1
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Cuénod A, Agnetti J, Seth-Smith HMB, Roloff T, Wälchli D, Shcherbakov D, Akbergenov R, Tschudin-Sutter S, Bassetti S, Siegemund M, Nickel CH, Moran-Gilad J, Keys TG, Pflüger V, Thomson NR, Egli A. Bacterial genome-wide association study substantiates papGII of Escherichia coli as a major risk factor for urosepsis. Genome Med 2023; 15:89. [PMID: 37904175 PMCID: PMC10614358 DOI: 10.1186/s13073-023-01243-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 06/06/2023] [Accepted: 10/02/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Urinary tract infections (UTIs) are among the most common bacterial infections worldwide, often caused by uropathogenic Escherichia coli. Multiple bacterial virulence factors or patient characteristics have been linked separately to progressive, more invasive infections. In this study, we aim to identify pathogen- and patient-specific factors that drive the progression to urosepsis by jointly analysing bacterial and host characteristics. METHODS We analysed 1076 E. coli strains isolated from 825 clinical cases with UTI and/or bacteraemia by whole-genome sequencing (Illumina). Sequence types (STs) were determined via srst2 and capsule loci via fastKaptive. We compared the isolates from urine and blood to confirm clonality. Furthermore, we performed a bacterial genome-wide association study (bGWAS) (pyseer) using bacteraemia as the primary clinical outcome. Clinical data were collected by an electronic patient chart review. We concurrently analysed the association of the most significant bGWAS hit and important patient characteristics with the clinical endpoint bacteraemia using a generalised linear model (GLM). Finally, we designed qPCR primers and probes to detect papGII-positive E. coli strains and prospectively screened E. coli from urine samples (n = 1657) at two healthcare centres. RESULTS Our patient cohort had a median age of 75.3 years (range: 18.00-103.1) and was predominantly female (574/825, 69.6%). The bacterial phylogroups B2 (60.6%; 500/825) and D (16.6%; 137/825), which are associated with extraintestinal infections, represent the majority of the strains in our collection, many of which encode a polysaccharide capsule (63.4%; 525/825). The most frequently observed STs were ST131 (12.7%; 105/825), ST69 (11.0%; 91/825), and ST73 (10.2%; 84/825). Of interest, in 12.3% (13/106) of cases, the E. coli pairs in urine and blood were only distantly related. In line with previous bGWAS studies, we identified the gene papGII (p-value < 0.001), which encodes the adhesin subunit of the E. coli P-pilus, to be associated with 'bacteraemia' in our bGWAS. In our GLM, correcting for patient characteristics, papGII remained highly significant (odds ratio = 5.27, 95% confidence interval = [3.48, 7.97], p-value < 0.001). An independent cohort of cases which we screened for papGII-carrying E. coli at two healthcare centres further confirmed the increased relative frequency of papGII-positive strains causing invasive infection, compared to papGII-negative strains (p-value = 0.033, chi-squared test). CONCLUSIONS This study builds on previous work linking papGII with invasive infection by showing that it is a major risk factor for progression from UTI to bacteraemia that has diagnostic potential.
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Affiliation(s)
- Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, UK.
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland.
- Department of Microbiology and Immunology, McGill University, Montréal, Canada.
| | - Jessica Agnetti
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Tim Roloff
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Denise Wälchli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Dimitri Shcherbakov
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Rashid Akbergenov
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Sarah Tschudin-Sutter
- Infectious Diseases and Hospital Epidemiology, University Hospital Basel and University of Basel, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Stefano Bassetti
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Martin Siegemund
- Department of Clinical Research, University of Basel, Basel, Switzerland
- Intensive Care Unit, University Hospital Basel, Basel, Switzerland
| | - Christian H Nickel
- Emergency Department, University Hospital Basel and University of Basel, Basel, Switzerland
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben Gurion University of the Negev, Be'er Sheva, Israel
| | - Timothy G Keys
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | | | - Nicholas R Thomson
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, UK
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
- Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland.
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2
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Shcherbakov D, Nigri M, Akbergenov R, Brilkova M, Mantovani M, Petit PI, Grimm A, Karol AA, Teo Y, Sanchón AC, Kumar Y, Eckert A, Thiam K, Seebeck P, Wolfer DP, Böttger EC. Premature aging in mice with error-prone protein synthesis. Sci Adv 2022; 8:eabl9051. [PMID: 35235349 PMCID: PMC8890705 DOI: 10.1126/sciadv.abl9051] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The main source of error in gene expression is messenger RNA decoding by the ribosome. Translational accuracy has been suggested on a purely correlative basis to positively coincide with maximum possible life span among different rodent species, but causal evidence that translation errors accelerate aging in vivo and limit life span is lacking. We have now addressed this question experimentally by creating heterozygous knock-in mice that express the ribosomal ambiguity mutation RPS9 D95N, resulting in genome-wide error-prone translation. Here, we show that Rps9 D95N knock-in mice exhibit reduced life span and a premature onset of numerous aging-related phenotypes, such as reduced weight, chest deformation, hunchback posture, poor fur condition, and urinary syndrome, together with lymphopenia, increased levels of reactive oxygen species-inflicted damage, accelerated age-related changes in DNA methylation, and telomere attrition. Our results provide an experimental link between translational accuracy, life span, and aging-related phenotypes in mammals.
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Affiliation(s)
- Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Martina Nigri
- Anatomisches Institut, Universität Zürich, and Institut für Bewegungswissenschaften und Sport, ETH Zürich, CH-8057 Zurich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Margarita Brilkova
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Matilde Mantovani
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | | | - Amandine Grimm
- Universitäre Psychiatrische Kliniken Basel, Transfaculty Research Platform Molecular and Cognitive Neurosciences, CH-4055 Basel, Switzerland
| | - Agnieszka A. Karol
- Musculoskeletal Research Unit (MSRU), Vetsuisse Faculty, University of Zurich, CH-8057 Zurich, Switzerland
| | - Youjin Teo
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Adrián Cortés Sanchón
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
| | - Yadhu Kumar
- Eurofins Genomics Europe Sequencing GmbH, D-78467 Konstanz, Germany
| | - Anne Eckert
- Universitäre Psychiatrische Kliniken Basel, Transfaculty Research Platform Molecular and Cognitive Neurosciences, CH-4055 Basel, Switzerland
| | | | - Petra Seebeck
- Zurich Integrative Rodent Physiology (ZIRP), University of Zurich, CH-8057 Zurich, Switzerland
| | - David P. Wolfer
- Anatomisches Institut, Universität Zürich, and Institut für Bewegungswissenschaften und Sport, ETH Zürich, CH-8057 Zurich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, CH-8006 Zurich, Switzerland
- Corresponding author.
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3
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Shcherbakov D, Teo Y, Boukari H, Cortes-Sanchon A, Mantovani M, Osinnii I, Moore J, Juskeviciene R, Brilkova M, Duscha S, Kumar HS, Laczko E, Rehrauer H, Westhof E, Akbergenov R, Böttger EC. Ribosomal mistranslation leads to silencing of the unfolded protein response and increased mitochondrial biogenesis. Commun Biol 2019; 2:381. [PMID: 31637312 PMCID: PMC6797716 DOI: 10.1038/s42003-019-0626-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/20/2019] [Indexed: 12/19/2022] Open
Abstract
Translation fidelity is the limiting factor in the accuracy of gene expression. With an estimated frequency of 10-4, errors in mRNA decoding occur in a mostly stochastic manner. Little is known about the response of higher eukaryotes to chronic loss of ribosomal accuracy as per an increase in the random error rate of mRNA decoding. Here, we present a global and comprehensive picture of the cellular changes in response to translational accuracy in mammalian ribosomes impaired by genetic manipulation. In addition to affecting established protein quality control pathways, such as elevated transcript levels for cytosolic chaperones, activation of the ubiquitin-proteasome system, and translational slowdown, ribosomal mistranslation led to unexpected responses. In particular, we observed increased mitochondrial biogenesis associated with import of misfolded proteins into the mitochondria and silencing of the unfolded protein response in the endoplasmic reticulum.
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Affiliation(s)
- Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Youjin Teo
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Adrian Cortes-Sanchon
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Matilde Mantovani
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Ivan Osinnii
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - James Moore
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Reda Juskeviciene
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Margarita Brilkova
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | | | - Endre Laczko
- Functional Genomics Center Zurich, ETH Zürich und Universität Zürich, 8057 Zurich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zürich und Universität Zürich, 8057 Zurich, Switzerland
| | - Eric Westhof
- Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 67084 Strasbourg, France
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zurich, Switzerland
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4
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Akbergenov R, Duscha S, Fritz AK, Juskeviciene R, Oishi N, Schmitt K, Shcherbakov D, Teo Y, Boukari H, Freihofer P, Isnard-Petit P, Oettinghaus B, Frank S, Thiam K, Rehrauer H, Westhof E, Schacht J, Eckert A, Wolfer D, Böttger EC. Mutant MRPS5 affects mitoribosomal accuracy and confers stress-related behavioral alterations. EMBO Rep 2018; 19:embr.201846193. [PMID: 30237157 PMCID: PMC6216279 DOI: 10.15252/embr.201846193] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 08/21/2018] [Accepted: 08/24/2018] [Indexed: 12/30/2022] Open
Abstract
The 1555 A to G substitution in mitochondrial 12S A‐site rRNA is associated with maternally transmitted deafness of variable penetrance in the absence of otherwise overt disease. Here, we recapitulate the suggested A1555G‐mediated pathomechanism in an experimental model of mitoribosomal mistranslation by directed mutagenesis of mitoribosomal protein MRPS5. We first establish that the ratio of cysteine/methionine incorporation and read‐through of mtDNA‐encoded MT‐CO1 protein constitute reliable measures of mitoribosomal misreading. Next, we demonstrate that human HEK293 cells expressing mutant V336Y MRPS5 show increased mitoribosomal mistranslation. As for immortalized lymphocytes of individuals with the pathogenic A1555G mutation, we find little changes in the transcriptome of mutant V336Y MRPS5 HEK cells, except for a coordinated upregulation of transcripts for cytoplasmic ribosomal proteins. Homozygous knock‐in mutant Mrps5 V338Y mice show impaired mitochondrial function and a phenotype composed of enhanced susceptibility to noise‐induced hearing damage and anxiety‐related behavioral alterations. The experimental data in V338Y mutant mice point to a key role of mitochondrial translation and function in stress‐related behavioral and physiological adaptations.
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Affiliation(s)
- Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Ann-Kristina Fritz
- Anatomisches Institut, Universität Zürich, Zürich, Switzerland.,Institut für Bewegungswissenschaften und Sport, ETH Zürich, Zürich, Switzerland
| | - Reda Juskeviciene
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Naoki Oishi
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI, USA
| | - Karen Schmitt
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, Universitäre Psychiatrische Kliniken Basel, Basel, Switzerland
| | - Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Youjin Teo
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Pietro Freihofer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | | | - Björn Oettinghaus
- Neuro- und Ophthalmopathologie, Universitätsspital Basel, Basel, Switzerland
| | - Stephan Frank
- Neuro- und Ophthalmopathologie, Universitätsspital Basel, Basel, Switzerland
| | | | - Hubert Rehrauer
- Functional Genomics Center Zurich, ETH Zürich und Universität Zürich, Zürich, Switzerland
| | - Eric Westhof
- Institut de biologie moléculaire et cellulaire du CNRS, Université de Strasbourg, Strasbourg, France
| | - Jochen Schacht
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, MI, USA
| | - Anne Eckert
- Transfaculty Research Platform Molecular and Cognitive Neurosciences, Universitäre Psychiatrische Kliniken Basel, Basel, Switzerland
| | - David Wolfer
- Anatomisches Institut, Universität Zürich, Zürich, Switzerland.,Institut für Bewegungswissenschaften und Sport, ETH Zürich, Zürich, Switzerland
| | - Erik C Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
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5
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Alexandrova A, Karpova O, Nargilova R, Kryldakov R, Nizkorodova A, Zhigaylov A, Yekaterinskaya E, Kushnarenko S, Akbergenov R, Iskakov B. Distribution of potato (Solanum tuberosum) viruses in Kazakhstan. IJBCh 2018. [DOI: 10.26577/ijbch-2018-1-311] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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6
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Freihofer P, Akbergenov R, Teo Y, Juskeviciene R, Andersson DI, Böttger EC. Nonmutational compensation of the fitness cost of antibiotic resistance in mycobacteria by overexpression of tlyA rRNA methylase. RNA 2016; 22:1836-1843. [PMID: 27698071 PMCID: PMC5113204 DOI: 10.1261/rna.057257.116] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/31/2016] [Indexed: 05/08/2023]
Abstract
Several studies over the last few decades have shown that antibiotic resistance mechanisms frequently confer a fitness cost and that these costs can be genetically ameliorated by intra- or extragenic second-site mutations, often without loss of resistance. Another, much less studied potential mechanism by which the fitness cost of antibiotic resistance could be reduced is via a regulatory response where the deleterious effect of the resistance mechanism is lowered by a physiological alteration that buffers the mutational effect. In mycobacteria, resistance to the clinically used tuberactinomycin antibiotic capreomycin involves loss-of-function mutations in rRNA methylase TlyA or point mutations in 16S rRNA (in particular the A1408G mutation). Both of these alterations result in resistance by reducing drug binding to the ribosome. Here we show that alterations of tlyA gene expression affect both antibiotic drug susceptibility and fitness cost of drug resistance. In particular, we demonstrate that the common resistance mutation A1408G is accompanied by a physiological change that involves increased expression of the tlyA gene. This gene encodes an enzyme that methylates neighboring 16S rRNA position C1409, and as a result of increased TlyA expression the fitness cost of the A1408G mutation is significantly reduced. Our findings suggest that in mycobacteria, a nonmutational mechanism (i.e., gene regulatory) can restore fitness to genetically resistant bacteria. Our results also point to a new and clinically relevant treatment strategy to combat evolution of resistance in multidrug-resistant tuberculosis. Thus, by utilizing antagonistic antibiotic interactions, resistance evolution could be reduced.
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Affiliation(s)
- Pietro Freihofer
- Institute of Medical Microbiology, University of Zurich, CH-8006 Zurich, Switzerland
| | - Rashid Akbergenov
- Institute of Medical Microbiology, University of Zurich, CH-8006 Zurich, Switzerland
| | - Youjin Teo
- Institute of Medical Microbiology, University of Zurich, CH-8006 Zurich, Switzerland
| | - Reda Juskeviciene
- Institute of Medical Microbiology, University of Zurich, CH-8006 Zurich, Switzerland
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 23 Uppsala, Sweden
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, CH-8006 Zurich, Switzerland
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7
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Abstract
RNA silencing pathways were first discovered in plants. Through genetic analysis, it has been established that the key silencing components called Dicer-like (DCL) genes have been shown to cooperatively process RNA substrates of multiple origin into distinct 21, 22 and 24 nt small RNAs. However, only few detailed biochemical analysis of the corresponding complexes has been carried out in plants, mainly due to the large unstable complexes that are hard to obtain or reconstitute in heterologous systems. Reconstitution of activity needs thorough understanding of all protein partners in the complex, something that is still an ongoing process in plant systems. Here, we use biochemical analysis to uncover properties of two previously identified native dicer-like activities from wheat germ. We find that standard wheat germ extract contains Dicer-like enzymes that convert double-stranded RNA (dsRNA) into two classes of small interfering RNAs of 21 and 24 nt in size. The 21 nt dicing activity, likely an siRNA producing complex known as DCL4, is 950 kDa-1.2 mDa in size and is highly unstable during purification processes but has a rather vast range for activity. On the contrary, the 24 nt dicing complex, likely the DCL3 activity, is relatively stable and comparatively smaller in size, but has stricter conditions for effective processing of dsRNA substrates. While both activities could process completely complementary dsRNA albeit with varying abilities, we show that DCL3-like 24 nt producing activity is equally good in processing incompletely complementary RNAs.
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Affiliation(s)
| | - Thomas Hohn
- Department of Plant Physiology, Botanical Institute, University of Basel, Basel, Switzerland
| | - Rashid Akbergenov
- Institute for Medical Microbiology, University of Zurich, Zurich, Switzerland
- * E-mail: (PVS); (RA)
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8
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Duscha S, Boukari H, Shcherbakov D, Salian S, Silva S, Kendall A, Kato T, Akbergenov R, Perez-Fernandez D, Bernet B, Vaddi S, Thommes P, Schacht J, Crich D, Vasella A, Böttger EC. Identification and evaluation of improved 4'-O-(alkyl) 4,5-disubstituted 2-deoxystreptamines as next-generation aminoglycoside antibiotics. mBio 2014; 5:e01827-14. [PMID: 25271289 PMCID: PMC4196235 DOI: 10.1128/mbio.01827-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [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: 08/27/2014] [Accepted: 08/29/2014] [Indexed: 01/15/2023] Open
Abstract
UNLABELLED The emerging epidemic of drug resistance places the development of efficacious and safe antibiotics in the spotlight of current research. Here, we report the design of next-generation aminoglycosides. Discovery efforts were driven by rational synthesis focusing on 4' alkylations of the aminoglycoside paromomycin, with the goal to alleviate the most severe and disabling side effect of aminoglycosides-irreversible hearing loss. Compounds were evaluated for target activity in in vitro ribosomal translation assays, antibacterial potency against selected pathogens, cytotoxicity against mammalian cells, and in vivo ototoxicity. The results of this study produced potent compounds with excellent selectivity at the ribosomal target, promising antibacterial activity, and little, if any, ototoxicity upon chronic administration. The favorable biocompatibility profile combined with the promising antibacterial activity emphasizes the potential of next-generation aminoglycosides in the treatment of infectious diseases without the risk of ototoxicity. IMPORTANCE The ever-widening epidemic of multidrug-resistant infectious diseases and the paucity of novel antibacterial agents emerging from modern screening platforms mandate the reinvestigation of established drugs with an emphasis on improved biocompatibility and overcoming resistance mechanisms. Here, we describe the preparation and evaluation of derivatives of the established aminoglycoside antibiotic paromomycin that effectively remove its biggest deficiency, ototoxicity, and overcome certain bacterial resistance mechanisms.
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Affiliation(s)
- Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Dimitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Sumantha Salian
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Sandrina Silva
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Ann Kendall
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - Takayuki Kato
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | | | - Bruno Bernet
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | | | - Pia Thommes
- Euprotec Limited, Manchester, United Kingdom
| | - Jochen Schacht
- Department of Otolaryngology, Kresge Hearing Research Institute, University of Michigan, Ann Arbor, Michigan, USA
| | - David Crich
- Department of Chemistry, Wayne State University, Detroit, Michigan, USA
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
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9
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Perez-Fernandez D, Shcherbakov D, Matt T, Leong NC, Kudyba I, Duscha S, Boukari H, Patak R, Dubbaka SR, Lang K, Meyer M, Akbergenov R, Freihofer P, Vaddi S, Thommes P, Ramakrishnan V, Vasella A, Böttger EC. 4'-O-substitutions determine selectivity of aminoglycoside antibiotics. Nat Commun 2014; 5:3112. [PMID: 24473108 PMCID: PMC3942853 DOI: 10.1038/ncomms4112] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [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: 04/02/2013] [Accepted: 12/16/2013] [Indexed: 02/04/2023] Open
Abstract
Clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. Here we present a series of 4',6'-O-acetal and 4'-O-ether modifications on glucopyranosyl ring I of aminoglycosides. Chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact poorly with the drug-binding pocket of eukaryotic mitochondrial or cytosolic ribosomes. Yet, these compounds largely retain their inhibitory activity for bacterial ribosomes and show antibacterial activity. Our data indicate that 4'-O-substituted aminoglycosides possess increased selectivity towards bacterial ribosomes and little activity for any of the human drug-binding pockets.
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Affiliation(s)
- Déborah Perez-Fernandez
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
- These authors contributed equally to this work
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
- These authors contributed equally to this work
| | - Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Ng Chyan Leong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- These authors contributed equally to this work
| | - Iwona Kudyba
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Heithem Boukari
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashmi Patak
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Srinivas Reddy Dubbaka
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Kathrin Lang
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Pietro Freihofer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
| | - Swapna Vaddi
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - Pia Thommes
- Euprotec Limited, Unit 12 Williams House, Manchester Science Park, Lloyd Street North, Manchester M15 6SE, UK
| | - V. Ramakrishnan
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, 8006 Zürich, Switzerland
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10
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Salian S, Matt T, Akbergenov R, Harish S, Meyer M, Duscha S, Shcherbakov D, Bernet BB, Vasella A, Westhof E, Böttger EC. Structure-activity relationships among the kanamycin aminoglycosides: role of ring I hydroxyl and amino groups. Antimicrob Agents Chemother 2012; 56:6104-8. [PMID: 22948879 PMCID: PMC3497201 DOI: 10.1128/aac.01326-12] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/26/2012] [Indexed: 11/20/2022] Open
Abstract
The kanamycins form an important subgroup of the 4,6-disubstituted 2-deoxystreptamine aminoglycoside antibiotics, comprising kanamycin A, kanamycin B, tobramycin, and dibekacin. These compounds interfere with protein synthesis by targeting the ribosomal decoding A site, and they differ in the numbers and locations of amino and hydroxy groups of the glucopyranosyl moiety (ring I). We synthesized kanamycin analogues characterized by subtle variations of the 2' and 6' substituents of ring I. The functional activities of the kanamycins and the synthesized analogues were investigated (i) in cell-free translation assays on wild-type and mutant bacterial ribosomes to study drug-target interaction, (ii) in MIC assays to assess antibacterial activity, and (iii) in rabbit reticulocyte translation assays to determine activity on eukaryotic ribosomes. Position 2' forms an intramolecular H bond with O5 of ring II, helping the relative orientations of the two rings with respect to each other. This bond becomes critical for drug activity when a 6'-OH substituent is present.
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Affiliation(s)
- Sumantha Salian
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Shinde Harish
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
| | - Bruno B. Bernet
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Andrea Vasella
- Laboratorium für Organische Chemie, ETH Zürich, Zürich, Switzerland
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire Centre National de la Recherche Scientifique, Strasbourg, France
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, Zürich, Switzerland
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11
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Matt T, Ng CL, Lang K, Sha SH, Akbergenov R, Shcherbakov D, Meyer M, Duscha S, Xie J, Dubbaka SR, Perez-Fernandez D, Vasella A, Ramakrishnan V, Schacht J, Böttger EC. Dissociation of antibacterial activity and aminoglycoside ototoxicity in the 4-monosubstituted 2-deoxystreptamine apramycin. Proc Natl Acad Sci U S A 2012; 109:10984-9. [PMID: 22699498 PMCID: PMC3390888 DOI: 10.1073/pnas.1204073109] [Citation(s) in RCA: 152] [Impact Index Per Article: 12.7] [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] [Indexed: 01/10/2023] Open
Abstract
Aminoglycosides are potent antibacterials, but therapy is compromised by substantial toxicity causing, in particular, irreversible hearing loss. Aminoglycoside ototoxicity occurs both in a sporadic dose-dependent and in a genetically predisposed fashion. We recently have developed a mechanistic concept that postulates a key role for the mitochondrial ribosome (mitoribosome) in aminoglycoside ototoxicity. We now report on the surprising finding that apramycin, a structurally unique aminoglycoside licensed for veterinary use, shows little activity toward eukaryotic ribosomes, including hybrid ribosomes which were genetically engineered to carry the mitoribosomal aminoglycoside-susceptibility A1555G allele. In ex vivo cultures of cochlear explants and in the in vivo guinea pig model of chronic ototoxicity, apramycin causes only little hair cell damage and hearing loss but it is a potent antibacterial with good activity against a range of clinical pathogens, including multidrug-resistant Mycobacterium tuberculosis. These data provide proof of concept that antibacterial activity can be dissected from aminoglycoside ototoxicity. Together with 3D structures of apramycin-ribosome complexes at 3.5-Å resolution, our results provide a conceptual framework for further development of less toxic aminoglycosides by hypothesis-driven chemical synthesis.
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Affiliation(s)
- Tanja Matt
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Chyan Leong Ng
- Structural Studies Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Kathrin Lang
- Structural Studies Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Su-Hua Sha
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109; and
| | - Rashid Akbergenov
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Dmitri Shcherbakov
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Martin Meyer
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Stefan Duscha
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
| | - Jing Xie
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109; and
| | - Srinivas R. Dubbaka
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Déborah Perez-Fernandez
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - Andrea Vasella
- Laboratorium für Organische Chemie, Eidgenössische Technische Hochschule Zürich, 8093 Zürich, Switzerland
| | - V. Ramakrishnan
- Structural Studies Division, Medical Research Council (MRC) Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Jochen Schacht
- Kresge Hearing Research Institute, Department of Otolaryngology, Head and Neck Surgery, University of Michigan, Ann Arbor, MI 48109; and
| | - Erik C. Böttger
- Institut für Medizinische Mikrobiologie, Universität Zürich, 8006 Zürich, Switzerland
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12
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Amin I, Hussain K, Akbergenov R, Yadav JS, Qazi J, Mansoor S, Hohn T, Fauquet CM, Briddon RW. Suppressors of RNA silencing encoded by the components of the cotton leaf curl begomovirus-betasatellite complex. Mol Plant Microbe Interact 2011; 24:973-83. [PMID: 21751853 DOI: 10.1094/mpmi-01-11-0001] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Begomoviruses (family Geminiviridae) are single-stranded DNA viruses transmitted by the whitefly Bemisia tabaci. Many economically important diseases in crops are caused by begomoviruses, particularly in tropical and subtropical environments. These include the betasatellite-associated begomoviruses causing cotton leaf curl disease (CLCuD) that causes significant losses to a mainstay of the economy of Pakistan, cotton. RNA interference (RNAi) or gene silencing is a natural defense response of plants against invading viruses. In counter-defense, viruses encode suppressors of gene silencing that allow them to effectively invade plants. Here, we have analyzed the ability of the begomovirus Cotton leaf curl Multan virus (CLCuMV) and its associated betasatellite, Cotton leaf curl Multan β-satellite (CLCuMB) which, together, cause CLCuD, and the nonessential alphasatellite (Cotton leaf curl Multan alphasatellite [CLCuMA]) for their ability to suppress gene silencing in Nicotiana benthamiana. The results showed that CLCuMV by itself was unable to efficiently block silencing. However, in the presence of the betasatellite, gene silencing was entirely suppressed. Silencing was not affected in any way when infections included CLCuMA, although the alphasatellite was, for the first time, shown to be a target of RNA silencing, inducing the production in planta of specific small interfering RNAs, the effectors of silencing. Subsequently, using a quantitative real-time polymerase chain reaction assay and Northern blot analysis, the ability of all proteins encoded by CLCuMV and CLCuMB were assessed for their ability to suppress RNAi and the relative strengths of their suppression activity were compared. The analysis showed that the V2, C2, C4, and βC1 proteins exhibited suppressor activity, with the V2 showing the strongest activity. In addition, V2, C4, and βC1 were examined for their ability to bind RNA and shown to have distinct specificities. Although each of these proteins has, for other begomoviruses or betasatellites, been previously shown to have suppressor activity, this is the first time all proteins encoded by a geminiviruses (or begomovirus-betasatellite complex) have been examined and also the first for which four separate suppressors have been identified.
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Affiliation(s)
- Imran Amin
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
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13
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14
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Shcherbakov D, Akbergenov R, Matt T, Sander P, Andersson DI, Böttger EC. Directed mutagenesis of Mycobacterium smegmatis 16S rRNA to reconstruct the in vivo evolution of aminoglycoside resistance in Mycobacterium tuberculosis. Mol Microbiol 2010; 77:830-40. [DOI: 10.1111/j.1365-2958.2010.07218.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Vogler H, Akbergenov R, Shivaprasad PV, Dang V, Fasler M, Kwon MO, Zhanybekova S, Hohn T, Heinlein M. Modification of small RNAs associated with suppression of RNA silencing by tobamovirus replicase protein. J Virol 2007; 81:10379-88. [PMID: 17634237 PMCID: PMC2045474 DOI: 10.1128/jvi.00727-07] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2007] [Accepted: 07/09/2007] [Indexed: 12/26/2022] Open
Abstract
Plant viruses act as triggers and targets of RNA silencing and have evolved proteins to suppress this plant defense response during infection. Although Tobacco mosaic tobamovirus (TMV) triggers the production of virus-specific small interfering RNAs (siRNAs), this does not lead to efficient silencing of TMV nor is a TMV-green fluorescent protein (GFP) hybrid able to induce silencing of a GFP-transgene in Nicotiana benthamiana, indicating that a TMV silencing suppressor is active and acts downstream of siRNA production. On the other hand, TMV-GFP is unable to spread into cells in which GFP silencing is established, suggesting that the viral silencing suppressor cannot revert silencing that is already established. Although previous evidence indicates that the tobamovirus silencing suppressing activity resides in the viral 126-kDa small replicase subunit, the mechanism of silencing suppression by this virus family is not known. Here, we connect the silencing suppressing activity of this protein with our previous finding that Oilseed rape mosaic tobamovirus infection leads to interference with HEN1-mediated methylation of siRNA and micro-RNA (miRNA). We demonstrate that TMV infection similarly leads to interference with HEN1-mediated methylation of small RNAs and that this interference and the formation of virus-induced disease symptoms are linked to the silencing suppressor activity of the 126-kDa protein. Moreover, we show that also Turnip crinkle virus interferes with the methylation of siRNA but, in contrast to tobamoviruses, not with the methylation of miRNA.
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Affiliation(s)
- Hannes Vogler
- Department of Plant Physiology, Botanical Institute, University of Basel, Switzerland
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16
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Vanderschuren H, Akbergenov R, Pooggin MM, Hohn T, Gruissem W, Zhang P. Transgenic cassava resistance to African cassava mosaic virus is enhanced by viral DNA-A bidirectional promoter-derived siRNAs. Plant Mol Biol 2007; 64:549-57. [PMID: 17492253 DOI: 10.1007/s11103-007-9175-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Accepted: 04/16/2007] [Indexed: 05/12/2023]
Abstract
Expression of double-stranded RNA (dsRNA) homologous to virus sequences can effectively interfere with RNA virus infection in plant cells by triggering RNA silencing. Here we applied this approach against a DNA virus, African cassava mosaic virus (ACMV), in its natural host cassava. Transgenic cassava plants were developed to express small interfering RNAs (siRNA) from a CaMV 35S promoter-controlled, intron-containing dsRNA cognate to the common region-containing bidirectional promoter of ACMV DNA-A. In two of three independent transgenic lines, accelerated plant recovery from ACMV-NOg infection was observed, which correlates with the presence of transgene-derived siRNAs 21-24 nt in length. Overall, cassava mosaic disease symptoms were dramatically attenuated in these two lines and less viral DNA accumulation was detected in their leaves than in those of wild-type plants. In a transient replication assay using leaf disks from the two transgenic lines, strongly reduced accumulation of viral single-stranded DNA was observed. Our study suggests that a natural RNA silencing mechanism targeting DNA viruses through production of virus-derived siRNAs is turned on earlier and more efficiently in transgenic plants expressing dsRNA cognate to the viral promoter and common region.
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Affiliation(s)
- Hervé Vanderschuren
- Institute of Plant Sciences, ETH Zurich, Universitätstrasse 2, Zürich, 8092, Switzerland
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17
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Noreen F, Akbergenov R, Hohn T, Richert-Pöggeler KR. Distinct expression of endogenous Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production. Plant J 2007; 50:219-29. [PMID: 17444906 DOI: 10.1111/j.1365-313x.2007.03040.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Endogenous viruses exist in all kingdoms. They usually have active mechanisms of integration, as in bacteriophage lambda and animal retroviruses, and sophisticated mechanisms to maintain a proviral state over decades and generations. Plant para retroviruses, however, neither have an integrase, nor genes for maintaining the proviral state. How are those elements controlled, and under what conditions can they be activated? Here we study the proviral state of endogenous petunia vein clearing virus (ePVCV). Our results support the hypothesis that the proviral state is associated with a host silencing mechanism manifested by DNA methylation, chromatin modification and production of small interfering (si) RNAs. PVCV may be induced by applying abiotic stress, leading to the development of viral symptoms and increased transcript and siRNA levels. Similar levels of ePVCV DNA methylation were observed in two different lines of Petunia hybrida, RdC (rose du ciel) and W138, the latter known for its active version of transposon dTph1. In contrast, significant differences in histone modification were detected. The predominant association of ePVCV sequences with histone H3 methylated at lysine 9 (H3mK9) in RdC and with about equal amounts of H3mK9 and H3mK4 in W138 indicates a less repressive proviral state in the latter cultivar.
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Affiliation(s)
- Faiza Noreen
- Friedrich Miescher Institute, Maulbeerstlasse 66, CH-4058 Basel, Switzerland
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18
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Noreen F, Akbergenov R, Hohn T, Richert-Pöggeler KR. Distinct expression of endogenous Petunia vein clearing virus and the DNA transposon dTph1 in two Petunia hybrida lines is correlated with differences in histone modification and siRNA production. Plant J 2007; 50:219-229. [PMID: 17444906 DOI: 10.1071/ap06016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Endogenous viruses exist in all kingdoms. They usually have active mechanisms of integration, as in bacteriophage lambda and animal retroviruses, and sophisticated mechanisms to maintain a proviral state over decades and generations. Plant para retroviruses, however, neither have an integrase, nor genes for maintaining the proviral state. How are those elements controlled, and under what conditions can they be activated? Here we study the proviral state of endogenous petunia vein clearing virus (ePVCV). Our results support the hypothesis that the proviral state is associated with a host silencing mechanism manifested by DNA methylation, chromatin modification and production of small interfering (si) RNAs. PVCV may be induced by applying abiotic stress, leading to the development of viral symptoms and increased transcript and siRNA levels. Similar levels of ePVCV DNA methylation were observed in two different lines of Petunia hybrida, RdC (rose du ciel) and W138, the latter known for its active version of transposon dTph1. In contrast, significant differences in histone modification were detected. The predominant association of ePVCV sequences with histone H3 methylated at lysine 9 (H3mK9) in RdC and with about equal amounts of H3mK9 and H3mK4 in W138 indicates a less repressive proviral state in the latter cultivar.
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Affiliation(s)
- Faiza Noreen
- Friedrich Miescher Institute, Maulbeerstlasse 66, CH-4058 Basel, Switzerland
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19
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Akbergenov R, Si-Ammour A, Blevins T, Amin I, Kutter C, Vanderschuren H, Zhang P, Gruissem W, Meins F, Hohn T, Pooggin MM. Molecular characterization of geminivirus-derived small RNAs in different plant species. Nucleic Acids Res 2006; 34:462-71. [PMID: 16421273 PMCID: PMC1342034 DOI: 10.1093/nar/gkj447] [Citation(s) in RCA: 191] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 12/23/2005] [Accepted: 01/03/2006] [Indexed: 11/23/2022] Open
Abstract
DNA geminiviruses are thought to be targets of RNA silencing. Here, we characterize small interfering (si) RNAs-the hallmarks of silencing-associated with Cabbage leaf curl begomovirus in Arabidopsis and African cassava mosaic begomovirus in Nicotiana benthamiana and cassava. We detected 21, 22 and 24 nt siRNAs of both polarities, derived from both the coding and the intergenic regions of these geminiviruses. Genetic evidence showed that all the 24 nt and a substantial fraction of the 22 nt viral siRNAs are generated by the dicer-like proteins DCL3 and DCL2, respectively. The viral siRNAs were 5' end phosphorylated, as shown by phosphatase treatments, and methylated at the 3'-nucleotide, as shown by HEN1 miRNA methylase-dependent resistance to beta-elimination. Similar modifications were found in all types of endogenous and transgene-derived siRNAs tested, but not in a major fraction of siRNAs from a cytoplasmic RNA tobamovirus. We conclude that several distinct silencing pathways are involved in DNA virus-plant interactions.
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Affiliation(s)
- Rashid Akbergenov
- Institute of Botany, University of BaselSchönbeinstrasse 6, 4056 Basel, Switzerland
| | - Azeddine Si-Ammour
- Friedrich Miescher Institute for Biomedical ResearchMaulbeerstrasse 66, 4058 Basel, Switzerland
| | - Todd Blevins
- Friedrich Miescher Institute for Biomedical ResearchMaulbeerstrasse 66, 4058 Basel, Switzerland
| | - Imran Amin
- Institute of Botany, University of BaselSchönbeinstrasse 6, 4056 Basel, Switzerland
| | - Claudia Kutter
- Friedrich Miescher Institute for Biomedical ResearchMaulbeerstrasse 66, 4058 Basel, Switzerland
| | - Herve Vanderschuren
- Institute of Plant Sciences, ETH-Zurich, LFW E17, Universitätstrasse 28092 Zürich, Switzerland
| | - Peng Zhang
- Institute of Plant Sciences, ETH-Zurich, LFW E17, Universitätstrasse 28092 Zürich, Switzerland
| | - Wilhelm Gruissem
- Institute of Plant Sciences, ETH-Zurich, LFW E17, Universitätstrasse 28092 Zürich, Switzerland
| | - Frederick Meins
- Friedrich Miescher Institute for Biomedical ResearchMaulbeerstrasse 66, 4058 Basel, Switzerland
| | - Thomas Hohn
- Institute of Botany, University of BaselSchönbeinstrasse 6, 4056 Basel, Switzerland
- Friedrich Miescher Institute for Biomedical ResearchMaulbeerstrasse 66, 4058 Basel, Switzerland
| | - Mikhail M. Pooggin
- Institute of Botany, University of BaselSchönbeinstrasse 6, 4056 Basel, Switzerland
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20
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Trinks D, Rajeswaran R, Shivaprasad PV, Akbergenov R, Oakeley EJ, Veluthambi K, Hohn T, Pooggin MM. Suppression of RNA silencing by a geminivirus nuclear protein, AC2, correlates with transactivation of host genes. J Virol 2005; 79:2517-27. [PMID: 15681452 PMCID: PMC546592 DOI: 10.1128/jvi.79.4.2517-2527.2005] [Citation(s) in RCA: 182] [Impact Index Per Article: 9.6] [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: 12/20/2022] Open
Abstract
Bipartite geminiviruses encode a small protein, AC2, that functions as a transactivator of viral transcription and a suppressor of RNA silencing. A relationship between these two functions had not been investigated before. We characterized both of these functions for AC2 from Mungbean yellow mosaic virus-Vigna (MYMV). When transiently expressed in plant protoplasts, MYMV AC2 strongly transactivated the viral promoter; AC2 was detected in the nucleus, and a split nuclear localization signal (NLS) was mapped. In a model Nicotiana benthamiana plant, in which silencing can be triggered biolistically, AC2 reduced local silencing and prevented its systemic spread. Mutations in the AC2 NLS or Zn finger or deletion of its activator domain abolished both these effects, suggesting that suppression of silencing by AC2 requires transactivation of host suppressor(s). In line with this, in Arabidopsis protoplasts, MYMV AC2 or its homologue from African cassava mosaic geminivirus coactivated >30 components of the plant transcriptome, as detected with Affymetrix ATH1 GeneChips. Several corresponding promoters cloned from Arabidopsis were strongly induced by both AC2 proteins. These results suggest that silencing suppression and transcription activation by AC2 are functionally connected and that some of the AC2-inducible host genes discovered here may code for components of an endogenous network that controls silencing.
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Affiliation(s)
- Daniela Trinks
- Institute of Botany, University of Basel, Schöenbeinstrasse 6, CH-4056 Basel, Switzerland
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21
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Shivaprasad PV, Akbergenov R, Trinks D, Rajeswaran R, Veluthambi K, Hohn T, Pooggin MM. Promoters, transcripts, and regulatory proteins of Mungbean yellow mosaic geminivirus. J Virol 2005; 79:8149-63. [PMID: 15956560 PMCID: PMC1143740 DOI: 10.1128/jvi.79.13.8149-8163.2005] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2004] [Accepted: 03/02/2005] [Indexed: 11/20/2022] Open
Abstract
Geminiviruses package circular single-stranded DNA and replicate in the nucleus via a double-stranded intermediate. This intermediate also serves as a template for bidirectional transcription by polymerase II. Here, we map promoters and transcripts and characterize regulatory proteins of Mungbean yellow mosaic virus-Vigna (MYMV), a bipartite geminivirus in the genus Begomovirus. The following new features, which might also apply to other begomoviruses, were revealed in MYMV. The leftward and rightward promoters on DNA-B share the transcription activator AC2-responsive region, which does not overlap the common region that is nearly identical in the two DNA components. The transcription unit for BC1 (movement protein) includes a conserved, leader-based intron. Besides negative-feedback regulation of its own leftward promoter on DNA-A, the replication protein AC1, in cooperation with AC2, synergistically transactivates the rightward promoter, which drives a dicistronic transcription unit for the coat protein AV1. AC2 and the replication enhancer AC3 are expressed from one dicistronic transcript driven by a strong promoter mapped within the upstream AC1 gene. Early and constitutive expression of AC2 is consistent with its essential dual function as an activator of viral transcription and a suppressor of silencing.
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Affiliation(s)
- P V Shivaprasad
- Institute of Botany, University of Basel, Schönbeinstrasse 6, CH-4056 Basel, Switzerland
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22
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Trinks D, Rajeswaran R, Shivaprasad PV, Akbergenov R, Oakeley EJ, Veluthambi K, Hohn T, Pooggin MM. Suppression of RNA silencing by a geminivirus nuclear protein, AC2, correlates with transactivation of host genes. J Virol 2005. [PMID: 15681452 DOI: 10.1128/jvi.79.4.2517-2527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Bipartite geminiviruses encode a small protein, AC2, that functions as a transactivator of viral transcription and a suppressor of RNA silencing. A relationship between these two functions had not been investigated before. We characterized both of these functions for AC2 from Mungbean yellow mosaic virus-Vigna (MYMV). When transiently expressed in plant protoplasts, MYMV AC2 strongly transactivated the viral promoter; AC2 was detected in the nucleus, and a split nuclear localization signal (NLS) was mapped. In a model Nicotiana benthamiana plant, in which silencing can be triggered biolistically, AC2 reduced local silencing and prevented its systemic spread. Mutations in the AC2 NLS or Zn finger or deletion of its activator domain abolished both these effects, suggesting that suppression of silencing by AC2 requires transactivation of host suppressor(s). In line with this, in Arabidopsis protoplasts, MYMV AC2 or its homologue from African cassava mosaic geminivirus coactivated >30 components of the plant transcriptome, as detected with Affymetrix ATH1 GeneChips. Several corresponding promoters cloned from Arabidopsis were strongly induced by both AC2 proteins. These results suggest that silencing suppression and transcription activation by AC2 are functionally connected and that some of the AC2-inducible host genes discovered here may code for components of an endogenous network that controls silencing.
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Affiliation(s)
- Daniela Trinks
- Institute of Botany, University of Basel, Schöenbeinstrasse 6, CH-4056 Basel, Switzerland
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