Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea
ABSTRACTThe identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes. However, interpretation of the LKP is complicated because a substantial fraction of the genes with this phenotype remains p...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2024-02-01
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| Series: | mBio |
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| Online Access: | https://journals.asm.org/doi/10.1128/mbio.03092-23 |
| _version_ | 1797309364425457664 |
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| author | Kira S. Makarova Changyi Zhang Yuri I. Wolf Svetlana Karamycheva Rachel J. Whitaker Eugene V. Koonin |
| author_facet | Kira S. Makarova Changyi Zhang Yuri I. Wolf Svetlana Karamycheva Rachel J. Whitaker Eugene V. Koonin |
| author_sort | Kira S. Makarova |
| collection | DOAJ |
| description | ABSTRACTThe identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes. However, interpretation of the LKP is complicated because a substantial fraction of the genes with this phenotype remains poorly functionally characterized. Furthermore, many genes can exhibit LKP not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes (conditionally essential genes). We analyzed the sets of LKP genes for two archaea, Methanococcus maripaludis and Sulfolobus islandicus, using a variety of computational approaches aiming to differentiate between essential and conditionally essential genes and to predict at least a general function for as many of the proteins encoded by these genes as possible. This analysis allowed us to predict the functions of several LKP genes including previously uncharacterized subunit of the GINS protein complex with an essential function in genome replication and of the KEOPS complex that is responsible for an essential tRNA modification as well as GRP protease implicated in protein quality control. Additionally, several novel antitoxins (conditionally essential genes) were predicted, and this prediction was experimentally validated by showing that the deletion of these genes together with the adjacent genes apparently encoding the cognate toxins caused no growth defect. We applied principal component analysis based on sequence and comparative genomic features showing that this approach can separate essential genes from conditionally essential ones and used it to predict essential genes in other archaeal genomes.IMPORTANCEOnly a relatively small fraction of the genes in any bacterium or archaeon is essential for survival as demonstrated by the lethal effect of their disruption. The identification of essential genes and their functions is crucial for understanding fundamental cell biology. However, many of the genes with a lethal knockout phenotype remain poorly functionally characterized, and furthermore, many genes can exhibit this phenotype not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes. We applied state-of-the-art computational methods to predict the functions of a number of uncharacterized genes with the lethal knockout phenotype in two archaeal species and developed a computational approach to predict genes involved in essential functions. These findings advance the current understanding of key functionalities of archaeal cells. |
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| format | Article |
| id | doaj.art-cb5d368cfa5e4f78a90c28049878ebbc |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-03-08T01:26:11Z |
| publishDate | 2024-02-01 |
| publisher | American Society for Microbiology |
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| series | mBio |
| spelling | doaj.art-cb5d368cfa5e4f78a90c28049878ebbc2024-02-14T14:00:56ZengAmerican Society for MicrobiologymBio2150-75112024-02-0115210.1128/mbio.03092-23Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaeaKira S. Makarova0Changyi Zhang1Yuri I. Wolf2Svetlana Karamycheva3Rachel J. Whitaker4Eugene V. Koonin5National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USACarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USANational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USANational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USACarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USANational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USAABSTRACTThe identification of microbial genes essential for survival as those with lethal knockout phenotype (LKP) is a common strategy for functional interrogation of genomes. However, interpretation of the LKP is complicated because a substantial fraction of the genes with this phenotype remains poorly functionally characterized. Furthermore, many genes can exhibit LKP not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes (conditionally essential genes). We analyzed the sets of LKP genes for two archaea, Methanococcus maripaludis and Sulfolobus islandicus, using a variety of computational approaches aiming to differentiate between essential and conditionally essential genes and to predict at least a general function for as many of the proteins encoded by these genes as possible. This analysis allowed us to predict the functions of several LKP genes including previously uncharacterized subunit of the GINS protein complex with an essential function in genome replication and of the KEOPS complex that is responsible for an essential tRNA modification as well as GRP protease implicated in protein quality control. Additionally, several novel antitoxins (conditionally essential genes) were predicted, and this prediction was experimentally validated by showing that the deletion of these genes together with the adjacent genes apparently encoding the cognate toxins caused no growth defect. We applied principal component analysis based on sequence and comparative genomic features showing that this approach can separate essential genes from conditionally essential ones and used it to predict essential genes in other archaeal genomes.IMPORTANCEOnly a relatively small fraction of the genes in any bacterium or archaeon is essential for survival as demonstrated by the lethal effect of their disruption. The identification of essential genes and their functions is crucial for understanding fundamental cell biology. However, many of the genes with a lethal knockout phenotype remain poorly functionally characterized, and furthermore, many genes can exhibit this phenotype not because their products perform essential cellular functions but because their knockout activates the toxicity of other genes. We applied state-of-the-art computational methods to predict the functions of a number of uncharacterized genes with the lethal knockout phenotype in two archaeal species and developed a computational approach to predict genes involved in essential functions. These findings advance the current understanding of key functionalities of archaeal cells.https://journals.asm.org/doi/10.1128/mbio.03092-23essential genesGINSKEOPS complextoxin/antitoxin systemsaspartic proteasearchaea |
| spellingShingle | Kira S. Makarova Changyi Zhang Yuri I. Wolf Svetlana Karamycheva Rachel J. Whitaker Eugene V. Koonin Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea mBio essential genes GINS KEOPS complex toxin/antitoxin systems aspartic protease archaea |
| title | Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea |
| title_full | Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea |
| title_fullStr | Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea |
| title_full_unstemmed | Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea |
| title_short | Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea |
| title_sort | computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea |
| topic | essential genes GINS KEOPS complex toxin/antitoxin systems aspartic protease archaea |
| url | https://journals.asm.org/doi/10.1128/mbio.03092-23 |
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