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Peyretaillade E, Akossi RF, Tournayre J, Delbac F, Wawrzyniak I. How to overcome constraints imposed by microsporidian genome features to ensure gene prediction? J Eukaryot Microbiol 2024:e13038. [PMID: 38934348 DOI: 10.1111/jeu.13038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/03/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024]
Abstract
Since the advent of sequencing techniques and due to their continuous evolution, it has become easier and less expensive to obtain the complete genome sequence of any organism. Nevertheless, to elucidate all biological processes governing organism development, quality annotation is essential. In genome annotation, predicting gene structure is one of the most important and captivating challenges for computational biology. This aspect of annotation requires continual optimization, particularly for genomes as unusual as those of microsporidia. Indeed, this group of fungal-related parasites exhibits specific features (highly reduced gene sizes, sequences with high rate of evolution) linked to their evolution as intracellular parasites, requiring the implementation of specific annotation approaches to consider all these features. This review aimed to outline these characteristics and to assess the increasingly efficient approaches and tools that have enhanced the accuracy of gene prediction for microsporidia, both in terms of sensitivity and specificity. Subsequently, a final part will be dedicated to postgenomic approaches aimed at reinforcing the annotation data generated by prediction software. These approaches include the characterization of other understudied genes, such as those encoding regulatory noncoding RNAs or very small proteins, which also play crucial roles in the life cycle of these microorganisms.
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Affiliation(s)
| | - Reginal F Akossi
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jérémy Tournayre
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, Saint-Genès-Champanelle, France
| | - Frédéric Delbac
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ivan Wawrzyniak
- LMGE, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
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Tripathi D, Kapoor A, Bulbul, Pankaj, Kant R, Saluja D, Sharma M. Functional annotation of Candida albicans hypothetical proteins: a bioinformatics approach. Arch Microbiol 2024; 206:118. [PMID: 38393407 DOI: 10.1007/s00203-024-03840-9] [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: 10/27/2023] [Revised: 12/24/2023] [Accepted: 01/07/2024] [Indexed: 02/25/2024]
Abstract
Candida albicans is a member of the ascomycetes class of fungi and it is an opportunistic pathogen species responsible for a wide range of fungal infections in humans. Bioinformatics and sequencing analysis of Candida proteomics has disclosed that around 69% proteome is still uncharacterized which needs to be annotated with functions. The NCBI-Genome has termed them as hypothetical proteins (HPs) in the whole proteome of Candida. Interpretation of this substantial portion of the proteome can reveal novel pharmacological targets for markers, drug development, and other therapeutics and so on. In this article, we have assigned functional annotation to these hypothetical proteins using bioinformatics methodologies. The advanced and robust computational models have been used to assign the preliminary functions to these putative HPs with high level of confidence. The findings of this study unveil some novel pharmacological targets for drug therapy and vaccines and it would help to identify novel molecular mechanisms underlying the fungal pathogenesis.
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Affiliation(s)
- Deepika Tripathi
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Arushi Kapoor
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Bulbul
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Pankaj
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Ravi Kant
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Daman Saluja
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India
| | - Meenakshi Sharma
- Dr. B.R. Ambedkar Center for Biomedical Research (ACBR), University of Delhi (DU), Delhi, India.
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Tournayre J, Polonais V, Wawrzyniak I, Akossi RF, Parisot N, Lerat E, Delbac F, Souvignet P, Reichstadt M, Peyretaillade E. MicroAnnot: A Dedicated Workflow for Accurate Microsporidian Genome Annotation. Int J Mol Sci 2024; 25:880. [PMID: 38255958 PMCID: PMC10815200 DOI: 10.3390/ijms25020880] [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: 10/27/2023] [Revised: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
With nearly 1700 species, Microsporidia represent a group of obligate intracellular eukaryotes with veterinary, economic and medical impacts. To help understand the biological functions of these microorganisms, complete genome sequencing is routinely used. Nevertheless, the proper prediction of their gene catalogue is challenging due to their taxon-specific evolutionary features. As innovative genome annotation strategies are needed to obtain a representative snapshot of the overall lifestyle of these parasites, the MicroAnnot tool, a dedicated workflow for microsporidian sequence annotation using data from curated databases of accurately annotated microsporidian genes, has been developed. Furthermore, specific modules have been implemented to perform small gene (<300 bp) and transposable element identification. Finally, functional annotation was performed using the signature-based InterProScan software. MicroAnnot's accuracy has been verified by the re-annotation of four microsporidian genomes for which structural annotation had previously been validated. With its comparative approach and transcriptional signal identification method, MicroAnnot provides an accurate prediction of translation initiation sites, an efficient identification of transposable elements, as well as high specificity and sensitivity for microsporidian genes, including those under 300 bp.
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Affiliation(s)
- Jérémy Tournayre
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Valérie Polonais
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Ivan Wawrzyniak
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Reginald Florian Akossi
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Nicolas Parisot
- UMR 203, BF2I, INRAE, INSA Lyon, Université de Lyon, 69621 Villeurbanne, France
| | - Emmanuelle Lerat
- VAS, CNRS, UMR5558, LBBE, Université Claude Bernard Lyon 1, 69622 Villeurbanne, France;
| | - Frédéric Delbac
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
| | - Pierre Souvignet
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Matthieu Reichstadt
- INRAE, UMR Herbivores, Université Clermont Auvergne, VetAgro Sup, 63122 Saint-Genès-Champanelle, France; (J.T.); (P.S.); (M.R.)
| | - Eric Peyretaillade
- LMGE, CNRS, Université Clermont Auvergne, 63000 Clermont-Ferrand, France; (V.P.); (I.W.); (R.F.A.); (F.D.)
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Svedberg D, Winiger RR, Berg A, Sharma H, Tellgren-Roth C, Debrunner-Vossbrinck BA, Vossbrinck CR, Barandun J. Functional annotation of a divergent genome using sequence and structure-based similarity. BMC Genomics 2024; 25:6. [PMID: 38166563 PMCID: PMC10759460 DOI: 10.1186/s12864-023-09924-y] [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: 08/27/2023] [Accepted: 12/18/2023] [Indexed: 01/04/2024] Open
Abstract
BACKGROUND Microsporidia are a large taxon of intracellular pathogens characterized by extraordinarily streamlined genomes with unusually high sequence divergence and many species-specific adaptations. These unique factors pose challenges for traditional genome annotation methods based on sequence similarity. As a result, many of the microsporidian genomes sequenced to date contain numerous genes of unknown function. Recent innovations in rapid and accurate structure prediction and comparison, together with the growing amount of data in structural databases, provide new opportunities to assist in the functional annotation of newly sequenced genomes. RESULTS In this study, we established a workflow that combines sequence and structure-based functional gene annotation approaches employing a ChimeraX plugin named ANNOTEX (Annotation Extension for ChimeraX), allowing for visual inspection and manual curation. We employed this workflow on a high-quality telomere-to-telomere sequenced tetraploid genome of Vairimorpha necatrix. First, the 3080 predicted protein-coding DNA sequences, of which 89% were confirmed with RNA sequencing data, were used as input. Next, ColabFold was used to create protein structure predictions, followed by a Foldseek search for structural matching to the PDB and AlphaFold databases. The subsequent manual curation, using sequence and structure-based hits, increased the accuracy and quality of the functional genome annotation compared to results using only traditional annotation tools. Our workflow resulted in a comprehensive description of the V. necatrix genome, along with a structural summary of the most prevalent protein groups, such as the ricin B lectin family. In addition, and to test our tool, we identified the functions of several previously uncharacterized Encephalitozoon cuniculi genes. CONCLUSION We provide a new functional annotation tool for divergent organisms and employ it on a newly sequenced, high-quality microsporidian genome to shed light on this uncharacterized intracellular pathogen of Lepidoptera. The addition of a structure-based annotation approach can serve as a valuable template for studying other microsporidian or similarly divergent species.
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Affiliation(s)
- Dennis Svedberg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Rahel R Winiger
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
| | - Alexandra Berg
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Himanshu Sharma
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, 90736, Sweden
| | - Christian Tellgren-Roth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Charles R Vossbrinck
- Department of Environmental Science, Connecticut Agricultural Experiment Station, New Haven, CT, 06504, USA
| | - Jonas Barandun
- Department of Molecular Biology, The Laboratory for Molecular Infection Medicine Sweden (MIMS), Science for Life Laboratory, Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, 90187, Sweden.
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