Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity
Abstract Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe inte...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-03-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-30829-z |
| _version_ | 1797865069900464128 |
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| author | Vikas Sharma Max Hünnefeld Tom Luthe Julia Frunzke |
| author_facet | Vikas Sharma Max Hünnefeld Tom Luthe Julia Frunzke |
| author_sort | Vikas Sharma |
| collection | DOAJ |
| description | Abstract Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe interactions. In this study, we performed a systematic analysis of prophage elements in 2406 complete actinobacterial genomes. Overall, 2106 prophage elements were predicted to be present in about 50% (1172/2406) of the analyzed datasets. Interestingly, these identified sequences compose a high prevalence of cryptic prophage elements, indicating genetic decay and domestication. Analysis of the sequence relationship of predicted prophages with known actinobacteriophage genomes revealed an exceptional high phylogenetic diversity of prophage elements. As a trend, we observed a higher prevalence of prophage elements in vicinity to the terminus. Analysis of the prophage-encoded gene functions revealed that prophage sequences significantly contribute to the bacterial antiviral immune system, but no biosynthetic gene clusters involved in the synthesis of known antiphage molecules were identified in prophage genomes. Overall, the current study highlights the remarkable diversity of prophages in actinobacterial genomes, with highly divergent prophages in actinobacterial genomes and thus provides an important basis for further investigation of phage-host interactions in this important bacterial phylum. |
| first_indexed | 2024-04-09T23:02:07Z |
| format | Article |
| id | doaj.art-bea04716defd4a358f4ba536ebd89778 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-09T23:02:07Z |
| publishDate | 2023-03-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-bea04716defd4a358f4ba536ebd897782023-03-22T10:56:26ZengNature PortfolioScientific Reports2045-23222023-03-0113111110.1038/s41598-023-30829-zSystematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversityVikas Sharma0Max Hünnefeld1Tom Luthe2Julia Frunzke3Institute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum JülichInstitute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum JülichInstitute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum JülichInstitute of Bio- and Geosciences (IBG-1) Biotechnology, Forschungszentrum JülichAbstract Actinobacteria represent one of the largest bacterial phyla harboring many species of high medical, biotechnological and ecological relevance. Prophage elements are major contributors to bacterial genome diversity and were shown to significantly shape bacterial fitness and host-microbe interactions. In this study, we performed a systematic analysis of prophage elements in 2406 complete actinobacterial genomes. Overall, 2106 prophage elements were predicted to be present in about 50% (1172/2406) of the analyzed datasets. Interestingly, these identified sequences compose a high prevalence of cryptic prophage elements, indicating genetic decay and domestication. Analysis of the sequence relationship of predicted prophages with known actinobacteriophage genomes revealed an exceptional high phylogenetic diversity of prophage elements. As a trend, we observed a higher prevalence of prophage elements in vicinity to the terminus. Analysis of the prophage-encoded gene functions revealed that prophage sequences significantly contribute to the bacterial antiviral immune system, but no biosynthetic gene clusters involved in the synthesis of known antiphage molecules were identified in prophage genomes. Overall, the current study highlights the remarkable diversity of prophages in actinobacterial genomes, with highly divergent prophages in actinobacterial genomes and thus provides an important basis for further investigation of phage-host interactions in this important bacterial phylum.https://doi.org/10.1038/s41598-023-30829-z |
| spellingShingle | Vikas Sharma Max Hünnefeld Tom Luthe Julia Frunzke Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity Scientific Reports |
| title | Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity |
| title_full | Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity |
| title_fullStr | Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity |
| title_full_unstemmed | Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity |
| title_short | Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity |
| title_sort | systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity |
| url | https://doi.org/10.1038/s41598-023-30829-z |
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