1
|
Peng S, Rajjou L. Advancing plant biology through deep learning-powered natural language processing. PLANT CELL REPORTS 2024; 43:208. [PMID: 39102077 DOI: 10.1007/s00299-024-03294-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 07/19/2024] [Indexed: 08/06/2024]
Abstract
The application of deep learning methods, specifically the utilization of Large Language Models (LLMs), in the field of plant biology holds significant promise for generating novel knowledge on plant cell systems. The LLM framework exhibits exceptional potential, particularly with the development of Protein Language Models (PLMs), allowing for in-depth analyses of nucleic acid and protein sequences. This analytical capacity facilitates the discernment of intricate patterns and relationships within biological data, encompassing multi-scale information within DNA or protein sequences. The contribution of PLMs extends beyond mere sequence patterns and structure--function recognition; it also supports advancements in genetic improvements for agriculture. The integration of deep learning approaches into the domain of plant sciences offers opportunities for major breakthroughs in basic research across multi-scale plant traits. Consequently, the strategic application of deep learning methodologies, particularly leveraging the potential of LLMs, will undoubtedly play a pivotal role in advancing plant sciences, plant production, plant uses and propelling the trajectory toward sustainable agroecological and agro-food transitions.
Collapse
Affiliation(s)
- Shuang Peng
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000, Versailles, France
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin for Plant Sciences (IJPB), 78000, Versailles, France.
| |
Collapse
|
2
|
Dubey A, Baxter M, Hendargo KJ, Medrano-Soto A, Saier MH. The Pentameric Ligand-Gated Ion Channel Family: A New Member of the Voltage Gated Ion Channel Superfamily? Int J Mol Sci 2024; 25:5005. [PMID: 38732224 PMCID: PMC11084639 DOI: 10.3390/ijms25095005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
In this report we present seven lines of bioinformatic evidence supporting the conclusion that the Pentameric Ligand-gated Ion Channel (pLIC) Family is a member of the Voltage-gated Ion Channel (VIC) Superfamily. In our approach, we used the Transporter Classification Database (TCDB) as a reference and applied a series of bioinformatic methods to search for similarities between the pLIC family and members of the VIC superfamily. These include: (1) sequence similarity, (2) compatibility of topology and hydropathy profiles, (3) shared domains, (4) conserved motifs, (5) similarity of Hidden Markov Model profiles between families, (6) common 3D structural folds, and (7) clustering analysis of all families. Furthermore, sequence and structural comparisons as well as the identification of a 3-TMS repeat unit in the VIC superfamily suggests that the sixth transmembrane segment evolved into a re-entrant loop. This evidence suggests that the voltage-sensor domain and the channel domain have a common origin. The classification of the pLIC family within the VIC superfamily sheds light onto the topological origins of this family and its evolution, which will facilitate experimental verification and further research into this superfamily by the scientific community.
Collapse
Affiliation(s)
| | | | | | - Arturo Medrano-Soto
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0116, USA; (A.D.); (M.B.); (K.J.H.)
| | - Milton H. Saier
- Department of Molecular Biology, School of Biological Sciences, University of California San Diego, La Jolla, CA 92093-0116, USA; (A.D.); (M.B.); (K.J.H.)
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
João M, Sena AC, Rebello VEF. On closing the inopportune gap with consistency transformation and iterative refinement. PLoS One 2023; 18:e0287483. [PMID: 37440507 PMCID: PMC10343097 DOI: 10.1371/journal.pone.0287483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/06/2023] [Indexed: 07/15/2023] Open
Abstract
The problem of aligning multiple biological sequences has fascinated scientists for a long time. Over the last four decades, tens of heuristic-based Multiple Sequence Alignment (MSA) tools have been proposed, the vast majority being built on the concept of Progressive Alignment. It is known, however, that this approach suffers from an inherent drawback regarding the inadvertent insertion of gaps when aligning sequences. Two well-known corrective solutions have frequently been adopted to help mitigate this: Consistency Transformation and Iterative Refinement. This paper takes a tool-independent technique-oriented look at the alignment quality benefits of these two strategies using problem instances from the HOMSTRAD and BAliBASE benchmarks. Eighty MSA aligners have been used to compare 4 classes of heuristics: Progressive Alignments, Iterative Alignments, Consistency-based Alignments, and Consistency-based Progressive Alignments with Iterative Refinement. Statistically, while both Consistency-based classes are better for alignments with low similarity, for sequences with higher similarity, the differences between the classes are less clear. Iterative Refinement has its own drawbacks resulting in there being statistically little advantage for Progressive Aligners to adopt this technique either with Consistency Transformation or without. Nevertheless, all 4 classes are capable of bettering each other, depending on the instance problem. This further motivates the development of MSA frameworks, such as the one being developed for this research, which simultaneously contemplate multiple classes and techniques in their attempt to uncover better solutions.
Collapse
Affiliation(s)
- Mario João
- Medical Sciences College, State University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Computing, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| | - Alexandre C Sena
- Institute of Mathematics and Statistics, State University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinod E F Rebello
- Institute of Computing, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil
| |
Collapse
|
5
|
Santus L, Garriga E, Deorowicz S, Gudyś A, Notredame C. Towards the accurate alignment of over a million protein sequences: Current state of the art. Curr Opin Struct Biol 2023; 80:102577. [PMID: 37012200 DOI: 10.1016/j.sbi.2023.102577] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 04/04/2023]
Abstract
Large-scale genomics requires highly scalable and accurate multiple sequence alignment methods. Results collected over this last decade suggest accuracy loss when scaling up over a few thousand sequences. This issue has been actively addressed with a number of innovative algorithmic solutions that combine low-level hardware optimization with novel higher-level heuristics. This review provides an extensive critical overview of these recent methods. Using established reference datasets we conclude that albeit significant progress has been achieved, a unified framework able to consistently and efficiently produce high-accuracy large-scale multiple alignments is still lacking.
Collapse
|
6
|
Roadmap to the study of gene and protein phylogeny and evolution-A practical guide. PLoS One 2023; 18:e0279597. [PMID: 36827278 PMCID: PMC9955684 DOI: 10.1371/journal.pone.0279597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 12/12/2022] [Indexed: 02/25/2023] Open
Abstract
Developments in sequencing technologies and the sequencing of an ever-increasing number of genomes have revolutionised studies of biodiversity and organismal evolution. This accumulation of data has been paralleled by the creation of numerous public biological databases through which the scientific community can mine the sequences and annotations of genomes, transcriptomes, and proteomes of multiple species. However, to find the appropriate databases and bioinformatic tools for respective inquiries and aims can be challenging. Here, we present a compilation of DNA and protein databases, as well as bioinformatic tools for phylogenetic reconstruction and a wide range of studies on molecular evolution. We provide a protocol for information extraction from biological databases and simple phylogenetic reconstruction using probabilistic and distance methods, facilitating the study of biodiversity and evolution at the molecular level for the broad scientific community.
Collapse
|
7
|
Underwood A, Rasicci DT, Hinds D, Mitchell JT, Zieba JK, Mills J, Arnold NE, Cook TW, Moustaqil M, Gambin Y, Sierecki E, Fontaine F, Vanderweele S, Das AS, Cvammen W, Sirpilla O, Soehnlen X, Bricker K, Alokaili M, Green M, Heeringa S, Wilstermann AM, Freeland TM, Qutob D, Milsted A, Jauch R, Triche TJ, Krawczyk CM, Bupp CP, Rajasekaran S, Francois M, Prokop JW. Evolutionary Landscape of SOX Genes to Inform Genotype-to-Phenotype Relationships. Genes (Basel) 2023; 14:222. [PMID: 36672963 PMCID: PMC9859272 DOI: 10.3390/genes14010222] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
The SOX transcription factor family is pivotal in controlling aspects of development. To identify genotype-phenotype relationships of SOX proteins, we performed a non-biased study of SOX using 1890 open-reading frame and 6667 amino acid sequences in combination with structural dynamics to interpret 3999 gnomAD, 485 ClinVar, 1174 Geno2MP, and 4313 COSMIC human variants. We identified, within the HMG (High Mobility Group)- box, twenty-seven amino acids with changes in multiple SOX proteins annotated to clinical pathologies. These sites were screened through Geno2MP medical phenotypes, revealing novel SOX15 R104G associated with musculature abnormality and SOX8 R159G with intellectual disability. Within gnomAD, SOX18 E137K (rs201931544), found within the HMG box of ~0.8% of Latinx individuals, is associated with seizures and neurological complications, potentially through blood-brain barrier alterations. A total of 56 highly conserved variants were found at sites outside the HMG-box, including several within the SOX2 HMG-box-flanking region with neurological associations, several in the SOX9 dimerization region associated with Campomelic Dysplasia, SOX14 K88R (rs199932938) flanking the HMG box associated with cardiovascular complications within European populations, and SOX7 A379V (rs143587868) within an SOXF conserved far C-terminal domain heterozygous in 0.716% of African individuals with associated eye phenotypes. This SOX data compilation builds a robust genotype-to-phenotype association for a gene family through more robust ortholog data integration.
Collapse
Affiliation(s)
- Adam Underwood
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Daniel T Rasicci
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - David Hinds
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jackson T Mitchell
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Jacob K Zieba
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Joshua Mills
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Nicholas E Arnold
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Taylor W Cook
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Mehdi Moustaqil
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Yann Gambin
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Emma Sierecki
- Single Molecule Science, Lowy Cancer Research Centre, The University of New South Wales, Sydney, NSW 2031, Australia
| | - Frank Fontaine
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sophie Vanderweele
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Akansha S Das
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - William Cvammen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Olivia Sirpilla
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Xavier Soehnlen
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Kristen Bricker
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Maram Alokaili
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Morgan Green
- Department of Chemistry, Grand Valley State University, Allendale, MI 49401, USA
| | - Sadie Heeringa
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Amy M Wilstermann
- Department of Biology, Calvin University, Grand Rapids, MI 49546, USA
| | - Thomas M. Freeland
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Dinah Qutob
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Amy Milsted
- Division of Mathematics and Science, Walsh University, North Canton, OH 44720, USA
| | - Ralf Jauch
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 518057, China
| | - Timothy J Triche
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - Connie M Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Caleb P Bupp
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Division of Medical Genetics, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Surender Rajasekaran
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
| | - Mathias Francois
- The Centenary Institute, The University of Sydney, Royal Prince Alfred Hospital, Sydney, NSW 2006, Australia
| | - Jeremy W. Prokop
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
- Office of Research, Spectrum Health, Grand Rapids, MI 49503, USA
- Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
8
|
Ben Boubaker R, Tiss A, Henrion D, Chabbert M. Homology Modeling in the Twilight Zone: Improved Accuracy by Sequence Space Analysis. Methods Mol Biol 2023; 2627:1-23. [PMID: 36959439 DOI: 10.1007/978-1-0716-2974-1_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
The analysis of the relationship between sequence and structure similarities during the evolution of a protein family has revealed a limit of sequence divergence for which structural conservation can be confidently assumed and homology modeling is reliable. Below this limit, the twilight zone corresponds to sequence divergence for which homology modeling becomes increasingly difficult and requires specific methods. Either with conventional threading methods or with recent deep learning methods, such as AlphaFold, the challenge relies on the identification of a template that shares not only a common ancestor (homology) but also a conserved structure with the query. As both homology and structural conservation are transitive properties, mining of sequence databases followed by multidimensional scaling (MDS) of the query sequence space can reveal intermediary sequences to infer homology and structural conservation between the query and the template. Here, as a case study, we studied the plethodontid receptivity factor isoform 1 (PRF1) from Plethodon jordani, a member of a pheromone protein family present only in lungless salamanders and weakly related to cytokines of the IL6 family. A variety of conventional threading methods led to the cytokine CNTF as a template. Sequence mining, followed by phylogenetic and MDS analysis, provided missing links between PRF1 and CNTF and allowed reliable homology modeling. In addition, we compared automated models obtained from web servers to a customized model to show how modeling can be improved by expert information.
Collapse
Affiliation(s)
- Rym Ben Boubaker
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Asma Tiss
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Daniel Henrion
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France
| | - Marie Chabbert
- UMR CNRS 6015 - INSERM 1083, Laboratoire MITOVASC, Université d'Angers, Angers, France.
| |
Collapse
|
9
|
Bohnsack KS, Kaden M, Abel J, Villmann T. Alignment-Free Sequence Comparison: A Systematic Survey From a Machine Learning Perspective. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:119-135. [PMID: 34990369 DOI: 10.1109/tcbb.2022.3140873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The encounter of large amounts of biological sequence data generated during the last decades and the algorithmic and hardware improvements have offered the possibility to apply machine learning techniques in bioinformatics. While the machine learning community is aware of the necessity to rigorously distinguish data transformation from data comparison and adopt reasonable combinations thereof, this awareness is often lacking in the field of comparative sequence analysis. With realization of the disadvantages of alignments for sequence comparison, some typical applications use more and more so-called alignment-free approaches. In light of this development, we present a conceptual framework for alignment-free sequence comparison, which highlights the delineation of: 1) the sequence data transformation comprising of adequate mathematical sequence coding and feature generation, from 2) the subsequent (dis-)similarity evaluation of the transformed data by means of problem-specific but mathematically consistent proximity measures. We consider coding to be an information-loss free data transformation in order to get an appropriate representation, whereas feature generation is inevitably information-lossy with the intention to extract just the task-relevant information. This distinction sheds light on the plethora of methods available and assists in identifying suitable methods in machine learning and data analysis to compare the sequences under these premises.
Collapse
|
10
|
Ragavendran PV, Tripathi V, Gandotra S. Structure prediction-based insights into the patatin family of Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36748562 DOI: 10.1099/mic.0.001270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Despite its genome sequencing more than two decades ago, the majority of the genes of Mycobacterium tuberculosis remain functionally uncharacterized. Patatins are one such class of proteins that, despite undergoing an expansion in this pathogenic species compared to their non-pathogenic cousins, remain largely unstudied. Recent advances in protein structure prediction using machine learning tools such as AlphaFold2 have provided high-confidence predicted structures for all M. tuberculosis proteins. Here we present detailed analyses of the patatin family of M. tuberculosis using AlphaFold-predicted structures, providing insights into likely modes of regulation, membrane interaction and substrate binding. Regulatory domains within this family of proteins include cyclic nucleotide binding, lid-like domains and other helical domains. Using structural homologues, we identified the likely membrane localization mechanisms and substrate-binding sites. These analyses reveal diversity in their regulatory capacity, mechanisms of membrane binding and likely length of fatty acid substrates. Together, this analysis suggests unique roles for the eight predicted patatins of M. tuberculosis.
Collapse
Affiliation(s)
- P V Ragavendran
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh- 201 002, India.,Immunology and Infectious Disease, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, New Delhi, India
| | - Vaishnavi Tripathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh- 201 002, India.,Immunology and Infectious Disease, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, New Delhi, India
| | - Sheetal Gandotra
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh- 201 002, India.,Immunology and Infectious Disease, CSIR-Institute of Genomics and Integrative Biology, New Delhi, India, New Delhi, India
| |
Collapse
|
11
|
Baltzis A, Mansouri L, Jin S, Langer BE, Erb I, Notredame C. Highly significant improvement of protein sequence alignments with AlphaFold2. Bioinformatics 2022; 38:5007-5011. [PMID: 36130276 PMCID: PMC9665868 DOI: 10.1093/bioinformatics/btac625] [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: 07/07/2022] [Revised: 08/29/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Protein sequence alignments are essential to structural, evolutionary and functional analysis, but their accuracy is often limited by sequence similarity unless molecular structures are available. Protein structures predicted at experimental grade accuracy, as achieved by AlphaFold2, could therefore have a major impact on sequence analysis. RESULTS Here, we find that multiple sequence alignments estimated on AlphaFold2 predictions are almost as accurate as alignments estimated on experimental structures and significantly closer to the structural reference than sequence-based alignments. We also show that AlphaFold2 structural models of relatively low quality can be used to obtain highly accurate alignments. These results suggest that, besides structure modeling, AlphaFold2 encodes higher-order dependencies that can be exploited for sequence analysis. AVAILABILITY AND IMPLEMENTATION All data, analyses and results are available on Zenodo (https://doi.org/10.5281/zenodo.7031286). The code and scripts have been deposited in GitHub (https://github.com/cbcrg/msa-af2-nf) and the various containers in (https://cloud.sylabs.io/library/athbaltzis/af2/alphafold, https://hub.docker.com/r/athbaltzis/pred). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
| | | | - Suzanne Jin
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Björn E Langer
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | - Ionas Erb
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain
| | | |
Collapse
|
12
|
Czech L, Stamatakis A, Dunthorn M, Barbera P. Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade. FRONTIERS IN BIOINFORMATICS 2022; 2:871393. [PMID: 36304302 PMCID: PMC9580882 DOI: 10.3389/fbinf.2022.871393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 12/20/2022] Open
Abstract
Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into a phylogenetic context using a set of known reference sequences and taking evolutionary history into account. Thereby, one can increase the accuracy of metagenomic surveys and eliminate the requirement for having exact or close matches with existing sequence databases. Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results. A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations with environmental variables. In this review, we provide an overview over the methods developed during the first 10 years. In particular, the goals of this review are 1) to motivate the usage of phylogenetic placement and illustrate some of its use cases, 2) to outline the full workflow, from raw sequences to publishable figures, including best practices, 3) to introduce the most common tools and methods and their capabilities, 4) to point out common placement pitfalls and misconceptions, 5) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.
Collapse
Affiliation(s)
- Lucas Czech
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany
- Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway
| | | |
Collapse
|
13
|
Kostenko DO, Korotkov EV. Application of the MAHDS Method for Multiple Alignment of Highly Diverged Amino Acid Sequences. Int J Mol Sci 2022; 23:ijms23073764. [PMID: 35409125 PMCID: PMC8998981 DOI: 10.3390/ijms23073764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/10/2022] Open
Abstract
The aim of this work was to compare the multiple alignment methods MAHDS, T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK in their ability to align highly divergent amino acid sequences. To accomplish this, we created test amino acid sequences with an average number of substitutions per amino acid (x) from 0.6 to 5.6, a total of 81 sets. Comparison of the performance of sequence alignments constructed by MAHDS and previously developed algorithms using the CS and Z score criteria and the benchmark alignment database (BAliBASE) indicated that, although the quality of the alignments built with MAHDS was somewhat lower than that of the other algorithms, it was compensated by greater statistical significance. MAHDS could construct statistically significant alignments of artificial sequences with x ≤ 4.8, whereas the other algorithms (T-Coffee, MUSCLE, Clustal Omega, Kalign, MAFFT, and PRANK) could not perform that at x > 2.4. The application of MAHDS to align 21 families of highly diverged proteins (identity < 20%) from Pfam and HOMSTRAD databases showed that it could calculate statistically significant alignments in cases when the other methods failed. Thus, MAHDS could be used to construct statistically significant multiple alignments of highly divergent protein sequences, which accumulated multiple mutations during evolution.
Collapse
|
14
|
Wang Y, Zhao Y, Pan Q. Advances, challenges and opportunities of phylogenetic and social network analysis using COVID-19 data. Brief Bioinform 2021; 23:6380452. [PMID: 34601563 DOI: 10.1093/bib/bbab406] [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: 06/30/2021] [Revised: 08/04/2021] [Accepted: 09/03/2021] [Indexed: 11/15/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) has attracted research interests from all fields. Phylogenetic and social network analyses based on connectivity between either COVID-19 patients or geographic regions and similarity between syndrome coronavirus 2 (SARS-CoV-2) sequences provide unique angles to answer public health and pharmaco-biological questions such as relationships between various SARS-CoV-2 mutants, the transmission pathways in a community and the effectiveness of prevention policies. This paper serves as a systematic review of current phylogenetic and social network analyses with applications in COVID-19 research. Challenges in current phylogenetic network analysis on SARS-CoV-2 such as unreliable inferences, sampling bias and batch effects are discussed as well as potential solutions. Social network analysis combined with epidemiology models helps to identify key transmission characteristics and measure the effectiveness of prevention and control strategies. Finally, future new directions of network analysis motivated by COVID-19 data are summarized.
Collapse
Affiliation(s)
- Yue Wang
- School of Mathematical and Natural Science, Arizona State University, 4701 W Thunderbird Rd, 85306, Arizona, USA
| | - Yunpeng Zhao
- School of Mathematical and Natural Science, Arizona State University, 4701 W Thunderbird Rd, 85306, Arizona, USA
| | - Qing Pan
- Department of Statistics, George Washington University, 801 22nd St. NW, 20052, Washington DC, USA
| |
Collapse
|
15
|
Li Y. Sequence Alignment with Q-Learning Based on the Actor-Critic Model. ACM T ASIAN LOW-RESO 2021. [DOI: 10.1145/3433540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Multiple sequence alignment methods refer to a series of algorithmic solutions for the alignment of evolutionary-related sequences while taking into account evolutionary events such as mutations, insertions, deletions, and rearrangements under certain conditions. In this article, we propose a method with Q-learning based on the Actor-Critic model for sequence alignment. We transform the sequence alignment problem into an agent's autonomous learning process. In this process, the reward of the possible next action taken is calculated, and the cumulative reward of the entire process is calculated. The results show that the method we propose is better than the gene algorithm and the dynamic programming method.
Collapse
Affiliation(s)
- Yarong Li
- The Experimental High School Attached to Beijing Normal University, Beijing, China
| |
Collapse
|
16
|
Meng X, Yang L, Liu H, Li Q, Xu G, Zhang Y, Guan F, Zhang Y, Zhang W, Wu N, Tian J. Protein engineering of stable IsPETase for PET plastic degradation by Premuse. Int J Biol Macromol 2021; 180:667-676. [PMID: 33753197 DOI: 10.1016/j.ijbiomac.2021.03.058] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/25/2022]
Abstract
Poly(ethylene terephthalate) (PET) is used widely by human beings, but is very difficult to degrade. Up to now, the PET degradation effect of PETase from Ideonella sakaiensis 201-F6 (IsPETase) variants with low stability and activity was not ideal. In this study, a mutation design tool, Premuse, was developed to integrate the sequence alignment and quantitative selection of the preferred mutations based on natural sequence evolution. Ten single point mutants were selected from 1486 homologous sequences using Premuse, and then two mutations (W159H and F229Y) with improved stability were screened from them. The derived double point mutant, W159H/F229Y, exhibited a strikingly enhanced enzymatic performance. Its Tm and catalytic efficiency values (kcat/Km) respectively increased by 10.4 °C and 2.0-fold using p-NPP as the substrate compared with wild type. The degradation activity for amorphous PET was increased by almost 40-fold in comparison with wild type at 40 °C in 24 h. Additionally, the variant could catalyze biodegradation of PET bottle preform at a mean rate of 23.4 mgPET/h/mgenzyme. This study allowed us to design the mutation more efficiently, and provides a tool for achieving biodegradation of PET pollution under mild natural environments.
Collapse
Affiliation(s)
- Xiangxi Meng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lixin Yang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hanqing Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qingbin Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Guoshun Xu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Food Science and Technology, Agricultural University of Hebei, Baoding, Hebei Province 071001, China
| | - Feifei Guan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuhong Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wei Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ningfeng Wu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Jian Tian
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
17
|
Akand EH, Murray JM. NGlyAlign: an automated library building tool to align highly divergent HIV envelope sequences. BMC Bioinformatics 2021; 22:54. [PMID: 33557755 PMCID: PMC7869453 DOI: 10.1186/s12859-020-03901-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/23/2020] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND The high variability in envelope regions of some viruses such as HIV allow the virus to establish infection and to escape subsequent immune surveillance. This variability, as well as increasing incorporation of N-linked glycosylation sites, is fundamental to this evasion. It also creates difficulties for multiple sequence alignment methods (MSA) that provide the first step in their analysis. Existing MSA tools often fail to properly align highly variable HIV envelope sequences requiring extensive manual editing that is impractical with even a moderate number of these variable sequences. RESULTS We developed an automated library building tool NGlyAlign, that organizes similar N-linked glycosylation sites as block constraints and statistically conserved global sites as single site constraints to automatically enforce partial columns in consistency-based MSA methods such as Dialign. This combined method accurately aligns variable HIV-1 envelope sequences. We tested the method on two datasets: a set of 156 founder and chronic gp160 HIV-1 subtype B sequences as well as a set of reference sequences of gp120 in the highly variable region 1. On measures such as entropy scores, sum of pair scores, column score, and similarity heat maps, NGlyAlign+Dialign proved superior against methods such as T-Coffee, ClustalOmega, ClustalW, Praline, HIValign and Muscle. The method is scalable to large sequence sets producing accurate alignments without requiring manual editing. As well as this application to HIV, our method can be used for other highly variable glycoproteins such as hepatitis C virus envelope. CONCLUSIONS NGlyAlign is an automated tool for mapping and building glycosylation motif libraries to accurately align highly variable regions in HIV sequences. It can provide the basis for many studies reliant on single robust alignments. NGlyAlign has been developed as an open-source tool and is freely available at https://github.com/UNSW-Mathematical-Biology/NGlyAlign_v1.0 .
Collapse
Affiliation(s)
- Elma H Akand
- School of Mathematics and Statistics, UNSW, Sydney, NSW, Australia.
| | - John M Murray
- School of Mathematics and Statistics, UNSW, Sydney, NSW, Australia
| |
Collapse
|
18
|
Korotkov EV, Suvorova YM, Kostenko DO, Korotkova MA. Multiple Alignment of Promoter Sequences from the Arabidopsis thaliana L. Genome. Genes (Basel) 2021; 12:135. [PMID: 33494278 PMCID: PMC7909805 DOI: 10.3390/genes12020135] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/16/2022] Open
Abstract
In this study, we developed a new mathematical method for performing multiple alignment of highly divergent sequences (MAHDS), i.e., sequences that have on average more than 2.5 substitutions per position (x). We generated sets of artificial DNA sequences with x ranging from 0 to 4.4 and applied MAHDS as well as currently used multiple sequence alignment algorithms, including ClustalW, MAFFT, T-Coffee, Kalign, and Muscle to these sets. The results indicated that most of the existing methods could produce statistically significant alignments only for the sets with x < 2.5, whereas MAHDS could operate on sequences with x = 4.4. We also used MAHDS to analyze a set of promoter sequences from the Arabidopsis thaliana genome and discovered many conserved regions upstream of the transcription initiation site (from -499 to +1 bp); a part of the downstream region (from +1 to +70 bp) also significantly contributed to the obtained alignments. The possibilities of applying the newly developed method for the identification of promoter sequences in any genome are discussed. A server for multiple alignment of nucleotide sequences has been created.
Collapse
Affiliation(s)
- Eugene V. Korotkov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia;
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoye Shosse, 115409 Moscow, Russia; (D.O.K.); (M.A.K.)
| | - Yulia M. Suvorova
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia;
| | - Dmitrii O. Kostenko
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoye Shosse, 115409 Moscow, Russia; (D.O.K.); (M.A.K.)
| | - Maria A. Korotkova
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 31 Kashirskoye Shosse, 115409 Moscow, Russia; (D.O.K.); (M.A.K.)
| |
Collapse
|
19
|
AnOxPePred: using deep learning for the prediction of antioxidative properties of peptides. Sci Rep 2020; 10:21471. [PMID: 33293615 PMCID: PMC7722737 DOI: 10.1038/s41598-020-78319-w] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 11/16/2020] [Indexed: 12/02/2022] Open
Abstract
Dietary antioxidants are an important preservative in food and have been suggested to help in disease prevention. With consumer demands for less synthetic and safer additives in food products, the food industry is searching for antioxidants that can be marketed as natural. Peptides derived from natural proteins show promise, as they are generally regarded as safe and potentially contain other beneficial bioactivities. Antioxidative peptides are usually obtained by testing various peptides derived from hydrolysis of proteins by a selection of proteases. This slow and cumbersome trial-and-error approach to identify antioxidative peptides has increased interest in developing computational approaches for prediction of antioxidant activity and thereby reduce laboratory work. A few antioxidant predictors exist, however, no tool predicting the antioxidative properties of peptides is, to the best of our knowledge, currently available as a web-server. We here present the AnOxPePred tool and web-server (http://services.bioinformatics.dtu.dk/service.php?AnOxPePred-1.0) that uses deep learning to predict the antioxidant properties of peptides. Our model was trained on a curated dataset consisting of experimentally-tested antioxidant and non-antioxidant peptides. For a variety of metrics our method displays a prediction performance better than a k-NN sequence identity-based approach. Furthermore, the developed tool will be a good benchmark for future predictors of antioxidant peptides.
Collapse
|
20
|
Portik DM, Wiens JJ. Do Alignment and Trimming Methods Matter for Phylogenomic (UCE) Analyses? Syst Biol 2020; 70:440-462. [PMID: 32797207 DOI: 10.1093/sysbio/syaa064] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/02/2020] [Accepted: 08/03/2020] [Indexed: 11/14/2022] Open
Abstract
Alignment is a crucial issue in molecular phylogenetics because different alignment methods can potentially yield very different topologies for individual genes. But it is unclear if the choice of alignment methods remains important in phylogenomic analyses, which incorporate data from hundreds or thousands of genes. For example, problematic biases in alignment might be multiplied across many loci, whereas alignment errors in individual genes might become irrelevant. The issue of alignment trimming (i.e., removing poorly aligned regions or missing data from individual genes) is also poorly explored. Here, we test the impact of 12 different combinations of alignment and trimming methods on phylogenomic analyses. We compare these methods using published phylogenomic data from ultraconserved elements (UCEs) from squamate reptiles (lizards and snakes), birds, and tetrapods. We compare the properties of alignments generated by different alignment and trimming methods (e.g., length, informative sites, missing data). We also test whether these data sets can recover well-established clades when analyzed with concatenated (RAxML) and species-tree methods (ASTRAL-III), using the full data ($\sim $5000 loci) and subsampled data sets (10% and 1% of loci). We show that different alignment and trimming methods can significantly impact various aspects of phylogenomic data sets (e.g., length, informative sites). However, these different methods generally had little impact on the recovery and support values for well-established clades, even across very different numbers of loci. Nevertheless, our results suggest several "best practices" for alignment and trimming. Intriguingly, the choice of phylogenetic methods impacted the phylogenetic results most strongly, with concatenated analyses recovering significantly more well-established clades (with stronger support) than the species-tree analyses. [Alignment; concatenated analysis; phylogenomics; sequence length heterogeneity; species-tree analysis; trimming].
Collapse
Affiliation(s)
- Daniel M Portik
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.,California Academy of Sciences, San Francisco, CA 94118, USA
| | - John J Wiens
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| |
Collapse
|
21
|
Abstract
Bioinformatics regularly poses new challenges to algorithm engineers and theoretical computer scientists. This work surveys recent developments of parameterized algorithms and complexity for important NP-hard problems in bioinformatics. We cover sequence assembly and analysis, genome comparison and completion, and haplotyping and phylogenetics. Aside from reporting the state of the art, we give challenges and open problems for each topic.
Collapse
|
22
|
Rozewicki J, Li S, Amada KM, Standley DM, Katoh K. MAFFT-DASH: integrated protein sequence and structural alignment. Nucleic Acids Res 2019; 47:W5-W10. [PMID: 31062021 PMCID: PMC6602451 DOI: 10.1093/nar/gkz342] [Citation(s) in RCA: 242] [Impact Index Per Article: 48.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/07/2019] [Accepted: 04/25/2019] [Indexed: 12/22/2022] Open
Abstract
Here, we describe a web server that integrates structural alignments with the MAFFT multiple sequence alignment (MSA) tool. For this purpose, we have prepared a web-based Database of Aligned Structural Homologs (DASH), which provides structural alignments at the domain and chain levels for all proteins in the Protein Data Bank (PDB), and can be queried interactively or by a simple REST-like API. MAFFT-DASH integration can be invoked with a single flag on either the web (https://mafft.cbrc.jp/alignment/server/) or command-line versions of MAFFT. In our benchmarks using 878 cases from the BAliBase, HomFam, OXFam, Mattbench and SISYPHUS datasets, MAFFT-DASH showed 10-20% improvement over standard MAFFT for MSA problems with weak similarity, in terms of Sum-of-Pairs (SP), a measure of how well a program succeeds at aligning input sequences in comparison to a reference alignment. When MAFFT alignments were supplemented with homologous sequences, further improvement was observed. Potential applications of DASH beyond MSA enrichment include functional annotation through detection of remote homology and assembly of template libraries for homology modeling.
Collapse
Affiliation(s)
- John Rozewicki
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Systems Immunology Laboratory, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Songling Li
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Systems Immunology Laboratory, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Karlou Mar Amada
- Systems Immunology Laboratory, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Daron M Standley
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Systems Immunology Laboratory, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| | - Kazutaka Katoh
- Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
- Systems Immunology Laboratory, Immunology Frontier Research Center, Osaka University, 3-1 Yamadaoka, Suita 565-0871, Japan
| |
Collapse
|
23
|
Gyimesi G, Albano G, Fuster DG, Hediger MA, Pujol-Giménez J. Unraveling the structural elements of pH sensitivity and substrate binding in the human zinc transporter SLC39A2 (ZIP2). J Biol Chem 2019; 294:8046-8063. [PMID: 30914478 PMCID: PMC6527156 DOI: 10.1074/jbc.ra118.006113] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 03/22/2019] [Indexed: 12/20/2022] Open
Abstract
The transport and ion-coupling mechanisms of ZIP transporters remain largely uncharacterized. Previous work in our laboratory has revealed that the solute carrier family 39 member A2 (SLC39A2/ZIP2) increases its substrate transport rate in the presence of extracellular H+. Here, we used a combination of in silico and in vitro techniques involving structural modeling, mutagenesis, and functional characterization in HEK293 cells to identify amino acid residues potentially relevant for both the ZIP2–H+ interaction and substrate binding. Our ZIP2 models revealed a cluster of charged residues close to the substrate–translocation pore. Interestingly, the H63A substitution completely abrogated pH sensitivity, and substitutions of Glu-67 and Phe-269 altered the pH and voltage modulation of transport. In contrast, substitution of Glu-106, which might be part of a dimerization interface, altered pH but not voltage modulation. Substitution of Phe-269, located close to the substrate-binding site, also affected substrate selectivity. These findings were supported by an additional model of ZIP2 that was based on the structure of a prokaryotic homolog, Bordetella bronchiseptica ZrT/Irt-like protein (bbZIP), and in silico pKa calculations. We also found that residues Glu-179, His-175, His-202, and Glu-276 are directly involved in the coordination of the substrate metal ion. We noted that, unlike bbZIP, human ZIP2 is predicted to harbor a single divalent metal-binding site, with the charged side chain of Lys-203 replacing the second bound ion. Our results provide the first structural evidence for the previously observed pH and voltage modulation of ZIP2-mediated metal transport, identify the substrate-binding site, and suggest a structure-based transport mechanism for the ZIP2 transporter.
Collapse
Affiliation(s)
- Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland; National Center of Competence in Research, NCCR TransCure, Bühlstrasse 28, 3012 Bern, Switzerland; Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 18, 3010 Bern, Switzerland
| | - Giuseppe Albano
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland; National Center of Competence in Research, NCCR TransCure, Bühlstrasse 28, 3012 Bern, Switzerland; Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 18, 3010 Bern, Switzerland
| | - Daniel G Fuster
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland; National Center of Competence in Research, NCCR TransCure, Bühlstrasse 28, 3012 Bern, Switzerland; Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 18, 3010 Bern, Switzerland
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland; National Center of Competence in Research, NCCR TransCure, Bühlstrasse 28, 3012 Bern, Switzerland; Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 18, 3010 Bern, Switzerland.
| | - Jonai Pujol-Giménez
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland; National Center of Competence in Research, NCCR TransCure, Bühlstrasse 28, 3012 Bern, Switzerland; Department of Nephrology and Hypertension, Inselspital, Bern University Hospital, University of Bern, Freiburgstrasse 18, 3010 Bern, Switzerland.
| |
Collapse
|
24
|
Catanach TA, Sweet AD, Nguyen NPD, Peery RM, Debevec AH, Thomer AK, Owings AC, Boyd BM, Katz AD, Soto-Adames FN, Allen JM. Fully automated sequence alignment methods are comparable to, and much faster than, traditional methods in large data sets: an example with hepatitis B virus. PeerJ 2019; 7:e6142. [PMID: 30627489 PMCID: PMC6321758 DOI: 10.7717/peerj.6142] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 11/14/2018] [Indexed: 01/05/2023] Open
Abstract
Aligning sequences for phylogenetic analysis (multiple sequence alignment; MSA) is an important, but increasingly computationally expensive step with the recent surge in DNA sequence data. Much of this sequence data is publicly available, but can be extremely fragmentary (i.e., a combination of full genomes and genomic fragments), which can compound the computational issues related to MSA. Traditionally, alignments are produced with automated algorithms and then checked and/or corrected "by eye" prior to phylogenetic inference. However, this manual curation is inefficient at the data scales required of modern phylogenetics and results in alignments that are not reproducible. Recently, methods have been developed for fully automating alignments of large data sets, but it is unclear if these methods produce alignments that result in compatible phylogenies when compared to more traditional alignment approaches that combined automated and manual methods. Here we use approximately 33,000 publicly available sequences from the hepatitis B virus (HBV), a globally distributed and rapidly evolving virus, to compare different alignment approaches. Using one data set comprised exclusively of whole genomes and a second that also included sequence fragments, we compared three MSA methods: (1) a purely automated approach using traditional software, (2) an automated approach including by eye manual editing, and (3) more recent fully automated approaches. To understand how these methods affect phylogenetic results, we compared resulting tree topologies based on these different alignment methods using multiple metrics. We further determined if the monophyly of existing HBV genotypes was supported in phylogenies estimated from each alignment type and under different statistical support thresholds. Traditional and fully automated alignments produced similar HBV phylogenies. Although there was variability between branch support thresholds, allowing lower support thresholds tended to result in more differences among trees. Therefore, differences between the trees could be best explained by phylogenetic uncertainty unrelated to the MSA method used. Nevertheless, automated alignment approaches did not require human intervention and were therefore considerably less time-intensive than traditional approaches. Because of this, we conclude that fully automated algorithms for MSA are fully compatible with older methods even in extremely difficult to align data sets. Additionally, we found that most HBV diagnostic genotypes did not correspond to evolutionarily-sound groups, regardless of alignment type and support threshold. This suggests there may be errors in genotype classification in the database or that HBV genotypes may need a revision.
Collapse
Affiliation(s)
- Therese A. Catanach
- Ornithology Department, Academy of Natural Sciences of Drexel University, Philadelphia, PA, United States of America
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Wildlife and Fisheries Sciences, Texas A&M University, College Station, TX, United States of America
| | - Andrew D. Sweet
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, Purdue University, West Lafayette, IN, United States of America
| | - Nam-phuong D. Nguyen
- Computer Science and Engineering, University of San Diego, California, La Jolla, CA, United States of America
| | - Rhiannon M. Peery
- Department of Biology, University of Alberta, Edmonton, Alberta, Canada
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrew H. Debevec
- School of Integrative Biology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Andrea K. Thomer
- School of Information, University of Michigan—Ann Arbor, Ann Arbor, MI, United States of America
| | - Amanda C. Owings
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Bret M. Boyd
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Georga, Athens, GA, United States of America
| | - Aron D. Katz
- Illinois Natural History Survey, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
- Department of Entomology, University of Illinois at Urbana-Champaign, Champaign, IL, United States of America
| | - Felipe N. Soto-Adames
- Florida State Collection of Arthropods, Florida Department of Agriculture and Consumer Services, Gainesville, FL, United States of America
- Department of Entomology and Nematology, University of Florida, Gainesville, FL, United States of America
| | - Julie M. Allen
- Biology Department, University of Nevada, Reno, Reno, NV, United States of America
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
Guyeux C, Al-Nuaimi B, AlKindy B, Couchot JF, Salomon M. On the reconstruction of the ancestral bacterial genomes in genus Mycobacterium and Brucella. BMC SYSTEMS BIOLOGY 2018; 12:100. [PMID: 30458842 PMCID: PMC6245693 DOI: 10.1186/s12918-018-0618-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
BACKGROUND To reconstruct the evolution history of DNA sequences, novel models of increasing complexity regarding the number of free parameters taken into account in the sequence evolution, as well as faster and more accurate algorithms, and statistical and computational methods, are needed. More particularly, as the principal forces that have led to major structural changes are genome rearrangements (such as translocations, fusions, and so on), understanding their underlying mechanisms, among other things via the ancestral genome reconstruction, are essential. In this problem, since finding the ancestral genomes that minimize the number of rearrangements in a phylogenetic tree is known to be NP-hard for three or more genomes, heuristics are commonly chosen to obtain approximations of the exact solution. The aim of this work is to show that another path is possible. RESULTS Various algorithms and software already deal with the difficult nature of the problem of reconstruction of the ancestral genome, but they do not function with precision, in particular when indels or single nucleotide polymorphisms fall into repeated sequences. In this article, and despite the theoretical NP-hardness of the ancestral reconstruction problem, we show that an exact solution can be found in practice in various cases, encompassing organelles and some bacteria. A practical example proves that an accurate reconstruction, which also allows to highlight homoplasic events, can be obtained. This is illustrated by the reconstruction of ancestral genomes of two bacterial pathogens, belonging in Mycobacterium and Brucella genera. CONCLUSIONS By putting together automatically reconstructed ancestral regions with handmade ones for problematic cases, we show that an accurate reconstruction of ancestors of the Brucella genus and of the Mycobacterium tuberculosis complex is possible. By doing so, we are able to investigate the evolutionary history of each pathogen by computing their common ancestors. They can be investigated extensively, by studying the gene content evolution over time, the resistance acquisition, and the impacts of mobile elements on genome plasticity.
Collapse
Affiliation(s)
- Christophe Guyeux
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, Besançon, 25000 France
| | - Bashar Al-Nuaimi
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, Besançon, 25000 France
- Department of Computer Science, Diyala University, Diyala, 32001 Iraq
| | - Bassam AlKindy
- Department of Computer Science, Al-Mustansiriyah University, Baghdad, 10052 Iraq
| | - Jean-François Couchot
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, Besançon, 25000 France
| | - Michel Salomon
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, Besançon, 25000 France
| |
Collapse
|
27
|
Levy Karin E, Ashkenazy H, Hein J, Pupko T. A Simulation-Based Approach to Statistical Alignment. Syst Biol 2018; 68:252-266. [DOI: 10.1093/sysbio/syy059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Accepted: 09/10/2018] [Indexed: 12/26/2022] Open
Affiliation(s)
- Eli Levy Karin
- School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Haim Ashkenazy
- School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Jotun Hein
- School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
- Department of Statistics, University of Oxford, Oxford, UK
| | - Tal Pupko
- School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| |
Collapse
|
28
|
Orlando G, Raimondi D, Khan T, Lenaerts T, Vranken WF. SVM-dependent pairwise HMM: an application to protein pairwise alignments. Bioinformatics 2018; 33:3902-3908. [PMID: 28666322 DOI: 10.1093/bioinformatics/btx391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 06/12/2017] [Indexed: 12/27/2022] Open
Abstract
Motivation Methods able to provide reliable protein alignments are crucial for many bioinformatics applications. In the last years many different algorithms have been developed and various kinds of information, from sequence conservation to secondary structure, have been used to improve the alignment performances. This is especially relevant for proteins with highly divergent sequences. However, recent works suggest that different features may have different importance in diverse protein classes and it would be an advantage to have more customizable approaches, capable to deal with different alignment definitions. Results Here we present Rigapollo, a highly flexible pairwise alignment method based on a pairwise HMM-SVM that can use any type of information to build alignments. Rigapollo lets the user decide the optimal features to align their protein class of interest. It outperforms current state of the art methods on two well-known benchmark datasets when aligning highly divergent sequences. Availability and implementation A Python implementation of the algorithm is available at http://ibsquare.be/rigapollo. Contact wim.vranken@vub.be. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Gabriele Orlando
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2.,Structural Biology Research Center, VIB.,Structural Machine Learning Group, Université Libre de Bruxelles
| | - Daniele Raimondi
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2.,Structural Biology Research Center, VIB.,Structural Machine Learning Group, Université Libre de Bruxelles
| | - Taushif Khan
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2
| | - Tom Lenaerts
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan.,Structural Machine Learning Group, Université Libre de Bruxelles.,Artificial Intelligence Lab, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Wim F Vranken
- Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, La Plaine Campus, Triomflaan.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2.,Structural Biology Research Center, VIB
| |
Collapse
|
29
|
Alves RJE, Minh BQ, Urich T, von Haeseler A, Schleper C. Unifying the global phylogeny and environmental distribution of ammonia-oxidising archaea based on amoA genes. Nat Commun 2018; 9:1517. [PMID: 29666365 PMCID: PMC5904100 DOI: 10.1038/s41467-018-03861-1] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/19/2018] [Indexed: 12/30/2022] Open
Abstract
Ammonia-oxidising archaea (AOA) are ubiquitous and abundant in nature and play a major role in nitrogen cycling. AOA have been studied intensively based on the amoA gene (encoding ammonia monooxygenase subunit A), making it the most sequenced functional marker gene. Here, based on extensive phylogenetic and meta-data analyses of 33,378 curated archaeal amoA sequences, we define a highly resolved taxonomy and uncover global environmental patterns that challenge many earlier generalisations. Particularly, we show: (i) the global frequency of AOA is extremely uneven, with few clades dominating AOA diversity in most ecosystems; (ii) characterised AOA do not represent most predominant clades in nature, including soils and oceans; (iii) the functional role of the most prevalent environmental AOA clade remains unclear; and (iv) AOA harbour molecular signatures that possibly reflect phenotypic traits. Our work synthesises information from a decade of research and provides the first integrative framework to study AOA in a global context.
Collapse
Affiliation(s)
- Ricardo J Eloy Alves
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Bui Quang Minh
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Campus Vienna Biocenter 5, Dr. Bohr Gasse 9, 1030, Vienna, Austria
- Ecology and Evolution, Research School of Biology, Australian National University, 2601, Canberra, ACT, Australia
| | - Tim Urich
- Institute of Microbiology, Ernst-Moritz-Arndt University, Felix-Hausdorff-Strasse 8, 17487, Greifswald, Germany
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Campus Vienna Biocenter 5, Dr. Bohr Gasse 9, 1030, Vienna, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria.
| |
Collapse
|
30
|
Mori H, Maruyama T, Yano M, Yamada T, Kurokawa K. VITCOMIC2: visualization tool for the phylogenetic composition of microbial communities based on 16S rRNA gene amplicons and metagenomic shotgun sequencing. BMC SYSTEMS BIOLOGY 2018; 12:30. [PMID: 29560821 PMCID: PMC5861490 DOI: 10.1186/s12918-018-0545-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Background The 16S rRNA gene-based amplicon sequencing analysis is widely used to determine the taxonomic composition of microbial communities. Once the taxonomic composition of each community is obtained, evolutionary relationships among taxa are inferred by a phylogenetic tree. Thus, the combined representation of taxonomic composition and phylogenetic relationships among taxa is a powerful method for understanding microbial community structure; however, applying phylogenetic tree-based representation with information on the abundance of thousands or more taxa in each community is a difficult task. For this purpose, we previously developed the tool VITCOMIC (VIsualization tool for Taxonomic COmpositions of MIcrobial Community), which is based on the genome-sequenced microbes’ phylogenetic information. Here, we introduce VITCOMIC2, which incorporates substantive improvements over VITCOMIC that were necessary to address several issues associated with 16S rRNA gene-based analysis of microbial communities. Results We developed VITCOMIC2 to provide (i) sequence identity searches against broad reference taxa including uncultured taxa; (ii) normalization of 16S rRNA gene copy number differences among taxa; (iii) rapid sequence identity searches by applying the graphics processing unit-based sequence identity search tool CLAST; (iv) accurate taxonomic composition inference and nearly full-length 16S rRNA gene sequence reconstructions for metagenomic shotgun sequencing; and (v) an interactive user interface for simultaneous representation of the taxonomic composition of microbial communities and phylogenetic relationships among taxa. We validated the accuracy of processes (ii) and (iv) by using metagenomic shotgun sequencing data from a mock microbial community. Conclusions The improvements incorporated into VITCOMIC2 enable users to acquire an intuitive understanding of microbial community composition based on the 16S rRNA gene sequence data obtained from both metagenomic shotgun and amplicon sequencing. Electronic supplementary material The online version of this article (10.1186/s12918-018-0545-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Hiroshi Mori
- Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan.
| | - Takayuki Maruyama
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Masahiro Yano
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Takuji Yamada
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 2-12-1 M6-3, Ookayama, Meguro-ku, Tokyo, 152-8550, Japan
| | - Ken Kurokawa
- Genome Evolution Laboratory, Center for Information Biology, National Institute of Genetics, Mishima, 411-8540, Japan
| |
Collapse
|
31
|
Bendiksby M, Næsborg RR, Timdal E. Xylopsora canopeorum (Umbilicariaceae), a new lichen species from the canopy of Sequoia sempervirens. MycoKeys 2018; 30:1-15. [PMID: 29559828 PMCID: PMC5804297 DOI: 10.3897/mycokeys.30.22271] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Accepted: 01/17/2018] [Indexed: 01/05/2023] Open
Abstract
Xylopsora canopeorum Timdal, Reese Næsborg & Bendiksby is described as a new species occupying the crowns of large Sequoia sempervirens trees in California, USA. The new species is supported by morphology, anatomy, secondary chemistry and DNA sequence data. While similar in external appearance to X. friesii, it is distinguished by forming smaller, partly coralloid squamules, by the occurrence of soralia and, in some specimens, by the presence of thamnolic acid in addition to friesiic acid in the thallus. Molecular phylogenetic results are based on nuclear (ITS and LSU) as well as mitochondrial (SSU) ribosomal DNA sequence alignments. Phylogenetic hypotheses obtained using Bayesian Inference, Maximum Likelihood and Maximum Parsimony all support X. canopeorum as a distinct evolutionary lineage belonging to the X. caradocensis-X. friesii clade.
Collapse
Affiliation(s)
- Mika Bendiksby
- NTNU University Museum, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Rikke Reese Næsborg
- Save the Redwoods League, 111 Sutter Street, 11th Floor, San Francisco, CA 94104, USA
| | - Einar Timdal
- Natural History Museum, University of Oslo, NO-0318 Oslo, Norway
| |
Collapse
|
32
|
Characterisation of Casein Kinase 1.1 in Leishmania donovani Using the CRISPR Cas9 Toolkit. BIOMED RESEARCH INTERNATIONAL 2017; 2017:4635605. [PMID: 29333442 PMCID: PMC5733176 DOI: 10.1155/2017/4635605] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/22/2017] [Accepted: 10/12/2017] [Indexed: 02/06/2023]
Abstract
The recent adaptation of CRISPR Cas9 genome editing to Leishmania spp. has opened a new era in deciphering Leishmania biology. The method was recently improved using a PCR-based CRISPR Cas9 approach, which eliminated the need for cloning. This new approach, which allows high-throughput gene deletion, was successfully validated in L. mexicana and L. major. In this study, we validated the toolkit in Leishmania donovani targeting the flagellar protein PF16, confirming that the tagged protein localizes to the flagellum and that null mutants lose their motility. We then used the technique to characterise CK1.1, a member of the casein kinase 1 family, which is involved in the regulation of many cellular processes. We showed that CK1.1 is a low-abundance protein present in promastigotes and in amastigotes. We demonstrated that CK1.1 is not essential for promastigote and axenic amastigote survival or for axenic amastigote differentiation, although it may have a role during stationary phase. Altogether, our data validate the use of PCR-based CRISPR Cas9 toolkit in L. donovani, which will be crucial for genetic modification of hamster-derived, disease-relevant parasites.
Collapse
|
33
|
Souza C, Zanchin NI, Krieger MA, Ludwig A. In silico analysis of amino acid variation in human respiratory syncytial virus: insights into immunodiagnostics. Mem Inst Oswaldo Cruz 2017; 112:655-663. [PMID: 28953993 PMCID: PMC5607514 DOI: 10.1590/0074-02760170013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/16/2017] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The highly contagious nature of human respiratory syncytial virus (HRSV) and the gravity of its infection in newborns and vulnerable adults pose a serious public health problem. Thus, a rapid and sensitive diagnostic test for viral detection that can be implemented upon the first appearance of symptoms is needed. The genetic variation of the virus must be considered for immunodiagnostic purposes. OBJECTIVES To analyse HRSV genetic variation and discuss the possible consequences for capture immunoassay development. METHODS We performed a wide analysis of N, F and G protein variation based on the HRSV sequences currently available in the GenBank database. We also evaluated their similarity with homologous proteins from other viruses. FINDINGS The mean amino acid divergences for the N, F, and G proteins between HRSV-A and HRSV-B were determined to be approximately 4%, 10% and 47%, respectively. Due to their high conservation, assays based on the full-length N and F proteins may not distinguish HRSV from human metapneumovirus and other Mononegavirales viruses, and the full-length G protein would most likely produce false negative results due to its high divergence. MAIN CONCLUSIONS We have identified specific regions in each of these three proteins that have higher potential to produce specific results, and their combined utilisation should be considered for immunoassay development.
Collapse
Affiliation(s)
- Claudemir Souza
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brasil.,Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Programa de Pós-Graduação em Biologia Celular e Molecular, Curitiba, PR, Brasil
| | - Nilson It Zanchin
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Programa de Pós-Graduação em Biologia Celular e Molecular, Curitiba, PR, Brasil
| | - Marco A Krieger
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brasil.,Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil.,Universidade Federal do Paraná, Programa de Pós-Graduação em Biologia Celular e Molecular, Curitiba, PR, Brasil
| | - Adriana Ludwig
- Fundação Oswaldo Cruz-Fiocruz, Instituto Carlos Chagas, Laboratório de Genômica Funcional, Curitiba, PR, Brasil.,Instituto de Biologia Molecular do Paraná, Curitiba, PR, Brasil
| |
Collapse
|
34
|
Schmitzberger F, Richter MM, Gordiyenko Y, Robinson CV, Dadlez M, Westermann S. Molecular basis for inner kinetochore configuration through RWD domain-peptide interactions. EMBO J 2017; 36:3458-3482. [PMID: 29046335 PMCID: PMC5709738 DOI: 10.15252/embj.201796636] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 07/31/2017] [Accepted: 09/08/2017] [Indexed: 01/05/2023] Open
Abstract
Kinetochores are dynamic cellular structures that connect chromosomes to microtubules. They form from multi‐protein assemblies that are evolutionarily conserved between yeasts and humans. One of these assemblies—COMA—consists of subunits Ame1CENP‐U, Ctf19CENP‐P, Mcm21CENP‐O and Okp1CENP‐Q. A description of COMA molecular organization has so far been missing. We defined the subunit topology of COMA, bound with inner kinetochore proteins Nkp1 and Nkp2, from the yeast Kluyveromyces lactis, with nanoflow electrospray ionization mass spectrometry, and mapped intermolecular contacts with hydrogen‐deuterium exchange coupled to mass spectrometry. Our data suggest that the essential Okp1 subunit is a multi‐segmented nexus with distinct binding sites for Ame1, Nkp1‐Nkp2 and Ctf19‐Mcm21. Our crystal structure of the Ctf19‐Mcm21 RWD domains bound with Okp1 shows the molecular contacts of this important inner kinetochore joint. The Ctf19‐Mcm21 binding motif in Okp1 configures a branch of mitotic inner kinetochores, by tethering Ctf19‐Mcm21 and Chl4CENP‐N‐Iml3CENP‐L. Absence of this motif results in dependence on the mitotic checkpoint for viability.
Collapse
Affiliation(s)
- Florian Schmitzberger
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA .,Research Institute of Molecular Pathology (IMP), Vienna, Austria
| | - Magdalena M Richter
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Yuliya Gordiyenko
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Carol V Robinson
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford, UK
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Institute of Genetics and Biotechnology, Biology Department, Warsaw University, Warsaw, Poland
| | | |
Collapse
|
35
|
Pujol-Giménez J, Hediger MA, Gyimesi G. A novel proton transfer mechanism in the SLC11 family of divalent metal ion transporters. Sci Rep 2017; 7:6194. [PMID: 28754960 PMCID: PMC5533754 DOI: 10.1038/s41598-017-06446-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 06/13/2017] [Indexed: 12/17/2022] Open
Abstract
In humans, the H+-coupled Fe2+ transporter DMT1 (SLC11A2) is essential for proper maintenance of iron homeostasis. While X-ray diffraction has recently unveiled the structure of the bacterial homologue ScaDMT as a LeuT-fold transporter, the exact mechanism of H+-cotransport has remained elusive. Here, we used a combination of molecular dynamics simulations, in silico pK a calculations and site-directed mutagenesis, followed by rigorous functional analysis, to discover two previously uncharacterized functionally relevant residues in hDMT1 that contribute to H+-coupling. E193 plays a central role in proton binding, thereby affecting transport properties and electrogenicity, while N472 likely coordinates the metal ion, securing an optimally "closed" state of the protein. Our molecular dynamics simulations provide insight into how H+-translocation through E193 is allosterically linked to intracellular gating, establishing a novel transport mechanism distinct from that of other H+-coupled transporters.
Collapse
Affiliation(s)
- Jonai Pujol-Giménez
- Institute of Biochemistry and Molecular Medicine and National Center of Competence in Research, NCCR TransCure, University of Bern, Bern, Switzerland
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine and National Center of Competence in Research, NCCR TransCure, University of Bern, Bern, Switzerland.
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine and National Center of Competence in Research, NCCR TransCure, University of Bern, Bern, Switzerland.
| |
Collapse
|
36
|
Seo H, Cho DH. A new alignment free genome comparison algorithm based on statistically estimated feature frequency profile. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017; 2017:4265-4268. [PMID: 29060839 DOI: 10.1109/embc.2017.8037798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The sequence comparison is an important part in bioinformatics to understand the biological property of genome. Although the alignment based sequence comparison is traditional and reliable algorithm, alignment free methods have been actively researched because of their advantage in terms of computational complexity. In this paper, we suggest a new alignment free genome comparison scheme based on statistical approach. From sequence components, word frequency information of the sequence is estimated. By investigating the relationship between estimated frequency information and actual word frequency, the characteristics of the sequence are numerically represented. The phylogenetic tree and the sequence classification of mammalian sequences are provided to reveal the remarkable performance of our statistical algorithm.
Collapse
|
37
|
Bagnato C, Have AT, Prados MB, Beligni MV. Computational Functional Analysis of Lipid Metabolic Enzymes. Methods Mol Biol 2017; 1609:195-216. [PMID: 28660584 DOI: 10.1007/978-1-4939-6996-8_17] [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] [Indexed: 06/07/2023]
Abstract
The computational analysis of enzymes that participate in lipid metabolism has both common and unique challenges when compared to the whole protein universe. Some of the hurdles that interfere with the functional annotation of lipid metabolic enzymes that are common to other pathways include the definition of proper starting datasets, the construction of reliable multiple sequence alignments, the definition of appropriate evolutionary models, and the reconstruction of phylogenetic trees with high statistical support, particularly for large datasets. Most enzymes that take part in lipid metabolism belong to complex superfamilies with many members that are not involved in lipid metabolism. In addition, some enzymes that do not have sequence similarity catalyze similar or even identical reactions. Some of the challenges that, albeit not unique, are more specific to lipid metabolism refer to the high compartmentalization of the routes, the catalysis in hydrophobic environments and, related to this, the function near or in biological membranes.In this work, we provide guidelines intended to assist in the proper functional annotation of lipid metabolic enzymes, based on previous experiences related to the phospholipase D superfamily and the annotation of the triglyceride synthesis pathway in algae. We describe a pipeline that starts with the definition of an initial set of sequences to be used in similarity-based searches and ends in the reconstruction of phylogenies. We also mention the main issues that have to be taken into consideration when using tools to analyze subcellular localization, hydrophobicity patterns, or presence of transmembrane domains in lipid metabolic enzymes.
Collapse
Affiliation(s)
- Carolina Bagnato
- Instituto de Energía y Desarrollo Sustentable-Comisión Nacional de Energía Atómica, Centro Atómico Bariloche, S. C. de Bariloche, 8400, Río Negro, Argentina
| | - Arjen Ten Have
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar del Plata, 7600, Argentina
| | - María B Prados
- Instituto de Energía y Desarrollo Sustentable-Comisión Nacional de Energía Atómica, Centro Atómico Bariloche, S. C. de Bariloche, 8400, Río Negro, Argentina
| | - María V Beligni
- Instituto de Investigaciones Biológicas (IIB-CONICET-UNMdP), Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, Mar del Plata, 7600, Argentina.
| |
Collapse
|
38
|
Iwai S, Weinmaier T, Schmidt BL, Albertson DG, Poloso NJ, Dabbagh K, DeSantis TZ. Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes. PLoS One 2016; 11:e0166104. [PMID: 27820856 PMCID: PMC5098786 DOI: 10.1371/journal.pone.0166104] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/07/2016] [Indexed: 01/30/2023] Open
Abstract
Functional analysis of a clinical microbiome facilitates the elucidation of mechanisms by which microbiome perturbation can cause a phenotypic change in the patient. The direct approach for the analysis of the functional capacity of the microbiome is via shotgun metagenomics. An inexpensive method to estimate the functional capacity of a microbial community is through collecting 16S rRNA gene profiles then indirectly inferring the abundance of functional genes. This inference approach has been implemented in the PICRUSt and Tax4Fun software tools. However, those tools have important limitations since they rely on outdated functional databases and uncertain phylogenetic trees and require very specific data pre-processing protocols. Here we introduce Piphillin, a straightforward algorithm independent of any proposed phylogenetic tree, leveraging contemporary functional databases and not obliged to any singular data pre-processing protocol. When all three inference tools were evaluated against actual shotgun metagenomics, Piphillin was superior in predicting gene composition in human clinical samples compared to both PICRUSt and Tax4Fun (p<0.01 and p<0.001, respectively) and Piphillin’s ability to predict disease associations with specific gene orthologs exhibited a 15% increase in balanced accuracy compared to PICRUSt. From laboratory animal samples, no performance advantage was observed for any one of the tools over the others and for environmental samples all produced unsatisfactory predictions. Our results demonstrate that functional inference using the direct method implemented in Piphillin is preferable for clinical biospecimens. Piphillin is publicly available for academic use at http://secondgenome.com/Piphillin.
Collapse
Affiliation(s)
- Shoko Iwai
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Thomas Weinmaier
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Brian L. Schmidt
- Bluestone Center for Clinical Research and the Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America
| | - Donna G. Albertson
- Bluestone Center for Clinical Research and the Department of Oral and Maxillofacial Surgery, New York University College of Dentistry, New York, New York, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
| | - Neil J. Poloso
- Research and External Scientific Innovation Department, Allergan PLC, Irvine, California, United States of America
| | - Karim Dabbagh
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
| | - Todd Z. DeSantis
- Informatics Department, Second Genome Inc., South San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
39
|
Rodriguez Y, Gonzalez-Mendez RR, Cadilla CL. Evolution of the Twist Subfamily Vertebrate Proteins: Discovery of a Signature Motif and Origin of the Twist1 Glycine-Rich Motifs in the Amino-Terminus Disordered Domain. PLoS One 2016; 11:e0161029. [PMID: 27556926 PMCID: PMC4996418 DOI: 10.1371/journal.pone.0161029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 07/28/2016] [Indexed: 11/18/2022] Open
Abstract
Twist proteins belong to the basic helix-loop-helix (bHLH) family of multifunctional transcriptional factors. These factors are known to use domains other than the common bHLH in protein-protein interactions. There has been much work characterizing the bHLH domain and the C-terminus in protein-protein interactions but despite a few attempts more focus is needed at the N-terminus. Since the region of highest diversity in Twist proteins is the N-terminus, we analyzed the conservation of this region in different vertebrate Twist proteins and study the sequence differences between Twist1 and Twist2 with emphasis on the glycine-rich regions found in Twist1. We found a highly conserved sequence motif in all Twist1 (SSSPVSPADDSLSNSEEE) and Twist2 (SSSPVSPVDSLGTSEEE) mammalian species with unknown function. Through sequence comparison we demonstrate that the Twist protein family ancestor was “Twist2-like” and the two glycine-rich regions found in Twist1 sequences were acquired late in evolution, apparently not at the same time. The second glycine-rich region started developing first in the fish vertebrate group, while the first glycine region arose afterwards within the reptiles. Disordered domain and secondary structure predictions showed that the amino acid sequence and disorder feature found at the N-terminus is highly evolutionary conserved and could be a functional site that interacts with other proteins. Detailed examination of the glycine-rich regions in the N-terminus of Twist1 demonstrate that the first region is completely aliphatic while the second region contains some polar residues that could be subject to post-translational modification. Phylogenetic and sequence space analysis showed that the Twist1 subfamily is the result of a gene duplication during Twist2 vertebrate fish evolution, and has undergone more evolutionary drift than Twist2. We identified a new signature motif that is characteristic of each Twist paralog and identified important residues within this motif that can be used to distinguish between these two paralogs, which will help reduce Twist1 and Twist2 sequence annotation errors in public databases.
Collapse
Affiliation(s)
- Yacidzohara Rodriguez
- Department of Biochemistry, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico, United States of America
| | - Ricardo R. Gonzalez-Mendez
- Department of Radiological Sciences, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico, United States of America
| | - Carmen L. Cadilla
- Department of Biochemistry, School of Medicine, University of Puerto Rico, San Juan, Puerto Rico, United States of America
- * E-mail:
| |
Collapse
|
40
|
Bromberg R, Grishin NV, Otwinowski Z. Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer. PLoS Comput Biol 2016; 12:e1004985. [PMID: 27336403 PMCID: PMC4918981 DOI: 10.1371/journal.pcbi.1004985] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 05/10/2016] [Indexed: 01/20/2023] Open
Abstract
Advances in sequencing have generated a large number of complete genomes. Traditionally, phylogenetic analysis relies on alignments of orthologs, but defining orthologs and separating them from paralogs is a complex task that may not always be suited to the large datasets of the future. An alternative to traditional, alignment-based approaches are whole-genome, alignment-free methods. These methods are scalable and require minimal manual intervention. We developed SlopeTree, a new alignment-free method that estimates evolutionary distances by measuring the decay of exact substring matches as a function of match length. SlopeTree corrects for horizontal gene transfer, for composition variation and low complexity sequences, and for branch-length nonlinearity caused by multiple mutations at the same site. We tested SlopeTree on 495 bacteria, 73 archaea, and 72 strains of Escherichia coli and Shigella. We compared our trees to the NCBI taxonomy, to trees based on concatenated alignments, and to trees produced by other alignment-free methods. The results were consistent with current knowledge about prokaryotic evolution. We assessed differences in tree topology over different methods and settings and found that the majority of bacteria and archaea have a core set of proteins that evolves by descent. In trees built from complete genomes rather than sets of core genes, we observed some grouping by phenotype rather than phylogeny, for instance with a cluster of sulfur-reducing thermophilic bacteria coming together irrespective of their phyla. The source-code for SlopeTree is available at: http://prodata.swmed.edu/download/pub/slopetree_v1/slopetree.tar.gz. Due to their lack of distinct morphological features, bacteria and archaea were extremely difficult to classify until technology was developed to obtain their DNA sequences; these sequences could then be compared to estimate evolutionary relationships. Now, due to technological advances, there is a flood of available sequences from a wide variety of organisms. These advances have spurred the development of algorithms which can estimate evolutionary relationships using whole genomes, in contrast to the more traditional methods which used single genes earlier and now typically use groups of conserved genes. However, there are many challenges when attempting to infer evolutionary relationships, in particular horizontal gene transfer, where DNA is transferred from one organism to another, resulting in an organism’s genome containing DNA that does not reflect its evolution by descent. We developed a new whole-genome method for estimating evolutionary distances which identifies and corrects for horizontal transfer. We found that for SlopeTree and all other whole-genome methods we applied, horizontal transfer causes some evolutionary distances to be grossly underestimated, and that our correction corrects for this.
Collapse
Affiliation(s)
- Raquel Bromberg
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Nick V. Grishin
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
| | - Zbyszek Otwinowski
- Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, Texas, United States of America
- * E-mail:
| |
Collapse
|
41
|
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.
Collapse
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
| |
Collapse
|
42
|
Floden EW, Tommaso PD, Chatzou M, Magis C, Notredame C, Chang JM. PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic Acids Res 2016; 44:W339-43. [PMID: 27106060 PMCID: PMC4987888 DOI: 10.1093/nar/gkw300] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/11/2016] [Indexed: 01/11/2023] Open
Abstract
The PSI/TM-Coffee web server performs multiple sequence alignment (MSA) of proteins by combining homology extension with a consistency based alignment approach. Homology extension is performed with Position Specific Iterative (PSI) BLAST searches against a choice of redundant and non-redundant databases. The main novelty of this server is to allow databases of reduced complexity to rapidly perform homology extension. This server also gives the possibility to use transmembrane proteins (TMPs) reference databases to allow even faster homology extension on this important category of proteins. Aside from an MSA, the server also outputs topological prediction of TMPs using the HMMTOP algorithm. Previous benchmarking of the method has shown this approach outperforms the most accurate alignment methods such as MSAProbs, Kalign, PROMALS, MAFFT, ProbCons and PRALINE™. The web server is available at http://tcoffee.crg.cat/tmcoffee.
Collapse
Affiliation(s)
- Evan W Floden
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Paolo D Tommaso
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Maria Chatzou
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Cedrik Magis
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Cedric Notredame
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona 08003, Spain
| | - Jia-Ming Chang
- Department of Computer Science, National Chengchi University, Taipei 11605, Taiwan
| |
Collapse
|
43
|
Magomedova Z, Grecu A, Sensen CW, Schwab H, Heidinger P. Characterization of two novel alcohol short-chain dehydrogenases/reductases from Ralstonia eutropha H16 capable of stereoselective conversion of bulky substrates. J Biotechnol 2016; 221:78-90. [DOI: 10.1016/j.jbiotec.2016.01.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/20/2016] [Accepted: 01/21/2016] [Indexed: 12/19/2022]
|
44
|
Kronenberg ZN, Osborne EJ, Cone KR, Kennedy BJ, Domyan ET, Shapiro MD, Elde NC, Yandell M. Wham: Identifying Structural Variants of Biological Consequence. PLoS Comput Biol 2015; 11:e1004572. [PMID: 26625158 PMCID: PMC4666669 DOI: 10.1371/journal.pcbi.1004572] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 09/30/2015] [Indexed: 11/22/2022] Open
Abstract
Existing methods for identifying structural variants (SVs) from short read datasets are inaccurate. This complicates disease-gene identification and efforts to understand the consequences of genetic variation. In response, we have created Wham (Whole-genome Alignment Metrics) to provide a single, integrated framework for both structural variant calling and association testing, thereby bypassing many of the difficulties that currently frustrate attempts to employ SVs in association testing. Here we describe Wham, benchmark it against three other widely used SV identification tools–Lumpy, Delly and SoftSearch–and demonstrate Wham’s ability to identify and associate SVs with phenotypes using data from humans, domestic pigeons, and vaccinia virus. Wham and all associated software are covered under the MIT License and can be freely downloaded from github (https://github.com/zeeev/wham), with documentation on a wiki (http://zeeev.github.io/wham/). For community support please post questions to https://www.biostars.org/.
Collapse
Affiliation(s)
- Zev N. Kronenberg
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Edward J. Osborne
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, United States of America
| | - Kelsey R. Cone
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Brett J. Kennedy
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, United States of America
| | - Eric T. Domyan
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Michael D. Shapiro
- Department of Biology, University of Utah, Salt Lake City, Utah, United States of America
| | - Nels C. Elde
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
| | - Mark Yandell
- Department of Human Genetics, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah, United States of America
- Utah Center for Genetic Discovery, University of Utah, Salt Lake City, Utah, United States of America
- * E-mail:
| |
Collapse
|
45
|
Chatzou M, Magis C, Chang JM, Kemena C, Bussotti G, Erb I, Notredame C. Multiple sequence alignment modeling: methods and applications. Brief Bioinform 2015; 17:1009-1023. [PMID: 26615024 DOI: 10.1093/bib/bbv099] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 10/16/2015] [Indexed: 12/20/2022] Open
Abstract
This review provides an overview on the development of Multiple sequence alignment (MSA) methods and their main applications. It is focused on progress made over the past decade. The three first sections review recent algorithmic developments for protein, RNA/DNA and genomic alignments. The fourth section deals with benchmarks and explores the relationship between empirical and simulated data, along with the impact on method developments. The last part of the review gives an overview on available MSA local reliability estimators and their dependence on various algorithmic properties of available methods.
Collapse
|
46
|
Wright ES. DECIPHER: harnessing local sequence context to improve protein multiple sequence alignment. BMC Bioinformatics 2015; 16:322. [PMID: 26445311 PMCID: PMC4595117 DOI: 10.1186/s12859-015-0749-z] [Citation(s) in RCA: 206] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 09/23/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Alignment of large and diverse sequence sets is a common task in biological investigations, yet there remains considerable room for improvement in alignment quality. Multiple sequence alignment programs tend to reach maximal accuracy when aligning only a few sequences, and then diminish steadily as more sequences are added. This drop in accuracy can be partly attributed to a build-up of error and ambiguity as more sequences are aligned. Most high-throughput sequence alignment algorithms do not use contextual information under the assumption that sites are independent. This study examines the extent to which local sequence context can be exploited to improve the quality of large multiple sequence alignments. RESULTS Two predictors based on local sequence context were assessed: (i) single sequence secondary structure predictions, and (ii) modulation of gap costs according to the surrounding residues. The results indicate that context-based predictors have appreciable information content that can be utilized to create more accurate alignments. Furthermore, local context becomes more informative as the number of sequences increases, enabling more accurate protein alignments of large empirical benchmarks. These discoveries became the basis for DECIPHER, a new context-aware program for sequence alignment, which outperformed other programs on large sequence sets. CONCLUSIONS Predicting secondary structure based on local sequence context is an efficient means of breaking the independence assumption in alignment. Since secondary structure is more conserved than primary sequence, it can be leveraged to improve the alignment of distantly related proteins. Moreover, secondary structure predictions increase in accuracy as more sequences are used in the prediction. This enables the scalable generation of large sequence alignments that maintain high accuracy even on diverse sequence sets. The DECIPHER R package and source code are freely available for download at DECIPHER.cee.wisc.edu and from the Bioconductor repository.
Collapse
Affiliation(s)
- Erik S Wright
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, 53715, USA. .,Wisconsin Institute for Discovery, University of Wisconsin-Madison, 330 N. Orchard St., Madison, WI, 53715, USA.
| |
Collapse
|
47
|
Ortuño FM, Valenzuela O, Prieto B, Saez-Lara MJ, Torres C, Pomares H, Rojas I. Comparing different machine learning and mathematical regression models to evaluate multiple sequence alignments. Neurocomputing 2015. [DOI: 10.1016/j.neucom.2015.01.080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
48
|
Structural basis for 2'-5'-oligoadenylate binding and enzyme activity of a viral RNase L antagonist. J Virol 2015; 89:6633-45. [PMID: 25878106 DOI: 10.1128/jvi.00701-15] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED Synthesis of 2'-5'-oligoadenylates (2-5A) by oligoadenylate synthetase (OAS) is an important innate cellular response that limits viral replication by activating the latent cellular RNase, RNase L, to degrade single-stranded RNA. Some rotaviruses and coronaviruses antagonize the OAS/RNase L pathway through the activity of an encoded 2H phosphoesterase domain that cleaves 2-5A. These viral 2H phosphoesterases are phylogenetically related to the cellular A kinase anchoring protein 7 (AKAP7) and share a core structure and an active site that contains two well-defined HΦ(S/T)Φ (where Φ is a hydrophobic residue) motifs, but their mechanism of substrate binding is unknown. Here, we report the structures of a viral 2H phosphoesterase, the C-terminal domain (CTD) of the group A rotavirus (RVA) VP3 protein, both alone and in complex with 2-5A. The domain forms a compact fold, with a concave β-sheet that contains the catalytic cleft, but it lacks two α-helical regions and two β-strands observed in AKAP7 and other 2H phosphoesterases. The cocrystal structure shows significant conformational changes in the R loop upon ligand binding. Bioinformatics and biochemical analyses reveal that conserved residues and residues required for catalytic activity and substrate binding comprise the catalytic motifs and a region on one side of the binding cleft. We demonstrate that the VP3 CTD of group B rotavirus, but not that of group G, cleaves 2-5A. These findings suggest that the VP3 CTD is a streamlined version of a 2H phosphoesterase with a ligand-binding mechanism that is shared among 2H phosphodiesterases that cleave 2-5A. IMPORTANCE The C-terminal domain (CTD) of rotavirus VP3 is a 2H phosphoesterase that cleaves 2'-5'-oligoadenylates (2-5A), potent activators of an important innate cellular antiviral pathway. 2H phosphoesterase superfamily proteins contain two conserved catalytic motifs and a proposed core structure. Here, we present structures of a viral 2H phosphoesterase, the rotavirus VP3 CTD, alone and in complex with its substrate, 2-5A. The domain lacks two α-helical regions and β-strands present in other 2H phosphoesterases. A loop of the protein undergoes significant structural changes upon substrate binding. Together with our bioinformatics and biochemical findings, the crystal structures suggest that the RVA VP3 CTD domain is a streamlined version of a cellular enzyme that shares a ligand-binding mechanism with other 2H phosphodiesterases that cleave 2-5A but differs from those of 2H phosphodiesterases that cleave other substrates. These findings may aid in the future design of antivirals targeting viral phosphodiesterases with cleavage specificity for 2-5A.
Collapse
|
49
|
Rojas M, Vasconcelos G, Dever TE. An eIF2α-binding motif in protein phosphatase 1 subunit GADD34 and its viral orthologs is required to promote dephosphorylation of eIF2α. Proc Natl Acad Sci U S A 2015; 112:E3466-75. [PMID: 26100893 PMCID: PMC4500263 DOI: 10.1073/pnas.1501557112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Transient protein synthesis inhibition, mediated by phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α), is an important protective mechanism cells use during stress conditions. Following relief of the stress, the growth arrest and DNA damage-inducible protein GADD34 associates with the broadly acting serine/threonine protein phosphatase 1 (PP1) to dephosphorylate eIF2α. Whereas the PP1-binding motif on GADD34 has been defined, it remains to be determined how GADD34 directs PP1 to specifically dephosphorylate eIF2α. In this report, we map a novel eIF2α-binding motif to the C terminus of GADD34 in a region distinct from where PP1 binds to GADD34. This motif is characterized by the consensus sequence Rx[Gnl]x(1-2)Wxxx[Arlv]x[Dn][Rg]xRFxx[Rlvk][Ivc], where capital letters are preferred and x is any residue. Point mutations altering the eIF2α-binding motif impair the ability of GADD34 to interact with eIF2α, promote eIF2α dephosphorylation, and suppress PKR toxicity in yeast. Interestingly, this eIF2α-docking motif is conserved among viral orthologs of GADD34, and is necessary for the proteins produced by African swine fever virus, Canarypox virus, and Herpes simplex virus to promote eIF2α dephosphorylation. Taken together, these data indicate that GADD34 and its viral orthologs direct specific dephosphorylation of eIF2α by interacting with both PP1 and eIF2α through independent binding motifs.
Collapse
Affiliation(s)
- Margarito Rojas
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Gabriel Vasconcelos
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| | - Thomas E Dever
- Laboratory of Gene Regulation and Development, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892
| |
Collapse
|
50
|
Yin C, Yau SST. An improved model for whole genome phylogenetic analysis by Fourier transform. J Theor Biol 2015; 382:99-110. [PMID: 26151589 DOI: 10.1016/j.jtbi.2015.06.033] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/19/2015] [Accepted: 06/22/2015] [Indexed: 01/07/2023]
Abstract
DNA sequence similarity comparison is one of the major steps in computational phylogenetic studies. The sequence comparison of closely related DNA sequences and genomes is usually performed by multiple sequence alignments (MSA). While the MSA method is accurate for some types of sequences, it may produce incorrect results when DNA sequences undergone rearrangements as in many bacterial and viral genomes. It is also limited by its computational complexity for comparing large volumes of data. Previously, we proposed an alignment-free method that exploits the full information contents of DNA sequences by Discrete Fourier Transform (DFT), but still with some limitations. Here, we present a significantly improved method for the similarity comparison of DNA sequences by DFT. In this method, we map DNA sequences into 2-dimensional (2D) numerical sequences and then apply DFT to transform the 2D numerical sequences into frequency domain. In the 2D mapping, the nucleotide composition of a DNA sequence is a determinant factor and the 2D mapping reduces the nucleotide composition bias in distance measure, and thus improving the similarity measure of DNA sequences. To compare the DFT power spectra of DNA sequences with different lengths, we propose an improved even scaling algorithm to extend shorter DFT power spectra to the longest length of the underlying sequences. After the DFT power spectra are evenly scaled, the spectra are in the same dimensionality of the Fourier frequency space, then the Euclidean distances of full Fourier power spectra of the DNA sequences are used as the dissimilarity metrics. The improved DFT method, with increased computational performance by 2D numerical representation, can be applicable to any DNA sequences of different length ranges. We assess the accuracy of the improved DFT similarity measure in hierarchical clustering of different DNA sequences including simulated and real datasets. The method yields accurate and reliable phylogenetic trees and demonstrates that the improved DFT dissimilarity measure is an efficient and effective similarity measure of DNA sequences. Due to its high efficiency and accuracy, the proposed DFT similarity measure is successfully applied on phylogenetic analysis for individual genes and large whole bacterial genomes.
Collapse
Affiliation(s)
- Changchuan Yin
- Department of Mathematics, Statistics and Computer Science, The University of Illinois at Chicago, Chicago, IL 60607-7045, USA
| | - Stephen S-T Yau
- Department of Mathematical Sciences, Tsinghua University, Beijing 100084, China.
| |
Collapse
|