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Iturbe P, Martín AS, Hamamoto H, Marcet-Houben M, Galbaldón T, Solano C, Lasa I. Noncontiguous operon atlas for the Staphylococcus aureus genome. MICROLIFE 2024; 5:uqae007. [PMID: 38651166 PMCID: PMC11034616 DOI: 10.1093/femsml/uqae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 03/20/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024]
Abstract
Bacteria synchronize the expression of genes with related functions by organizing genes into operons so that they are cotranscribed together in a single polycistronic messenger RNA. However, some cellular processes may benefit if the simultaneous production of the operon proteins coincides with the inhibition of the expression of an antagonist gene. To coordinate such situations, bacteria have evolved noncontiguous operons (NcOs), a subtype of operons that contain one or more genes that are transcribed in the opposite direction to the other operon genes. This structure results in overlapping transcripts whose expression is mutually repressed. The presence of NcOs cannot be predicted computationally and their identification requires a detailed knowledge of the bacterial transcriptome. In this study, we used direct RNA sequencing methodology to determine the NcOs map in the Staphylococcus aureus genome. We detected the presence of 18 NcOs in the genome of S. aureus and four in the genome of the lysogenic prophage 80α. The identified NcOs comprise genes involved in energy metabolism, metal acquisition and transport, toxin-antitoxin systems, and control of the phage life cycle. Using the menaquinone operon as a proof of concept, we show that disarrangement of the NcO architecture results in a reduction of bacterial fitness due to an increase in menaquinone levels and a decrease in the rate of oxygen consumption. Our study demonstrates the significance of NcO structures in bacterial physiology and emphasizes the importance of combining operon maps with transcriptomic data to uncover previously unnoticed functional relationships between neighbouring genes.
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Affiliation(s)
- Pablo Iturbe
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
| | - Alvaro San Martín
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
| | - Hiroshi Hamamoto
- Faculty of Medicine, Department of Infectious diseases, Yamagata University, 2-2-2 Lida-Nishi, 990-9585 Yamagata, Japan
| | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Galbaldón
- Barcelona Supercomputing Centre (BSC-CNS). Plaça Eusebi Güell, 1-3, 08034 Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Cristina Solano
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
| | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed-Universidad Pública de Navarra (UPNA)-Hospital Universitario de Navarra (HUN), IdiSNA, Irunlarrea 3, Pamplona, 31008 Navarra, Spain
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Kakuk B, Dörmő Á, Csabai Z, Kemenesi G, Holoubek J, Růžek D, Prazsák I, Dani VÉ, Dénes B, Torma G, Jakab F, Tóth GE, Földes FV, Zana B, Lanszki Z, Harangozó Á, Fülöp Á, Gulyás G, Mizik M, Kiss AA, Tombácz D, Boldogkői Z. In-depth Temporal Transcriptome Profiling of Monkeypox and Host Cells using Nanopore Sequencing. Sci Data 2023; 10:262. [PMID: 37160911 PMCID: PMC10170163 DOI: 10.1038/s41597-023-02149-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023] Open
Abstract
The recent human Monkeypox outbreak underlined the importance of studying basic biology of orthopoxviruses. However, the transcriptome of its causative agent has not been investigated before neither with short-, nor with long-read sequencing approaches. This Oxford Nanopore long-read RNA-Sequencing dataset fills this gap. It will enable the in-depth characterization of the transcriptomic architecture of the monkeypox virus, and may even make possible to annotate novel host transcripts. Moreover, our direct cDNA and native RNA sequencing reads will allow the estimation of gene expression changes of both the virus and the host cells during the infection. Overall, our study will lead to a deeper understanding of the alterations caused by the viral infection on a transcriptome level.
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Affiliation(s)
- Balázs Kakuk
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Ákos Dörmő
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Zsolt Csabai
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Gábor Kemenesi
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Jiří Holoubek
- Veterinary Research Institute, Hudcova 70, CZ-62100, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, 753/5, Brno, CZ-62500, Czech Republic
| | - Daniel Růžek
- Veterinary Research Institute, Hudcova 70, CZ-62100, Brno, Czech Republic
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005, Ceske Budejovice, Czech Republic
- Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice, 753/5, Brno, CZ-62500, Czech Republic
| | - István Prazsák
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Virág Éva Dani
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Béla Dénes
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143, Budapest, Hungária krt. 23-25, Hungary
| | - Gábor Torma
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Ferenc Jakab
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Gábor E Tóth
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Fanni V Földes
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Brigitta Zana
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Zsófia Lanszki
- National Laboratory of Virology, Szentágothai Research Centre, University of Pécs, Pécs, Hungary
- Institute of Biology, Faculty of Sciences, University of Pécs, Pécs, Hungary
| | - Ákos Harangozó
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Ádám Fülöp
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Gábor Gulyás
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Máté Mizik
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - András Attila Kiss
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Dóra Tombácz
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary
| | - Zsolt Boldogkői
- Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4., 6720, Szeged, Hungary.
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