Innovative Hybrid-Alignment Annotation Method for Bioinformatics Identification and Functional Verification of a Novel Nitric Oxide Synthase in Trichomonas vaginalis
Both the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a wi...
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| Published in | Biology (Basel, Switzerland) Vol. 11; no. 8; p. 1210 |
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| Main Authors | , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
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MDPI AG
12.08.2022
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| ISSN | 2079-7737 2079-7737 |
| DOI | 10.3390/biology11081210 |
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| Abstract | Both the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV via the Smith–Waterman and Needleman–Wunsch algorithms through in-depth and repeated alignment of whole coding sequences of TV against thousands of sequences of known proteins from other organisms. A novel NOS of TV (TV NOS), which was annotated as hydrogenase in the NCBI database, was successfully identified; this TV NOS had a high witness-to-suspect ratio and contained all the NOS cofactor-binding motifs (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD) motifs). To confirm this identification, we performed in silico modeling of the protein structure and cofactor docking, cloned the gene, expressed and purified the protein, performed mass spectrometry analysis, and ultimately performed an assay to measure enzymatic activity. Our data showed that although the predicted structure of the TV NOS protein was not similar to the structure of NOSs of other species, all cofactor-binding motifs could interact with their ligands with high affinities. We clearly showed that the purified protein had high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes in TV and highlights a novel NOS that might serve as a virulence factor of TV. |
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| AbstractList | Both the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV via the Smith-Waterman and Needleman-Wunsch algorithms through in-depth and repeated alignment of whole coding sequences of TV against thousands of sequences of known proteins from other organisms. A novel NOS of TV (TV NOS), which was annotated as hydrogenase in the NCBI database, was successfully identified; this TV NOS had a high witness-to-suspect ratio and contained all the NOS cofactor-binding motifs (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD) motifs). To confirm this identification, we performed in silico modeling of the protein structure and cofactor docking, cloned the gene, expressed and purified the protein, performed mass spectrometry analysis, and ultimately performed an assay to measure enzymatic activity. Our data showed that although the predicted structure of the TV NOS protein was not similar to the structure of NOSs of other species, all cofactor-binding motifs could interact with their ligands with high affinities. We clearly showed that the purified protein had high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes in TV and highlights a novel NOS that might serve as a virulence factor of TV.Both the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV via the Smith-Waterman and Needleman-Wunsch algorithms through in-depth and repeated alignment of whole coding sequences of TV against thousands of sequences of known proteins from other organisms. A novel NOS of TV (TV NOS), which was annotated as hydrogenase in the NCBI database, was successfully identified; this TV NOS had a high witness-to-suspect ratio and contained all the NOS cofactor-binding motifs (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD) motifs). To confirm this identification, we performed in silico modeling of the protein structure and cofactor docking, cloned the gene, expressed and purified the protein, performed mass spectrometry analysis, and ultimately performed an assay to measure enzymatic activity. Our data showed that although the predicted structure of the TV NOS protein was not similar to the structure of NOSs of other species, all cofactor-binding motifs could interact with their ligands with high affinities. We clearly showed that the purified protein had high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes in TV and highlights a novel NOS that might serve as a virulence factor of TV. Both the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV via the Smith–Waterman and Needleman–Wunsch algorithms through in-depth and repeated alignment of whole coding sequences of TV against thousands of sequences of known proteins from other organisms. A novel NOS of TV (TV NOS), which was annotated as hydrogenase in the NCBI database, was successfully identified; this TV NOS had a high witness-to-suspect ratio and contained all the NOS cofactor-binding motifs (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD) motifs). To confirm this identification, we performed in silico modeling of the protein structure and cofactor docking, cloned the gene, expressed and purified the protein, performed mass spectrometry analysis, and ultimately performed an assay to measure enzymatic activity. Our data showed that although the predicted structure of the TV NOS protein was not similar to the structure of NOSs of other species, all cofactor-binding motifs could interact with their ligands with high affinities. We clearly showed that the purified protein had high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes in TV and highlights a novel NOS that might serve as a virulence factor of TV. Simple SummaryBoth the annotation and identification of genes in pathogenic parasites remain challenging. As a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV). However, nitric oxide synthase (NOS) has not yet been annotated in the TV genome. By aligning whole coding sequences of TV against a thousand sequences of known proteins from other organisms via the Smith–Waterman and Needleman–Wunsch algorithms, we developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV. A novel NOS of TV (TV NOS) with a high witness-to-suspect ratio, which was originally annotated as a hydrogenase in the NCBI database, was successfully identified. We then performed in silico modeling of the protein structure and the molecular docking of all cofactors (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD)), cloned the gene, expressed and purified the protein, and ultimately performed mass spectrometry analysis and enzymatic activity assays. We clearly showed that although the predicted structure of TV NOS is not similar to that of NOS proteins of other species, all cofactor-binding motifs can interact with their ligands with high affinities. Most importantly, the purified protein is a functional NOS, as it has a high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes.AbstractBoth the annotation and identification of genes in pathogenic parasites are still challenging. Although, as a survival factor, nitric oxide (NO) has been proven to be synthesized in Trichomonas vaginalis (TV), nitric oxide synthase (NOS) has not yet been annotated in the TV genome. We developed a witness-to-suspect strategy to identify incorrectly annotated genes in TV via the Smith–Waterman and Needleman–Wunsch algorithms through in-depth and repeated alignment of whole coding sequences of TV against thousands of sequences of known proteins from other organisms. A novel NOS of TV (TV NOS), which was annotated as hydrogenase in the NCBI database, was successfully identified; this TV NOS had a high witness-to-suspect ratio and contained all the NOS cofactor-binding motifs (NADPH, tetrahydrobiopterin (BH4), heme and flavin adenine dinucleotide (FAD) motifs). To confirm this identification, we performed in silico modeling of the protein structure and cofactor docking, cloned the gene, expressed and purified the protein, performed mass spectrometry analysis, and ultimately performed an assay to measure enzymatic activity. Our data showed that although the predicted structure of the TV NOS protein was not similar to the structure of NOSs of other species, all cofactor-binding motifs could interact with their ligands with high affinities. We clearly showed that the purified protein had high enzymatic activity for generating NO in vitro. This study provides an innovative approach to identify incorrectly annotated genes in TV and highlights a novel NOS that might serve as a virulence factor of TV. |
| Author | Chen, Guan-Ru Chang, Yu-Tien Lin, Hung-Che Chu, Chi-Ming Huang, Yuahn-Sieh Chang, Hsin-Yi Wu, Yi-Syuan Lee, Hwei-Jen Liu, Hsiu-Lin Lin, Wei-Zhi Ko, Ching-Lung Huang, Kuo-Yang Lee, Jih-Chin Yang, Ya-Ting Shui, Hao-Ai Lin, Ying-Chih Wang, Chih-Hung Cheng, Chia-Shiang Lin, Chen-Shien |
| AuthorAffiliation | 1 Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan 8 Department of Biology and Anatomy, National Defense Medical Center, Taipei 114, Taiwan 12 Department of Public Health, China Medical University, Taichung 406, Taiwan 7 School of Public Health, National Defense Medical Center, Taipei 114, Taiwan 11 Department of Public Health, Kaohsiung Medical University, Kaohsiung 807, Taiwan 5 Department of Research and Development, National Defense Medical Center, Taipei 11490, Taiwan 4 Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan 3 Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei 114, Taiwan 10 Big Data Research Center, College of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan 6 Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan 2 Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medic |
| AuthorAffiliation_xml | – name: 2 Department of Otolaryngology-Head and Neck Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei 114, Taiwan – name: 10 Big Data Research Center, College of Medicine, Fu-Jen Catholic University, New Taipei City 242, Taiwan – name: 8 Department of Biology and Anatomy, National Defense Medical Center, Taipei 114, Taiwan – name: 7 School of Public Health, National Defense Medical Center, Taipei 114, Taiwan – name: 9 Chinese Medicine Department, Taipei Hospital, Ministry of Health and Welfare, New Taipei City 242, Taiwan – name: 5 Department of Research and Development, National Defense Medical Center, Taipei 11490, Taiwan – name: 1 Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei 114, Taiwan – name: 3 Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei 114, Taiwan – name: 6 Department of Biochemistry, National Defense Medical Center, Taipei 114, Taiwan – name: 12 Department of Public Health, China Medical University, Taichung 406, Taiwan – name: 4 Graduate Institute of Life Sciences, National Defense Medical Center, Taipei 114, Taiwan – name: 11 Department of Public Health, Kaohsiung Medical University, Kaohsiung 807, Taiwan |
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| SubjectTerms | Algorithms Annotations Bacteria bioinformatic Bioinformatics Biosynthesis Cofactors computer simulation Enzymatic activity enzyme activity Flavin Flavin-adenine dinucleotide gene annotation Genes Genomes Heme Hydrogenase Identification Ligands Mammals mass spectrometry Mass spectroscopy Nitric oxide Nitric-oxide synthase novel nitric oxide synthase Organisms Parasitic diseases Protein structure protein structure prediction Proteins Queries Sexually transmitted diseases STD Survival Survival factor Tetrahydrobiopterin Trichomonas vaginalis virulence Virulence factors |
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| Title | Innovative Hybrid-Alignment Annotation Method for Bioinformatics Identification and Functional Verification of a Novel Nitric Oxide Synthase in Trichomonas vaginalis |
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