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Kjellin J, Lee D, Steinsland H, Dwane R, Barth Vedoy O, Hanevik K, Koskiniemi S. Colicins and T6SS-based competition systems enhance enterotoxigenic E. coli (ETEC) competitiveness. Gut Microbes 2024; 16:2295891. [PMID: 38149626 PMCID: PMC10761095 DOI: 10.1080/19490976.2023.2295891] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023] Open
Abstract
Diarrheal diseases are still a significant problem for humankind, causing approximately half a million deaths annually. To cause diarrhea, enteric bacterial pathogens must first colonize the gut, which is a niche occupied by the normal bacterial microbiota. Therefore, the ability of pathogenic bacteria to inhibit the growth of other bacteria can facilitate the colonization process. Although enterotoxigenic Escherichia coli (ETEC) is one of the major causative agents of diarrheal diseases, little is known about the competition systems found in and used by ETEC and how they contribute to the ability of ETEC to colonize a host. Here, we collected a set of 94 fully assembled ETEC genomes by performing whole-genome sequencing and mining the NCBI RefSeq database. Using this set, we performed a comprehensive search for delivered bacterial toxins and investigated how these toxins contribute to ETEC competitiveness in vitro. We found that type VI secretion systems (T6SS) were widespread among ETEC (n = 47). In addition, several closely related ETEC strains were found to encode Colicin Ia and T6SS (n = 8). These toxins provide ETEC competitive advantages during in vitro competition against other E. coli, suggesting that the role of T6SS as well as colicins in ETEC biology has until now been underappreciated.
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Affiliation(s)
- Jonas Kjellin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Danna Lee
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Hans Steinsland
- CISMAC, Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Rachel Dwane
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Oda Barth Vedoy
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kurt Hanevik
- Department of Clinical Science, University of Bergen, Bergen, Norway
- National centre for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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2
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Baldanzi G, Sayols-Baixeras S, Theorell-Haglöw J, Dekkers KF, Hammar U, Nguyen D, Lin YT, Ahmad S, Holm JB, Nielsen HB, Brunkwall L, Benedict C, Cedernaes J, Koskiniemi S, Phillipson M, Lind L, Sundström J, Bergström G, Engström G, Smith JG, Orho-Melander M, Ärnlöv J, Kennedy B, Lindberg E, Fall T. OSA Is Associated With the Human Gut Microbiota Composition and Functional Potential in the Population-Based Swedish CardioPulmonary bioImage Study. Chest 2023; 164:503-516. [PMID: 36925044 PMCID: PMC10410248 DOI: 10.1016/j.chest.2023.03.010] [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: 11/08/2022] [Revised: 02/17/2023] [Accepted: 03/05/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND OSA is a common sleep-breathing disorder linked to increased risk of cardiovascular disease. Intermittent upper airway obstruction and hypoxia, hallmarks of OSA, have been shown in animal models to induce substantial changes to the gut microbiota composition, and subsequent transplantation of fecal matter to other animals induced changes in BP and glucose metabolism. RESEARCH QUESTION Does OSA in adults associate with the composition and functional potential of the human gut microbiota? STUDY DESIGN AND METHODS We used respiratory polygraphy data from up to 3,570 individuals 50 to 64 years of age from the population-based Swedish Cardiopulmonary bioimage Study combined with deep shotgun metagenomics of fecal samples to identify cross-sectional associations between three OSA parameters covering apneas and hypopneas, cumulative sleep time in hypoxia, and number of oxygen desaturation events with gut microbiota composition. Data collection about potential confounders was based on questionnaires, onsite anthropometric measurements, plasma metabolomics, and linkage with the Swedish Prescribed Drug Register. RESULTS We found that all three OSA parameters were associated with lower diversity of species in the gut. Furthermore, in multivariable-adjusted analysis, the OSA-related hypoxia parameters were associated with the relative abundance of 128 gut bacterial species, including higher abundance of Blautia obeum and Collinsella aerofaciens. The latter species was also independently associated with increased systolic BP. Furthermore, the cumulative time in hypoxia during sleep was associated with the abundance of genes involved in nine gut microbiota metabolic pathways, including propionate production from lactate. Finally, we observed two heterogeneous sets of plasma metabolites with opposite association with species positively and negatively associated with hypoxia parameters, respectively. INTERPRETATION OSA-related hypoxia, but not the number of apneas/hypopneas, is associated with specific gut microbiota species and functions. Our findings lay the foundation for future research on the gut microbiota-mediated health effects of OSA.
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Affiliation(s)
- Gabriel Baldanzi
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sergi Sayols-Baixeras
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; CIBER Cardiovascular Diseases (CIBERCV), Instituto de Salud Carlos III, Madrid, Spain
| | - Jenny Theorell-Haglöw
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Department of Medical Sciences, Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
| | - Koen F Dekkers
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Hammar
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Diem Nguyen
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Yi-Ting Lin
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Division of Family Medicine and Primary Care, Department of Neurobiology, Care Science and Society, Karolinska Institute, Huddinge, Sweden; Department of Family Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Taiwan
| | - Shafqat Ahmad
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden; Preventive Medicine Division, Harvard Medical School, Brigham and Women's Hospital, Boston, MA
| | | | | | - Louise Brunkwall
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Christian Benedict
- Molecular Neuropharmacology (Sleep Science Lab), Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, Sweden
| | - Jonathan Cedernaes
- Department of Medical Sciences, Transplantation and Regenerative Medicine, Uppsala University, Uppsala, Sweden; Department of Medical Cell Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Mia Phillipson
- Department of Medical Cell Biology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Lind
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden
| | - Johan Sundström
- Department of Medical Sciences, Clinical Epidemiology, Uppsala University, Uppsala, Sweden; The George Institute for Global Health, University of New South Wales, Sydney, NSW, Australia
| | - Göran Bergström
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden; Department of Clinical Physiology, Sahlgrenska University Hospital, Region Västra Götaland, Gothenburg, Sweden
| | - Gunnar Engström
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - J Gustav Smith
- The Wallenberg Laboratory/Department of Molecular and Clinical Medicine, Institute of Medicine, Gothenburg University and the Department of Cardiology, Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Cardiology, Clinical Sciences, Lund University and Skåne University Hospital, Lund, Sweden; Wallenberg Center for Molecular Medicine and Lund University Diabetes Center, Lund University, Lund, Sweden
| | - Marju Orho-Melander
- Department of Clinical Sciences in Malmö, Lund University Diabetes Center, Lund University, Malmö, Sweden
| | - Johan Ärnlöv
- Division of Family Medicine and Primary Care, Department of Neurobiology, Care Science and Society, Karolinska Institute, Huddinge, Sweden; School of Health and Social Studies, Dalarna University, Falun, Sweden
| | - Beatrice Kennedy
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Eva Lindberg
- Department of Medical Sciences, Respiratory, Allergy and Sleep Research, Uppsala University, Uppsala, Sweden
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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3
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Stenum TS, Kumar AD, Sandbaumhüter FA, Kjellin J, Jerlström-Hultqvist J, Andrén PE, Koskiniemi S, Jansson ET, Holmqvist E. RNA interactome capture in Escherichia coli globally identifies RNA-binding proteins. Nucleic Acids Res 2023; 51:4572-4587. [PMID: 36987847 DOI: 10.1093/nar/gkad216] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 03/03/2023] [Accepted: 03/16/2023] [Indexed: 03/30/2023] Open
Abstract
RNA-binding proteins (RPBs) are deeply involved in fundamental cellular processes in bacteria and are vital for their survival. Despite this, few studies have so far been dedicated to direct and global identification of bacterial RBPs. We have adapted the RNA interactome capture (RIC) technique, originally developed for eukaryotic systems, to globally identify RBPs in bacteria. RIC takes advantage of the base pairing potential of poly(A) tails to pull-down RNA-protein complexes. Overexpressing poly(A) polymerase I in Escherichia coli drastically increased transcriptome-wide RNA polyadenylation, enabling pull-down of crosslinked RNA-protein complexes using immobilized oligo(dT) as bait. With this approach, we identified 169 putative RBPs, roughly half of which are already annotated as RNA-binding. We experimentally verified the RNA-binding ability of a number of uncharacterized RBPs, including YhgF, which is exceptionally well conserved not only in bacteria, but also in archaea and eukaryotes. We identified YhgF RNA targets in vivo using CLIP-seq, verified specific binding in vitro, and reveal a putative role for YhgF in regulation of gene expression. Our findings present a simple and robust strategy for RBP identification in bacteria, provide a resource of new bacterial RBPs, and lay the foundation for further studies of the highly conserved RBP YhgF.
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Affiliation(s)
- Thomas Søndergaard Stenum
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Ankith D Kumar
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Friederike A Sandbaumhüter
- Medical Mass Spectrometry, Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
| | - Jonas Kjellin
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Jon Jerlström-Hultqvist
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Per E Andrén
- Medical Mass Spectrometry, Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
- Science for Life Laboratory, Spatial Mass Spectrometry, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
| | - Sanna Koskiniemi
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
| | - Erik T Jansson
- Medical Mass Spectrometry, Department of Pharmaceutical Biosciences, Biomedical Centre, Uppsala University, Box 591, 75124 Uppsala, Sweden
| | - Erik Holmqvist
- Microbiology and Immunology, Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Box 596, 75124 Uppsala, Sweden
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Wäneskog M, Halvorsen T, Filek K, Xu F, Hammarlöf DL, Hayes CS, Braaten BA, Low DA, Poole SJ, Koskiniemi S. Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions. Microb Genom 2021; 7:mgen000534. [PMID: 33646095 PMCID: PMC8190604 DOI: 10.1099/mgen.0.000534] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/29/2021] [Indexed: 01/27/2023] Open
Abstract
The phenomenon of contact-dependent growth inhibition (CDI) and the genes required for CDI (cdiBAI) were identified and isolated in 2005 from an Escherichia coli isolate (EC93) from rats. Although the cdiBAIEC93 locus has been the focus of extensive research during the past 15 years, little is known about the EC93 isolate from which it originates. Here we sequenced the EC93 genome and find two complete and functional cdiBAI loci (including the previously identified cdi locus), both carried on a large 127 kb plasmid. These cdiBAI systems are differentially expressed in laboratory media, enabling EC93 to outcompete E. coli cells lacking cognate cdiI immunity genes. The two CDI systems deliver distinct effector peptides that each dissipate the membrane potential of target cells, although the two toxins display different toxic potencies. Despite the differential expression and toxic potencies of these CDI systems, both yielded similar competitive advantages against E. coli cells lacking immunity. This can be explained by the fact that the less expressed cdiBAI system (cdiBAIEC93-2) delivers a more potent toxin than the highly expressed cdiBAIEC93-1 system. Moreover, our results indicate that unlike most sequenced CDI+ bacterial isolates, the two cdi loci of E. coli EC93 are located on a plasmid and are expressed in laboratory media.
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Affiliation(s)
- Marcus Wäneskog
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Tiffany Halvorsen
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, California, USA
| | - Klara Filek
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Present address: Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Feifei Xu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Disa L. Hammarlöf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- Present address: Science for Life Laboratory, KTH, Sweden
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, California, USA
| | - Bruce A. Braaten
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, California, USA
| | - David A. Low
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, California, USA
| | - Stephen J. Poole
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, California, USA
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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5
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Stårsta M, Hammarlöf DL, Wäneskog M, Schlegel S, Xu F, Heden Gynnå A, Borg M, Herschend S, Koskiniemi S. RHS-elements function as type II toxin-antitoxin modules that regulate intra-macrophage replication of Salmonella Typhimurium. PLoS Genet 2020; 16:e1008607. [PMID: 32053596 PMCID: PMC7043789 DOI: 10.1371/journal.pgen.1008607] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 02/26/2020] [Accepted: 01/12/2020] [Indexed: 11/19/2022] Open
Abstract
RHS elements are components of conserved toxin-delivery systems, wide-spread within the bacterial kingdom and some of the most positively selected genes known. However, very little is known about how Rhs toxins affect bacterial biology. Salmonella Typhimurium contains a full-length rhs gene and an adjacent orphan rhs gene, which lacks the conserved delivery part of the Rhs protein. Here we show that, in addition to the conventional delivery, Rhs toxin-antitoxin pairs encode for functional type-II toxin-antitoxin (TA) loci that regulate S. Typhimurium proliferation within macrophages. Mutant S. Typhimurium cells lacking both Rhs toxins proliferate 2-times better within macrophages, mainly because of an increased growth rate. Thus, in addition to providing strong positive selection for the rhs loci under conditions when there is little or no toxin delivery, internal expression of the toxin-antitoxin system regulates growth in the stressful environment found inside macrophages. Bacteria that reside and multiply inside of phagocytic cells are hard to treat with common antibiotics, partly because subpopulations of bacteria are non-growing. Very little is known about how bacteria regulate their growth in the phagocytic vesicle. We show that RHS elements, previously known to function as mobilizable toxins that inhibit growth of neighboring bacteria, also function as internally expressed toxin-antitoxin systems that regulate Salmonella Typhimurium growth in macrophages. RHS elements were discovered more than 30 years ago, but their role in biology has long remained unclear even though they are some of the most positively selected genes known. Our results suggest an explanation to why rhs genes are under such strong positive selection in addition to suggesting a novel function for these toxins in regulating bacterial growth.
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Affiliation(s)
- Magnus Stårsta
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Disa L. Hammarlöf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Marcus Wäneskog
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Susan Schlegel
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Feifei Xu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Arvid Heden Gynnå
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Malin Borg
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sten Herschend
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
- * E-mail:
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6
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7
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Virtanen P, Wäneskog M, Koskiniemi S. Class II contact-dependent growth inhibition (CDI) systems allow for broad-range cross-species toxin delivery within the Enterobacteriaceae family. Mol Microbiol 2019; 111:1109-1125. [PMID: 30710431 PMCID: PMC6850196 DOI: 10.1111/mmi.14214] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2019] [Indexed: 12/17/2022]
Abstract
Contact‐dependent growth inhibition (CDI) allows bacteria to recognize kin cells in mixed bacterial populations. In Escherichia coli, CDI mediated effector delivery has been shown to be species‐specific, with a preference for the own strain over others. This specificity is achieved through an interaction between a receptor‐binding domain in the CdiA protein and its cognate receptor protein on the target cell. But how conserved this specificity is has not previously been investigated in detail. Here, we show that class II CdiA receptor‐binding domains and their Enterobacter cloacae analog are highly promiscuous, and can allow for efficient effector delivery into several different Enterobacteriaceae species, including Escherichia,Enterobacter,Klebsiella and Salmonella spp. In addition, although we observe a preference for the own receptors over others for two of the receptor‐binding domains, this did not limit cross‐species effector delivery in all experimental conditions. These results suggest that class II CdiA proteins could allow for broad‐range and cross‐species growth inhibition in mixed bacterial populations.
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Affiliation(s)
- Petra Virtanen
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden
| | - Marcus Wäneskog
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, 75124, Sweden
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8
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Michalska K, Quan Nhan D, Willett JLE, Stols LM, Eschenfeldt WH, Jones AM, Nguyen JY, Koskiniemi S, Low DA, Goulding CW, Joachimiak A, Hayes CS. Functional plasticity of antibacterial EndoU toxins. Mol Microbiol 2018; 109:509-527. [PMID: 29923643 PMCID: PMC6173971 DOI: 10.1111/mmi.14007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/15/2018] [Indexed: 01/05/2023]
Abstract
Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact-dependent growth inhibition toxin CdiA-CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His-His-Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate-specific ribonuclease activity that characterizes the superfamily. Comparative sequence analysis indicates that bacterial EndoU domains segregate into at least three major clades based on structural variations in the N-terminal subdomain. Representative EndoU nucleases from clades I and II degrade tRNA molecules with little specificity. In contrast, CdiA-CTSTECO31 and other clade III toxins are specific anticodon nucleases that cleave tRNAGlu between nucleotides C37 and m2 A38. These findings suggest that the EndoU fold is a versatile scaffold for the evolution of novel substrate specificities. Such functional plasticity may account for the widespread use of EndoU effectors by diverse inter-bacterial toxin delivery systems.
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Affiliation(s)
- Karolina Michalska
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA
| | - Dinh Quan Nhan
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Julia L E Willett
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Lucy M Stols
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA
| | - William H Eschenfeldt
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA
| | - Allison M Jones
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Josephine Y Nguyen
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - David A Low
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
| | - Celia W Goulding
- Department of Molecular Biology & Biochemistry, University of California, Irvine, CA, USA.,Pharmaceutical Sciences, University of California, Irvine, CA, USA
| | - Andrzej Joachimiak
- Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL, USA.,Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, CA, USA.,Biomolecular Science and Engineering Program, University of California, Santa Barbara, CA, USA
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9
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Wistrand-Yuen E, Knopp M, Hjort K, Koskiniemi S, Berg OG, Andersson DI. Evolution of high-level resistance during low-level antibiotic exposure. Nat Commun 2018; 9:1599. [PMID: 29686259 PMCID: PMC5913237 DOI: 10.1038/s41467-018-04059-1|] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/01/2023] Open
Abstract
It has become increasingly clear that low levels of antibiotics present in many environments can select for resistant bacteria, yet the evolutionary pathways for resistance development during exposure to low amounts of antibiotics remain poorly defined. Here we show that Salmonella enterica exposed to sub-MIC levels of streptomycin evolved high-level resistance via novel mechanisms that are different from those observed during lethal selections. During lethal selection only rpsL mutations are found, whereas at sub-MIC selection resistance is generated by several small-effect resistance mutations that combined confer high-level resistance via three different mechanisms: (i) alteration of the ribosomal RNA target (gidB mutations), (ii) reduction in aminoglycoside uptake (cyoB, nuoG, and trkH mutations), and (iii) induction of the aminoglycoside-modifying enzyme AadA (znuA mutations). These results demonstrate how the strength of the selective pressure influences evolutionary trajectories and that even weak selective pressures can cause evolution of high-level resistance.
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Affiliation(s)
- Erik Wistrand-Yuen
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden
| | - Michael Knopp
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden
| | - Karin Hjort
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, 75237, Uppsala, Sweden
| | - Otto G Berg
- Department of Cell and Molecular Biology, Uppsala University, 75237, Uppsala, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75237, Uppsala, Sweden.
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10
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Ghosh A, Baltekin Ö, Wäneskog M, Elkhalifa D, Hammarlöf DL, Elf J, Koskiniemi S. Contact-dependent growth inhibition induces high levels of antibiotic-tolerant persister cells in clonal bacterial populations. EMBO J 2018; 37:embj.201798026. [PMID: 29572241 DOI: 10.15252/embj.201798026] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 02/08/2018] [Accepted: 02/21/2018] [Indexed: 12/31/2022] Open
Abstract
Bacterial populations can use bet-hedging strategies to cope with rapidly changing environments. One example is non-growing cells in clonal bacterial populations that are able to persist antibiotic treatment. Previous studies suggest that persisters arise in bacterial populations either stochastically through variation in levels of global signalling molecules between individual cells, or in response to various stresses. Here, we show that toxins used in contact-dependent growth inhibition (CDI) create persisters upon direct contact with cells lacking sufficient levels of CdiI immunity protein, which would otherwise bind to and neutralize toxin activity. CDI-mediated persisters form through a feedforward cycle where the toxic activity of the CdiA toxin increases cellular (p)ppGpp levels, which results in Lon-mediated degradation of the immunity protein and more free toxin. Thus, CDI systems mediate a population density-dependent bet-hedging strategy, where the fraction of non-growing cells is increased only when there are many cells of the same genotype. This may be one of the mechanisms of how CDI systems increase the fitness of their hosts.
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Affiliation(s)
- Anirban Ghosh
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Özden Baltekin
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Marcus Wäneskog
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Dina Elkhalifa
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Disa L Hammarlöf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sanna Koskiniemi
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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Koskiniemi S, Garza-Sánchez F, Edman N, Chaudhuri S, Poole SJ, Manoil C, Hayes CS, Low DA. Genetic analysis of the CDI pathway from Burkholderia pseudomallei 1026b. PLoS One 2015; 10:e0120265. [PMID: 25786241 PMCID: PMC4364669 DOI: 10.1371/journal.pone.0120265] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/21/2015] [Indexed: 12/03/2022] Open
Abstract
Contact-dependent growth inhibition (CDI) is a mode of inter-bacterial competition mediated by the CdiB/CdiA family of two-partner secretion systems. CdiA binds to receptors on susceptible target bacteria, then delivers a toxin domain derived from its C-terminus. Studies with Escherichia coli suggest the existence of multiple CDI growth-inhibition pathways, whereby different systems exploit distinct target-cell proteins to deliver and activate toxins. Here, we explore the CDI pathway in Burkholderia using the CDIIIBp1026b system encoded on chromosome II of Burkholderia pseudomallei 1026b as a model. We took a genetic approach and selected Burkholderia thailandensis E264 mutants that are resistant to growth inhibition by CDIIIBp1026b. We identified mutations in three genes, BTH_I0359, BTH_II0599, and BTH_I0986, each of which confers resistance to CDIIIBp1026b. BTH_I0359 encodes a small peptide of unknown function, whereas BTH_II0599 encodes a predicted inner membrane transport protein of the major facilitator superfamily. The inner membrane localization of BTH_II0599 suggests that it may facilitate translocation of CdiA-CTIIBp1026b toxin from the periplasm into the cytoplasm of target cells. BTH_I0986 encodes a putative transglycosylase involved in lipopolysaccharide (LPS) synthesis. ∆BTH_I0986 mutants have altered LPS structure and do not interact with CDI+ inhibitor cells to the same extent as BTH_I0986+ cells, suggesting that LPS could function as a receptor for CdiAIIBp1026b. Although ∆BTH_I0359, ∆BTH_II0599, and ∆BTH_I0986 mutations confer resistance to CDIIIBp1026b, they provide no protection against the CDIE264 system deployed by B. thailandensis E264. Together, these findings demonstrate that CDI growth-inhibition pathways are distinct and can differ significantly even between closely related species.
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Affiliation(s)
- Sanna Koskiniemi
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Fernando Garza-Sánchez
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Natasha Edman
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Swarnava Chaudhuri
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Stephen J. Poole
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Colin Manoil
- Department of Genome Sciences, Box 355065, University of Washington, Seattle, Washington, United States of America
| | - Christopher S. Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - David A. Low
- Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
- Biomolecular Science and Engineering Program, University of California Santa Barbara, Santa Barbara, California, United States of America
- * E-mail:
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Hayes CS, Koskiniemi S, Ruhe ZC, Poole SJ, Low DA. Mechanisms and biological roles of contact-dependent growth inhibition systems. Cold Spring Harb Perspect Med 2014; 4:4/2/a010025. [PMID: 24492845 DOI: 10.1101/cshperspect.a010025] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Bacterial contact-dependent growth inhibition (CDI) is mediated by the CdiA/CdiB family of two-partner secretion proteins. CDI(+) cells bind to susceptible target bacteria and deliver a toxic effector domain derived from the carboxyl terminus of CdiA (CdiA-CT). More than 60 distinct CdiA-CT sequence types have been identified, and all CDI toxins characterized thus far display RNase, DNase, or pore-forming activities. CDI systems also encode CdiI immunity proteins, which specifically bind and inactivate cognate CdiA-CT toxins to prevent autoinhibition. CDI activity appears to be limited to target cells of the same species, suggesting that these systems play a role in competition between closely related bacteria. Recent work on the CDI system from uropathogenic Escherichia coli (UPEC 536) has revealed that its CdiA-CT toxin binds tightly to a cysteine biosynthetic enzyme (CysK) in the cytoplasm of target cells. The unanticipated complexity in the UPEC CDI pathway raises the possibility that these systems perform other functions in addition to growth inhibition. Finally, we propose that the phenomenon of CDI is more widespread than previously appreciated. Rhs (rearrangement hotspot) systems encode toxin-immunity pairs, some of which share significant sequence identity with CdiA-CT/CdiI proteins. A number of recent observations suggest that Rhs proteins mediate a distinct form of CDI.
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Affiliation(s)
- Christopher S Hayes
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, Santa Barbara, California 93106-9625
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Abstract
Aminoglycoside resistance in bacteria can be acquired by several mechanisms, including drug modification, target alteration, reduced uptake and increased efflux. Here we demonstrate that increased resistance to the aminoglycosides streptomycin and spectinomycin in Salmonella enterica can be conferred by increased expression of an aminoglycoside adenyl transferase encoded by the cryptic, chromosomally located aadA gene. During growth in rich medium the wild-type strain was susceptible but mutations that impaired electron transport and conferred a small colony variant (SCV) phenotype or growth in glucose/glycerol minimal media resulted in activation of the aadA gene and aminoglycoside resistance. Expression of the aadA gene was positively regulated by the stringent response regulator guanosine penta/tetraphosphate ((p)ppGpp). SCV mutants carrying stop codon mutations in the hemA and ubiA genes showed a streptomycin pseudo-dependent phenotype, where growth was stimulated by streptomycin. Our data suggest that this phenotype is due to streptomycin-induced readthrough of the stop codons, a resulting increase in HemA/UbiA levels and improved electron transport and growth. Our results demonstrate that environmental and mutational activation of a cryptic resistance gene can confer clinically significant resistance and that a streptomycin-pseudo-dependent phenotype can be generated via a novel mechanism that does not involve the classical rpsL mutations.
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Affiliation(s)
- Sanna Koskiniemi
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
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Koskiniemi S, Andersson DI. Translesion DNA polymerases are required for spontaneous deletion formation in Salmonella typhimurium. Proc Natl Acad Sci U S A 2009; 106:10248-53. [PMID: 19525399 PMCID: PMC2700912 DOI: 10.1073/pnas.0904389106] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [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: 04/19/2008] [Indexed: 01/12/2023] Open
Abstract
How spontaneous deletions form in bacteria is still a partly unresolved problem. Here, we show that deletion formation in Salmonella typhimurium requires the presence of functional translesion polymerases. First, in wild-type bacteria, removal of the known translesion DNA polymerases, PolII (polB), PolIV (dinB), PolV (umuDC), and SamAB (samAB), resulted in a 10-fold decrease in the deletion rate, indicating that 90% of all spontaneous deletions require these polymerases for their formation. Second, overexpression of these polymerases by derepression of the DNA damage-inducible LexA regulon caused a 25-fold increase in deletion rate that depended on the presence of functional translesion polymerases. Third, overexpression of the polymerases PolII and PolIV from a plasmid increased the deletion rate 12- to 30-fold, respectively. Last, in a recBC(-) mutant where dsDNA ends are stabilized due to the lack of the end-processing nuclease RecBC, the deletion rate was increased 20-fold. This increase depended on the translesion polymerases. In lexA(def) mutant cells with constitutive SOS expression, a 10-fold increase in DNA breaks was observed. Inactivation of all 4 translesion polymerases in the lexA(def) mutant reduced the deletion rate 250-fold without any concomitant reduction in the amount of DNA breaks. Mutational inactivation of 3 endonucleases under LexA control reduced the number of DNA breaks to the wild-type level in a lexA(def) mutant with a concomitant 50-fold reduction in deletion rate. These findings suggest that the translesion polymerases are not involved in forming the DNA breaks, but that they require them to stimulate deletion formation.
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Affiliation(s)
- Sanna Koskiniemi
- Department of Medical Biochemistry and Microbiology, Uppsala University, S-751 23 Uppsala, Sweden
| | - Dan I. Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, S-751 23 Uppsala, Sweden
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Nilsson AI, Koskiniemi S, Eriksson S, Kugelberg E, Hinton JCD, Andersson DI. Bacterial genome size reduction by experimental evolution. Proc Natl Acad Sci U S A 2005; 102:12112-6. [PMID: 16099836 PMCID: PMC1189319 DOI: 10.1073/pnas.0503654102] [Citation(s) in RCA: 166] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacterial evolution toward endosymbiosis with eukaryotic cells is associated with extensive bacterial genome reduction and loss of metabolic and regulatory capabilities. Here we examined the rate and process of genome reduction in the bacterium Salmonella enterica by a serial passage experimental evolution procedure. The initial rate of DNA loss was estimated to be 0.05 bp per chromosome per generation for a WT bacterium and approximately 50-fold higher for a mutS mutant defective in methyl-directed DNA mismatch repair. The endpoints were identified for seven chromosomal deletions isolated during serial passage and in two separate genetic selections. Deletions ranged in size from 1 to 202 kb, and most of them were not associated with DNA repeats, indicating that they were formed via RecA-independent recombination events. These results suggest that extensive genome reduction can occur on a short evolutionary time scale and that RecA-dependent homologous recombination only plays a limited role in this process of jettisoning superfluous DNA.
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Affiliation(s)
- A I Nilsson
- Microbiology and Tumor Biology Center, Karolinska Institute, SE-171 77 Stockholm, Sweden
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Koskiniemi M, Rantalaiho T, Piiparinen H, von Bonsdorff CH, Färkkilä M, Järvinen A, Kinnunen E, Koskiniemi S, Mannonen L, Muttilainen M, Linnavuori K, Porras J, Puolakkainen M, Räihä K, Salonen EM, Ukkonen P, Vaheri A, Valtonen V. Infections of the central nervous system of suspected viral origin: a collaborative study from Finland. J Neurovirol 2001; 7:400-8. [PMID: 11582512 DOI: 10.1080/135502801753170255] [Citation(s) in RCA: 147] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
We studied 3231 patients with acute central nervous system (CNS) symptoms of suspected viral origin to elucidate the current etiologic spectrum. In 46% of the cases, a viral finding was observed. Varicella-zoster virus (VZV) was the main agent associated with encephalitis, as well as meningitis and myelitis. VZV comprised 29% of all confirmed or probable etiologic agents. Herpes simplex virus (HSV) and enteroviruses accounted 11% each, and influenza A virus 7%. VZV seems to have achieved a major role in viral infections of CNS. In encephalitis in our population, VZV is clearly more commonly associated with these neurological diseases than HSV. The increase in VZV findings may in part be a pseudophenomenon due to improved diagnostic methods, however, a true increase may have occurred and the pathogenetic mechanisms behind this should be elucidated.
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MESH Headings
- Adenoviridae Infections/epidemiology
- Adenoviridae Infections/virology
- Adolescent
- Adult
- Age Distribution
- Aged
- Child
- Child, Preschool
- Chlamydia Infections/epidemiology
- Chlamydophila pneumoniae
- Encephalitis/epidemiology
- Encephalitis/microbiology
- Encephalitis, Herpes Simplex/diagnosis
- Encephalitis, Herpes Simplex/epidemiology
- Encephalitis, Tick-Borne/epidemiology
- Encephalitis, Tick-Borne/virology
- Encephalitis, Varicella Zoster/diagnosis
- Encephalitis, Viral/diagnosis
- Encephalitis, Viral/epidemiology
- Encephalitis, Viral/virology
- Enterovirus Infections/diagnosis
- Enterovirus Infections/epidemiology
- Female
- Finland/epidemiology
- Herpesviridae Infections/diagnosis
- Herpesviridae Infections/epidemiology
- Humans
- Immunoenzyme Techniques
- Incidence
- Infant
- Infant, Newborn
- Male
- Meningitis/diagnosis
- Meningitis/epidemiology
- Meningitis/virology
- Middle Aged
- Myelitis/diagnosis
- Myelitis/epidemiology
- Myelitis/virology
- Polymerase Chain Reaction
- Puumala virus/isolation & purification
- Retrospective Studies
- Rotavirus Infections/epidemiology
- Rotavirus Infections/virology
- Seroepidemiologic Studies
- Vaccination
- Viral Vaccines
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Affiliation(s)
- M Koskiniemi
- The Haartman Institute, Department of Virology, University of Helsinki, Finland.
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Koskiniemi S, Sellin M, Norgren M. Identification of two genes, cpsX and cpsY, with putative regulatory function on capsule expression in group B streptococci. FEMS Immunol Med Microbiol 1998; 21:159-68. [PMID: 9685006 DOI: 10.1111/j.1574-695x.1998.tb01162.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Two divergently transcribed open reading frames: cpsX and cpsY separated by a common regulatory region was identified upstream of the cpsA-D genes involved in polysaccharide capsule biosynthesis in group B streptococci (GBS). We suggest that these genes are involved in the regulation of capsule expression in GBS, since the CpsX protein shares sequence similarities with LytR of Bacillus subtilis, an attenuator of transcription while CpsY has similarity to a wide variety of members of the LysR family of transcriptional regulators. No deletions, insertions, DNA rearrangements, or apparent differences were discovered in the postulated regulatory genes when the gene region was compared in GBS with different capsule phenotypes. Thus, other yet unidentified gene loci may control capsule phase variation in GBS.
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Affiliation(s)
- S Koskiniemi
- Department of Clinical Bacteriology, Umeå University, Sweden
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Nilsson J, Koskiniemi S, Persson K, Grahn B, Holm I. Polyamines regulate both transcription and translation of the gene encoding ornithine decarboxylase antizyme in mouse. Eur J Biochem 1997; 250:223-31. [PMID: 9428668 DOI: 10.1111/j.1432-1033.1997.0223a.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The degradation of ornithine decarboxylase (ODC) is mediated by antizyme, a protein regulated by the end-products of ODC activity, the polyamines. High levels of polyamines induce a +1 ribosomal frameshift in the translation of the rat antizyme message leading to the expression of a full-length protein. We have studied whether the regulation of antizyme expression occurs only at the level of translation or whether polyamine levels also affect the transcription of the antizyme gene. Thus, we have cloned and sequenced the mouse homologues of the rat ODC-antizyme gene and cDNA. Northern blot analysis shows that although high concentrations of polyamines do not affect the steady-state levels of antizyme message in L1210 leukemia cells, polyamine depletion using 2-(difluoromethyl)ornithine [Orn(F2Me)] leads to a marked decrease in mRNA levels. Results of transient transfections of luciferase-reporter-gene constructs driven by antizyme promoter fragments in untreated and Orn(F2Me)-treated Balb/C 3T3 cells indicate that the transcription of the antizyme gene is altered upon polyamine depletion. The amount of antizyme protein on Western blots was also altered by polyamine depletion and addition, and the polysomal distribution of antizyme message suggests a general translational increase of the message when polyamine concentrations are high. These results indicate a role for polyamines in the transcriptional and translational regulation of ornithine decarboxylase antizyme.
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Affiliation(s)
- J Nilsson
- Department of Cellular and Developmental Biology, Umeå University, Sweden
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