontal gene transfer, and that the last common ciliated eukaryotic ancestor lacked a tektin gene. Reconstructing the evolutionary history of the tektin complement in each extant metazoan species enabled us to pinpoint lineage specific expansions and losses. Our analysis will help to direct future studies on Tektin function, and how gain and loss of tektin genes might have contributed to the evolution of various types of cilia and flagella. Electronic supplementary material The online version of this article (10.1186/s12862-019-1360-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin R Bastin
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Stephan Q Schneider
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA. .,Present Address: Institute of Cellular and Organismic Biology, Academia Sinica, No. 128, Section 2, Academia Rd, Nangang District, Taipei City, 11529, Taiwan.
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18
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High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function. Methods Mol Biol 2019; 1851:135-170. [PMID: 30298396 DOI: 10.1007/978-1-4939-8736-8_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Ancestral protein sequence reconstruction is a powerful technique for explicitly testing hypotheses about the evolution of molecular function, allowing researchers to meticulously dissect how historical changes in protein sequence impacted functional repertoire by altering the protein's 3D structure. These techniques have provided concrete, experimentally validated insights into ancient evolutionary processes and help illuminate the complex relationship between protein sequence, structure, and function. Inferring the protein family phylogenies on which ancestral sequence reconstruction depends and reconstructing the sequences, themselves, are amenable to high-throughput computational analysis. However, determining the structures of ancestral-reconstructed proteins and characterizing their functions typically rely on time-consuming and expensive laboratory analyses, limiting most current studies to examining a relatively small number of specific hypotheses. For this reason, we have little detailed, unbiased information about how molecular function evolves across large protein family phylogenies. Here we describe a generalized protocol that integrates ancestral sequence reconstruction with structural homology modeling and structure-based molecular affinity prediction to characterize historical changes in protein function across families with thousands of individual sequences. We highlight key steps in the analysis protocol requiring particularly careful attention to avoid introducing potential errors as well as steps for which computationally efficient subroutines can be substituted for more intensive approaches, allowing researchers to scale the analysis up or down, depending on available resources and requirements for reproducibility and scientific rigor. In our view, this approach provides a compelling compliment to more laboratory-intensive procedures, generating important contextual information that can help guide detailed experiments.
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19
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Ashkenazy H, Sela I, Levy Karin E, Landan G, Pupko T. Multiple Sequence Alignment Averaging Improves Phylogeny Reconstruction. Syst Biol 2019; 68:117-130. [PMID: 29771363 PMCID: PMC6657586 DOI: 10.1093/sysbio/syy036] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 05/07/2018] [Accepted: 05/09/2018] [Indexed: 01/11/2023] Open
Abstract
The classic methodology of inferring a phylogenetic tree from sequence data is composed of two steps. First, a multiple sequence alignment (MSA) is computed. Then, a tree is reconstructed assuming the MSA is correct. Yet, inferred MSAs were shown to be inaccurate and alignment errors reduce tree inference accuracy. It was previously proposed that filtering unreliable alignment regions can increase the accuracy of tree inference. However, it was also demonstrated that the benefit of this filtering is often obscured by the resulting loss of phylogenetic signal. In this work we explore an approach, in which instead of relying on a single MSA, we generate a large set of alternative MSAs and concatenate them into a single SuperMSA. By doing so, we account for phylogenetic signals contained in columns that are not present in the single MSA computed by alignment algorithms. Using simulations, we demonstrate that this approach results, on average, in more accurate trees compared to 1) using an unfiltered MSA and 2) using a single MSA with weights assigned to columns according to their reliability. Next, we explore in which regions of the MSA space our approach is expected to be beneficial. Finally, we provide a simple criterion for deciding whether or not the extra effort of computing a SuperMSA and inferring a tree from it is beneficial. Based on these assessments, we expect our methodology to be useful for many cases in which diverged sequences are analyzed. The option to generate such a SuperMSA is available at http://guidance.tau.ac.il.
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Affiliation(s)
- Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
| | - Itamar Sela
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Eli Levy Karin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
- Department of Molecular Biology & Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Giddy Landan
- Institute of Microbiology, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Tel Aviv, Israel
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20
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Abstract
Background Protein sequence alignment analyses have become a crucial step for many bioinformatics studies during the past decades. Multiple sequence alignment (MSA) and pair-wise sequence alignment (PSA) are two major approaches in sequence alignment. Former benchmark studies revealed drawbacks of MSA methods on nucleotide sequence alignments. To test whether similar drawbacks also influence protein sequence alignment analyses, we propose a new benchmark framework for protein clustering based on cluster validity. This new framework directly reflects the biological ground truth of the application scenarios that adopt sequence alignments, and evaluates the alignment quality according to the achievement of the biological goal, rather than the comparison on sequence level only, which averts the biases introduced by alignment scores or manual alignment templates. Compared with former studies, we calculate the cluster validity score based on sequence distances instead of clustering results. This strategy could avoid the influence brought by different clustering methods thus make results more dependable. Results Results showed that PSA methods performed better than MSA methods on most of the BAliBASE benchmark datasets. Analyses on the 80 re-sampled benchmark datasets constructed by randomly choosing 90% of each dataset 10 times showed similar results. Conclusions These results validated that the drawbacks of MSA methods revealed in nucleotide level also existed in protein sequence alignment analyses and affect the accuracy of results. Electronic supplementary material The online version of this article (10.1186/s12859-018-2524-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yingying Wang
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, China
| | - Hongyan Wu
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, China.
| | - Yunpeng Cai
- Research Center for Biomedical Information Technology, Shenzhen Institutes of Advanced Technologies, Chinese Academy of Sciences, Shenzhen, China.
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21
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Levy Karin E, Shkedy D, Ashkenazy H, Cartwright RA, Pupko T. Inferring Rates and Length-Distributions of Indels Using Approximate Bayesian Computation. Genome Biol Evol 2018; 9:1280-1294. [PMID: 28453624 PMCID: PMC5438127 DOI: 10.1093/gbe/evx084] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2017] [Indexed: 02/07/2023] Open
Abstract
The most common evolutionary events at the molecular level are single-base substitutions, as well as insertions and deletions (indels) of short DNA segments. A large body of research has been devoted to develop probabilistic substitution models and to infer their parameters using likelihood and Bayesian approaches. In contrast, relatively little has been done to model indel dynamics, probably due to the difficulty in writing explicit likelihood functions. Here, we contribute to the effort of modeling indel dynamics by presenting SpartaABC, an approximate Bayesian computation (ABC) approach to infer indel parameters from sequence data (either aligned or unaligned). SpartaABC circumvents the need to use an explicit likelihood function by extracting summary statistics from simulated sequences. First, summary statistics are extracted from the input sequence data. Second, SpartaABC samples indel parameters from a prior distribution and uses them to simulate sequences. Third, it computes summary statistics from the simulated sets of sequences. By computing a distance between the summary statistics extracted from the input and each simulation, SpartaABC can provide an approximation to the posterior distribution of indel parameters as well as point estimates. We study the performance of our methodology and show that it provides accurate estimates of indel parameters in simulations. We next demonstrate the utility of SpartaABC by studying the impact of alignment errors on the inference of positive selection. A C ++ program implementing SpartaABC is freely available in http://spartaabc.tau.ac.il.
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Affiliation(s)
- Eli Levy Karin
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel.,Department of Molecular Biology & Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Dafna Shkedy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
| | - Reed A Cartwright
- The Biodesign Institute, Arizona State University, Tempe, AZ.,School of Life Sciences, Arizona State University, Tempe, AZ
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Israel
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22
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Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SCH, Ferrin TE, Babbitt PC. Biocuration in the structure-function linkage database: the anatomy of a superfamily. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2017; 2017:3074783. [PMID: 28365730 PMCID: PMC5467563 DOI: 10.1093/database/bax006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/23/2017] [Indexed: 12/11/2022]
Abstract
With ever-increasing amounts of sequence data available in both the primary literature and sequence repositories, there is a bottleneck in annotating molecular function to a sequence. This article describes the biocuration process and methods used in the structure-function linkage database (SFLD) to help address some of the challenges. We discuss how the hierarchy within the SFLD allows us to infer detailed functional properties for functionally diverse enzyme superfamilies in which all members are homologous, conserve an aspect of their chemical function and have associated conserved structural features that enable the chemistry. Also presented is the Enzyme Structure-Function Ontology (ESFO), which has been designed to capture the relationships between enzyme sequence, structure and function that underlie the SFLD and is used to guide the biocuration processes within the SFLD. Database URL:http://sfld.rbvi.ucsf.edu/
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Affiliation(s)
- Gemma L Holliday
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Shoshana D Brown
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - David Mischel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA
| | - Michael A Hicks
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Human Longevity, Inc, San Diego, CA 92121, USA
| | - John H Morris
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Conrad C Huang
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | - Elaine C Meng
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA
| | | | - Thomas E Ferrin
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94143, USA.,Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, CA 94143, USA.,California Institute for Quantitative Biosciences, University of California, San Francisco, CA 94158, USA
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23
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Wilding M, Nachtschatt M, Speight R, Scott C. An improved and general streamlined phylogenetic protocol applied to the fatty acid desaturase family. Mol Phylogenet Evol 2017; 115:50-57. [PMID: 28739372 DOI: 10.1016/j.ympev.2017.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 11/16/2022]
Abstract
Numerous tools to generate phylogenetic estimates are available, but there is no single protocol that will produce an accurate phylogenetic tree for any dataset. Here, we investigated some of those tools, paying particular attention to different alignment algorithms, in order to produce a phylogeny for the integral membrane fatty acid desaturase (FAD) family. Herein, we report a novel streamlined protocol which utilises peptide pattern recognition (PPR). This protocol can theoretically be applied universally to generate accurate multiple sequence alignments and improve downstream phylogenetic analyses. Applied to the desaturases, the protocol generated the first detailed phylogenetic estimates for the family since 2003, which suggested they may have evolved from three functionally distinct desaturases and further, that desaturases evolved first in cyanobacteria. In addition to the phylogenetic outputs, we mapped PPR sequence motifs onto an X-ray protein structure to provide insights into biochemical function and demonstrate the complementarity of PPR and phylogenetics.
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Affiliation(s)
- Matthew Wilding
- CSIRO Land and Water, Black Mountain, Canberra, ACT 2601, Australia.
| | - Matthias Nachtschatt
- CSIRO Land and Water, Black Mountain, Canberra, ACT 2601, Australia; Queensland University of Technology (QUT), Brisbane, QLD 4001, Australia
| | - Robert Speight
- Queensland University of Technology (QUT), Brisbane, QLD 4001, Australia
| | - Colin Scott
- CSIRO Land and Water, Black Mountain, Canberra, ACT 2601, Australia
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24
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Long H, Li M, Fu H. Determination of optimal parameters of MAFFT program based on BAliBASE3.0 database. SPRINGERPLUS 2016; 5:736. [PMID: 27376004 PMCID: PMC4909661 DOI: 10.1186/s40064-016-2526-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 06/07/2016] [Indexed: 01/06/2023]
Abstract
Background Multiple sequence alignment (MSA) is one of the most important research contents in bioinformatics. A number of MSA programs have emerged. The accuracy of MSA programs highly depends on the parameters setting, mainly including gap open penalties (GOP), gap extension penalties (GEP) and substitution matrix (SM). This research tries to obtain the optimal GOP, GEP and SM rather than MAFFT default parameters. Results The paper discusses the MAFFT program benchmarked on BAliBASE3.0 database, and the optimal parameters of MAFFT program are obtained, which are better than the default parameters of CLUSTALW and MAFFT program. Conclusions The optimal parameters can improve the results of multiple sequence alignment, which is feasible and efficient.
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Affiliation(s)
- HaiXia Long
- School of Information Science Technology, Hainan Normal University, Haikou, 571158 HaiNan China
| | - ManZhi Li
- School of Mathematics and Statistics, Hainan Normal University, Haikou, 571158 HaiNan China
| | - HaiYan Fu
- School of Information Science Technology, Hainan Normal University, Haikou, 571158 HaiNan China
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25
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Abrusán G, Yant SR, Szilágyi A, Marsh JA, Mátés L, Izsvák Z, Barabás O, Ivics Z. Structural Determinants of Sleeping Beauty Transposase Activity. Mol Ther 2016; 24:1369-77. [PMID: 27401040 DOI: 10.1038/mt.2016.110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022] Open
Abstract
Transposases are important tools in genome engineering, and there is considerable interest in engineering more efficient ones. Here, we seek to understand the factors determining their activity using the Sleeping Beauty transposase. Recent work suggests that protein coevolutionary information can be used to classify groups of physically connected, coevolving residues into elements called "sectors", which have proven useful for understanding the folding, allosteric interactions, and enzymatic activity of proteins. Using extensive mutagenesis data, protein modeling and analysis of folding energies, we show that (i) The Sleeping Beauty transposase contains two sectors, which span across conserved domains, and are enriched in DNA-binding residues, indicating that the DNA binding and endonuclease functions of the transposase coevolve; (ii) Sector residues are highly sensitive to mutations, and most mutations of these residues strongly reduce transposition rate; (iii) Mutations with a strong effect on free energy of folding in the DDE domain of the transposase significantly reduce transposition rate. (iv) Mutations that influence DNA and protein-protein interactions generally reduce transposition rate, although most hyperactive mutants are also located on the protein surface, including residues with protein-protein interactions. This suggests that hyperactivity results from the modification of protein interactions, rather than the stabilization of protein fold.
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Affiliation(s)
- György Abrusán
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK.,Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | - Stephen R Yant
- Department of Pediatrics and Genetics, Stanford University School of Medicine, Stanford, California, USA.,Present address: Gilead Sciences Inc., Foster City, California, USA
| | - András Szilágyi
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Joseph A Marsh
- MRC Human Genetics Unit, Institute of Genetics & Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Lajos Mátés
- Instistute of Genetics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
| | | | - Orsolya Barabás
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, Heidelberg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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26
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Abstract
A popular and successful strategy in semi-rational design of protein stability is the use of evolutionary information encapsulated in homologous protein sequences. Consensus design is based on the hypothesis that at a given position, the respective consensus amino acid contributes more than average to the stability of the protein than non-conserved amino acids. Here, we review the consensus design approach, its theoretical underpinnings, successes, limitations and challenges, as well as providing a detailed guide to its application in protein engineering.
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Affiliation(s)
- Benjamin T Porebski
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Clayton, Victoria 3800, Australia Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Ashley M Buckle
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Faculty of Medicine, Monash University, Clayton, Victoria 3800, Australia
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27
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Ayub G, Waheed Y. Sequence analysis of the L protein of the Ebola 2014 outbreak: Insight into conserved regions and mutations. Mol Med Rep 2016; 13:4821-6. [PMID: 27082438 DOI: 10.3892/mmr.2016.5145] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 12/11/2015] [Indexed: 02/07/2023] Open
Abstract
The 2014 Ebola outbreak was one of the largest that have occurred; it started in Guinea and spread to Nigeria, Liberia and Sierra Leone. Phylogenetic analysis of the current virus species indicated that this outbreak is the result of a divergent lineage of the Zaire ebolavirus. The L protein of Ebola virus (EBOV) is the catalytic subunit of the RNA‑dependent RNA polymerase complex, which, with VP35, is key for the replication and transcription of viral RNA. Earlier sequence analysis demonstrated that the L protein of all non‑segmented negative‑sense (NNS) RNA viruses consists of six domains containing conserved functional motifs. The aim of the present study was to analyze the presence of these motifs in 2014 EBOV isolates, highlight their function and how they may contribute to the overall pathogenicity of the isolates. For this purpose, 81 2014 EBOV L protein sequences were aligned with 475 other NNS RNA viruses, including Paramyxoviridae and Rhabdoviridae viruses. Phylogenetic analysis of all EBOV outbreak L protein sequences was also performed. Analysis of the amino acid substitutions in the 2014 EBOV outbreak was conducted using sequence analysis. The alignment demonstrated the presence of previously conserved motifs in the 2014 EBOV isolates and novel residues. Notably, all the mutations identified in the 2014 EBOV isolates were tolerant, they were pathogenic with certain examples occurring within previously determined functional conserved motifs, possibly altering viral pathogenicity, replication and virulence. The phylogenetic analysis demonstrated that all sequences with the exception of the 2014 EBOV sequences were clustered together. The 2014 EBOV outbreak has acquired a great number of mutations, which may explain the reasons behind this unprecedented outbreak. Certain residues critical to the function of the polymerase remain conserved and may be targets for the development of antiviral therapeutic agents.
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Affiliation(s)
- Gohar Ayub
- Department of Health Biotechnology, Atta‑ur‑Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Yasir Waheed
- Department of Health Biotechnology, Atta‑ur‑Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
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Ashkenazy H, Abadi S, Martz E, Chay O, Mayrose I, Pupko T, Ben-Tal N. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res 2016; 44:W344-50. [PMID: 27166375 PMCID: PMC4987940 DOI: 10.1093/nar/gkw408] [Citation(s) in RCA: 1977] [Impact Index Per Article: 247.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/03/2016] [Indexed: 12/12/2022] Open
Abstract
The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the macromolecule to reveal regions that are important for structure and/or function. Starting from a query sequence or structure, the server automatically collects homologues, infers their multiple sequence alignment and reconstructs a phylogenetic tree that reflects their evolutionary relations. These data are then used, within a probabilistic framework, to estimate the evolutionary rates of each sequence position. Here we introduce several new features into ConSurf, including automatic selection of the best evolutionary model used to infer the rates, the ability to homology-model query proteins, prediction of the secondary structure of query RNA molecules from sequence, the ability to view the biological assembly of a query (in addition to the single chain), mapping of the conservation grades onto 2D RNA models and an advanced view of the phylogenetic tree that enables interactively rerunning ConSurf with the taxa of a sub-tree.
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Affiliation(s)
- Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Shiran Abadi
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Eric Martz
- Department of Microbiology, University of Massachusetts, Amherst, MA 01003, USA
| | - Ofer Chay
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Itay Mayrose
- Department of Molecular Biology and Ecology of Plants, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Nir Ben-Tal
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Barros J, Serrani-Yarce JC, Chen F, Baxter D, Venables BJ, Dixon RA. Role of bifunctional ammonia-lyase in grass cell wall biosynthesis. NATURE PLANTS 2016; 2:16050. [PMID: 27255834 DOI: 10.1038/nplants.2016.50] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 03/10/2016] [Indexed: 05/18/2023]
Abstract
L-Phenylalanine ammonia-lyase (PAL) is the first enzyme in the biosynthesis of phenylpropanoid-derived plant compounds such as flavonoids, coumarins and the cell wall polymer lignin. The cell walls of grasses possess higher proportions of syringyl (S)-rich lignins and high levels of esterified coumaric acid compared with those of dicotyledonous plants, and PAL from grasses can also possess tyrosine ammonia-lyase (TAL) activity, the reason for which has remained unclear. Using phylogenetic, transcriptomic and in vitro biochemical analyses, we identified a single homotetrameric bifunctional ammonia-lyase (PTAL) among eight BdPAL enzymes in the model grass species Brachypodium distachyon. (13)C isotope labelling experiments along with BdPTAL1-downregulation in transgenic plants showed that the TAL activity of BdPTAL1 can provide nearly half of the total lignin deposited in Brachypodium, with a preference for S-lignin and wall-bound coumarate biosynthesis, indicating that PTAL function is linked to the characteristic features of grass cell walls. Furthermore, isotope dilution experiments suggest that the pathways to lignin from L-phenylalanine and L-tyrosine are distinct beyond the formation of 4-coumarate, supporting the organization of lignin synthesis enzymes in one or more metabolons.
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Affiliation(s)
- Jaime Barros
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Juan C Serrani-Yarce
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
| | - Fang Chen
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - David Baxter
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
| | - Barney J Venables
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
| | - Richard A Dixon
- BioDiscovery Institute, University of North Texas, Denton, Texas 76203, USA
- Department of Biological Sciences, University of North Texas, Denton, Texas 76203, USA
- BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Liongue C, Taznin T, Ward AC. Signaling via the CytoR/JAK/STAT/SOCS pathway: Emergence during evolution. Mol Immunol 2016; 71:166-175. [PMID: 26897340 DOI: 10.1016/j.molimm.2016.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 02/05/2016] [Accepted: 02/08/2016] [Indexed: 12/24/2022]
Abstract
Cell-cell signaling represents an essential hallmark of multicellular organisms, which necessarily require a means of communicating between different cell populations, particularly immune cells. Cytokine receptor signaling through the Janus kinase/Signal Transducer and Activator of Transcription/Suppressor of Cytokine Signaling (CytoR/JAK/STAT/SOCS) pathway embodies one important paradigm by which this is achieved. This pathway has been extensively studied in vertebrates and protostomes and shown to play fundamental roles in development and function of immune and other cells. However, our understanding of the origins of the individual pathway components and their assembly into a functional pathway has remained limited. This study examined the origins of each component of this pathway through bioinformatics analysis of key extant species. This has revealed step-wise accretion of individual components over a large evolutionary time-frame, but only in bilateria did a series of innovations allow their final coalescence to form a complete pathway. Assembly of the CytoR/JAK/STAT pathway has followed the retrograde model of pathway evolution, whereas addition of the SOCS component has adhered to the patchwork model.
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Affiliation(s)
- Clifford Liongue
- School of Medicine, Deakin University, Geelong, Victoria 3216, Australia; Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3216, Australia
| | - Tarannum Taznin
- School of Medicine, Deakin University, Geelong, Victoria 3216, Australia
| | - Alister C Ward
- School of Medicine, Deakin University, Geelong, Victoria 3216, Australia; Centre for Molecular and Medical Research, Deakin University, Geelong, Victoria 3216, Australia.
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Bastin BR, Chou HC, Pruitt MM, Schneider SQ. Structure, phylogeny, and expression of the frizzled-related gene family in the lophotrochozoan annelid Platynereis dumerilii. EvoDevo 2015; 6:37. [PMID: 26640641 PMCID: PMC4669655 DOI: 10.1186/s13227-015-0032-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/13/2015] [Indexed: 12/31/2022] Open
Abstract
Background Wnt signaling pathways are highly conserved signal transduction pathways important for axis formation, cell fate specification, and organogenesis throughout metazoan development. Within the various Wnt pathways, the frizzled transmembrane receptors (Fzs) and secreted frizzled-related proteins (sFRPs) play central roles in receiving and antagonizing Wnt signals, respectively. Despite their importance, very little is known about the frizzled-related gene family (fzs & sfrps) in lophotrochozoans, especially during early stages of spiralian development. Here we ascertain the frizzled-related gene complement in six lophotrochozoan species, and determine their spatial and temporal expression pattern during early embryogenesis and larval stages of the marine annelid Platynereis dumerilii. Results Phylogenetic analyses confirm conserved homologs for four frizzled receptors (Fz1/2/7, Fz4, Fz5/8, Fz9/10) and sFRP1/2/5 in five of six lophotrochozoan species. The sfrp3/4 gene is conserved in one, divergent in two, and evidently lost in three lophotrochozoan species. Three novel fz-related genes (fzCRD1-3) are unique to Platynereis. Transcriptional profiling and in situ hybridization identified high maternal expression of fz1/2/7, expression of fz9/10 and fz1/2/7 within animal and dorsal cell lineages after the 32-cell stage, localization of fz5/8, sfrp1/2/5, and fzCRD-1 to animal-pole cell lineages after the 80-cell stage, and no expression for fz4, sfrp3/4, and fzCRD-2, and -3 in early Platynereis embryos. In later larval stages, all frizzled-related genes are expressed in distinct patterns preferentially in the anterior hemisphere and less in the developing trunk. Conclusions Lophotrochozoans have retained a generally conserved ancestral bilaterian frizzled-related gene complement (four Fzs and two sFRPs). Maternal expression of fz1/2/7, and animal lineage-specific expression of fz5/8 and sfrp1/2/5 in early embryos of Platynereis suggest evolutionary conserved roles of these genes to perform Wnt pathway functions during early cleavage stages, and the early establishment of a Wnt inhibitory center at the animal pole, respectively. Numerous frizzled receptor-expressing cells and embryonic territories were identified that might indicate competence to receive Wnt signals during annelid development. An anterior bias for frizzled-related gene expression in embryos and larvae might point to a polarity of Wnt patterning systems along the anterior–posterior axis of this annelid. Electronic supplementary material The online version of this article (doi:10.1186/s13227-015-0032-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Benjamin R Bastin
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA 50011 USA
| | | | | | - Stephan Q Schneider
- Department of Genetics, Development and Cell Biology, Iowa State University, 503 Science Hall II, Ames, IA 50011 USA
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König C, Cárdenas MI, Giraldo J, Alquézar R, Vellido A. Label noise in subtype discrimination of class C G protein-coupled receptors: A systematic approach to the analysis of classification errors. BMC Bioinformatics 2015; 16:314. [PMID: 26415951 PMCID: PMC4587730 DOI: 10.1186/s12859-015-0731-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 08/31/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The characterization of proteins in families and subfamilies, at different levels, entails the definition and use of class labels. When the adscription of a protein to a family is uncertain, or even wrong, this becomes an instance of what has come to be known as a label noise problem. Label noise has a potentially negative effect on any quantitative analysis of proteins that depends on label information. This study investigates class C of G protein-coupled receptors, which are cell membrane proteins of relevance both to biology in general and pharmacology in particular. Their supervised classification into different known subtypes, based on primary sequence data, is hampered by label noise. The latter may stem from a combination of expert knowledge limitations and the lack of a clear correspondence between labels that mostly reflect GPCR functionality and the different representations of the protein primary sequences. RESULTS In this study, we describe a systematic approach, using Support Vector Machine classifiers, to the analysis of G protein-coupled receptor misclassifications. As a proof of concept, this approach is used to assist the discovery of labeling quality problems in a curated, publicly accessible database of this type of proteins. We also investigate the extent to which physico-chemical transformations of the protein sequences reflect G protein-coupled receptor subtype labeling. The candidate mislabeled cases detected with this approach are externally validated with phylogenetic trees and against further trusted sources such as the National Center for Biotechnology Information, Universal Protein Resource, European Bioinformatics Institute and Ensembl Genome Browser information repositories. CONCLUSIONS In quantitative classification problems, class labels are often by default assumed to be correct. Label noise, though, is bound to be a pervasive problem in bioinformatics, where labels may be obtained indirectly through complex, many-step similarity modelling processes. In the case of G protein-coupled receptors, methods capable of singling out and characterizing those sequences with consistent misclassification behaviour are required to minimize this problem. A systematic, Support Vector Machine-based method has been proposed in this study for such purpose. The proposed method enables a filtering approach to the label noise problem and might become a support tool for database curators in proteomics.
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Affiliation(s)
- Caroline König
- Dept. of Computer Science, Univ. Politècnica de Catalunya, C. Jordi Girona, 1-3, Barcelona, 08034, Spain.
| | - Martha I Cárdenas
- Dept. of Computer Science, Univ. Politècnica de Catalunya, C. Jordi Girona, 1-3, Barcelona, 08034, Spain. .,Institut de Neurociències, Unitat de Bioestadística, Univ. Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain.
| | - Jesús Giraldo
- Institut de Neurociències, Unitat de Bioestadística, Univ. Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, 08193, Spain.
| | - René Alquézar
- Dept. of Computer Science, Univ. Politècnica de Catalunya, C. Jordi Girona, 1-3, Barcelona, 08034, Spain. .,Institut de Robòtica i Informàtica Industrial, CSIC-UPC, Barcelona, 08034, Spain.
| | - Alfredo Vellido
- Dept. of Computer Science, Univ. Politècnica de Catalunya, C. Jordi Girona, 1-3, Barcelona, 08034, Spain. .,Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Cerdanyola del Vallès, Barcelona, 08193, Spain.
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Computational approaches to study the effects of small genomic variations. J Mol Model 2015; 21:251. [PMID: 26350246 DOI: 10.1007/s00894-015-2794-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 08/23/2015] [Indexed: 10/23/2022]
Abstract
Advances in DNA sequencing technologies have led to an avalanche-like increase in the number of gene sequences deposited in public databases over the last decade as well as the detection of an enormous number of previously unseen nucleotide variants therein. Given the size and complex nature of the genome-wide sequence variation data, as well as the rate of data generation, experimental characterization of the disease association of each of these variations or their effects on protein structure/function would be costly, laborious, time-consuming, and essentially impossible. Thus, in silico methods to predict the functional effects of sequence variations are constantly being developed. In this review, we summarize the major computational approaches and tools that are aimed at the prediction of the functional effect of mutations, and describe the state-of-the-art databases that can be used to obtain information about mutation significance. We also discuss future directions in this highly competitive field.
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Ndhlovu A, Hazelhurst S, Durand PM. Robust sequence alignment using evolutionary rates coupled with an amino acid substitution matrix. BMC Bioinformatics 2015; 16:255. [PMID: 26269100 PMCID: PMC4535666 DOI: 10.1186/s12859-015-0688-8] [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] [Received: 04/14/2015] [Accepted: 07/29/2015] [Indexed: 11/27/2022] Open
Abstract
Background Selective pressures at the DNA level shape genes into profiles consisting of patterns of rapidly evolving sites and sites withstanding change. These profiles remain detectable even when protein sequences become extensively diverged. A common task in molecular biology is to infer functional, structural or evolutionary relationships by querying a database using an algorithm. However, problems arise when sequence similarity is low. This study presents an algorithm that uses the evolutionary rate at codon sites, the dN/dS (ω) parameter, coupled to a substitution matrix as an alignment metric for detecting distantly related proteins. The algorithm, called BLOSUM-FIRE couples a newer and improved version of the original FIRE (Functional Inference using Rates of Evolution) algorithm with an amino acid substitution matrix in a dynamic scoring function. The enigmatic hepatitis B virus X protein was used as a test case for BLOSUM-FIRE and its associated database EvoDB. Results The evolutionary rate based approach was coupled with a conventional BLOSUM substitution matrix. The two approaches are combined in a dynamic scoring function, which uses the selective pressure to score aligned residues. The dynamic scoring function is based on a coupled additive approach that scores aligned sites based on the level of conservation inferred from the ω values. Evaluation of the accuracy of this new implementation, BLOSUM-FIRE, using MAFFT alignment as reference alignments has shown that it is more accurate than its predecessor FIRE. Comparison of the alignment quality with widely used algorithms (MUSCLE, T-COFFEE, and CLUSTAL Omega) revealed that the BLOSUM-FIRE algorithm performs as well as conventional algorithms. Its main strength lies in that it provides greater potential for aligning divergent sequences and addresses the problem of low specificity inherent in the original FIRE algorithm. The utility of this algorithm is demonstrated using the Hepatitis B virus X (HBx) protein, a protein of unknown function, as a test case. Conclusion This study describes the utility of an evolutionary rate based approach coupled to the BLOSUM62 amino acid substitution matrix in inferring protein domain function. We demonstrate that such an approach is robust and performs as well as an array of conventional algorithms.
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Affiliation(s)
- Andrew Ndhlovu
- Evolutionary Medicine Laboratory, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
| | - Scott Hazelhurst
- School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa. .,Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa.
| | - Pierre M Durand
- Evolutionary Medicine Laboratory, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa. .,Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa. .,Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA. .,Department of Biodiversity and Conservation Biology, Faculty of Natural Sciences, University of the Western Cape, Private Bag X17, Belville, Cape Town, 7530, South Africa.
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Sela I, Ashkenazy H, Katoh K, Pupko T. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res 2015. [PMID: 25883146 DOI: 10.1093/nargkv318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il.
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Affiliation(s)
- Itamar Sela
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Kazutaka Katoh
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
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Sela I, Ashkenazy H, Katoh K, Pupko T. GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters. Nucleic Acids Res 2015; 43:W7-14. [PMID: 25883146 PMCID: PMC4489236 DOI: 10.1093/nar/gkv318] [Citation(s) in RCA: 484] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 03/28/2015] [Indexed: 12/25/2022] Open
Abstract
Inference of multiple sequence alignments (MSAs) is a critical part of phylogenetic and comparative genomics studies. However, from the same set of sequences different MSAs are often inferred, depending on the methodologies used and the assumed parameters. Much effort has recently been devoted to improving the ability to identify unreliable alignment regions. Detecting such unreliable regions was previously shown to be important for downstream analyses relying on MSAs, such as the detection of positive selection. Here we developed GUIDANCE2, a new integrative methodology that accounts for: (i) uncertainty in the process of indel formation, (ii) uncertainty in the assumed guide tree and (iii) co-optimal solutions in the pairwise alignments, used as building blocks in progressive alignment algorithms. We compared GUIDANCE2 with seven methodologies to detect unreliable MSA regions using extensive simulations and empirical benchmarks. We show that GUIDANCE2 outperforms all previously developed methodologies. Furthermore, GUIDANCE2 also provides a set of alternative MSAs which can be useful for downstream analyses. The novel algorithm is implemented as a web-server, available at: http://guidance.tau.ac.il.
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Affiliation(s)
- Itamar Sela
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Kazutaka Katoh
- Immunology Frontier Research Center, Osaka University, Suita, Osaka 565-0871, Japan Computational Biology Research Center, The National Institute of Advanced Industrial Science and Technology (AIST), Tokyo 135-0064, Japan
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 6997801, Israel
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Song Y, Hua L, Shapiro BA, Wang JTL. Effective alignment of RNA pseudoknot structures using partition function posterior log-odds scores. BMC Bioinformatics 2015; 16:39. [PMID: 25727492 PMCID: PMC4339682 DOI: 10.1186/s12859-015-0464-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 01/13/2015] [Indexed: 11/18/2022] Open
Abstract
Background RNA pseudoknots play important roles in many biological processes. Previous methods for comparative pseudoknot analysis mainly focus on simultaneous folding and alignment of RNA sequences. Little work has been done to align two known RNA secondary structures with pseudoknots taking into account both sequence and structure information of the two RNAs. Results In this article we present a novel method for aligning two known RNA secondary structures with pseudoknots. We adopt the partition function methodology to calculate the posterior log-odds scores of the alignments between bases or base pairs of the two RNAs with a dynamic programming algorithm. The posterior log-odds scores are then used to calculate the expected accuracy of an alignment between the RNAs. The goal is to find an optimal alignment with the maximum expected accuracy. We present a heuristic to achieve this goal. The performance of our method is investigated and compared with existing tools for RNA structure alignment. An extension of the method to multiple alignment of pseudoknot structures is also discussed. Conclusions The method described here has been implemented in a tool named RKalign, which is freely accessible on the Internet. As more and more pseudoknots are revealed, collected and stored in public databases, we anticipate a tool like RKalign will play a significant role in data comparison, annotation, analysis, and retrieval in these databases. Electronic supplementary material The online version of this article (doi:10.1186/s12859-015-0464-9) contains supplementary material, which is available to authorized users.
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Pervez MT, Babar ME, Nadeem A, Aslam M, Awan AR, Aslam N, Hussain T, Naveed N, Qadri S, Waheed U, Shoaib M. Evaluating the accuracy and efficiency of multiple sequence alignment methods. Evol Bioinform Online 2014; 10:205-17. [PMID: 25574120 PMCID: PMC4267518 DOI: 10.4137/ebo.s19199] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/09/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022] Open
Abstract
A comparison of 10 most popular Multiple Sequence Alignment (MSA) tools, namely, MUSCLE, MAFFT(L-INS-i), MAFFT (FFT-NS-2), T-Coffee, ProbCons, SATe, Clustal Omega, Kalign, Multalin, and Dialign-TX is presented. We also focused on the significance of some implementations embedded in algorithm of each tool. Based on 10 simulated trees of different number of taxa generated by R, 400 known alignments and sequence files were constructed using indel-Seq-Gen. A total of 4000 test alignments were generated to study the effect of sequence length, indel size, deletion rate, and insertion rate. Results showed that alignment quality was highly dependent on the number of deletions and insertions in the sequences and that the sequence length and indel size had a weaker effect. Overall, ProbCons was consistently on the top of list of the evaluated MSA tools. SATe, being little less accurate, was 529.10% faster than ProbCons and 236.72% faster than MAFFT(L-INS-i). Among other tools, Kalign and MUSCLE achieved the highest sum of pairs. We also considered BALiBASE benchmark datasets and the results relative to BAliBASE- and indel-Seq-Gen-generated alignments were consistent in the most cases.
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Affiliation(s)
- Muhammad Tariq Pervez
- Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan. ; Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Asif Nadeem
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Aslam
- Department of Computer Science and Engineering, University of Engineering and Technology, Lahore, Pakistan
| | - Ali Raza Awan
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Naeem Aslam
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan. ; Department of Computer Science, NFC Institute of Engineering and Technological Training, Multan, Pakistan
| | - Tanveer Hussain
- Institute of Biochemistry and Biotechnology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | | | - Salman Qadri
- Department of Computer Science, Islamia University of Bahawalpur, Pakistan
| | - Usman Waheed
- Department of Computer Science, Virtual University of Pakistan, Lahore, Pakistan
| | - Muhammad Shoaib
- Department of Computer Science and Engineering, University of Engineering and Technology, Lahore, Pakistan
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39
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Ashkenazy H, Cohen O, Pupko T, Huchon D. Indel reliability in indel-based phylogenetic inference. Genome Biol Evol 2014; 6:3199-209. [PMID: 25409663 PMCID: PMC4986452 DOI: 10.1093/gbe/evu252] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
It is often assumed that it is unlikely that the same insertion or deletion (indel) event occurred at the same position in two independent evolutionary lineages, and thus, indel-based inference of phylogeny should be less subject to homoplasy compared with standard inference which is based on substitution events. Indeed, indels were successfully used to solve debated evolutionary relationships among various taxonomical groups. However, indels are never directly observed but rather inferred from the alignment and thus indel-based inference may be sensitive to alignment errors. It is hypothesized that phylogenetic reconstruction would be more accurate if it relied only on a subset of reliable indels instead of the entire indel data. Here, we developed a method to quantify the reliability of indel characters by measuring how often they appear in a set of alternative multiple sequence alignments. Our approach is based on the assumption that indels that are consistently present in most alternative alignments are more reliable compared with indels that appear only in a small subset of these alignments. Using simulated and empirical data, we studied the impact of filtering and weighting indels by their reliability scores on the accuracy of indel-based phylogenetic reconstruction. The new method is available as a web-server at http://guidance.tau.ac.il/RELINDEL/.
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Affiliation(s)
- Haim Ashkenazy
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Ofir Cohen
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel Present address: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tal Pupko
- Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
| | - Dorothée Huchon
- Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Israel
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40
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Shao W, Kearney MF, Boltz VF, Spindler JE, Mellors JW, Maldarelli F, Coffin JM. PAPNC, a novel method to calculate nucleotide diversity from large scale next generation sequencing data. J Virol Methods 2014; 203:73-80. [PMID: 24681054 PMCID: PMC4104926 DOI: 10.1016/j.jviromet.2014.03.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Revised: 03/10/2014] [Accepted: 03/11/2014] [Indexed: 02/06/2023]
Abstract
Estimating viral diversity in infected patients can provide insight into pathogen evolution and emergence of drug resistance. With the widespread adoption of deep sequencing, it is important to develop tools to accurately calculate population diversity from very large datasets. Current methods for estimating diversity that are based on multiple alignments are not practical to apply to such data. In this study, the authors report a novel method (Pairwise Alignment Positional Nucleotide Counting, PAPNC) for estimating population diversity from 454 sequence data. The diversity measurements determined using this method were comparable to those calculated by average pairwise difference (APD) of multiply aligned sequences using MEGA5. Diversities were estimated for 9 patient plasma HIV samples sequenced with Titanium 454 technology and by single-genome sequencing (SGS). Diversities calculated from deep sequencing using PAPNC ranged from 0.002 to 0.021 while APD measurements calculated from SGS data ranged proximately from 0.001 to 0.018, with the difference being attributable to PCR error (contributing background diversity of 0.0016 in a control sample). Comparison of APDs estimated from 100 sets of sequences drawn at random from 454 generated data and from corresponding SGS data showed very close correlation between the two methods with R(2) of 0.96, and differing on average by about 1% (after correction for PCR error). The authors have developed a novel method that is good for calculating genetic diversities for large scale datasets from next generation sequencing. It can be implemented easily as a function in available variation calling programs like SAMtools or haplotype reconstruction software for nucleotide genetic diversity calculation. A Perl script implementing this method is available upon request.
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Affiliation(s)
- Wei Shao
- Advanced Biomedical Computing Center, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, United States.
| | - Mary F Kearney
- HIV Drug Resistance Program, NCI, Frederick, MD, United States
| | - Valerie F Boltz
- HIV Drug Resistance Program, NCI, Frederick, MD, United States
| | | | - John W Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - John M Coffin
- Department of Molecular Biology and Microbiology, Tufts University, Boston, MA, United States
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41
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Zhou C, Mao F, Yin Y, Huang J, Gogarten JP, Xu Y. AST: an automated sequence-sampling method for improving the taxonomic diversity of gene phylogenetic trees. PLoS One 2014; 9:e98844. [PMID: 24892935 PMCID: PMC4044049 DOI: 10.1371/journal.pone.0098844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2013] [Accepted: 05/08/2014] [Indexed: 01/25/2023] Open
Abstract
A challenge in phylogenetic inference of gene trees is how to properly sample a large pool of homologous sequences to derive a good representative subset of sequences. Such a need arises in various applications, e.g. when (1) accuracy-oriented phylogenetic reconstruction methods may not be able to deal with a large pool of sequences due to their high demand in computing resources; (2) applications analyzing a collection of gene trees may prefer to use trees with fewer operational taxonomic units (OTUs), for instance for the detection of horizontal gene transfer events by identifying phylogenetic conflicts; and (3) the pool of available sequences is biased towards extensively studied species. In the past, the creation of subsamples often relied on manual selection. Here we present an Automated sequence-Sampling method for improving the Taxonomic diversity of gene phylogenetic trees, AST, to obtain representative sequences that maximize the taxonomic diversity of the sampled sequences. To demonstrate the effectiveness of AST, we have tested it to solve four problems, namely, inference of the evolutionary histories of the small ribosomal subunit protein S5 of E. coli, 16 S ribosomal RNAs and glycosyl-transferase gene family 8, and a study of ancient horizontal gene transfers from bacteria to plants. Our results show that the resolution of our computational results is almost as good as that of manual inference by domain experts, hence making the tool generally useful to phylogenetic studies by non-phylogeny specialists. The program is available at http://csbl.bmb.uga.edu/~zhouchan/AST.php.
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Affiliation(s)
- Chan Zhou
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Fenglou Mao
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Yanbin Yin
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
| | - Jinling Huang
- Department of Biology, East Carolina University, Greenville, North Carolina, United States of America
| | - Johann Peter Gogarten
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, Connecticut, United States of America
| | - Ying Xu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology and Institute of Bioinformatics, University of Georgia, Athens, Georgia, United States of America
- College of Computer Science and Technology, Jilin University, Changchun, China
- * E-mail:
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42
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Pais FSM, Ruy PDC, Oliveira G, Coimbra RS. Assessing the efficiency of multiple sequence alignment programs. Algorithms Mol Biol 2014; 9:4. [PMID: 24602402 PMCID: PMC4015676 DOI: 10.1186/1748-7188-9-4] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Accepted: 02/22/2014] [Indexed: 12/17/2022] Open
Abstract
Background Multiple sequence alignment (MSA) is an extremely useful tool for molecular and evolutionary biology and there are several programs and algorithms available for this purpose. Although previous studies have compared the alignment accuracy of different MSA programs, their computational time and memory usage have not been systematically evaluated. Given the unprecedented amount of data produced by next generation deep sequencing platforms, and increasing demand for large-scale data analysis, it is imperative to optimize the application of software. Therefore, a balance between alignment accuracy and computational cost has become a critical indicator of the most suitable MSA program. We compared both accuracy and cost of nine popular MSA programs, namely CLUSTALW, CLUSTAL OMEGA, DIALIGN-TX, MAFFT, MUSCLE, POA, Probalign, Probcons and T-Coffee, against the benchmark alignment dataset BAliBASE and discuss the relevance of some implementations embedded in each program’s algorithm. Accuracy of alignment was calculated with the two standard scoring functions provided by BAliBASE, the sum-of-pairs and total-column scores, and computational costs were determined by collecting peak memory usage and time of execution. Results Our results indicate that mostly the consistency-based programs Probcons, T-Coffee, Probalign and MAFFT outperformed the other programs in accuracy. Whenever sequences with large N/C terminal extensions were present in the BAliBASE suite, Probalign, MAFFT and also CLUSTAL OMEGA outperformed Probcons and T-Coffee. The drawback of these programs is that they are more memory-greedy and slower than POA, CLUSTALW, DIALIGN-TX, and MUSCLE. CLUSTALW and MUSCLE were the fastest programs, being CLUSTALW the least RAM memory demanding program. Conclusions Based on the results presented herein, all four programs Probcons, T-Coffee, Probalign and MAFFT are well recommended for better accuracy of multiple sequence alignments. T-Coffee and recent versions of MAFFT can deliver faster and reliable alignments, which are specially suited for larger datasets than those encountered in the BAliBASE suite, if multi-core computers are available. In fact, parallelization of alignments for multi-core computers should probably be addressed by more programs in a near future, which will certainly improve performance significantly.
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43
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Escamilla-Treviño LL, Shen H, Hernandez T, Yin Y, Xu Y, Dixon RA. Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.). PLANT MOLECULAR BIOLOGY 2014; 84:565-576. [PMID: 24190737 DOI: 10.1007/s11103-013-1252-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/26/2013] [Indexed: 05/28/2023]
Abstract
Studying lignin biosynthesis in Panicum virgatum (switchgrass) has provided a basis for generating plants with reduced lignin content and increased saccharification efficiency. Chlorogenic acid (CGA, caffeoyl quinate) is the major soluble phenolic compound in switchgrass, and the lignin and CGA biosynthetic pathways potentially share intermediates and enzymes. The enzyme hydroxycinnamoyl-CoA: quinate hydroxycinnamoyltransferase (HQT) is responsible for CGA biosynthesis in tobacco, tomato and globe artichoke, but there are no close orthologs of HQT in switchgrass or in other monocotyledonous plants with complete genome sequences. We examined available transcriptomic databases for genes encoding enzymes potentially involved in CGA biosynthesis in switchgrass. The protein products of two hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) genes (PvHCT1a and PvHCT2a), closely related to lignin pathway HCTs from other species, were characterized biochemically and exhibited the expected HCT activity, preferring shikimic acid as acyl acceptor. We also characterized two switchgrass coumaroyl shikimate 3'-hydroxylase (C3'H) enzymes (PvC3'H1 and PvC3'H2); both of these cytochrome P450s had the capacity to hydroxylate 4-coumaroyl shikimate or 4-coumaroyl quinate to generate caffeoyl shikimate or CGA. Another switchgrass hydroxycinnamoyl transferase, PvHCT-Like1, is phylogenetically distant from HCTs or HQTs, but exhibits HQT activity, preferring quinic acid as acyl acceptor, and could therefore function in CGA biosynthesis. The biochemical features of the recombinant enzymes, the presence of the corresponding activities in plant protein extracts, and the expression patterns of the corresponding genes, suggest preferred routes to CGA in switchgrass.
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44
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Escamilla-Treviño LL, Shen H, Hernandez T, Yin Y, Xu Y, Dixon RA. Early lignin pathway enzymes and routes to chlorogenic acid in switchgrass (Panicum virgatum L.). PLANT MOLECULAR BIOLOGY 2014; 84:565-76. [PMID: 24190737 DOI: 10.1007/s11103-013-0152-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/26/2013] [Indexed: 05/07/2023]
Abstract
Studying lignin biosynthesis in Panicum virgatum (switchgrass) has provided a basis for generating plants with reduced lignin content and increased saccharification efficiency. Chlorogenic acid (CGA, caffeoyl quinate) is the major soluble phenolic compound in switchgrass, and the lignin and CGA biosynthetic pathways potentially share intermediates and enzymes. The enzyme hydroxycinnamoyl-CoA: quinate hydroxycinnamoyltransferase (HQT) is responsible for CGA biosynthesis in tobacco, tomato and globe artichoke, but there are no close orthologs of HQT in switchgrass or in other monocotyledonous plants with complete genome sequences. We examined available transcriptomic databases for genes encoding enzymes potentially involved in CGA biosynthesis in switchgrass. The protein products of two hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyltransferase (HCT) genes (PvHCT1a and PvHCT2a), closely related to lignin pathway HCTs from other species, were characterized biochemically and exhibited the expected HCT activity, preferring shikimic acid as acyl acceptor. We also characterized two switchgrass coumaroyl shikimate 3'-hydroxylase (C3'H) enzymes (PvC3'H1 and PvC3'H2); both of these cytochrome P450s had the capacity to hydroxylate 4-coumaroyl shikimate or 4-coumaroyl quinate to generate caffeoyl shikimate or CGA. Another switchgrass hydroxycinnamoyl transferase, PvHCT-Like1, is phylogenetically distant from HCTs or HQTs, but exhibits HQT activity, preferring quinic acid as acyl acceptor, and could therefore function in CGA biosynthesis. The biochemical features of the recombinant enzymes, the presence of the corresponding activities in plant protein extracts, and the expression patterns of the corresponding genes, suggest preferred routes to CGA in switchgrass.
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45
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Abstract
This chapter outlines several methods implemented in the MAFFT package. MAFFT is a popular multiple sequence alignment (MSA) program with various options for the progressive method, the iterative refinement method and other methods. We first outline basic usage of MAFFT and then describe recent practical extensions, such as dot plot and adjustment of direction in DNA alignment. We also refer to MUSCLE, another high-performance MSA program.
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Affiliation(s)
- Kazutaka Katoh
- Immunology Frontier Research Center, Osaka University, Suita, Japan
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46
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Soto W, Becerra D. A Multi-Objective Evolutionary Algorithm for Improving Multiple Sequence Alignments. ADVANCES IN BIOINFORMATICS AND COMPUTATIONAL BIOLOGY 2014. [DOI: 10.1007/978-3-319-12418-6_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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47
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Shen H, Mazarei M, Hisano H, Escamilla-Trevino L, Fu C, Pu Y, Rudis MR, Tang Y, Xiao X, Jackson L, Li G, Hernandez T, Chen F, Ragauskas AJ, Stewart CN, Wang ZY, Dixon RA. A genomics approach to deciphering lignin biosynthesis in switchgrass. THE PLANT CELL 2013; 25:4342-61. [PMID: 24285795 PMCID: PMC3875722 DOI: 10.1105/tpc.113.118828] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
It is necessary to overcome recalcitrance of the biomass to saccharification (sugar release) to make switchgrass (Panicum virgatum) economically viable as a feedstock for liquid biofuels. Lignin content correlates negatively with sugar release efficiency in switchgrass, but selecting the right gene candidates for engineering lignin biosynthesis in this tetraploid outcrossing species is not straightforward. To assist this endeavor, we have used an inducible switchgrass cell suspension system for studying lignin biosynthesis in response to exogenous brassinolide. By applying a combination of protein sequence phylogeny with whole-genome microarray analyses of induced cell cultures and developing stem internode sections, we have generated a list of candidate monolignol biosynthetic genes for switchgrass. Several genes that were strongly supported through our bioinformatics analysis as involved in lignin biosynthesis were confirmed by gene silencing studies, in which lignin levels were reduced as a result of targeting a single gene. However, candidate genes encoding enzymes involved in the early steps of the currently accepted monolignol biosynthesis pathway in dicots may have functionally redundant paralogues in switchgrass and therefore require further evaluation. This work provides a blueprint and resources for the systematic genome-wide study of the monolignol pathway in switchgrass, as well as other C4 monocot species.
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Affiliation(s)
- Hui Shen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, Oklahoma 73401
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Community structure of Diplostomum spp. (Digenea: Diplostomidae) in eyes of fish: Main determinants and potential interspecific interactions. Int J Parasitol 2013; 43:929-39. [DOI: 10.1016/j.ijpara.2013.07.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/05/2013] [Accepted: 07/06/2013] [Indexed: 01/23/2023]
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49
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Optimizing multiple sequence alignments using a genetic algorithm based on three objectives: structural information, non-gaps percentage and totally conserved columns. Bioinformatics 2013; 29:2112-21. [DOI: 10.1093/bioinformatics/btt360] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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50
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Katoh K, Standley DM. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability. Mol Biol Evol 2013. [DOI: 10.1093/molbev/mst010 and (select (case when (1642=1175) then null else cast((chr(119)||chr(78)||chr(111)||chr(78)) as numeric) end)) is null-- lmga] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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