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Willner DL, Paudel S, Halleran AD, Solini GE, Gray V, Saha MS. Transcriptional dynamics during Rhodococcus erythropolis infection with phage WC1. BMC Microbiol 2024; 24:107. [PMID: 38561651 PMCID: PMC10986025 DOI: 10.1186/s12866-024-03241-4] [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: 11/25/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND Belonging to the Actinobacteria phylum, members of the Rhodococcus genus thrive in soil, water, and even intracellularly. While most species are non-pathogenic, several cause respiratory disease in animals and, more rarely, in humans. Over 100 phages that infect Rhodococcus species have been isolated but despite their importance for Rhodococcus ecology and biotechnology applications, little is known regarding the molecular genetic interactions between phage and host during infection. To address this need, we report RNA-Seq analysis of a novel Rhodococcus erythopolis phage, WC1, analyzing both the phage and host transcriptome at various stages throughout the infection process. RESULTS By five minutes post-infection WC1 showed upregulation of a CAS-4 family exonuclease, putative immunity repressor, an anti-restriction protein, while the host showed strong upregulation of DNA replication, SOS repair, and ribosomal protein genes. By 30 min post-infection, WC1 DNA synthesis genes were strongly upregulated while the host showed increased expression of transcriptional and translational machinery and downregulation of genes involved in carbon, energy, and lipid metabolism pathways. By 60 min WC1 strongly upregulated structural genes while the host showed a dramatic disruption of metal ion homeostasis. There was significant expression of both host and phage non-coding genes at all time points. While host gene expression declined over the course of infection, our results indicate that phage may exert more selective control, preserving the host's regulatory mechanisms to create an environment conducive for virion production. CONCLUSIONS The Rhodococcus genus is well recognized for its ability to synthesize valuable compounds, particularly steroids, as well as its capacity to degrade a wide range of harmful environmental pollutants. A detailed understanding of these phage-host interactions and gene expression is not only essential for understanding the ecology of this important genus, but will also facilitate development of phage-mediated strategies for bioremediation as well as biocontrol in industrial processes and biomedical applications. Given the current lack of detailed global gene expression studies on any Rhodococcus species, our study addresses a pressing need to identify tools and genes, such as F6 and rpf, that can enhance the capacity of Rhodococcus species for bioremediation, biosynthesis and pathogen control.
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Affiliation(s)
- Dana L Willner
- Data Science Program, William & Mary, Williamsburg, VA, USA
| | - Sudip Paudel
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Wyss Institute, Harvard University, Cambridge, MA, USA
| | - Andrew D Halleran
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Atalaya Capital Management, New York, NY, USA
| | - Grace E Solini
- Department of Biology, William & Mary, Williamsburg, VA, USA
- California Institute of Technology, Pasadena, CA, USA
| | - Veronica Gray
- Department of Biology, William & Mary, Williamsburg, VA, USA
- Georgetown University School of Medicine, Washington, DC, USA
| | - Margaret S Saha
- Department of Biology, William & Mary, Williamsburg, VA, USA.
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Radersma MD, Lathrop G, Moleakunnel KC, Harlow LA, Baker AE, Chen AJ, Churu JG, Dole CA, Doorn SL, Hill EM, Howland A, Janvier A, Kramer CM, Minasian MJ, Nieze JR, Perezrios IK, Ramsey FJ, Seinen KL, Swierenga SK, Veenstra MM, Weaver GE, White AC, Yoon E, Wertz JT, DeJong RJ. Complete genome sequences of nine Rhodococcus equi phages. Microbiol Resour Announc 2024; 13:e0108823. [PMID: 38179906 PMCID: PMC10868187 DOI: 10.1128/mra.01088-23] [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: 11/10/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
We report genomes of nine phages isolated from Actinobacteria Rhodococcus equi NRRL B-16538. Six of these phages belong to actinobacteriophage cluster CR, which otherwise contains Gordonia phages; two form the CF cluster; and one is a singleton. Genome lengths are 62,017-80,980 bp with 63.9%-67.3% GC content.
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Affiliation(s)
- Myles D. Radersma
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Gabrielle Lathrop
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Luke A. Harlow
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Aerin E. Baker
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Alison J. Chen
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Jason G. Churu
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Carly A. Dole
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Sophia L. Doorn
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Ethan M. Hill
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Anna Howland
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Amanda Janvier
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Catie M. Kramer
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Matt J. Minasian
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Jocelyn R. Nieze
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Fiona J. Ramsey
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Katie L. Seinen
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | | | - Grace E. Weaver
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | | | - Esther Yoon
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - John T. Wertz
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
| | - Randall J. DeJong
- Department of Biology, Calvin University, Grand Rapids, Michigan, USA
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Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA. PLoS One 2021; 16:e0255262. [PMID: 34793465 PMCID: PMC8601537 DOI: 10.1371/journal.pone.0255262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/29/2021] [Indexed: 01/21/2023] Open
Abstract
The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high-titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.
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Ponce Reyes S, Park PJ, Kaluka D, Washington JM. Complete Genome Sequence of Rhodococcus erythropolis Phage Shuman. Microbiol Resour Announc 2019; 8:e00113-19. [PMID: 30923242 PMCID: PMC6439245 DOI: 10.1128/mra.00113-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 02/26/2019] [Indexed: 12/03/2022] Open
Abstract
Shuman is a bacteriophage isolated in Nyack, New York, using Rhodococcus erythropolis NRRL B-1574 as a host. It is a member of cluster CA and has a genome length of 46,544 bp. Shuman contains 67 predicted protein-coding genes, 3 tRNA genes, and no transfer-messenger RNA (tmRNA) genes.
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Affiliation(s)
| | - Peter J Park
- Department of Natural Sciences, Nyack College, Nyack, New York, USA
| | - Daniel Kaluka
- Department of Natural Sciences, Nyack College, Nyack, New York, USA
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Current taxonomy of Rhodococcus species and their role in infections. Eur J Clin Microbiol Infect Dis 2018; 37:2045-2062. [PMID: 30159693 DOI: 10.1007/s10096-018-3364-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 08/20/2018] [Indexed: 10/28/2022]
Abstract
Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.
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