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Mac Donagh J, Marchesini A, Spiga A, Fallico MJ, Arrías PN, Monzon AM, Vagiona AC, Gonçalves-Kulik M, Mier P, Andrade-Navarro MA. Structured Tandem Repeats in Protein Interactions. Int J Mol Sci 2024; 25:2994. [PMID: 38474241 DOI: 10.3390/ijms25052994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Tandem repeats (TRs) in protein sequences are consecutive, highly similar sequence motifs. Some types of TRs fold into structural units that pack together in ensembles, forming either an (open) elongated domain or a (closed) propeller, where the last unit of the ensemble packs against the first one. Here, we examine TR proteins (TRPs) to see how their sequence, structure, and evolutionary properties favor them for a function as mediators of protein interactions. Our observations suggest that TRPs bind other proteins using large, structured surfaces like globular domains; in particular, open-structured TR ensembles are favored by flexible termini and the possibility to tightly coil against their targets. While, intuitively, open ensembles of TRs seem prone to evolve due to their potential to accommodate insertions and deletions of units, these evolutionary events are unexpectedly rare, suggesting that they are advantageous for the emergence of the ancestral sequence but are early fixed. We hypothesize that their flexibility makes it easier for further proteins to adapt to interact with them, which would explain their large number of protein interactions. We provide insight into the properties of open TR ensembles, which make them scaffolds for alternative protein complexes to organize genes, RNA and proteins.
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Affiliation(s)
- Juan Mac Donagh
- Science and Technology Department, National University of Quilmes, Bernal B1876, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Abril Marchesini
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
- Biotechnology and Molecular Biology Institute (IBBM, UNLP-CONICET), Faculty of Exact Sciences, University of La Plata, La Plata 1900, Argentina
| | - Agostina Spiga
- Science and Technology Department, National University of Quilmes, Bernal B1876, Argentina
- National Scientific and Technical Research Council (CONICET), Buenos Aires C1033AAJ, Argentina
| | - Maximiliano José Fallico
- Laboratory of Bioactive Compound Research and Development, Faculty of Exact Sciences, University of La Plata, La Plata 1900, Argentina
| | - Paula Nazarena Arrías
- Department of Biomedical Sciences, University of Padova, Via U. Bassi 58/b, 35121 Padova, Italy
| | - Alexander Miguel Monzon
- Department of Information Engineering, University of Padova, Via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Aimilia-Christina Vagiona
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Mariane Gonçalves-Kulik
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
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2
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Balakrishnan S, Bhasker R, Ramasamy Y, Dev SA. Genome-wide analysis of cellulose synthase gene superfamily in Tectona grandis L.f. 3 Biotech 2024; 14:86. [PMID: 38385141 PMCID: PMC10876501 DOI: 10.1007/s13205-024-03927-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 01/08/2024] [Indexed: 02/23/2024] Open
Abstract
This study aimed to explore Cellulose synthase gene superfamily of teak, and its evolutionary relationship with homologous genes of other woody species. The incidence of evolutionary events like gene duplication and gene loss, influence of the selection pressure, and consequent adaptive functional divergence of the duplicated TgCes gene were assessed alongside it's role in wood coloration. This study identified 39 full-length non-redundant proteins belonging to CesA and Csl gene families. TgCesA and TgCsl proteins with Cellulose synthase domain repeats indicated tandem gene duplication and probable genetic variability, enabling local adaptation. Further, multi-domain protein (MYB-like DNA-binding domain and CesA domain) with maximum introns was also identified indicating gene fusion and formation of complex protein with novel functions. Phylogenetic analysis grouped the genes into seven subfamilies (CesA, CslA, CslC, CslD, CslE, CslG, and CslM) with each undergoing gene duplication and loss along their evolutionary history. Post-species gene duplications and probable neofunctionalization were identified in TgCesA and TgCsl gene families. Each subfamily was found to be under strong purifying selection with a few or no sites under positive selection. Functional divergence analysis further revealed site-specific selective constraints in CesA and Csl genes of the teak Cellulose synthase gene family. Furthermore, protein-protein interaction network analysis identified co-expression of Cellulose synthase gene with flavonoid 3',5'-hydroxylase (F3'5'H, CYP75A), involved in the biosynthesis of xylem anthocyanin compounds, probably responsible for wood coloration. This study thus offers a foundation for future research in wood formation and wood property traits specific to teak and its provenances. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-03927-6.
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Affiliation(s)
- Swathi Balakrishnan
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
- Cochin University of Science and Technology, Kochi, Kerala India
| | - Reshma Bhasker
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
- Cochin University of Science and Technology, Kochi, Kerala India
| | - Yasodha Ramasamy
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, 641002 India
| | - Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala 680653 India
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3
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Palit S, Bhide AJ, Mohanasundaram B, Pala M, Banerjee AK. Peptides from conserved tandem direct repeats of SHORT-LEAF regulate gametophore development in moss P. patens. PLANT PHYSIOLOGY 2023; 194:434-455. [PMID: 37770073 DOI: 10.1093/plphys/kiad515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/29/2023] [Accepted: 09/06/2023] [Indexed: 10/03/2023]
Abstract
Tandem direct repeat (TDR)-containing proteins, present across all domains of life, play crucial roles in plant development and defense mechanisms. Previously, we identified that disruption of a bryophyte-specific protein family, SHORT-LEAF (SHLF), possessing the longest reported TDRs, is the cause of the shlf mutant phenotype in Physcomitrium patens. shlf exhibits reduced apical dominance, altered auxin distribution, and 2-fold shorter leaves. However, the molecular role of SHLF was unclear due to the absence of known conserved domains. Through a series of protein domain deletion analyses, here, we demonstrate the importance of the signal peptide and the conserved TDRs and report a minimal functional protein (miniSHLF) containing the N-terminal signal peptide and first two TDRs (N-TDR1-2). We also demonstrate that SHLF behaves as a secretory protein and that the TDRs contribute to a pool of secreted peptides essential for SHLF function. Further, we identified that the mutant secretome lacks SHLF peptides, which are abundant in WT and miniSHLF secretomes. Interestingly, shlf mutants supplemented with the secretome or peptidome from WT or miniSHLF showed complete or partial phenotypic recovery. Transcriptomic and metabolomic analyses revealed that shlf displays an elevated stress response, including high ROS activity and differential accumulation of genes and metabolites involved in the phenylpropanoid pathway, which may affect auxin distribution. The TDR-specific synthetic peptide SHLFpep3 (INIINAPLQGFKIA) also rescued the mutant phenotypes, including the altered auxin distribution, in a dosage-dependent manner and restored the mutant's stress levels. Our study shows that secretory SHLF peptides derived from conserved TDRs regulate moss gametophore development.
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Affiliation(s)
- Shirsa Palit
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Amey J Bhide
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | | | - Madhusmita Pala
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Anjan K Banerjee
- Department of Biology, Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
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4
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Monzon AM, Arrías PN, Elofsson A, Mier P, Andrade-Navarro MA, Bevilacqua M, Clementel D, Bateman A, Hirsh L, Fornasari MS, Parisi G, Piovesan D, Kajava AV, Tosatto SCE. A STRP-ed definition of Structured Tandem Repeats in Proteins. J Struct Biol 2023; 215:108023. [PMID: 37652396 DOI: 10.1016/j.jsb.2023.108023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 07/31/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
Tandem Repeat Proteins (TRPs) are a class of proteins with repetitive amino acid sequences that have been studied extensively for over two decades. Different features at the level of sequence, structure, function and evolution have been attributed to them by various authors. And yet many of its salient features appear only when looking at specific subclasses of protein tandem repeats. Here, we attempt to rationalize the existing knowledge on Tandem Repeat Proteins (TRPs) by pointing out several dichotomies. The emerging picture is more nuanced than generally assumed and allows us to draw some boundaries of what is not a "proper" TRP. We conclude with an operational definition of a specific subset, which we have denominated STRPs (Structural Tandem Repeat Proteins), which separates a subclass of tandem repeats with distinctive features from several other less well-defined types of repeats. We believe that this definition will help researchers in the field to better characterize the biological meaning of this large yet largely understudied group of proteins.
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Affiliation(s)
- Alexander Miguel Monzon
- Dept. of Information Engineering, University of Padova, via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Paula Nazarena Arrías
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Arne Elofsson
- Dept. of Biochemistry and Biophysics and Science for Life Laboratory, Stockholm University, Tomtebodavägen 23, 171 21 Solna, Sweden
| | - Pablo Mier
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Institute of Organismic and Molecular Evolution, Faculty of Biology, Johannes Gutenberg University of Mainz, Hanns-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Martina Bevilacqua
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Damiano Clementel
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Layla Hirsh
- Dept. of Engineering, Faculty of Science and Engineering, Pontifical Catholic University of Peru, Av. Universitaria 1801 San Miguel, Lima 32, Lima, Peru
| | - Maria Silvina Fornasari
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Gustavo Parisi
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, CONICET, Bernal, Buenos Aires, Argentina
| | - Damiano Piovesan
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France
| | - Silvio C E Tosatto
- Dept. of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy.
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5
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Li G, Dang J, Pan J, Liu J, Peng T, Chen G, Wang R, Hu S, Li X, Hu X. Genome-Wide Analysis of the DC1 Domain Protein Gene Family in Tomatoes under Abiotic Stress. Int J Mol Sci 2023; 24:16994. [PMID: 38069320 PMCID: PMC10707348 DOI: 10.3390/ijms242316994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
DC1 (Divergent C1) domain proteins are a new class of proteins that have been discovered in recent years, which play an important role in plant growth, development, and stress response. In order to better study the distribution and function of DC1 domain proteins in tomatoes, a genome-wide identification was conducted. It was found that there are twenty-one DC1 domain protein genes distributed on nine chromosomes of tomatoes, named SlCHP1-21. Phylogenetic analysis shows that twenty-one SlCHP genes are divided into six subfamilies. Most of the SlCHP genes in tomatoes have no or very short introns. All SlCHP proteins, with the exception of SlCHP8 and SlCHP17, contain variable amounts of C1 domain. Analysis of the SlCHP gene promoter sequence revealed multiple cis-elements responsive to plant stress. qRT-CR analysis showed that most members of SlCHP gene expressed in the roots. The SlCHP11, 13, 16, 17, and SlCHP20 genes showed specific responses to high temperature, low temperature, salt, and drought stress. In addition, the subcellular localization and interaction proteins of SlCHP were analyzed and predicted. Together, these results provides a theoretical basis for further exploration of the function and mechanism of the SlCHP gene in tomatoes.
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Affiliation(s)
- Guobin Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Jiao Dang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Jiaqi Pan
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Jingyi Liu
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
| | - Tieli Peng
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Guo Chen
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
| | - Rongqun Wang
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
| | - Songshen Hu
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Xiaojing Li
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
| | - Xiaohui Hu
- College of Horticulture, Northwest A&F University, Yangling 712100, China; (G.L.); (J.D.); (J.P.); (J.L.); (T.P.); (G.C.); (R.W.); (S.H.); (X.L.)
- Key Laboratory of Protected Horticultural Engineering in Northwest, Ministry of Agriculture, Yangling 712100, China
- Shaanxi Protected Agriculture Research Centre, Yangling 712100, China
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6
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Muslimov A, Tereshchenko V, Shevyrev D, Rogova A, Lepik K, Reshetnikov V, Ivanov R. The Dual Role of the Innate Immune System in the Effectiveness of mRNA Therapeutics. Int J Mol Sci 2023; 24:14820. [PMID: 37834268 PMCID: PMC10573212 DOI: 10.3390/ijms241914820] [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: 07/13/2023] [Revised: 09/24/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Advances in molecular biology have revolutionized the use of messenger RNA (mRNA) as a therapeutic. The concept of nucleic acid therapy with mRNA originated in 1990 when Wolff et al. reported successful expression of proteins in target organs by direct injection of either plasmid DNA or mRNA. It took decades to bring the transfection efficiency of mRNA closer to that of DNA. The next few decades were dedicated to turning in vitro-transcribed (IVT) mRNA from a promising delivery tool for gene therapy into a full-blown therapeutic modality, which changed the biotech market rapidly. Hundreds of clinical trials are currently underway using mRNA for prophylaxis and therapy of infectious diseases and cancers, in regenerative medicine, and genome editing. The potential of IVT mRNA to induce an innate immune response favors its use for vaccination and immunotherapy. Nonetheless, in non-immunotherapy applications, the intrinsic immunostimulatory activity of mRNA directly hinders the desired therapeutic effect since it can seriously impair the target protein expression. Targeting the same innate immune factors can increase the effectiveness of mRNA therapeutics for some indications and decrease it for others, and vice versa. The review aims to present the innate immunity-related 'barriers' or 'springboards' that may affect the development of immunotherapies and non-immunotherapy applications of mRNA medicines.
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Affiliation(s)
- Albert Muslimov
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
- Laboratory of Nano- and Microencapsulation of Biologically Active Substances, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, 195251 St. Petersburg, Russia;
- RM Gorbacheva Research Institute, Pavlov University, L’va Tolstogo 6-8, 197022 St. Petersburg, Russia;
| | - Valeriy Tereshchenko
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
| | - Daniil Shevyrev
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
| | - Anna Rogova
- Laboratory of Nano- and Microencapsulation of Biologically Active Substances, Peter the Great St. Petersburg Polytechnic University, Polytechnicheskaya 29, 195251 St. Petersburg, Russia;
- Saint-Petersburg Chemical-Pharmaceutical University, Professora Popova 14, 197376 St. Petersburg, Russia
- School of Physics and Engineering, ITMO University, Lomonosova 9, 191002 St. Petersburg, Russia
| | - Kirill Lepik
- RM Gorbacheva Research Institute, Pavlov University, L’va Tolstogo 6-8, 197022 St. Petersburg, Russia;
| | - Vasiliy Reshetnikov
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Prospekt Akad. Lavrentyeva 10, 630090 Novosibirsk, Russia
| | - Roman Ivanov
- Scientific Center for Translational Medicine, Sirius University of Science and Technology, Olympic Ave 1, 354340 Sirius, Russia; (V.T.); (D.S.); (V.R.); (R.I.)
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7
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Arrías PN, Monzon AM, Clementel D, Mozaffari S, Piovesan D, Kajava AV, Tosatto SCE. The repetitive structure of DNA clamps: An overlooked protein tandem repeat. J Struct Biol 2023; 215:108001. [PMID: 37467824 DOI: 10.1016/j.jsb.2023.108001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/12/2023] [Accepted: 07/16/2023] [Indexed: 07/21/2023]
Abstract
Structured tandem repeats proteins (STRPs) are a specific kind of tandem repeat proteins characterized by a modular and repetitive three-dimensional structure arrangement. The majority of STRPs adopt solenoid structures, but with the increasing availability of experimental structures and high-quality predicted structural models, more STRP folds can be characterized. Here, we describe "Box repeats", an overlooked STRP fold present in the DNA sliding clamp processivity factors, which has eluded classification although structural data has been available since the late 1990s. Each Box repeat is a β⍺βββ module of about 60 residues, which forms a class V "beads-on-a-string" type STRP. The number of repeats present in processivity factors is organism dependent. Monomers of PCNA proteins in both Archaea and Eukarya have 4 repeats, while the monomers of bacterial beta-sliding clamps have 6 repeats. This new repeat fold has been added to the RepeatsDB database, which now provides structural annotation for 66 Box repeat proteins belonging to different organisms, including viruses.
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Affiliation(s)
- Paula Nazarena Arrías
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Alexander Miguel Monzon
- Department of Information Engineering, University of Padova, via Giovanni Gradenigo 6/B, 35131 Padova, Italy
| | - Damiano Clementel
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Soroush Mozaffari
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier (CRBM), UMR 5237 CNRS, Université Montpellier, 1919 Route de Mende, Cedex 5, 34293 Montpellier, France
| | - Silvio C E Tosatto
- Department of Biomedical Sciences, University of Padova, via U. Bassi 58/b, 35121 Padova, Italy.
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8
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Nowakowska AW, Wojciechowski JW, Szulc N, Kotulska M. The role of tandem repeats in bacterial functional amyloids. J Struct Biol 2023; 215:108002. [PMID: 37482232 DOI: 10.1016/j.jsb.2023.108002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration. However, recent discoveries showed that amyloid structure of a protein could also be beneficial and desired, e.g., to promote cell adhesion. Functional amyloids are proteins which differ in their characteristics from pathological amyloids, so that the fibril formation could be more under control of an organism. We propose that repeats in the sequence could regulate the aggregation propensity of these proteins. The inclusion of multiple symmetric interactions, due to the presence of the repeats, could be supporting and strengthening the desirable structural properties of functional amyloids. Our results show that tandem repeats in bacterial functional amyloids have a distinct characteristic. The pattern of repeats supports the appropriate level of fibril formation and better controllability of fibril stability. The repeats tend to be more imperfect, which attenuates excessive aggregation propensity. Their desired structure and function are also reinforced by their amino acid profile. Although in the study we focused on bacterial functional amyloids, due to their importance in biofilm formation, we propose that similar mechanisms could be employed in other functional amyloids which are designed by evolution to aggregate in a desirable manner, but not necessarily in pathological amyloids.
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Affiliation(s)
- Alicja W Nowakowska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
| | - Jakub W Wojciechowski
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland
| | - Natalia Szulc
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland; Wrocław University of Environmental and Life Sciences, Department of Physics and Biophysics, Poland; LPCT, CNRS, Universite de Lorraine, F-54000 Nancy, France
| | - Malgorzata Kotulska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
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9
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Oladzad A, Roy J, Mamidi S, Miklas PN, Lee R, Clevenger J, Myers Z, Korani W, McClean PE. Linked candidate genes of different functions for white mold resistance in common bean ( Phaseolus vulgaris L) are identified by multiple QTL mapping approaches. FRONTIERS IN PLANT SCIENCE 2023; 14:1233285. [PMID: 37583595 PMCID: PMC10425182 DOI: 10.3389/fpls.2023.1233285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/11/2023] [Indexed: 08/17/2023]
Abstract
White mold (WM) is a major disease in common bean (Phaseolus vulgaris L.), and its complex quantitative genetic control limits the development of WM resistant cultivars. WM2.2, one of the nine meta-QTL with a major effect on WM tolerance, explains up to 35% of the phenotypic variation and was previously mapped to a large genomic interval on Pv02. Our objective was to narrow the interval of this QTL using combined approach of classic QTL mapping and QTL-based bulk segregant analysis (BSA), and confirming those results with Khufu de novo QTL-seq. The phenotypic and genotypic data from two RIL populations, 'Raven'/I9365-31 (R31) and 'AN-37'/PS02-029C-20 (Z0726-9), were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing. The QTL physical interval was determined by considering overlapping interval of the identified QTL or peak region in both populations by three independent QTL mapping analyses. Our findings revealed that meta-QTL WM2.2 consists of three regions, WM2.2a (4.27-5.76 Mb; euchromatic), WM 2.2b (12.19 to 17.61 Mb; heterochromatic), and WM2.2c (23.01-25.74 Mb; heterochromatic) found in both populations. Gene models encoding for gibberellin 2-oxidase 8, pentatricopeptide repeat, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein (Phvul.002G09200) and LRR domain containing family proteins are potential candidate genes associated with WM2.2b resistance. Nine gene models encoding disease resistance protein [pathogenesis-related thaumatin superfamily protein and disease resistance-responsive (dirigent-like protein) family protein etc] found within the WM2.2c QTL interval are putative candidate genes. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b and WM2.2c regions trigger physiological resistance based on putative candidate genes.
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Affiliation(s)
- Atena Oladzad
- Genomics Data Scientist II, Sound Agriculture, Emeryville, CA, United States
| | - Jayanta Roy
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Sujan Mamidi
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Prosser, WA, United States
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Josh Clevenger
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Zachary Myers
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Walid Korani
- Hudson Alpha Institute for Biotechnology, Huntsville, AL, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Genomics, Phenomics, and Bioinformatics Program, North Dakota State University, Fargo, ND, United States
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10
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Annotation of Siberian Larch (Larix sibirica Ledeb.) Nuclear Genome—One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in Pinaceae. PLANTS 2022; 11:plants11152062. [PMID: 35956540 PMCID: PMC9370799 DOI: 10.3390/plants11152062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 11/17/2022]
Abstract
The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly. About 66% of the larch genome consists of highly repetitive elements (REs), with the likely wave of retrotransposons insertions into the larch genome estimated to occur 4–5 MYA. In total, 39,370 gene models were predicted, with 87% of them having homology to the Arabidopsis-annotated proteins and 78% having at least one GO term assignment. The current state of the genome annotations allows for the exploration of the gymnosperm and angiosperm species for relative gene abundance in different functional categories. Comparative analysis of functional gene categories across different angiosperm and gymnosperm species finds that the Siberian larch genome has an overabundance of genes associated with programmed cell death (PCD), autophagy, stress hormone biosynthesis and regulatory pathways; genes that may play important roles in seasonal senescence and stress response to extreme cold in larch. Despite being incomplete, the draft assemblies and annotations of the conifer genomes are at a point of development where they now represent a valuable source for further genomic, genetic and population studies.
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11
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Xu Z, He J, Tehseen Azhar M, Zhang Z, Fan S, Jiang X, Jia T, Shang H, Yuan Y. UDP-glucose pyrophosphorylase: genome-wide identification, expression and functional analyses in Gossypium hirsutum. PeerJ 2022; 10:e13460. [PMID: 35663522 PMCID: PMC9161816 DOI: 10.7717/peerj.13460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/27/2022] [Indexed: 01/14/2023] Open
Abstract
In this study, a total of 66 UDP-glucose pyrophosphorylase (UGP) (EC 2.7.7.9) genes were identified from the genomes of four cotton species, which are the members of Pfam glycosyltransferase family (PF01702) and catalyze the reaction between glucose-1-phosphate and UTP to produce UDPG. The analysis of evolutionary relationship, gene structure, and expression provides the basis for studies on function of UGP genes in cotton. The evolutionary tree and gene structure analysis revealed that the UGP gene family is evolutionarily conserved. Collinearity and Ka/Ks analysis indicated that amplification of UGP genes is due to repetitive crosstalk generating between new family genes, while being under strong selection pressure. The analysis of cis-acting elements exhibited that UGP genes play important role in cotton growth, development, abiotic and hormonal stresses. Six UGP genes that were highly expressed in cotton fiber at 15 DPA were screened by transcriptome data and qRT-PCR analysis. The addition of low concentrations of IAA and GA3 to ovule cultures revealed that energy efficiency promoted the development of ovules and fiber clusters, and qRT-PCR showed that expression of these six UGP genes was differentially increased. These results suggest that the UGP gene may play an important role in fiber development, and provides the opportunity to plant researchers to explore the mechanisms involve in fiber development in cotton.
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Affiliation(s)
- Zhongyang Xu
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Jiasen He
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Muhammad Tehseen Azhar
- Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
| | - Haihong Shang
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministryof Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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12
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Luo X, Chen S, Zhang Y. PlantRep: a database of plant repetitive elements. PLANT CELL REPORTS 2022; 41:1163-1166. [PMID: 34977976 PMCID: PMC9035001 DOI: 10.1007/s00299-021-02817-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/19/2021] [Indexed: 05/14/2023]
Abstract
We re-annotated repeats of 459 plant genomes and released a new database: PlantRep ( http://www.plantrep.cn/ ). PlantRep sheds lights of repeat evolution and provides fundamental data for deep exploration of genome.
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Affiliation(s)
- Xizhi Luo
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Shiyu Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Yu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
- School of Agriculture, Sun Yat-sen University, Shenzhen, 518107, China.
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13
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Wu C, Zuo D, Xiao S, Wang Q, Cheng H, Lv L, Zhang Y, Li P, Song G. Genome-Wide Identification and Characterization of GhCOMT Gene Family during Fiber Development and Verticillium Wilt Resistance in Cotton. PLANTS 2021; 10:plants10122756. [PMID: 34961226 PMCID: PMC8706182 DOI: 10.3390/plants10122756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/04/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022]
Abstract
Caffeic acid O-methyltransferases (COMTs) play an essential role in lignin synthesis procession, especially in the plant’s phenylalanine metabolic pathway. The content of COMT genes in cotton and the relationship between their expression patterns have not been studied clearly in cotton. In this study, we have identified 190 COMT genes in cotton, which were classified into three groups (I, II and III), and mapped on the cotton chromosomes. In addition, we found that 135 of the 190 COMT genes result from dispersed duplication (DSD) and whole-genome duplication (WGD), indicating that DSD and WGD were the main forces driving COMT gene expansion. The Ka/Ks analysis showed that GhCOMT43 and GhCOMT41 evolved from GaCOMT27 and GrCOMT14 through positive selection. The results of qRT-PCR showed that GhCOMT13, GhCOMT28, GhCOMT39 and GhCOMT55 were related to lignin content during the cotton fiber development. GhCOMT28, GhCOMT39, GhCOMT55, GhCOMT56 and GhCOMT57 responded to Verticillium Wilt (VW) and maybe related to VW resistance through lignin synthesis. Conclusively, this study found that GhCOMTs were highly expressed in the secondary wall thickening stage and VW. These results provide a clue for studying the functions of GhCOMTs in the development of cotton fiber and VW resistance and could lay a foundation for breeding cotton cultivates with higher quantity and high resistance to VW.
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Affiliation(s)
- Cuicui Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
- Cotton Research Institute, Shanxi Agricultural University, Yuncheng 044000, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
| | - Shuiping Xiao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
- Cotton Research Institute of Jiangxi Province, Jiujiang 332105, China
| | - Qiaolian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
| | - Limin Lv
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
| | - Youping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
| | - Pengbo Li
- Cotton Research Institute, Shanxi Agricultural University, Yuncheng 044000, China
- Correspondence: (P.L.); (G.S.); Tel.: +86-372-2562377 (P.L. & G.S.)
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China; (C.W.); (D.Z.); (S.X.); (Q.W.); (H.C.); (L.L.); (Y.Z.)
- Correspondence: (P.L.); (G.S.); Tel.: +86-372-2562377 (P.L. & G.S.)
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14
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Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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15
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Mohanasundaram B, Bhide AJ, Palit S, Chaturvedi G, Lingwan M, Masakapalli SK, Banerjee AK. The unique bryophyte-specific repeat-containing protein SHORT-LEAF regulates gametophore development in moss. PLANT PHYSIOLOGY 2021; 187:203-217. [PMID: 34618137 PMCID: PMC8418407 DOI: 10.1093/plphys/kiab261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/18/2021] [Indexed: 05/29/2023]
Abstract
Convergent evolution of shoot development across plant lineages has prompted numerous comparative genetic studies. Though functional conservation of gene networks governing flowering plant shoot development has been explored in bryophyte gametophore development, the role of bryophyte-specific genes remains unknown. Previously, we have reported Tnt1 insertional mutants of moss defective in gametophore development. Here, we report a mutant (short-leaf; shlf) having two-fold shorter leaves, reduced apical dominance, and low plasmodesmata frequency. UHPLC-MS/MS-based auxin quantification and analysis of soybean (Glycine max) auxin-responsive promoter (GH3:GUS) lines exhibited a striking differential auxin distribution pattern in the mutant gametophore. Whole-genome sequencing and functional characterization of candidate genes revealed that a novel bryophyte-specific gene (SHORT-LEAF; SHLF) is responsible for the shlf phenotype. SHLF represents a unique family of near-perfect tandem direct repeat (TDR)-containing proteins conserved only among mosses and liverworts, as evident from our phylogenetic analysis. Cross-complementation with a Marchantia homolog partially recovered the shlf phenotype, indicating possible functional specialization. The distinctive structure (longest known TDRs), absence of any known conserved domain, localization in the endoplasmic reticulum, and proteolytic cleavage pattern of SHLF imply its function in bryophyte-specific cellular mechanisms. This makes SHLF a potential candidate to study gametophore development and evolutionary adaptations of early land plants.
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Affiliation(s)
- Boominathan Mohanasundaram
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Amey J. Bhide
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Shirsa Palit
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Gargi Chaturvedi
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
| | - Maneesh Lingwan
- School of Basic Sciences, Indian Institute of Technology (IIT), Himachal Pradesh, Mandi 175005, India
| | - Shyam Kumar Masakapalli
- School of Basic Sciences, Indian Institute of Technology (IIT), Himachal Pradesh, Mandi 175005, India
| | - Anjan K. Banerjee
- Indian Institute of Science Education and Research (IISER-Pune), Dr. Homi Bhabha Road, Maharashtra, Pune 411008, India
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16
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Delucchi M, Näf P, Bliven S, Anisimova M. TRAL 2.0: Tandem Repeat Detection With Circular Profile Hidden Markov Models and Evolutionary Aligner. FRONTIERS IN BIOINFORMATICS 2021; 1:691865. [PMID: 36303789 PMCID: PMC9581039 DOI: 10.3389/fbinf.2021.691865] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/11/2021] [Indexed: 11/13/2022] Open
Abstract
The Tandem Repeat Annotation Library (TRAL) focuses on analyzing tandem repeat units in genomic sequences. TRAL can integrate and harmonize tandem repeat annotations from a large number of external tools, and provides a statistical model for evaluating and filtering the detected repeats. TRAL version 2.0 includes new features such as a module for identifying repeats from circular profile hidden Markov models, a new repeat alignment method based on the progressive Poisson Indel Process, an improved installation procedure and a docker container. TRAL is an open-source Python 3 library and is available, together with documentation and tutorials viavital-it.ch/software/tral.
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Affiliation(s)
- Matteo Delucchi
- Institute of Applied Simulations, School of Life Sciences und Facility Management, Zurich University of Applied Sciences, Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paulina Näf
- Institute of Applied Simulations, School of Life Sciences und Facility Management, Zurich University of Applied Sciences, Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Spencer Bliven
- Institute of Applied Simulations, School of Life Sciences und Facility Management, Zurich University of Applied Sciences, Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Laboratory for Scientific Computing and Modelling, Paul Scherrer Institute, Villigen PSI, Villigen, Switzerland
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences und Facility Management, Zurich University of Applied Sciences, Wädenswil, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- *Correspondence: Maria Anisimova,
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17
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Kamel M, Kastano K, Mier P, Andrade-Navarro MA. REP2: A Web Server to Detect Common Tandem Repeats in Protein Sequences. J Mol Biol 2021; 433:166895. [PMID: 33972020 DOI: 10.1016/j.jmb.2021.166895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 02/01/2021] [Accepted: 02/21/2021] [Indexed: 12/13/2022]
Abstract
Ensembles of tandem repeats (TRs) in protein sequences expand rapidly to form domains well suited for interactions with proteins. For this reason, they are relatively frequent. Some TRs have known structures and therefore it is advantageous to predict their presence in a protein sequence. However, since most TRs diverge quickly, their detection by classical sequence comparison algorithms is not very accurate. Previously, we developed a method and a web server that used curated profiles and thresholds for the detection of 11 common TRs. Here we present a new web server (REP2) that allows the analysis of TRs in both individual and aligned sequences. We provide currently precomputed analyses for a selection of 78 UniProt reference proteomes. We illustrate how these data can be used to study the evolution of TRs using comparative genomics. REP2 can be accessed at http://cbdm-01.zdv.uni-mainz.de/~munoz/rep/.
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Affiliation(s)
- Mohamed Kamel
- Department of Computer Science, Faculty of Mathematics and Informatics, University of M'sila, 28000 M'sila, Algeria; Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Kristina Kastano
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University of Mainz, 55128 Mainz, Germany
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18
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Jia T, Ge Q, Zhang S, Zhang Z, Liu A, Fan S, Jiang X, Feng Y, Zhang L, Niu D, Huang S, Gong W, Yuan Y, Shang H. UDP-Glucose Dehydrogenases: Identification, Expression, and Function Analyses in Upland Cotton ( Gossypium hirsutum). Front Genet 2021; 11:597890. [PMID: 33505427 PMCID: PMC7831515 DOI: 10.3389/fgene.2020.597890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 11/27/2020] [Indexed: 11/17/2022] Open
Abstract
UDP-glucose dehydrogenase (UGD; EC1.1.1.22) is a NAD+-dependent enzyme that catalyzes the two-fold oxidation of UDP-glucose (UDP-Glc) to produce UDP-glucuronic acid and plays an important role in plant cell wall synthesis. A total of 42 UGD genes from four Gossypium genomes including G. hirsutum, G. arboretum, G. barbadense, and G. raimondii were identified and found that the UGD gene family has conservative evolution patterns in gene structure and protein domain. The growth of fibers can be effectively promoted after adding the UDP-Glc to the medium, and the GhUGD gene expression enhanced. In addition, the transgenic Arabidopsis lines over-expressing GH_D12G1806 had longer root lengths and higher gene expression level than the wild-type plants of Columbia-0. These results indicated that UGD may play important roles in cotton fiber development and has a guiding significance for dissecting fiber development mechanism.
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Affiliation(s)
- Tingting Jia
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qun Ge
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shuya Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhen Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Aiying Liu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Senmiao Fan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiao Jiang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yulong Feng
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Lipeng Zhang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Doudou Niu
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shen Huang
- Zhengzhou University of Light Industry College of Food and Bioengineering, Zhengzhou, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Youlu Yuan
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Haihong Shang
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
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19
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Kumar V, Donev EN, Barbut FR, Kushwah S, Mannapperuma C, Urbancsok J, Mellerowicz EJ. Genome-Wide Identification of Populus Malectin/Malectin-Like Domain-Containing Proteins and Expression Analyses Reveal Novel Candidates for Signaling and Regulation of Wood Development. FRONTIERS IN PLANT SCIENCE 2020; 11:588846. [PMID: 33414796 PMCID: PMC7783096 DOI: 10.3389/fpls.2020.588846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/18/2020] [Indexed: 05/21/2023]
Abstract
Malectin domain (MD) is a ligand-binding protein motif of pro- and eukaryotes. It is particularly abundant in Viridiplantae, where it occurs as either a single (MD, PF11721) or tandemly duplicated domain (PF12819) called malectin-like domain (MLD). In herbaceous plants, MD- or MLD-containing proteins (MD proteins) are known to regulate development, reproduction, and resistance to various stresses. However, their functions in woody plants have not yet been studied. To unravel their potential role in wood development, we carried out genome-wide identification of MD proteins in the model tree species black cottonwood (Populus trichocarpa), and analyzed their expression and co-expression networks. P. trichocarpa had 146 MD genes assigned to 14 different clades, two of which were specific to the genus Populus. 87% of these genes were located on chromosomes, the rest being associated with scaffolds. Based on their protein domain organization, and in agreement with the exon-intron structures, the MD genes identified here could be classified into five superclades having the following domains: leucine-rich repeat (LRR)-MD-protein kinase (PK), MLD-LRR-PK, MLD-PK (CrRLK1L), MLD-LRR, and MD-Kinesin. Whereas the majority of MD genes were highly expressed in leaves, particularly under stress conditions, eighteen showed a peak of expression during secondary wall formation in the xylem and their co-expression networks suggested signaling functions in cell wall integrity, pathogen-associated molecular patterns, calcium, ROS, and hormone pathways. Thus, P. trichocarpa MD genes having different domain organizations comprise many genes with putative foliar defense functions, some of which could be specific to Populus and related species, as well as genes with potential involvement in signaling pathways in other tissues including developing wood.
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Affiliation(s)
- Vikash Kumar
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Evgeniy N. Donev
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Félix R. Barbut
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Sunita Kushwah
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Chanaka Mannapperuma
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - János Urbancsok
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Ewa J. Mellerowicz
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, Sweden
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20
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González R, Butković A, Rivarez MPS, Elena SF. Natural variation in Arabidopsis thaliana rosette area unveils new genes involved in plant development. Sci Rep 2020; 10:17600. [PMID: 33077802 PMCID: PMC7788084 DOI: 10.1038/s41598-020-74723-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 10/06/2020] [Indexed: 11/08/2022] Open
Abstract
Growth is a complex trait influenced by multiple genes that act at different moments during the development of an organism. This makes it difficult to spot its underlying genetic mechanisms. Since plant growth is intimately related to the effective leaf surface area (ELSA), identifying genes controlling this trait will shed light on our understanding of plant growth. To find new genes with a significant contribution to plant growth, here we used the natural variation in Arabidopsis thaliana to perform a genome-wide association study of ELSA. To do this, the projected rosette area of 710 worldwide distributed natural accessions was measured and analyzed using the genome-wide efficient mixed model association algorithm. From this analysis, ten genes were identified having SNPs with a significant association with ELSA. To validate the implication of these genes into A. thaliana growth, six of them were further studied by phenotyping knock-out mutant plants. It was observed that rem1.2, orc1a, ppd1, and mcm4 mutants showed different degrees of reduction in rosette size, thus confirming the role of these genes in plant growth. Our study identified genes already known to be involved in plant growth but also assigned this role, for the first time, to other genes.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain.
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain
| | - Mark Paul Selda Rivarez
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980, Valencia, Spain
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA
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21
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Beedessee G, Kubota T, Arimoto A, Nishitsuji K, Waller RF, Hisata K, Yamasaki S, Satoh N, Kobayashi J, Shoguchi E. Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate. BMC Biol 2020; 18:139. [PMID: 33050904 PMCID: PMC7557087 DOI: 10.1186/s12915-020-00873-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/18/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Some dinoflagellates cause harmful algal blooms, releasing toxic secondary metabolites, to the detriment of marine ecosystems and human health. Our understanding of dinoflagellate toxin biosynthesis has been hampered by their unusually large genomes. To overcome this challenge, for the first time, we sequenced the genome, microRNAs, and mRNA isoforms of a basal dinoflagellate, Amphidinium gibbosum, and employed an integrated omics approach to understand its secondary metabolite biosynthesis. RESULTS We assembled the ~ 6.4-Gb A. gibbosum genome, and by probing decoded dinoflagellate genomes and transcriptomes, we identified the non-ribosomal peptide synthetase adenylation domain as essential for generation of specialized metabolites. Upon starving the cells of phosphate and nitrogen, we observed pronounced shifts in metabolite biosynthesis, suggestive of post-transcriptional regulation by microRNAs. Using Iso-Seq and RNA-seq data, we found that alternative splicing and polycistronic expression generate different transcripts for secondary metabolism. CONCLUSIONS Our genomic findings suggest intricate integration of various metabolic enzymes that function iteratively to synthesize metabolites, providing mechanistic insights into how dinoflagellates synthesize secondary metabolites, depending upon nutrient availability. This study provides insights into toxin production associated with dinoflagellate blooms. The genome of this basal dinoflagellate provides important clues about dinoflagellate evolution and overcomes the large genome size, which has been a challenge previously.
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Affiliation(s)
- Girish Beedessee
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan.
- Present address: Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK.
| | - Takaaki Kubota
- Showa Pharmaceutical University, 3-3165 Higashi-Tamagawagakuen, Machida, Tokyo, 194-8543, Japan
| | - Asuka Arimoto
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
- Marine Biological Laboratory, Graduate School of Integrated Sciences for Life, Hiroshima University, Onomichi, Hiroshima, 722-0073, Japan
| | - Koki Nishitsuji
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Kanako Hisata
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Shinichi Yamasaki
- DNA Sequencing Section, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Noriyuki Satoh
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
| | - Jun'ichi Kobayashi
- Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo, 060-0812, Japan
| | - Eiichi Shoguchi
- Marine Genomics Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, 904-0495, Japan
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22
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Paladin L, Necci M, Piovesan D, Mier P, Andrade-Navarro MA, Tosatto SCE. A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication. J Struct Biol 2020; 212:107608. [PMID: 32896658 DOI: 10.1016/j.jsb.2020.107608] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 11/30/2022]
Abstract
Tandem Repeat Proteins (TRPs) are ubiquitous in cells and are enriched in eukaryotes. They contributed to the evolution of organism complexity, specializing for functions that require quick adaptability such as immunity-related functions. To investigate the hypothesis of repeat protein evolution through exon duplication and rearrangement, we designed a tool to analyze the relationships between exon/intron patterns and structural symmetries. The tool allows comparison of the structure fragments as defined by exon/intron boundaries from Ensembl against the structural element repetitions from RepeatsDB. The all-against-all pairwise structural alignment between fragments and comparison of the two definitions (structural units and exons) are visualized in a single matrix, the "repeat/exon plot". An analysis of different repeat protein families, including the solenoids Leucine-Rich, Ankyrin, Pumilio, HEAT repeats and the β propellers Kelch-like, WD40 and RCC1, shows different behaviors, illustrated here through examples. For each example, the analysis of the exon mapping in homologous proteins supports the conservation of their exon patterns. We propose that when a clear-cut relationship between exon and structural boundaries can be identified, it is possible to infer a specific "evolutionary pattern" which may improve TRPs detection and classification.
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Affiliation(s)
| | - Marco Necci
- Dept. of Biomedical Sciences, University of Padova, Italy
| | | | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University of Mainz, Germany
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23
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Gě Q, Cūi Y, Lǐ J, Gōng J, Lú Q, Lǐ P, Shí Y, Shāng H, Liú À, Dèng X, Pān J, Chén Q, Yuán Y, Gǒng W. Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species. BMC Genomics 2020; 21:379. [PMID: 32482161 PMCID: PMC7262775 DOI: 10.1186/s12864-020-6773-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 05/06/2020] [Indexed: 11/26/2022] Open
Abstract
Background Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of FBPs has been reported in Gossypium species. Results A total of 41 FBP genes from four Gossypium species were identified and analyzed. These FBP genes were sorted into two groups and seven subgroups. Results revealed that FBP family genes were under purifying selection pressure that rendered FBP family members as being conserved evolutionarily, and there was no tandem or fragmental DNA duplication in FBP family genes. Collinearity analysis revealed that a FBP gene was located in a translocated DNA fragment and the whole FBP gene family was under disequilibrium evolution that led to a faster evolutionary progress of the members in G. barbadense and in At subgenome than those in other Gossypium species and in the Dt subgenome, respectively, in this study. Through RNA-seq analyses and qRT-PCR verification, different FBP genes had diversified biological functions in cotton fiber development (two genes in 0 DPA and 1DPA ovules and four genes in 20–25 DPA fibers), in plant responses to Verticillium wilt onset (two genes) and to salt stress (eight genes). Conclusion The FBP gene family displayed a disequilibrium evolution pattern in Gossypium species, which led to diversified functions affecting not only fiber development, but also responses to Verticillium wilt and salt stress. All of these findings provide the foundation for further study of the function of FBP genes in cotton fiber development and in environmental adaptability.
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Affiliation(s)
- Qún Gě
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Yànli Cūi
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jùnwén Lǐ
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jǔwǔ Gōng
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Quánwěi Lú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang, China
| | - Péngtāo Lǐ
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang, China
| | - Yùzhēn Shí
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Hǎihóng Shāng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Àiyīng Liú
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiǎoyīng Dèng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jìngtāo Pān
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Qúanjiā Chén
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China.
| | - Yǒulù Yuán
- College of Agriculture, Engineering Research Centre of Cotton of Ministry of Education, Xinjiang Agricultural University, Urumqi, China, 311 Nongda East Road, Urumqi, 830052, China. .,State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China. .,Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| | - Wànkuí Gǒng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China. .,Research Base, State Key Laboratory of Cotton Biology, Anyang Institute of Technology, Anyang, China.
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24
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Vermamoeba vermiformis CDC-19 draft genome sequence reveals considerable gene trafficking including with candidate phyla radiation and giant viruses. Sci Rep 2020; 10:5928. [PMID: 32246084 PMCID: PMC7125106 DOI: 10.1038/s41598-020-62836-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 03/08/2020] [Indexed: 12/31/2022] Open
Abstract
Vermamoeba vermiformis is a predominant free-living amoeba in human environments and amongst the most common amoebae that can cause severe infections in humans. It is a niche for numerous amoeba-resisting microorganisms such as bacteria and giant viruses. Differences in the susceptibility to these giant viruses have been observed. V. vermiformis and amoeba-resisting microorganisms share a sympatric lifestyle that can promote exchanges of genetic material. This work analyzed the first draft genome sequence of a V. vermiformis strain (CDC-19) through comparative genomic, transcriptomic and phylogenetic analyses. The genome of V. vermiformis is 59.5 megabase pairs in size, and 22,483 genes were predicted. A high proportion (10% (n = 2,295)) of putative genes encoded proteins showed the highest sequence homology with a bacterial sequence. The expression of these genes was demonstrated for some bacterial homologous genes. In addition, for 30 genes, we detected best BLAST hits with members of the Candidate Phyla Radiation. Moreover, 185 genes (0.8%) best matched with giant viruses, mostly those related to the subfamily Klosneuvirinae (101 genes), in particular Bodo saltans virus (69 genes). Lateral sequence transfers between V. vermiformis and amoeba-resisting microorganisms were strengthened by Sanger sequencing, transcriptomic and phylogenetic analyses. This work provides important insights and genetic data for further studies about this amoeba and its interactions with microorganisms.
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25
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Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, Gruca A, Grynberg M, Kajava AV, Promponas VJ, Anisimova M, Jakobsen KS, Linke D. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res 2019; 47:10994-11006. [PMID: 31584084 PMCID: PMC6868369 DOI: 10.1093/nar/gkz841] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/03/2019] [Accepted: 10/01/2019] [Indexed: 12/13/2022] Open
Abstract
The widespread occurrence of repetitive stretches of DNA in genomes of organisms across the tree of life imposes fundamental challenges for sequencing, genome assembly, and automated annotation of genes and proteins. This multi-level problem can lead to errors in genome and protein databases that are often not recognized or acknowledged. As a consequence, end users working with sequences with repetitive regions are faced with 'ready-to-use' deposited data whose trustworthiness is difficult to determine, let alone to quantify. Here, we provide a review of the problems associated with tandem repeat sequences that originate from different stages during the sequencing-assembly-annotation-deposition workflow, and that may proliferate in public database repositories affecting all downstream analyses. As a case study, we provide examples of the Atlantic cod genome, whose sequencing and assembly were hindered by a particularly high prevalence of tandem repeats. We complement this case study with examples from other species, where mis-annotations and sequencing errors have propagated into protein databases. With this review, we aim to raise the awareness level within the community of database users, and alert scientists working in the underlying workflow of database creation that the data they omit or improperly assemble may well contain important biological information valuable to others.
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Affiliation(s)
- Ole K Tørresen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Bastiaan Star
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Pablo Mier
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Miguel A Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg University Mainz, Hans-Dieter-Husch-Weg 15, 55128 Mainz, Germany
| | - Alex Bateman
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton. CB10 1SD, UK
| | - Patryk Jarnot
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Aleksandra Gruca
- Institute of Informatics, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Marcin Grynberg
- Institute of Biochemistry and Biophysics PAS, Pawińskiego 5A, 02-106 Warsaw, Poland
| | - Andrey V Kajava
- Centre de Recherche en Biologie cellulaire de Montpellier, UMR 5237 CNRS, Universite Montpellier 1919 Route de Mende, CEDEX 5, 34293 Montpellier, France
- Institut de Biologie Computationnelle, 34095 Montpellier, France
| | - Vasilis J Promponas
- Bioinformatics Research Laboratory, Department of Biological Sciences, University of Cyprus, PO Box 20537, CY 1678 Nicosia, Cyprus
| | - Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
- Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland
| | - Kjetill S Jakobsen
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, NO-0316 Oslo, Norway
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26
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López-Galiano MJ, Sentandreu V, Martínez-Ramírez AC, Rausell C, Real MD, Camañes G, Ruiz-Rivero O, Crespo-Salvador O, García-Robles I. Identification of Stress Associated microRNAs in Solanum lycopersicum by High-Throughput Sequencing. Genes (Basel) 2019; 10:genes10060475. [PMID: 31234458 PMCID: PMC6627569 DOI: 10.3390/genes10060475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Revised: 06/13/2019] [Accepted: 06/17/2019] [Indexed: 11/16/2022] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most important crops around the world and also a model plant to study response to stress. High-throughput sequencing was used to analyse the microRNA (miRNA) profile of tomato plants undergoing five biotic and abiotic stress conditions (drought, heat, P. syringae infection, B. cinerea infection, and herbivore insect attack with Leptinotarsa decemlineata larvae) and one chemical treatment with a plant defence inducer, hexanoic acid. We identified 104 conserved miRNAs belonging to 37 families and we predicted 61 novel tomato miRNAs. Among those 165 miRNAs, 41 were stress-responsive. Reverse transcription quantitative PCR (RT-qPCR) was used to validate high-throughput expression analysis data, confirming the expression profiles of 10 out of 11 randomly selected miRNAs. Most of the differentially expressed miRNAs were stress-specific, except for sly-miR167c-3p upregulated in B. cinerea and P. syringae infection, sly-newmiR26-3p upregulated in drought and Hx treatment samples, and sly-newmiR33-3p, sly-newmiR6-3p and sly-newmiR8-3p differentially expressed both in biotic and abiotic stresses. From mature miRNAs sequences of the 41 stress-responsive miRNAs 279 targets were predicted. An inverse correlation between the expression profiles of 4 selected miRNAs (sly-miR171a, sly-miR172c, sly-newmiR22-3p and sly-miR167c-3p) and their target genes (Kinesin, PPR, GRAS40, ABC transporter, GDP and RLP1) was confirmed by RT-qPCR. Altogether, our analysis of miRNAs in different biotic and abiotic stress conditions highlight the interest to understand the functional role of miRNAs in tomato stress response as well as their putative targets which could help to elucidate plants molecular and physiological adaptation to stress.
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Affiliation(s)
| | - Vicente Sentandreu
- Servicios Centrales de Soporte a la Investigación Experimental (SCSIE), University of Valencia, 46100 Burjassot, Valencia, Spain.
| | - Amparo C Martínez-Ramírez
- Servicios Centrales de Soporte a la Investigación Experimental (SCSIE), University of Valencia, 46100 Burjassot, Valencia, Spain.
| | - Carolina Rausell
- Department of Genetics, University of Valencia, 46100 Burjassot, Valencia, Spain.
| | - M Dolores Real
- Department of Genetics, University of Valencia, 46100 Burjassot, Valencia, Spain.
| | - Gemma Camañes
- Plant Physiology Area, Biochemistry and Biotechnology Laboratory, Department CAMN, University Jaume I, 12071 Castellón, Spain.
| | - Omar Ruiz-Rivero
- Department of Genetics, University of Valencia, 46100 Burjassot, Valencia, Spain.
| | - Oscar Crespo-Salvador
- Department of Biochemistry and Molecular Biology, University of Valencia, IATA (CSIC), 46980 Paterna, Valencia, Spain.
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27
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Banguera-Hinestroza E, Ferrada E, Sawall Y, Flot JF. Computational Characterization of the mtORF of Pocilloporid Corals: Insights into Protein Structure and Function in Stylophora Lineages from Contrasting Environments. Genes (Basel) 2019; 10:E324. [PMID: 31035578 PMCID: PMC6562464 DOI: 10.3390/genes10050324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/15/2023] Open
Abstract
More than a decade ago, a new mitochondrial Open Reading Frame (mtORF) was discovered in corals of the family Pocilloporidae and has been used since then as an effective barcode for these corals. Recently, mtORF sequencing revealed the existence of two differentiated Stylophora lineages occurring in sympatry along the environmental gradient of the Red Sea (18.5°C to 33.9°C). In the endemic Red Sea lineage RS_LinB, the mtORF and the heat shock protein gene hsp70 uncovered similar phylogeographic patterns strongly correlated with environmental variations. This suggests that the mtORF too might be involved in thermal adaptation. Here, we used computational analyses to explore the features and putative function of this mtORF. In particular, we tested the likelihood that this gene encodes a functional protein and whether it may play a role in adaptation. Analyses of full mitogenomes showed that the mtORF originated in the common ancestor of Madracis and other pocilloporids, and that it encodes a transmembrane protein differing in length and domain architecture among genera. Homology-based annotation and the relative conservation of metal-binding sites revealed traces of an ancient hydrolase catalytic activity. Furthermore, signals of pervasive purifying selection, lack of stop codons in 1830 sequences analyzed, and a codon-usage bias similar to that of other mitochondrial genes indicate that the protein is functional, i.e., not a pseudogene. Other features, such as intrinsically disordered regions, tandem repeats, and signals of positive selection particularly in StylophoraRS_LinB populations, are consistent with a role of the mtORF in adaptive responses to environmental changes.
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Affiliation(s)
- Eulalia Banguera-Hinestroza
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
| | - Evandro Ferrada
- Center for Genomics and Bioinformatics, Universidad Mayor, Santiago, Chile.
| | - Yvonne Sawall
- Coral Reef Ecology, Bermuda Institute of Ocean Sciences (BIOS), St.George's GE 01, Bermuda.
| | - Jean-François Flot
- Evolutionary Biology and Ecology, Université libre de Bruxelles, B-1050 Brussels, Belgium.
- Interuniversity Institute of Bioinformatics in Brussels-(IB)2, 1050 Brussels, Belgium.
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Podia V, Milioni D, Katsareli E, Valassakis C, Roussis A, Haralampidis K. Molecular and functional characterization of Arabidopsis thaliana VPNB1 gene involved in plant vascular development. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 277:11-19. [PMID: 30466575 DOI: 10.1016/j.plantsci.2018.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/31/2018] [Accepted: 09/05/2018] [Indexed: 06/09/2023]
Abstract
Armadillo (ARM) repeat containing proteins constitute a large family in plants and are involved in diverse cellular functions, like signal transduction, proliferation and differentiation. In animals, ARM repeat proteins have been implicated in cancer development. In this study, we aimed in characterizing the VPNB1 gene from Arabidopsis thaliana and its role in plant development, by implementing a number of genetic and molecular approaches. AtVPNB1 encodes for an ARM repeat protein of unknown function, exclusively expressed in the cambium as well as in the differentiating xylem and phloem cells of the vascular system. Subcellular localization experiments showed that VPNB is confined in nucleoplasmic speckle-like structures unrelated to cajal bodies. Transgenic VPNB-impaired plants exhibit a slower growing phenotype and a non-canonical pattern of xylem tissue. On the contrary, VPNB overexpression lines display an inverted phenotype of increased growth, accompanied by an increased deposition of phloem and xylem cell layers. In line with the above data, qPCR analysis revealed a deregulation of several key master genes of secondary wall biosynthesis, underlining the involvement of VPNB1 in the regulation and differentiation of the root and shoot vascular tissue.
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Affiliation(s)
- Varvara Podia
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Dimitra Milioni
- Agricultural University of Athens, Department of Agricultural Biotechnology, Iera Odos 75, 11855 Athens, Greece.
| | - Efthimia Katsareli
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Chryssanthi Valassakis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Andreas Roussis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
| | - Kosmas Haralampidis
- National and Kapodistrian University of Athens, Faculty of Biology, Department of Botany, 15784 Athens, Greece.
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Sharma C, Saripalli G, Kumar S, Gautam T, Kumar A, Rani S, Jain N, Prasad P, Raghuvanshi S, Jain M, Sharma JB, Prabhu KV, Sharma PK, Balyan HS, Gupta PK. A study of transcriptome in leaf rust infected bread wheat involving seedling resistance gene Lr28. FUNCTIONAL PLANT BIOLOGY : FPB 2018; 45:1046-1064. [PMID: 32291004 DOI: 10.1071/fp17326] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 04/09/2018] [Indexed: 05/02/2023]
Abstract
Leaf rust disease causes severe yield losses in wheat throughout the world. During the present study, high-throughput RNA-Seq analysis was used to gain insights into the role of Lr28 gene in imparting seedling leaf rust resistance in wheat. Differential expression analysis was conducted using a pair of near-isogenic lines (NILs) (HD 2329 and HD 2329+Lr28) at early (0h before inoculation (hbi), 24 and 48h after inoculation (hai)) and late stages (72, 96 and 168 hai) after inoculation with a virulent pathotype of pathogen Puccinia triticina. Expression of a large number of genes was found to be affected due to the presence/absence of Lr28. Gene ontology analysis of the differentially expressed transcripts suggested enrichment of transcripts involved in carbohydrate and amino acid metabolism, oxidative stress and hormone metabolism, in resistant and/or susceptible NILs. Genes encoding receptor like kinases (RLKs) (including ATP binding; serine threonine kinases) and other kinases were the most abundant class of genes, whose expression was affected. Genes involved in reactive oxygen species (ROS) homeostasis and several genes encoding transcription factors (TFs) (most abundant being WRKY TFs) were also identified along with some ncRNAs and histone variants. Quantitative real-time PCR was also used for validation of 39 representative selected genes. In the long term, the present study should prove useful in developing leaf rust resistant wheat cultivars through molecular breeding.
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Affiliation(s)
- Chanchal Sharma
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Gautam Saripalli
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Santosh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Tinku Gautam
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Avneesh Kumar
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - Sushma Rani
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Neelu Jain
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - Pramod Prasad
- Regional Station, Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, 171002, India
| | - Saurabh Raghuvanshi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - J B Sharma
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - K V Prabhu
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi, 110022, India
| | - P K Sharma
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - H S Balyan
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
| | - P K Gupta
- Department of Genetics and Plant Breeding, Ch.Charan Singh University, Meerut, 250004, India
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Pablos I, Eichhorn S, Machado Y, Briza P, Neunkirchner A, Jahn-Schmid B, Wildner S, Soh WT, Ebner C, Park JW, Pickl WF, Arora N, Vieths S, Ferreira F, Gadermaier G. Distinct epitope structures of defensin-like proteins linked to proline-rich regions give rise to differences in their allergenic activity. Allergy 2018; 73:431-441. [PMID: 28960341 PMCID: PMC5771466 DOI: 10.1111/all.13298] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2017] [Indexed: 01/17/2023]
Abstract
Background Art v 1, Amb a 4, and Par h 1 are allergenic defensin‐polyproline–linked proteins present in mugwort, ragweed, and feverfew pollen, respectively. We aimed to investigate the physicochemical and immunological features underlying the different allergenic capacities of those allergens. Methods Recombinant defensin‐polyproline–linked proteins were expressed in E. coli and physicochemically characterized in detail regarding identity, secondary structure, and aggregation status. Allergenic activity was assessed by mediator releases assay, serum IgE reactivity, and IgE inhibition ELISA using sera of patients from Austria, Canada, and Korea. Endolysosomal protein degradation and T‐cell cross‐reactivity were studied in vitro. Results Despite variations in the proline‐rich region, similar secondary structure elements were observed in the defensin‐like domains. Seventy‐four percent and 52% of the Austrian and Canadian patients reacted to all three allergens, while Korean patients were almost exclusively sensitized to Art v 1. This was reflected by IgE inhibition assays demonstrating high cross‐reactivity for Austrian, medium for Canadian, and low for Korean sera. In a subgroup of patients, IgE reactivity toward structurally altered Amb a 4 and Par h 1 was not changed suggesting involvement of linear epitopes. Immunologically relevant endolysosomal stability of the defensin‐like domain was limited to Art v 1 and no T‐cell cross‐reactivity with Art v 125‐36 was observed. Conclusions Despite structural similarity, different IgE‐binding profiles and proteolytic processing impacted the allergenic capacity of defensin‐polyproline–linked molecules. Based on the fact that Amb a 4 demonstrated distinct IgE‐binding epitopes, we suggest inclusion in molecule‐based allergy diagnosis.
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Affiliation(s)
- I. Pablos
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
| | - S. Eichhorn
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
| | - Y. Machado
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
| | - P. Briza
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
| | - A. Neunkirchner
- Center for Pathophysiology, Infectiology and Immunology; Institute of Immunology; Medical University of Vienna; Vienna Austria
| | - B. Jahn-Schmid
- Department of Pathophysiology and Allergy Research; Medical University of Vienna; Vienna Austria
| | - S. Wildner
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
- Christian Doppler Laboratory for Biosimilar Characterization; University of Salzburg; Salzburg Austria
| | - W. T. Soh
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
| | - C. Ebner
- Allergy Clinic Reumannplatz; Vienna Austria
| | - J.-W. Park
- Department of Internal Medicine and Institute of Allergy; Yonsei University College of Medicine; Seoul Korea
| | - W. F. Pickl
- Center for Pathophysiology, Infectiology and Immunology; Institute of Immunology; Medical University of Vienna; Vienna Austria
| | - N. Arora
- Allergy and Immunology Section; CSIR-Institute of Genomic and Integrative Biology; Delhi India
| | - S. Vieths
- Division of Allergology; Paul-Ehrlich-Institut; Langen Germany
| | - F. Ferreira
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
| | - G. Gadermaier
- Division of Allergy and Immunology; Department of Molecular Biology; University of Salzburg; Salzburg Austria
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Wang C, Ulloa M, Duong TT, Roberts PA. QTL Analysis of Transgressive Nematode Resistance in Tetraploid Cotton Reveals Complex Interactions in Chromosome 11 Regions. FRONTIERS IN PLANT SCIENCE 2017; 8:1979. [PMID: 29209344 PMCID: PMC5702019 DOI: 10.3389/fpls.2017.01979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 11/02/2017] [Indexed: 05/24/2023]
Abstract
Transgressive segregation in cotton (Gossypium spp.) provides an important approach to enhance resistance to the major pest root-knot nematode (RKN) Meloidogyne incognita. Our previous studies reported transgressive RKN resistance in an intraspecific Gossypium hirsutum resistant NemX × susceptible SJ-2 recombinant inbred line (RIL) population and early generations of interspecific cross Gossypium barbadense (susceptible Pima S-7) × G. hirsutum (NemX). However, the underlying functional mechanisms for this phenomenon are not known. In this study, the region of RKN resistance gene rkn1 on chromosome (Chr) 11 and its homoeologous Chr 21 was fine mapped with G. raimondii D5 genome reference sequence. Transgressive resistance was found in the later generation of a new RIL population F2:7 (Pima S-7 × NemX) and one interspecific F2 (susceptible Pima S-7 × susceptible SJ-2). QTL analysis revealed similar contributions to root-galling and egg-production resistance phenotypes associated with SSR marker CIR316 linked to resistance gene rkn1 in NemX on Chr 11 in all seven populations analyzed. In testcross NemX × F1 (Pima S-7 × SJ-2) marker allele CIR069-271 from Pima S-7 linked to CIR316 contributed 63% of resistance to galling phenotype in the presence of rkn1. Similarly, in RIL population F2:8 (NemX × SJ-2), SJ-2 markers closely linked to CIR316 contributed up to 82% of resistance to root-galling. These results were confirmed in BC1F1 SJ-2 × F1 (NemX × SJ-2), F2 (NemX × SJ-2), and F2 (Pima S-7 × SJ-2) populations in which up to 44, 36, and 15% contribution in resistance to galling was found, respectively. Transgressive segregation for resistance was universal in all intra- and inter-specific populations, although stronger transgressive resistance occurred in later than in early generations in the intraspecific cross compared with the interspecific cross. Transgressive effects on progeny from susceptible parents are possibly provided in the rkn1 resistance region of chromosome 11 by tandemly arrayed allele (TAA) or gene (TAG) interactions contributing to transgressive resistance. Complex TAA and TAG recombination and interactions in the rkn1 resistance region provide three genes and a model to study disease and transgressive resistance in polyploid plants, and novel genotypes for plant breeding.
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Affiliation(s)
- Congli Wang
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, China
| | - Mauricio Ulloa
- Plant Stress and Germplasm Development Research, PA, CSRL, USDA-ARS, Lubbock, TX, United States
| | - Tra T. Duong
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
| | - Philip A. Roberts
- Department of Nematology, University of California, Riverside, Riverside, CA, United States
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Van Holle S, De Schutter K, Eggermont L, Tsaneva M, Dang L, Van Damme EJM. Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics. Int J Mol Sci 2017; 18:ijms18061136. [PMID: 28587095 PMCID: PMC5485960 DOI: 10.3390/ijms18061136] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Revised: 05/20/2017] [Accepted: 05/22/2017] [Indexed: 01/07/2023] Open
Abstract
Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsisthaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica). The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST), hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.
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Affiliation(s)
- Sofie Van Holle
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Kristof De Schutter
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
- Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Lore Eggermont
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Mariya Tsaneva
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Liuyi Dang
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
| | - Els J M Van Damme
- Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium.
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Van Holle S, Rougé P, Van Damme EJM. Evolution and structural diversification of Nictaba-like lectin genes in food crops with a focus on soybean (Glycine max). ANNALS OF BOTANY 2017; 119:901-914. [PMID: 28087663 PMCID: PMC5379587 DOI: 10.1093/aob/mcw259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/24/2016] [Accepted: 11/17/2016] [Indexed: 05/10/2023]
Abstract
Background and Aims The Nictaba family groups all proteins that show homology to Nictaba, the tobacco lectin. So far, Nictaba and an Arabidopsis thaliana homologue have been shown to be implicated in the plant stress response. The availability of more than 50 sequenced plant genomes provided the opportunity for a genome-wide identification of Nictaba -like genes in 15 species, representing members of the Fabaceae, Poaceae, Solanaceae, Musaceae, Arecaceae, Malvaceae and Rubiaceae. Additionally, phylogenetic relationships between the different species were explored. Furthermore, this study included domain organization analysis, searching for orthologous genes in the legume family and transcript profiling of the Nictaba -like lectin genes in soybean. Methods Using a combination of BLASTp, InterPro analysis and hidden Markov models, the genomes of Medicago truncatula , Cicer arietinum , Lotus japonicus , Glycine max , Cajanus cajan , Phaseolus vulgaris , Theobroma cacao , Solanum lycopersicum , Solanum tuberosum , Coffea canephora , Oryza sativa , Zea mays, Sorghum bicolor , Musa acuminata and Elaeis guineensis were searched for Nictaba -like genes. Phylogenetic analysis was performed using RAxML and additional protein domains in the Nictaba-like sequences were identified using InterPro. Expression analysis of the soybean Nictaba -like genes was investigated using microarray data. Key Results Nictaba -like genes were identified in all studied species and analysis of the duplication events demonstrated that both tandem and segmental duplication contributed to the expansion of the Nictaba gene family in angiosperms. The single-domain Nictaba protein and the multi-domain F-box Nictaba architectures are ubiquitous among all analysed species and microarray analysis revealed differential expression patterns for all soybean Nictaba-like genes. Conclusions Taken together, the comparative genomics data contributes to our understanding of the Nictaba -like gene family in species for which the occurrence of Nictaba domains had not yet been investigated. Given the ubiquitous nature of these genes, they have probably acquired new functions over time and are expected to take on various roles in plant development and defence.
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Affiliation(s)
- Sofie Van Holle
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
| | - Pierre Rougé
- UMR 152 PHARMA-DEV, Université de Toulouse, IRD, UPS, Chemin des Maraîchers 35, 31400 Toulouse, France
| | - Els J. M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Molecular Biotechnology, Ghent University, Coupure Links 653, 9000 Ghent, Belgium
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Persi E, Wolf YI, Koonin EV. Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins. Nat Commun 2016; 7:13570. [PMID: 27857066 PMCID: PMC5120217 DOI: 10.1038/ncomms13570] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 10/17/2016] [Indexed: 01/21/2023] Open
Abstract
Protein repeats are considered hotspots of protein evolution, associated with acquisition of new functions and novel phenotypic traits, including disease. Paradoxically, however, repeats are often strongly conserved through long spans of evolution. To resolve this conundrum, it is necessary to directly compare paralogous (horizontal) evolution of repeats within proteins with their orthologous (vertical) evolution through speciation. Here we develop a rigorous methodology to identify highly periodic repeats with significant sequence similarity, for which evolutionary rates and selection (dN/dS) can be estimated, and systematically characterize their evolution. We show that horizontal evolution of repeats is markedly accelerated compared with their divergence from orthologues in closely related species. This observation is universal across the diversity of life forms and implies a biphasic evolutionary regime whereby new copies experience rapid functional divergence under combined effects of strongly relaxed purifying selection and positive selection, followed by fixation and conservation of each individual repeat.
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Affiliation(s)
- Erez Persi
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
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Wei S, Wang X, Bi C, Xu Y, Wu D, Ye N. Assembly and analysis of the complete Salix purpurea L. (Salicaceae) mitochondrial genome sequence. SPRINGERPLUS 2016; 5:1894. [PMID: 27843751 PMCID: PMC5084139 DOI: 10.1186/s40064-016-3521-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 10/11/2016] [Indexed: 11/10/2022]
Abstract
Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55.06%. The S. purpurea mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. Eighteen tandem repeats and 404 microsatellites are distributed unevenly throughout the S. purpurea mt genome. A phylogenetic tree of 23 representative terrestrial plants strongly supports S. purpurea inclusion in the Malpighiales clade. Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species.
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Affiliation(s)
- Suyun Wei
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Xuelin Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Yiqing Xu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; School of Computer Science and Engineering, Southeast University, Nanjing, 211189 Jiangsu China
| | - Dongyang Wu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Ning Ye
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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Abstract
Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a significant fraction of noteworthy volatile outliers with very high indel rates. Analysis of structural data indicates that repeats with an open structure and independently folding units are more volatile and more likely to be intrinsically disordered. Such disordered repeats are also significantly enriched in sites with a high functional potential such as linear motifs. Furthermore, the most volatile repeats have a high sequence similarity between their units. Since many volatile repeats also show signs of recombination, we conclude they are often shaped by concerted evolution. Intriguingly, many of these conserved yet volatile repeats are involved in host-pathogen interactions where they might foster fast but subtle adaptation in biological arms races. KEY WORDS: protein evolution, domain rearrangements, protein repeats, concerted evolution.
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Affiliation(s)
- Andreas Schüler
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Huefferstrasse 1, Muenster, Germany
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, Westfalian Wilhelms University, Huefferstrasse 1, Muenster, Germany
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Pellegrini M. Tandem Repeats in Proteins: Prediction Algorithms and Biological Role. Front Bioeng Biotechnol 2015; 3:143. [PMID: 26442257 PMCID: PMC4585158 DOI: 10.3389/fbioe.2015.00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/07/2015] [Indexed: 12/30/2022] Open
Abstract
Tandem repetitions in protein sequence and structure is a fascinating subject of research which has been a focus of study since the late 1990s. In this survey, we give an overview on the multi-faceted aspects of research on protein tandem repeats (PTR for short), including prediction algorithms, databases, early classification efforts, mechanisms of PTR formation and evolution, and synthetic PTR design. We also touch on the rather open issue of the relationship between PTR and flexibility (or disorder) in proteins. Detection of PTR either from protein sequence or structure data is challenging due to inherent high (biological) signal-to-noise ratio that is a key feature of this problem. As early in silico analytic tools have been key enablers for starting this field of study, we expect that current and future algorithmic and statistical breakthroughs will have a high impact on the investigations of the biological role of PTR.
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Affiliation(s)
- Marco Pellegrini
- Laboratory for Integrative Systems Medicine (LISM), Istituto di Informatica e Telematica, and Istituto di Fisiologia Clinica, Consiglio Nazionale delle Ricerche , Pisa , Italy
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Schaper E, Korsunsky A, Pečerska J, Messina A, Murri R, Stockinger H, Zoller S, Xenarios I, Anisimova M. TRAL: tandem repeat annotation library. Bioinformatics 2015; 31:3051-3. [PMID: 25987568 DOI: 10.1093/bioinformatics/btv306] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 05/08/2015] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Currently, more than 40 sequence tandem repeat detectors are published, providing heterogeneous, partly complementary, partly conflicting results. RESULTS We present TRAL, a tandem repeat annotation library that allows running and parsing of various detection outputs, clustering of redundant or overlapping annotations, several statistical frameworks for filtering false positive annotations, and importantly a tandem repeat annotation and refinement module based on circular profile hidden Markov models (cpHMMs). Using TRAL, we evaluated the performance of a multi-step tandem repeat annotation workflow on 547 085 sequences in UniProtKB/Swiss-Prot. The researcher can use these results to predict run-times for specific datasets, and to choose annotation complexity accordingly. AVAILABILITY AND IMPLEMENTATION TRAL is an open-source Python 3 library and is available, together with documentation and tutorials via http://www.vital-it.ch/software/tral. CONTACT elke.schaper@isb-sib.ch.
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Affiliation(s)
- Elke Schaper
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wäde
| | - Alexander Korsunsky
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Jūlija Pečerska
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wäde
| | - Antonio Messina
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Riccardo Murri
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Heinz Stockinger
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Stefan Zoller
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Ioannis Xenarios
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
| | - Maria Anisimova
- Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland Vital-IT group, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland, Department of Computer Science, ETH Zürich, 8092 Zürich, Switzerland, Graz University of Technology, Institute of Molecular Biotechnology, 8010 Graz, Austria, Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland, Services and Support for Science IT, University of Zürich, 8057 Zürich, Switzerland and Institute of Applied Simulations, School of Life Sciences und Facility Management, Zürich University of Applied Sciences, 8820 Wädenswil, Switzerland
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Anisimova M. Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry. BMC Evol Biol 2015; 15:76. [PMID: 25928234 PMCID: PMC4422139 DOI: 10.1186/s12862-015-0352-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 04/15/2015] [Indexed: 12/22/2022] Open
Abstract
Background Today computational molecular evolution is a vibrant research field that benefits from the availability of large and complex new generation sequencing data – ranging from full genomes and proteomes to microbiomes, metabolomes and epigenomes. The grounds for this progress were established long before the discovery of the DNA structure. Specifically, Darwin’s theory of evolution by means of natural selection not only remains relevant today, but also provides a solid basis for computational research with a variety of applications. But a long-term progress in biology was ensured by the mathematical sciences, as exemplified by Sir R. Fisher in early 20th century. Now this is true more than ever: The data size and its complexity require biologists to work in close collaboration with experts in computational sciences, modeling and statistics. Results Natural selection drives function conservation and adaptation to emerging pathogens or new environments; selection plays key role in immune and resistance systems. Here I focus on computational methods for evaluating selection in molecular sequences, and argue that they have a high potential for applications. Pharma and biotech industries can successfully use this potential, and should take the initiative to enhance their research and development with state of the art bioinformatics approaches. Conclusions This review provides a quick guide to the current computational approaches that apply the evolutionary principles of natural selection to real life problems – from drug target validation, vaccine design and protein engineering to applications in agriculture, ecology and conservation.
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Affiliation(s)
- Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Einsiedlerstrasse 31a, Wädenswil, 8820, Switzerland. .,Department of Computer Science, ETH, Zurich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Anisimova M, Pečerska J, Schaper E. Statistical approaches to detecting and analyzing tandem repeats in genomic sequences. Front Bioeng Biotechnol 2015; 3:31. [PMID: 25853125 PMCID: PMC4362331 DOI: 10.3389/fbioe.2015.00031] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/26/2015] [Indexed: 11/13/2022] Open
Abstract
Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions and can be associated with virulence, resistance, and infectious/neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this review, we discuss these intricacies and their consequences. We present our recent contributions to computational and statistical approaches for TR significance testing, sequence profile-based TR annotation, TR-aware sequence alignment, phylogenetic analyses of TR unit number and order, and TR benchmarks. Importantly, all these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features.
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Affiliation(s)
- Maria Anisimova
- Institute of Applied Simulation, School of Life Sciences and Facility Management, Zürich University of Applied Sciences (ZHAW) , Wädenswil , Switzerland
| | - Julija Pečerska
- Department of Biosystems Science and Engineering, ETH Zürich , Basel , Switzerland ; Department of Computer Science, ETH Zürich , Zürich , Switzerland
| | - Elke Schaper
- Department of Computer Science, ETH Zürich , Zürich , Switzerland ; Vital-IT Competency Center, Swiss Institute for Bioinformatics , Lausanne , Switzerland
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Sharma M, Pandey GK. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants. FRONTIERS IN PLANT SCIENCE 2015; 6:1218. [PMID: 26793205 PMCID: PMC4707873 DOI: 10.3389/fpls.2015.01218] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 12/17/2015] [Indexed: 05/18/2023]
Abstract
The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants.
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