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Khan N, Graham T, Franciszkiewicz K, Bloch S, Nejman-Faleńczyk B, Wegrzyn A, Donaldson LW. The NMR structure of the Orf63 lytic developmental protein from lambda bacteriophage. Sci Rep 2024; 14:3793. [PMID: 38360900 PMCID: PMC10869804 DOI: 10.1038/s41598-024-54508-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 02/13/2024] [Indexed: 02/17/2024] Open
Abstract
The orf63 gene resides in a region of the lambda bacteriophage genome between the exo and xis genes and is among the earliest genes transcribed during infection. In lambda phage and Shiga toxin (Stx) producing phages found in enterohemorrhagic Escherichia coli (EHEC) associated with food poisoning, Orf63 expression reduces the host survival and hastens the period between infection and lysis thereby giving it pro-lytic qualities. The NMR structure of dimeric Orf63 reveals a fold consisting of two helices and one strand that all make extensive intermolecular contacts. Structure-based data mining failed to identify any Orf63 homolog beyond the family of temperate bacteriophages. A machine learning approach was used to design an amphipathic helical ligand that bound a hydrophobic cleft on Orf63 with micromolar affinity. This approach may open a new path towards designing therapeutics that antagonize the contributions of Stx phages in EHEC outbreaks.
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Affiliation(s)
- Naushaba Khan
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada
| | - Tavawn Graham
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada
| | | | - Sylwia Bloch
- Department of Molecular Biology, University of Gdańsk, 80-308, Gdańsk, Poland
| | | | - Alicja Wegrzyn
- Phage Therapy Center, University Center for Applied and Interdisciplinary Research, University of Gdańsk, 80-822, Gdańsk, Poland
| | - Logan W Donaldson
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada.
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Bloch S, Nejman-Faleńczyk B, Licznerska K, Dydecka A, Topka-Bielecka G, Necel A, Węgrzyn A, Węgrzyn G. Complex effects of the exo-xis region of the Shiga toxin-converting bacteriophage Φ24 B genome on the phage development and the Escherichia coli host physiology. J Appl Genet 2024; 65:191-211. [PMID: 37968427 PMCID: PMC10789677 DOI: 10.1007/s13353-023-00799-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 11/17/2023]
Abstract
Lambdoid bacteriophages are excellent models in studies on molecular aspects of virus-host interactions. However, some of them carry genes encoding toxins which are responsible for virulence of pathogenic strains of bacteria. Shiga toxin-converting bacteriophages (Stx phages) encode Shiga toxins that cause virulence of enterohemorrhagic Escherichia coli (EHEC), and their effective production depends on Stx prophage induction. The exo-xis region of the lambdoid phage genome consists of genes which are dispensable for the phage multiplication under laboratory conditions; however, they might modulate the virus development. Nevertheless, their exact effects on the phage and host physiology remained unclear. Here, we present results of complex studies on the role of the exo-xis region of bacteriophage Φ24B, one of Stx2b phages. Transcriptomic analyses, together with proteomic and metabolomic studies, provided the basis for understanding the functions of the exo-xis region. Genes from this region promoted lytic development of the phage over lysogenization. Moreover, expression of the host genes coding for DnaK, DnaJ, GrpE, and GroELS chaperones was impaired in the cells infected with the Δexo-xis phage mutant, relative to the wild-type virus, corroborating the conclusion about lytic development promotion by the exo-xis region. Proteomic and metabolomic analyses indicated also modulation of gad and nrf operons, and levels of amino acids and acylcarnitines, respectively. In conclusion, the exo-xis region controls phage propagation and host metabolism by influencing expression of different phage and bacterial genes, directing the virus to the lytic rather than lysogenic developmental mode.
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Affiliation(s)
- Sylwia Bloch
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | | | | | | | | | - Agnieszka Necel
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Alicja Węgrzyn
- Phage Therapy Center, University Center for Applied and Interdisciplinary Research, University of Gdansk, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, Faculty of Biology, University of Gdansk, Gdansk, Poland.
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Goddard C, Nejman-Faleńczyk B, Donaldson LW. The NMR structure of the Ea22 lysogenic developmental protein from lambda bacteriophage. Sci Rep 2024; 14:2685. [PMID: 38302537 PMCID: PMC10834534 DOI: 10.1038/s41598-024-52996-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024] Open
Abstract
The ea22 gene resides in a relatively uncharacterized region of the lambda bacteriophage genome between the exo and xis genes and is among the earliest genes transcribed upon infection. In lambda and Shiga toxin-producing phages found in enterohemorrhagic E. coli (EHEC) associated with food poisoning, Ea22 favors a lysogenic over lytic developmental state. The Ea22 protein may be considered in terms of three domains: a short amino-terminal domain, a coiled-coiled domain, and a carboxy-terminal domain (CTD). While the full-length protein is tetrameric, the CTD is dimeric when expressed individually. Here, we report the NMR solution structure of the Ea22 CTD that is described by a mixed alpha-beta fold with a dimer interface reinforced by salt bridges. A conserved mobile loop may serve as a ligand for an unknown host protein that works with Ea22 to promote bacterial survival and the formation of new lysogens. From sequence and structural comparisons, the CTD distinguishes lambda Ea22 from homologs encoded by Shiga toxin-producing bacteriophages.
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Affiliation(s)
- Cameron Goddard
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada
| | | | - Logan W Donaldson
- Department of Biology, York University, Toronto, ON, M3J1P3, Canada.
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Donaldson LW. Molecular Modeling the Proteins from the exo-xis Region of Lambda and Shigatoxigenic Bacteriophages. Antibiotics (Basel) 2021; 10:1282. [PMID: 34827220 PMCID: PMC8614690 DOI: 10.3390/antibiotics10111282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/09/2021] [Accepted: 10/19/2021] [Indexed: 11/17/2022] Open
Abstract
Despite decades of intensive research on bacteriophage lambda, a relatively uncharacterized region remains between the exo and xis genes. Collectively, exo-xis region genes are expressed during the earliest stages of the lytic developmental cycle and are capable of affecting the molecular events associated with the lysogenic-lytic developmental decision. In Shiga toxin-producing E. coli (STEC) and enterohemorragic E. coli (EHEC) that are responsible for food- and water-borne outbreaks throughout the world, there are distinct differences of exo-xis region genes from their counterparts in lambda phage. Together, these differences may help EHEC-specific phage and their bacterial hosts adapt to the complex environment within the human intestine. Only one exo-xis region protein, Ea8.5, has been solved to date. Here, I have used the AlphaFold and RoseTTAFold machine learning algorithms to predict the structures of six exo-xis region proteins from lambda and STEC/EHEC phages. Together, the models suggest possible roles for exo-xis region proteins in transcription and the regulation of RNA polymerase.
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Rodríguez-Rubio L, Haarmann N, Schwidder M, Muniesa M, Schmidt H. Bacteriophages of Shiga Toxin-Producing Escherichia coli and Their Contribution to Pathogenicity. Pathogens 2021; 10:404. [PMID: 33805526 PMCID: PMC8065619 DOI: 10.3390/pathogens10040404] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/18/2021] [Accepted: 03/24/2021] [Indexed: 12/25/2022] Open
Abstract
Shiga toxins (Stx) of Shiga toxin-producing Escherichia coli (STEC) are generally encoded in the genome of lambdoid bacteriophages, which spend the most time of their life cycle integrated as prophages in specific sites of the bacterial chromosome. Upon spontaneous induction or induction by chemical or physical stimuli, the stx genes are co-transcribed together with the late phase genes of the prophages. After being assembled in the cytoplasm, and after host cell lysis, mature bacteriophage particles are released into the environment, together with Stx. As members of the group of lambdoid phages, Stx phages share many genetic features with the archetypical temperate phage Lambda, but are heterogeneous in their DNA sequences due to frequent recombination events. In addition to Stx phages, the genome of pathogenic STEC bacteria may contain numerous prophages, which are either cryptic or functional. These prophages may carry foreign genes, some of them related to virulence, besides those necessary for the phage life cycle. Since the production of one or more Stx is considered the major pathogenicity factor of STEC, we aim to highlight the new insights on the contribution of Stx phages and other STEC phages to pathogenicity.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Nadja Haarmann
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maike Schwidder
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
| | - Maite Muniesa
- Department of Genetics, Microbiology and Statistics, University of Barcelona, Diagonal 643, 08028 Barcelona, Spain; (L.R.-R.); (M.M.)
| | - Herbert Schmidt
- Department of Food Microbiology and Hygiene, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany; (N.H.); (M.S.)
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Tong J, Nejman-Faleńczyk B, Bloch S, Węgrzyn A, Węgrzyn G, Donaldson LW. Ea22 Proteins from Lambda and Shiga Toxin-Producing Bacteriophages Balance Structural Diversity with Functional Similarity. ACS Omega 2020; 5:12236-12244. [PMID: 32548406 PMCID: PMC7271347 DOI: 10.1021/acsomega.0c00894] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/11/2020] [Indexed: 06/11/2023]
Abstract
Enterohemorrhagic Escherichia coli (EHEC) outbreaks are commonly associated with contaminated food sources. Unlike normal intestinal bacteria, EHEC are lysogens of lambdoid bacteriophages that also carry a gene for Shiga toxin. Oxidative attack by the immune system or other stressors on the bacterial host can activate the lytic pathway of the latent phage genome to produce phage progeny and the release of Shiga toxin into the surrounding tissues. Within the genomes of bacteriophage λ and Shiga toxin-expressing (Stx+) phages such as φ24B and φP27, there is a conserved set of open reading frames that is located between the exo and xis genes that influences the lysogenic-lytic decision. In this report, we have focused on the largest exo-xis region open reading frame termed ea22 that has been shown previously to have prolysogenic properties. Using a variety of biophysical and bioinformatic methods, we demonstrate that λ and φP27 Ea22 proteins are tetrameric in solution and can be considered in terms of an amino-terminal region, a central coiled-coil region, and a carboxy-terminal region. The carboxy-terminal regions of λ and φ24B Ea22, expressed on their own, form dimers with exceptional thermostability. Limited proteolysis of φP27 Ea22 also identified a C-terminal region along the predicted boundaries. While the three Ea22 proteins all appear to have the hallmarks of a domain in their respective C-terminal regions, each sequence is remarkably dissimilar. To reconcile this difference among Ea22 proteins from λ and Stx+ phages alike, we speculate that each Ea22 may achieve the same function by targeting different components of the same regulatory process in the host.
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Affiliation(s)
- Jinge Tong
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, Canada M3J 1P3
| | - Bożena Nejman-Faleńczyk
- Department of Molecular Biology, University
of Gdansk, Wita Stwosza
59, 80-308 Gdansk, Poland
| | - Sylwia Bloch
- Department of Molecular Biology, University
of Gdansk, Wita Stwosza
59, 80-308 Gdansk, Poland
| | - Alicja Węgrzyn
- Laboratory of Molecular Biology, Institute
of Biochemistry and Biophysics, Polish Academy
of Sciences, Kładki
24, 80-822 Gdańsk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University
of Gdansk, Wita Stwosza
59, 80-308 Gdansk, Poland
| | - Logan W. Donaldson
- Department of Biology, York University, 4700 Keele Street, Toronto, ON, Canada M3J 1P3
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