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Bhoobalan-Chitty Y, Xu S, Martinez-Alvarez L, Karamycheva S, Makarova KS, Koonin EV, Peng X. Regulatory sequence-based discovery of anti-defense genes in archaeal viruses. Nat Commun 2024; 15:3699. [PMID: 38698035 PMCID: PMC11065993 DOI: 10.1038/s41467-024-48074-x] [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: 09/06/2023] [Accepted: 04/19/2024] [Indexed: 05/05/2024] Open
Abstract
In silico identification of viral anti-CRISPR proteins (Acrs) has relied largely on the guilt-by-association method using known Acrs or anti-CRISPR associated proteins (Acas) as the bait. However, the low number and limited spread of the characterized archaeal Acrs and Aca hinders our ability to identify Acrs using guilt-by-association. Here, based on the observation that the few characterized archaeal Acrs and Aca are transcribed immediately post viral infection, we hypothesize that these genes, and many other unidentified anti-defense genes (ADG), are under the control of conserved regulatory sequences including a strong promoter, which can be used to predict anti-defense genes in archaeal viruses. Using this consensus sequence based method, we identify 354 potential ADGs in 57 archaeal viruses and 6 metagenome-assembled genomes. Experimental validation identified a CRISPR subtype I-A inhibitor and the first virally encoded inhibitor of an archaeal toxin-antitoxin based immune system. We also identify regulatory proteins potentially akin to Acas that can facilitate further identification of ADGs combined with the guilt-by-association approach. These results demonstrate the potential of regulatory sequence analysis for extensive identification of ADGs in viruses of archaea and bacteria.
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Affiliation(s)
| | - Shuanshuan Xu
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark
| | | | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Kira S Makarova
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD, USA
| | - Xu Peng
- Department of Biology, University of Copenhagen, Copenhagen N, Denmark.
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Makarova KS, Zhang C, Wolf YI, Karamycheva S, Whitaker RJ, Koonin EV. Computational analysis of genes with lethal knockout phenotype and prediction of essential genes in archaea. mBio 2024; 15:e0309223. [PMID: 38189270 PMCID: PMC10865827 DOI: 10.1128/mbio.03092-23] [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: 11/15/2023] [Accepted: 11/27/2023] [Indexed: 01/09/2024] Open
Abstract
The 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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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Changyi Zhang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Svetlana Karamycheva
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Rachel J. Whitaker
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
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Saini N, Aamir M, Singh VK, Deepak B, Mona S. Unveiling the microbial diversity and functional dynamics of Shiv Kund, Sohna hot spring, India through a shotgun metagenomics approach. Arch Microbiol 2023; 205:323. [PMID: 37651004 DOI: 10.1007/s00203-023-03664-z] [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: 05/03/2023] [Revised: 08/07/2023] [Accepted: 08/18/2023] [Indexed: 09/01/2023]
Abstract
In this research, we examined the microbial diversity in Sohna hot spring, Haryana, India using shotgun metagenome sequencing based on the Illumina Hiseq 4000 sequencing technology. The raw sequence data from metagenomic paired-end libraries were analysed for taxonomic classification, diversity, and functional annotation using MG-RAST online server. The results showed the presence of total of 57 phyla, 931 genera, and 2068 species, predominantly occupied by Moraxellaceae (Gammaproteobacteria). However, at the species level, we reported the presence of some representative pathogenic taxa, such as Acinetobacter baumannii and Moraxella osloensis. The functional annotation predicted at various levels based on SEED-based subsystem, KEGG ortholog identity (KO), Cluster of Orthologous Groups (COGs) database identified the predominance of genes associated with primary and secondary metabolism along with a crucial role in environmental and genetic signals, cellular communication, and cell signalling. Comparative Genome Analysis (CGA) using The Pathosystem Resource Integration Centre (PATRIC) tool based on genome annotation and assembly of the metagenomic libraries for representative taxon Acinetobacter baumannii (NCBI tax id:470) characterized the reads with a unique genome identifier of 470.20380 (A. baumannii DDLJ4) which is evolutionary closer to A. baumannii ATCC 470.17978 400667.7. In addition, the CARD database results about the presence of potential AMR pathotypes and the prevalence of adeABC, adeIJK, abeM gene-specific clusters that function as multidrug efflux pumps. Overall, the results provided a comprehensive insight into virulence and anti-microbial resistance mechanism and could be useful for developing potential drug targets against the possible AMR pathotypes.
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Affiliation(s)
- Neha Saini
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Mohd Aamir
- Division of Plant Pathology, ICAR-Indian Council of Agricultural Research, Pusa Campus, New Delhi, India
| | - Vinay Kumar Singh
- Centre for Bioinformatics, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, India
| | - Bansal Deepak
- Department of Environmental Science and Engineering, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Sharma Mona
- Department of Environmental Studies, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendragarh, India.
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Lyubetsky VA, Rubanov LI, Tereshina MB, Ivanova AS, Araslanova KR, Uroshlev LA, Goremykina GI, Yang JR, Kanovei VG, Zverkov OA, Shitikov AD, Korotkova DD, Zaraisky AG. Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations. Biol Direct 2023; 18:45. [PMID: 37568147 PMCID: PMC10416458 DOI: 10.1186/s13062-023-00405-6] [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: 02/02/2023] [Accepted: 08/07/2023] [Indexed: 08/13/2023] Open
Abstract
BACKGROUND It is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid contents of proteins. Recently, evidence has accumulated that significant evolutionary transformations could also be associated with the loss/emergence of whole genes. The targeted identification of such genes is a challenging problem for both bioinformatics and evo-devo research. RESULTS To solve this problem we propose the WINEGRET method, named after the first letters of the title. Its main idea is to search for genes that satisfy two requirements: first, the desired genes were lost/emerged at the same evolutionary stage at which the phenotypic trait of interest was lost/emerged, and second, the expression of these genes changes significantly during the development of the trait of interest in the model organism. To verify the first requirement, we do not use existing databases of orthologs, but rely purely on gene homology and local synteny by using some novel quickly computable conditions. Genes satisfying the second requirement are found by deep RNA sequencing. As a proof of principle, we used our method to find genes absent in extant amniotes (reptiles, birds, mammals) but present in anamniotes (fish and amphibians), in which these genes are involved in the regeneration of large body appendages. As a result, 57 genes were identified. For three of them, c-c motif chemokine 4, eotaxin-like, and a previously unknown gene called here sod4, essential roles for tail regeneration were demonstrated. Noteworthy, we established that the latter gene belongs to a novel family of Cu/Zn-superoxide dismutases lost by amniotes, SOD4. CONCLUSIONS We present a method for targeted identification of genes whose loss/emergence in evolution could be associated with the loss/emergence of a phenotypic trait of interest. In a proof-of-principle study, we identified genes absent in amniotes that participate in body appendage regeneration in anamniotes. Our method provides a wide range of opportunities for studying the relationship between the loss/emergence of phenotypic traits and the loss/emergence of specific genes in evolution.
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Affiliation(s)
- Vassily A Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
- Department of Mechanics and Mathematics, Lomonosov Moscow State University, Kolmogorova Str., 1, Moscow, Russia, 119234
| | - Lev I Rubanov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Maria B Tereshina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Anastasiya S Ivanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, USA
| | - Karina R Araslanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
| | - Leonid A Uroshlev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32, Vavilova Str., Moscow, Russia, 119991
| | - Galina I Goremykina
- Plekhanov Russian University of Economics, Stremyanny Lane 36, Moscow, Russia
| | - Jian-Rong Yang
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
- Department of Genetics and Biomedical Informatics, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China
| | - Vladimir G Kanovei
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Oleg A Zverkov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), 19 Build. 1, Bolshoy Karetny per., Moscow, Russia, 127051
| | - Alexander D Shitikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
| | - Daria D Korotkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997
- Global Health Institute, School of Life Sciences, EPFL, Lausanne, Switzerland
| | - Andrey G Zaraisky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10, Miklukho-Maklaya Str., Moscow, Russia, 117997.
- Pirogov Russian National Research Medical University, Moscow, Russia.
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