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Calia G, Porracciolo P, Chen Y, Kozlowski D, Schuler H, Cestaro A, Quentin M, Favery B, Danchin EGJ, Bottini S. Identification and characterization of specific motifs in effector proteins of plant parasites using MOnSTER. Commun Biol 2024; 7:850. [PMID: 38992096 PMCID: PMC11239862 DOI: 10.1038/s42003-024-06515-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/27/2024] [Indexed: 07/13/2024] Open
Abstract
Plant pathogens cause billions of dollars of crop loss every year and are a major threat to global food security. Identifying and characterizing pathogens effectors is crucial towards their improved control. Because of their poor sequence conservation, effector identification is challenging, and current methods generate too many candidates without indication for prioritizing experimental studies. In most phyla, effectors contain specific sequence motifs which influence their localization and targets in the plant. Therefore, there is an urgent need to develop bioinformatics tools tailored for pathogen effectors. To circumvent these limitations, we have developed MOnSTER a specific tool that identifies clusters of motifs of protein sequences (CLUMPs). MOnSTER can be fed with motifs identified by de novo tools or from databases such as Pfam and InterProScan. The advantage of MOnSTER is the reduction of motif redundancy by clustering them and associating a score. This score encompasses the physicochemical properties of AAs and the motif occurrences. We built up our method to identify discriminant CLUMPs in oomycetes effectors. Consequently, we applied MOnSTER on plant parasitic nematodes and identified six CLUMPs in about 60% of the known nematode candidate parasitism proteins. Furthermore, we found co-occurrences of CLUMPs with protein domains important for invasion and pathogenicity. The potentiality of this tool goes beyond the effector characterization and can be used to easily cluster motifs and calculate the CLUMP-score on any set of protein sequences.
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Affiliation(s)
- Giulia Calia
- Free University of Bolzano, Faculty of Agricultural Environmental and Food Science, Bolzano, Italy
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Paola Porracciolo
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Yongpan Chen
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
- Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Djampa Kozlowski
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France
| | - Hannes Schuler
- Free University of Bolzano, Faculty of Agricultural Environmental and Food Science, Bolzano, Italy
- Free University of Bolzano, Competence Centre for Plant Health, Bolzano, Italy
| | - Alessandro Cestaro
- Fondazione Edmund Mach, Research and Innovation Centre, San Michele all'Adige, Italy
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), National Research Council (CNR), Bari, Italy
| | - Michaël Quentin
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Bruno Favery
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Etienne G J Danchin
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France
| | - Silvia Bottini
- INRAE, Université Côte d'Azur, CNRS, Institut Sophia Agrobiotech, Sophia-Antipolis, France.
- Université Côte d'Azur, Center of Modeling, Simulation and Interactions, Nice, France.
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Huang T, Xiao H, Tian Q, He Z, Yuan C, Lin Z, Gao X, Yao M. Identification of upstream transcription factor binding sites in orthologous genes using mixed Student’s t-test statistics. PLoS Comput Biol 2022; 18:e1009773. [PMID: 35671296 PMCID: PMC9205514 DOI: 10.1371/journal.pcbi.1009773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 06/17/2022] [Accepted: 04/30/2022] [Indexed: 11/18/2022] Open
Abstract
Background Transcription factor (TF) regulates the transcription of DNA to messenger RNA by binding to upstream sequence motifs. Identifying the locations of known motifs in whole genomes is computationally intensive. Methodology/Principal findings This study presents a computational tool, named “Grit”, for screening TF-binding sites (TFBS) by coordinating transcription factors to their promoter sequences in orthologous genes. This tool employs a newly developed mixed Student’s t-test statistical method that detects high-scoring binding sites utilizing conservation information among species. The program performs sequence scanning at a rate of 3.2 Mbp/s on a quad-core Amazon server and has been benchmarked by the well-established ChIP-Seq datasets, putting Grit amongst the top-ranked TFBS predictors. It significantly outperforms the well-known transcription factor motif scanning tools, Pscan (4.8%) and FIMO (17.8%), in analyzing well-documented ChIP-Atlas human genome Chip-Seq datasets. Significance Grit is a good alternative to current available motif scanning tools. Locating transcription factor-binding (TF-binding) site in the genome and identification their function is fundamental in understanding various biological processes. Improve the performance of the prediction tools is important because accurate TF-binding site prediction can save cost and time for wet-lab experiments. Also, genome wide TF-binding site prediction can provide new insights for transcriptome regulation in system biology perspective. This study developed a new TF-binding site prediction tool based on mixed Student’s t-test statistical method. The tool is amongst the top-ranked TF-binding site predictors, as such, it can help the researchers in TF-binding site identification and transcriptional regulation mechanism interpretation of genes.
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Affiliation(s)
- Tinghua Huang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Hong Xiao
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Qi Tian
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Zhen He
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Cheng Yuan
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Zezhao Lin
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Xuejun Gao
- College of Animal Science, Yangtze University, Jingzhou, China
- * E-mail: (XG); (MY)
| | - Min Yao
- College of Animal Science, Yangtze University, Jingzhou, China
- * E-mail: (XG); (MY)
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Roberson EDO. A catalog of CasX genome editing sites in common model organisms. BMC Genomics 2019; 20:528. [PMID: 31248380 PMCID: PMC6598274 DOI: 10.1186/s12864-019-5924-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/23/2019] [Indexed: 11/18/2022] Open
Abstract
DpbCasX, also called Cas12e, is an RNA-guided DNA endonuclease isolated from Deltaproteobacteria. In this paper I characterized the CasX-compatible genome editing sites in the reference genomes of yeast (Saccharomyces cerevisiae), flatworms (Caenorhabditis elegans), flies (Drosophila melanogaster), zebrafish (Danio rerio), mouse (Mus musculus), rats (Rattus norvegicus), and humans (Homo sapiens). Across those genomes there were > 27,000 CasX sites per megabase on average. More than 90% of genes in each genome had at least one unique site overlapping an exon, with median unique sites per gene of 6–45. I also annotated sites in the GRCm38 reference and 15 additional mouse strain genomes. The presence of specific guide sequences varied amongst the strains, with CAST/EiJ and PWK/PhJ showing the greatest divergence from the reference strain. The high density of CasX sites and number of exon overlapping sites suggests that CasX has the potential to be used as a common genome editor.
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Affiliation(s)
- Elisha D O Roberson
- Department of Medicine, Division of Rheumatology, Washington University, St. Louis, MO, 63110, USA. .,Department of Genetics, Washington University, St. Louis, MO, 63110, USA.
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