101
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Drecktrah D, Lybecker M, Popitsch N, Rescheneder P, Hall LS, Samuels DS. The Borrelia burgdorferi RelA/SpoT Homolog and Stringent Response Regulate Survival in the Tick Vector and Global Gene Expression during Starvation. PLoS Pathog 2015; 11:e1005160. [PMID: 26371761 PMCID: PMC4570706 DOI: 10.1371/journal.ppat.1005160] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/21/2015] [Indexed: 01/09/2023] Open
Abstract
As the Lyme disease bacterium Borrelia burgdorferi traverses its enzootic cycle, alternating between a tick vector and a vertebrate host, the spirochete must adapt and persist in the tick midgut under prolonged nutrient stress between blood meals. In this study, we examined the role of the stringent response in tick persistence and in regulation of gene expression during nutrient limitation. Nutritionally starving B. burgdorferi in vitro increased the levels of guanosine tetraphosphate (ppGpp) and guanosine pentaphosphate (pppGpp), collectively referred to as (p)ppGpp, products of the bifunctional synthetase/hydrolase RelBbu (RelA/SpoT homolog). Conversely, returning B. burgdorferi to a nutrient-rich medium decreased (p)ppGpp levels. B. burgdorferi survival in ticks between the larval and nymph blood meals, and during starvation in vitro, was dependent on RelBbu. Furthermore, normal morphological conversion from a flat-wave shape to a condensed round body (RB) form during starvation was dependent on RelBbu; relBbu mutants more frequently formed RBs, but their membranes were compromised. By differential RNA sequencing analyses, we found that RelBbu regulates an extensive transcriptome, both dependent and independent of nutrient stress. The RelBbu regulon includes the glp operon, which is important for glycerol utilization and persistence in the tick, virulence factors and the late phage operon of the 32-kb circular plasmid (cp32) family. In summary, our data suggest that RelBbu globally modulates transcription in response to nutrient stress by increasing (p)ppGpp levels to facilitate B. burgdorferi persistence in the tick.
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Affiliation(s)
- Dan Drecktrah
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Meghan Lybecker
- Department of Biology, University of Colorado, Colorado Springs, Colorado, United States of America
- Department of Biochemistry and Cell Biology, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Niko Popitsch
- Oxford NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, Vienna, Austria
| | - Philipp Rescheneder
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna & Medical University of Vienna, Vienna, Austria
| | - Laura S. Hall
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - D. Scott Samuels
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
- Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana, United States of America
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102
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Wu Q, Law YS, Shah NP. Dairy Streptococcus thermophilus improves cell viability of Lactobacillus brevis NPS-QW-145 and its γ-aminobutyric acid biosynthesis ability in milk. Sci Rep 2015; 5:12885. [PMID: 26245488 PMCID: PMC4526857 DOI: 10.1038/srep12885] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 07/06/2015] [Indexed: 11/13/2022] Open
Abstract
Most high γ-aminobutyric acid (GABA) producers are Lactobacillus brevis of plant origin, which may be not able to ferment milk well due to its poor proteolytic nature as evidenced by the absence of genes encoding extracellular proteinases in its genome. In the present study, two glutamic acid decarboxylase (GAD) genes, gadA and gadB, were found in high GABA-producing L. brevis NPS-QW-145. Co-culturing of this organism with conventional dairy starters was carried out to manufacture GABA-rich fermented milk. It was observed that all the selected strains of Streptococcus thermophilus, but not Lactobacillus delbrueckii subsp. bulgaricus, improved the viability of L. brevis NPS-QW-145 in milk. Only certain strains of S. thermophilus improved the gadA mRNA level in L. brevis NPS-QW-145, thus enhanced GABA biosynthesis by the latter. These results suggest that certain S. thermophilus strains are highly recommended to co-culture with high GABA producer for manufacturing GABA-rich fermented milk.
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Affiliation(s)
- Qinglong Wu
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Yee-Song Law
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Nagendra P Shah
- Food and Nutritional Science, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong
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103
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Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. FRONTIERS IN PLANT SCIENCE 2015; 6:431. [PMID: 26136759 DOI: 10.3389/fpls.2015.00431.ecollection2015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/27/2015] [Indexed: 05/24/2023]
Abstract
Pathogenic bacteria in the genus Xanthomonas cause diseases on over 350 plant species, including cannabis (Cannabis sativa L.). Because of regulatory limitations, the biology of the Xanthomonas-cannabis pathosystem remains largely unexplored. To gain insight into the evolution of Xanthomonas strains pathogenic to cannabis, we sequenced the genomes of two geographically distinct Xanthomonas strains, NCPPB 3753 and NCPPB 2877, which were previously isolated from symptomatic plant tissue in Japan and Romania. Comparative multilocus sequence analysis of housekeeping genes revealed that they belong to Group 2, which comprises most of the described species of Xanthomonas. Interestingly, both strains lack the Hrp Type III secretion system and do not contain any of the known Type III effectors. Yet their genomes notably encode two key Hrp pathogenicity regulators HrpG and HrpX, and hrpG and hrpX are in the same genetic organization as in the other Group 2 xanthomonads. Promoter prediction of HrpX-regulated genes suggests the induction of an aminopeptidase, a lipase and two polygalacturonases upon plant colonization, similar to other plant-pathogenic xanthomonads. Genome analysis of the distantly related Xanthomonas maliensis strain 97M, which was isolated from a rice leaf in Mali, similarly demonstrated the presence of HrpG, HrpX, and a HrpX-regulated polygalacturonase, and the absence of the Hrp Type III secretion system and known Type III effectors. Given the observation that some Xanthomonas strains across distinct taxa do not contain hrpG and hrpX, we speculate a stepwise evolution of pathogenicity, which involves (i) acquisition of key regulatory genes and cell wall-degrading enzymes, followed by (ii) acquisition of the Hrp Type III secretion system, which is ultimately accompanied by (iii) successive acquisition of Type III effectors.
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Affiliation(s)
- Jonathan M Jacobs
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France
| | - Céline Pesce
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France ; Department of Applied Microbiology, Earth and Life Institute, Université Catholique de Louvain Louvain-la-Neuve, Belgium
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, Cirad, UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical Saint-Pierre, Ile de la Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement - Cirad - Université Montpellier, Interactions Plantes Microorganismes Environnement Montpellier, France
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104
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Optical and analytical investigations on dengue virus rapid diagnostic test for IgM antibody detection. Med Biol Eng Comput 2015; 53:679-87. [DOI: 10.1007/s11517-015-1262-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 02/27/2015] [Indexed: 10/23/2022]
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105
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Makariti I, Printezi A, Kapetanakou A, Zeaki N, Skandamis P. Investigating boundaries of survival, growth and expression of genes associated with stress and virulence of Listeria monocytogenes in response to acid and osmotic stress. Food Microbiol 2015; 45:231-44. [DOI: 10.1016/j.fm.2014.06.023] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 06/18/2014] [Accepted: 06/22/2014] [Indexed: 01/03/2023]
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106
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Jacobs JM, Pesce C, Lefeuvre P, Koebnik R. Comparative genomics of a cannabis pathogen reveals insight into the evolution of pathogenicity in Xanthomonas. FRONTIERS IN PLANT SCIENCE 2015; 6:431. [PMID: 26136759 PMCID: PMC4468381 DOI: 10.3389/fpls.2015.00431] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Accepted: 05/27/2015] [Indexed: 05/05/2023]
Abstract
Pathogenic bacteria in the genus Xanthomonas cause diseases on over 350 plant species, including cannabis (Cannabis sativa L.). Because of regulatory limitations, the biology of the Xanthomonas-cannabis pathosystem remains largely unexplored. To gain insight into the evolution of Xanthomonas strains pathogenic to cannabis, we sequenced the genomes of two geographically distinct Xanthomonas strains, NCPPB 3753 and NCPPB 2877, which were previously isolated from symptomatic plant tissue in Japan and Romania. Comparative multilocus sequence analysis of housekeeping genes revealed that they belong to Group 2, which comprises most of the described species of Xanthomonas. Interestingly, both strains lack the Hrp Type III secretion system and do not contain any of the known Type III effectors. Yet their genomes notably encode two key Hrp pathogenicity regulators HrpG and HrpX, and hrpG and hrpX are in the same genetic organization as in the other Group 2 xanthomonads. Promoter prediction of HrpX-regulated genes suggests the induction of an aminopeptidase, a lipase and two polygalacturonases upon plant colonization, similar to other plant-pathogenic xanthomonads. Genome analysis of the distantly related Xanthomonas maliensis strain 97M, which was isolated from a rice leaf in Mali, similarly demonstrated the presence of HrpG, HrpX, and a HrpX-regulated polygalacturonase, and the absence of the Hrp Type III secretion system and known Type III effectors. Given the observation that some Xanthomonas strains across distinct taxa do not contain hrpG and hrpX, we speculate a stepwise evolution of pathogenicity, which involves (i) acquisition of key regulatory genes and cell wall-degrading enzymes, followed by (ii) acquisition of the Hrp Type III secretion system, which is ultimately accompanied by (iii) successive acquisition of Type III effectors.
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Affiliation(s)
- Jonathan M. Jacobs
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
| | - Céline Pesce
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
- Department of Applied Microbiology, Earth and Life Institute, Université Catholique de LouvainLouvain-la-Neuve, Belgium
| | - Pierre Lefeuvre
- Pôle de Protection des Plantes, Cirad, UMR Peuplements Végétaux et Bioagresseurs en Milieu TropicalSaint-Pierre, Ile de la Réunion, France
| | - Ralf Koebnik
- Institut de Recherche pour le Développement – Cirad – Université Montpellier, Interactions Plantes Microorganismes EnvironnementMontpellier, France
- *Correspondence: Ralf Koebnik, Institut de Recherche pour le Développement, UMR Interactions – Plantes – Microorganismes – Environnement, Génomique et Transcriptomique des Interactions Plantes-Procaryotes, 921 avenue Agropolis, 34394 Montpellier, France
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107
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Hamidou Soumana I, Tchicaya B, Simo G, Geiger A. Comparative gene expression of Wigglesworthia inhabiting non-infected and Trypanosoma brucei gambiense-infected Glossina palpalis gambiensis flies. Front Microbiol 2014; 5:620. [PMID: 25452752 PMCID: PMC4233935 DOI: 10.3389/fmicb.2014.00620] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Accepted: 10/30/2014] [Indexed: 12/29/2022] Open
Abstract
Tsetse flies (Glossina sp.) that transmit trypanosomes causing human (and animal) African trypanosomiasis (HAT and AAT, respectively) harbor symbiotic microorganisms, including the obligate primary symbiont Wigglesworthia glossinidia. A relationship between Wigglesworthia and tsetse fly infection by trypanosomes has been suggested, as removal of the symbiont results in a higher susceptibility to midgut infection in adult flies. To investigate this relationship and to decipher the role of W. glossinidia in the fly's susceptibility to trypanosome infection, we challenged flies with trypanosomes and subsequently analyzed and compared the transcriptomes of W. glossinidia from susceptible and refractory tsetse flies at three time points (3, 10, and 20 days). More than 200 W. glossinidia genes were found to be differentially expressed between susceptible and refractory flies. The high specificity of these differentially expressed genes makes it possible to distinguish Wigglesworthia inhabiting these two distinct groups of flies. Furthermore, gene expression patterns were observed to evolve during the infection time course, such that very few differentially expressed genes were found in common in Wigglesworthia from the 3-, 10- and 20-day post-feeding fly samples. The overall results clearly demonstrate that the taking up of trypanosomes by flies, regardless of whether flies proceed with the developmental program of Trypanosoma brucei gambiense, strongly alters gene expression in Wigglesworthia. These results therefore provide a novel framework for studies that aim to decrease or even abolish tsetse fly vector competence.
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Affiliation(s)
| | - Bernadette Tchicaya
- UMR 177, Institut de Recherche pour le Développement-CIRAD Montpellier, France
| | - Gustave Simo
- Department of Biochemistry, Faculty of Science, University of Dschang Dschang, Cameroon
| | - Anne Geiger
- UMR 177, Institut de Recherche pour le Développement-CIRAD Montpellier, France
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108
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Mutation-driven β-lactam resistance mechanisms among contemporary ceftazidime-nonsusceptible Pseudomonas aeruginosa isolates from U.S. hospitals. Antimicrob Agents Chemother 2014; 58:6844-50. [PMID: 25182652 DOI: 10.1128/aac.03681-14] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
OprD loss and hyperexpression of AmpC, MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM were evaluated among 120 Pseudomonas aeruginosa isolates collected during 2012 in U.S. hospitals and selected based on ceftazidime MIC values (1 to >32 μg/ml). AmpC derepression (10-fold greater than that with the control) and OprD loss (decreased/no band) were the most prevalent resistance mechanisms: 47.5 and 45.8% of the isolates were considered positive, respectively. Elevated expression of the efflux pumps MexAB-OprM, MexCD-OprJ, MexEF-OprN, and MexXY-OprM was observed in 32.5, 8.3, 0.0, and 28.4% of the isolates, respectively. A total of 21 different combinations of resistance mechanisms were noted, and the most prevalent included AmpC derepression with OprD loss with and without efflux hyperexpression (38 and 10 isolates, respectively). A total of 26 isolates had no changes in the resistance mechanisms tested and had lower MIC values for all β-lactams or β-lactam/β-lactamase inhibitor combinations analyzed. OprD loss had a strong correlation with elevated MIC results for imipenem and meropenem (median MIC values of 8 and 4 μg/ml, respectively), with all combinations displaying OprD loss also displaying elevated median MIC values for these carbapenems (4 to >8 μg/ml). AmpC expression levels were greater in isolates displaying elevated cefepime, ceftazidime, or piperacillin-tazobactam MIC values (≥4, ≥4, and ≥16 μg/ml, respectively). Isolates displaying derepressed AmpC had ceftolozane-tazobactam MIC values ranging from 1 to 16 μg/ml. No strong correlation was noticed with MIC values for this β-lactam/β-lactamase inhibitor combination and OprD loss or hyperexpression of efflux systems. Two KPC-producing isolates were detected among 16 isolates displaying ceftolozane-tazobactam MIC values of ≥8 μg/ml.
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109
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Martins R, Queiroz J, Sousa F. Ribonucleic acid purification. J Chromatogr A 2014; 1355:1-14. [DOI: 10.1016/j.chroma.2014.05.075] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 11/24/2022]
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110
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Holmes A, Birse L, Jackson RW, Holden NJ. An optimized method for the extraction of bacterial mRNA from plant roots infected with Escherichia coli O157:H7. Front Microbiol 2014; 5:286. [PMID: 25018749 PMCID: PMC4071639 DOI: 10.3389/fmicb.2014.00286] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 05/23/2014] [Indexed: 01/08/2023] Open
Abstract
Analysis of microbial gene expression during host colonization provides valuable information on the nature of interaction, beneficial or pathogenic, and the adaptive processes involved. Isolation of bacterial mRNA for in planta analysis can be challenging where host nucleic acid may dominate the preparation, or inhibitory compounds affect downstream analysis, e.g., quantitative reverse transcriptase PCR (qPCR), microarray, or RNA-seq. The goal of this work was to optimize the isolation of bacterial mRNA of food-borne pathogens from living plants. Reported methods for recovery of phytopathogen-infected plant material, using hot phenol extraction and high concentration of bacterial inoculation or large amounts of infected tissues, were found to be inappropriate for plant roots inoculated with Escherichia coli O157:H7. The bacterial RNA yields were too low and increased plant material resulted in a dominance of plant RNA in the sample. To improve the yield of bacterial RNA and reduce the number of plants required, an optimized method was developed which combines bead beating with directed bacterial lysis using SDS and lysozyme. Inhibitory plant compounds, such as phenolics and polysaccharides, were counteracted with the addition of high-molecular-weight polyethylene glycol and hexadecyltrimethyl ammonium bromide. The new method increased the total yield of bacterial mRNA substantially and allowed assessment of gene expression by qPCR. This method can be applied to other bacterial species associated with plant roots, and also in the wider context of food safety.
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Affiliation(s)
- Ashleigh Holmes
- Cell and Molecular Sciences, The James Hutton Institute Invergowrie, Dundee, UK
| | - Louise Birse
- Cell and Molecular Sciences, The James Hutton Institute Invergowrie, Dundee, UK
| | - Robert W Jackson
- School of Biological Sciences, The University of Reading Knight Building, Whiteknights, Reading, UK
| | - Nicola J Holden
- Cell and Molecular Sciences, The James Hutton Institute Invergowrie, Dundee, UK
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111
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Burbank L, Roper MC. OxyR and SoxR modulate the inducible oxidative stress response and are implicated during different stages of infection for the bacterial phytopathogen Pantoea stewartii subsp. stewartii. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:479-490. [PMID: 24450773 DOI: 10.1094/mpmi-11-13-0348-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Reactive oxygen species (ROS) from a variety of sources are often encountered by invading plant pathogens during the infection process. Pantoea stewartii subsp. stewartii, the etiological agent of Stewart's wilt, is a serious bacterial pathogen of sweet corn that colonizes both the apoplast and xylem tissues in which ROS are produced. The P. stewartii genome predicts the presence of two redox-sensing transcriptional regulators, OxyR and SoxR, which both activate gene expression in response to oxidative stress. ROS exposure in the form of hydrogen peroxide and the superoxide-generating compound paraquat initiates an induced stress response through OxyR and SoxR that includes activation of the ROS-detoxifying enzymes alkyl hydroperoxide reductase and superoxide dismutase. P. stewartii ΔsoxR was more sensitive to paraquat and was compromised in the ability to form water-soaked lesions, while ΔoxyR was more sensitive to hydrogen peroxide treatment and was deficient in exopolysaccharide production and the elicitation of wilting symptoms. This demonstrates that both SoxR and OxyR play an important role in virulence in the different niches that P. stewartii colonize during the infection process.
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112
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Bocsanczy AM, Achenbach UCM, Mangravita-Novo A, Chow M, Norman DJ. Proteomic comparison of Ralstonia solanacearum strains reveals temperature dependent virulence factors. BMC Genomics 2014; 15:280. [PMID: 24725348 PMCID: PMC4023598 DOI: 10.1186/1471-2164-15-280] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 04/09/2014] [Indexed: 11/29/2022] Open
Abstract
Background Ralstonia solanacearum, the causal agent of bacterial wilt, is a genetically diverse bacterial plant pathogen present in tropical and subtropical regions of the world that infects more than 200 plant species, including economically important solanaceous crops. Most strains of R. solanacearum are only pathogenic at temperatures between 25 to 30°C with strains that can cause disease below 20°C considered a threat to agriculture in temperate areas. Identifying key molecular factors that distinguish strains virulent at cold temperatures from ones that are not is needed to develop effective management tools for this pathogen. We compared protein profiles of two strains virulent at low temperature and two strains not virulent at low temperature when incubated in the rhizosphere of tomato seedlings at 30 and 18°C using quantitative 2D DIGE gel methods. Spot intensities were quantified and compared, and differentially expressed proteins were sequenced and identified by mass spectrometry (MS/MS). Results Four hundred and eighteen (418) differentially expressed protein spots sequenced produced 101 unique proteins. The identified proteins were classified in the Gene Ontology biological processes categories of metabolism, cell processes, stress response, transport, secretion, motility, and virulence. Identified virulence factors included catalase (KatE), exoglucanase A (ChbA), drug efflux pump, and twitching motility porin (PilQ). Other proteins identified included two components of a putative type VI secretion system. We confirmed differential expression of 13 candidate genes using real time PCR techniques. Global regulators HrpB and HrpG also had temperature dependent expression when quantified by real time PCR. Conclusions The putative involvement of the identified proteins in virulence at low temperature is discussed. The discovery of a functional type VI secretion system provides a new potential virulence mechanism to explore. The global regulators HrpG and HrpB, and the protein expression profiles identified suggest that virulence at low temperatures can be partially explained by differences in regulation of virulence factors present in all the strains.
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Affiliation(s)
| | | | | | | | - David J Norman
- Department of Plant Pathology, University of Florida, IFAS, Mid-Florida Research and Education Center, 2725 Binion Rd,, Apopka, FL 32703, USA.
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113
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Castanheira M, Deshpande LM, Costello A, Davies TA, Jones RN. Epidemiology and carbapenem resistance mechanisms of carbapenem-non-susceptible Pseudomonas aeruginosa collected during 2009-11 in 14 European and Mediterranean countries. J Antimicrob Chemother 2014; 69:1804-14. [PMID: 24603963 DOI: 10.1093/jac/dku048] [Citation(s) in RCA: 146] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
OBJECTIVES To evaluate the genetic relatedness and carbapenem resistance mechanisms among carbapenem-non-susceptible Pseudomonas aeruginosa collected during 2009-11 in 14 European and Mediterranean countries. METHODS Doripenem-non-susceptible (MIC >2 mg/L) isolates were tested for susceptibility to imipenem, meropenem, doripenem, aztreonam, ceftazidime and cefepime with and without phenyl-arginine-β-naphthylamide (PAβN) (efflux inhibitor) and/or cloxacillin (AmpC inhibitor). Carbapenemase screening was performed by PCR and sequencing. Expression of chromosomal ampC, mexA, mexC, mexE and mexX was determined by quantitative real-time PCR using P. aeruginosa PAO1 or a group of susceptible isolates as baseline. Clonality was evaluated by PFGE and multilocus sequence typing. RESULTS Among 529 (25.6% overall) carbapenem-non-susceptible P. aeruginosa, 106 were positive for metallo-β-lactamase (MβL) genes encoding VIM-2 (76 strains), VIM-4 (14), VIM-1 (7) and VIM-5 (5). IMP-15 and three new MβLs (IMP-33, VIM-36 and VIM-37) were detected in one strain each. An increasing prevalence of MβL producers was noted in 2011 (30.6%) compared with previous years (13.4% and 12.3% in 2009 and 2010, respectively). Isolates displayed high genetic diversity, with 401 unique profiles detected. CC235 and ST111 were detected among MβL-producing clusters. The PAβN/cloxacillin effect ranged from 90.0% to 56.5%/from 1.3% to 21.2%. OprD decrease/loss was the most prevalent intrinsic mechanism and was detected among 94.9% of the P. aeruginosa, followed by AmpC (44.4%) and MexAB-OprM (20.1%). When using the susceptible group of isolates as baseline, MexAB-OprM became as prevalent as OprD decrease/loss. CONCLUSIONS Increasing MβL prevalence is worrisome in various European countries; however, intrinsic resistance mechanisms in a highly genetically diverse population of carbapenem-non-susceptible P. aeruginosa are probably a matter for greater concern in these countries.
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Affiliation(s)
| | | | | | - Todd A Davies
- Janssen Research & Development, Raritan, NJ 08869, USA
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114
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Characterization of LgnR, an IclR family transcriptional regulator involved in the regulation of l-gluconate catabolic genes in Paracoccus sp. 43P. Microbiology (Reading) 2014; 160:623-634. [DOI: 10.1099/mic.0.074286-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five genes encoding enzymes required for l-gluconate catabolism, together with genes encoding components of putative ABC transporters, are located in a cluster in the genome of Paracoccus sp. 43P. A gene encoding a transcriptional regulator in the IclR family, lgnR, is located in front of the cluster in the opposite direction. Reverse transcription PCR analysis indicated that the cluster was transcribed as an operon, termed the lgn operon. Two promoters, P
lgnA
and P
lgnR
, are divergently located in the intergenic region, and transcription from these promoters was induced by addition of l-gluconate or d-idonate, a catabolite of l-gluconate. Deletion of lgnR resulted in constitutive expression of lgnA, lgnH and lgnR, indicating that lgnR encodes a repressor protein for the expression of the lgn operon and lgnR itself. Electrophoretic mobility shift assay and DNase I footprinting analyses revealed that recombinant LgnR binds to both P
lgnA
and P
lgnR
, indicating that LgnR represses transcription from these promoters by competing with RNA polymerase for binding to these sequences. d-Idonate was identified as a candidate effector molecule for dissociation of LgnR from these promoters. Phylogenetic analysis revealed that LgnR formed a cluster with putative proteins from other genome sequences, which is distinct from those proteins of known regulatory functions, in the IclR family of transcriptional regulators. Additionally, the phylogeny suggests an evolutionary linkage between the l-gluconate catabolic pathway and d-galactonate catabolic pathways distributed in Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria and Actinobacteria.
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115
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Abstract
Advances in high-throughput transcriptome analyses have revealed hundreds of antisense RNAs (asRNAs) for many bacteria, although few have been characterized, and the number of functional asRNAs remains unknown. We have developed a genome-wide high-throughput method to identify functional asRNAs in vivo. Most mechanisms of gene regulation via asRNAs require an RNA-RNA interaction with its target RNA, and we hypothesized that a functional asRNA would be found in a double strand (dsRNA), duplexed with its cognate RNA in a single cell. We developed a method of isolating dsRNAs from total RNA by immunoprecipitation with a ds-RNA specific antibody. Total RNA and immunoprecipitated dsRNA from Escherichia coli RNase III WT and mutant strains were deep-sequenced. A statistical model was applied to filter for biologically relevant dsRNA regions, which were subsequently categorized by location relative to annotated genes. A total of 316 potentially functional asRNAs were identified in the RNase III mutant strain and are encoded primarily opposite to the 5' ends of transcripts, but are also found opposite ncRNAs, gene junctions, and the 3' ends. A total of 21 sense/antisense RNA pairs identified in dsRNAs were confirmed by Northern blot analyses. Most of the RNA steady-state levels were higher or detectable only in the RNase III mutant strain. Taken together, our data indicate that a significant amount of dsRNA is formed in the cell, that RNase III degrades or processes these dsRNAs, and that dsRNA plays a major role in gene regulation in E. coli.
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116
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Shu C, Sun S, Chen J, Chen J, Zhou E. Comparison of different methods for total RNA extraction from sclerotia of Rhizoctonia solani. ELECTRON J BIOTECHN 2014. [DOI: 10.1016/j.ejbt.2013.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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117
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Next-generation sequencing-based transcriptome analysis of L-lysine-producing Corynebacterium glutamicum ATCC 21300 strain. J Microbiol 2013; 51:877-80. [PMID: 24385368 DOI: 10.1007/s12275-013-3236-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 07/15/2013] [Indexed: 10/25/2022]
Abstract
In the present study, 151 genes showed a significant change in their expression levels in Corynebacterium glutamicum ATCC 21300 compared with those of C. glutamicum ATCC 13032. Of these 151 genes, 56 genes (2%) were up-regulated and 95 genes (3%) were down-regulated. RNA sequencing analysis also revealed that 11 genes, involved in the L-lysine biosynthetic pathway of C. glutamicum, were up- or down-regulated compared with those of C. glutamicum ATCC 13032. Of the 151 genes, 10 genes were identified to have mutations including SNP (9 genes) and InDel (1 gene). This information will be useful for genome breeding of C. glutamicum to develop an industrial amino acid-producing strain with minimal mutation.
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118
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Mailu BM, Ramasamay G, Mudeppa DG, Li L, Lindner SE, Peterson MJ, DeRocher AE, Kappe SHI, Rathod PK, Gardner MJ. A nondiscriminating glutamyl-tRNA synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway. J Biol Chem 2013; 288:32539-32552. [PMID: 24072705 PMCID: PMC3820887 DOI: 10.1074/jbc.m113.507467] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/23/2013] [Indexed: 11/06/2022] Open
Abstract
The malaria parasite Plasmodium falciparum and related organisms possess a relict plastid known as the apicoplast. Apicoplast protein synthesis is a validated drug target in malaria because antibiotics that inhibit translation in prokaryotes also inhibit apicoplast protein synthesis and are sometimes used for malaria prophylaxis or treatment. We identified components of an indirect aminoacylation pathway for Gln-tRNA(Gln) biosynthesis in Plasmodium that we hypothesized would be essential for apicoplast protein synthesis. Here, we report our characterization of the first enzyme in this pathway, the apicoplast glutamyl-tRNA synthetase (GluRS). We expressed the recombinant P. falciparum enzyme in Escherichia coli, showed that it is nondiscriminating because it glutamylates both apicoplast tRNA(Glu) and tRNA(Gln), determined its kinetic parameters, and demonstrated its inhibition by a known bacterial GluRS inhibitor. We also localized the Plasmodium berghei ortholog to the apicoplast in blood stage parasites but could not delete the PbGluRS gene. These data show that Gln-tRNA(Gln) biosynthesis in the Plasmodium apicoplast proceeds via an essential indirect aminoacylation pathway that is reminiscent of bacteria and plastids.
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Affiliation(s)
- Boniface M Mailu
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | | | - Devaraja G Mudeppa
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Ling Li
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Scott E Lindner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Megan J Peterson
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Amy E DeRocher
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Stefan H I Kappe
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Pradipsinh K Rathod
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Malcolm J Gardner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195.
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119
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Salazar MA, Fernando LP, Baig F, Harcum SW. The effects of protein solubility on the RNA Integrity Number (RIN) for recombinant Escherichia coli. Biochem Eng J 2013; 79:129-135. [PMID: 24151430 PMCID: PMC3799817 DOI: 10.1016/j.bej.2013.07.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
High quality, intact messenger RNA (mRNA) is required for DNA microarray and reverse transcriptase polymerase chain reaction analysis and is generally obtained from total RNA isolations. The most widely recognized measure of RNA integrity is the RNA Integrity Number (RIN) obtained from the Agilent Bioanalyzer, as it provides sizing, quantification, and quality control measures. This work describes comparisons of the RIN values obtained for recombinant E. coli. Uninduced recombinant E. coli cultures were examined, as well as induced cultures that produced either a soluble or insoluble recombinant protein. The uninduced cultures and the induced cultures producing soluble protein had higher RIN values than the induced cultures producing insoluble protein. These lower RIN values for E. coli producing the insoluble protein indicate that cellular degradation of the ribosomal RNA species is the likely cause of the lower RIN values. As the use of DNA microarrays and other gene expression tools increase in usage in the industrial recombinant protein production community, these results suggest the need for further studies to determine acceptable RIN ranges for gene expression analysis and effects of various culture conditions on RIN values for recombinant E. coli.
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Affiliation(s)
| | | | - Faraz Baig
- Department of Bioengineering, Clemson University
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120
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Stark L, Giersch T, Wünschiers R. Efficiency of RNA extraction from selected bacteria in the context of biogas production and metatranscriptomics. Anaerobe 2013; 29:85-90. [PMID: 24096086 DOI: 10.1016/j.anaerobe.2013.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Revised: 09/05/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
Abstract
Understanding the microbial population in anaerobic digestion is an essential task to increase efficient substrate use and process stability. The metabolic state, represented e.g. by the transcriptome, of a fermenting system can help to find markers for monitoring industrial biogas production to prevent failures or to model the whole process. Advances in next-generation sequencing make transcriptomes accessible for large-scale analyses. In order to analyze the metatranscriptome of a mixed-species sample, isolation of high-quality RNA is the first step. However, different extraction methods may yield different efficiencies in different species. Especially in mixed-species environmental samples, unbiased isolation of transcripts is important for meaningful conclusions. We applied five different RNA-extraction protocols to nine taxonomic diverse bacterial species. Chosen methods are based on various lysis and extraction principles. We found that the extraction efficiency of different methods depends strongly on the target organism. RNA isolation of gram-positive bacteria was characterized by low yield whilst from gram-negative species higher concentrations can be obtained. Transferring our results to mixed-species investigations, such as metatranscriptomics with biofilms or biogas plants, leads to the conclusion that particular microorganisms might be over- or underrepresented depending on the method applied. Special care must be taken when using such metatranscriptomics data for, e.g. process modeling.
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Affiliation(s)
- Lucy Stark
- Faculty of Mathematics, Natural Sciences and Computer Sciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany.
| | - Tina Giersch
- Faculty of Mathematics, Natural Sciences and Computer Sciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany
| | - Röbbe Wünschiers
- Faculty of Mathematics, Natural Sciences and Computer Sciences, University of Applied Sciences Mittweida, Technikumplatz 17, 09648 Mittweida, Germany
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121
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Carvalhais V, Delgado-Rastrollo M, Melo LDR, Cerca N. Controlled RNA contamination and degradation and its impact on qPCR gene expression in S. epidermidis biofilms. J Microbiol Methods 2013; 95:195-200. [PMID: 23999274 DOI: 10.1016/j.mimet.2013.08.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 08/14/2013] [Accepted: 08/14/2013] [Indexed: 10/26/2022]
Abstract
RNA quality is of utmost importance to perform gene expression quantification by qPCR. The classical methods used to determine RNA quality are based on electrophoresis and spectrophotometer assessment, namely A(260)/A(280) and A(260)/A(230) ratios. It was previously shown that due to the complex nature of Staphylococcus epidermidis biofilms, RNA extraction procedures could impact mRNA quality and thus accurate quantification. Herein, we contaminated and degraded RNA extracted from S. epidermidis biofilms, and assessed the effect on gene expression by qPCR. As expected, thermal degradation of RNA had a significant impact on gene expression on two out of the three tested genes. On the other hand, the contamination of the extracted RNA yielded an interesting result: while most contaminants did not changed the purity indicators or the integrity of RNA, significant changes on gene expression levels were found. This work confirms that poor RNA extraction has an important impact in qPCR quantification, emphasizing the consequences of carry-over contaminants on gene expression studies. Additionally, our results show that the parameters commonly used to assess the quality of extracted RNA from bacterial cultures seem to be insufficient to ensure reliable gene expression determination.
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Affiliation(s)
- Virginia Carvalhais
- IBB - Institute for Biotechnology and Bioengineering, Centre of Biological Engineering, University of Minho, Braga, Portugal
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122
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Poboży E, Filaber M, Koc A, Garcia-Reyes JF. Application of capillary electrophoretic chips in protein profiling of plant extracts for identification of genetic modifications of maize. Electrophoresis 2013; 34:2740-53. [DOI: 10.1002/elps.201300103] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 06/05/2013] [Accepted: 06/10/2013] [Indexed: 12/15/2022]
Affiliation(s)
- Ewa Poboży
- Department of Chemistry; University of Warsaw; Warsaw; Poland
| | - Monika Filaber
- Department of Chemistry; University of Warsaw; Warsaw; Poland
| | - Anna Koc
- Department of Chemistry; University of Warsaw; Warsaw; Poland
| | - Juan F. Garcia-Reyes
- Analytical Chemistry Research Group, Department of Physical and Analytical Chemistry; University of Jaén; Jaén; Spain
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123
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Chionh YH, Ho CH, Pruksakorn D, Ramesh Babu I, Ng CS, Hia F, McBee ME, Su D, Pang YLJ, Gu C, Dong H, Prestwich EG, Shi PY, Preiser PR, Alonso S, Dedon PC. A multidimensional platform for the purification of non-coding RNA species. Nucleic Acids Res 2013; 41:e168. [PMID: 23907385 PMCID: PMC3783195 DOI: 10.1093/nar/gkt668] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.
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Affiliation(s)
- Yok Hian Chionh
- Singapore-MIT Alliance for Research and Technology, Infectious Disease Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Department of Microbiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA, Applied Biological Science Program, Chulabhorn Graduate Institute, Bangkok 10210, Thailand, Division of Molecular Genetics & Cell Biology, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Immunology Programme, Life Science Institute, Centre for Life Science, Singapore 117456 and Novartis Institute for Tropical Disease, Singapore 138670
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Hogan CS, Mole BM, Grant SR, Willis DK, Charkowski AO. The type III secreted effector DspE is required early in solanum tuberosum leaf infection by Pectobacterium carotovorum to cause cell death, and requires Wx(3-6)D/E motifs. PLoS One 2013; 8:e65534. [PMID: 23755246 PMCID: PMC3670860 DOI: 10.1371/journal.pone.0065534] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 04/29/2013] [Indexed: 11/23/2022] Open
Abstract
Pectobacterium species are enterobacterial plant-pathogens that cause soft rot disease in diverse plant species. Unlike hemi-biotrophic plant pathogenic bacteria, the type III secretion system (T3SS) of Pectobacterium carotovorum subsp. carotovorum (P. carotovorum) appears to secrete only one effector protein, DspE. Previously, we found that the T3SS regulator HrpL and the effector DspE are required for P. carotovorum pathogenesis on leaves. Here, we identified genes up-regulated by HrpL, visualized expression of dspE in leaves, and established that DspE causes host cell death. DspE required its full length and WxxxE-like motifs, which are characteristic of the AvrE-family effectors, for host cell death. We also examined expression in plant leaves and showed that hrpL is required for the expression of dspE and hrpN, and that the loss of a functional T3SS had unexpected effects on expression of other genes during leaf infection. These data support a model where P. carotovorum uses the T3SS early in leaf infection to initiate pathogenesis through elicitation of DspE-mediated host cell death.
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Affiliation(s)
- Clifford S. Hogan
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Beth M. Mole
- Department of Biology and Curriculum in Molecular Biology and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Sarah R. Grant
- Department of Biology and Curriculum in Molecular Biology and Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - David K. Willis
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Vegetable Crops Research Unit, United States Department of Agriculture – Agricultural Research Service, Madison, Wisconsin, United States of America
| | - Amy O. Charkowski
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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125
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A robust and efficient method for the isolation of DNA-free, pure and intact RNA from Mycobacterium tuberculosis. J Microbiol Methods 2013; 93:198-202. [DOI: 10.1016/j.mimet.2013.03.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Revised: 03/21/2013] [Accepted: 03/21/2013] [Indexed: 11/19/2022]
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126
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Tu B, Li J, Guo Y, Guo X, Lu X, Han X. Compensation phenomena found inAcidithiobacillus ferrooxidansafter starvation stress. J Basic Microbiol 2013; 54:598-606. [DOI: 10.1002/jobm.201200637] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Accepted: 01/26/2013] [Indexed: 11/06/2022]
Affiliation(s)
- Bowen Tu
- Jiangsu Key Laboratory of Molecular Medicine; Nanjing University; Nanjing P.R. China
- Centers for Disease Control and Prevention of Changzhou; Changzhou P.R. China
- State Key Laboratory of Analytical Chemistry for Life Science; Nanjing University; Nanjing P.R. China
| | - Juan Li
- State Key Laboratory of Mineral Deposits Research; School of Earth Sciences and Engineering, Nanjing University; Nanjing P.R. China
| | - Yueshuai Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology; Nanjing Medical University; Nanjing P.R. China
| | - Xuejiang Guo
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology; Nanjing Medical University; Nanjing P.R. China
| | - Xiancai Lu
- State Key Laboratory of Mineral Deposits Research; School of Earth Sciences and Engineering, Nanjing University; Nanjing P.R. China
| | - Xiaodong Han
- Jiangsu Key Laboratory of Molecular Medicine; Nanjing University; Nanjing P.R. China
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127
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Gadkar VJ, Filion M. Development of a versatile TaqMan™ real-time quantitative PCR (RT-qPCR) compliant anchor sequence to quantify bacterial gene transcripts from RNA samples containing carryover genomic DNA. BMC Biotechnol 2013; 13:7. [PMID: 23369378 PMCID: PMC3689636 DOI: 10.1186/1472-6750-13-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 01/22/2013] [Indexed: 12/23/2022] Open
Abstract
Background In bacterial systems, the sequence congruence of genomic DNA (gDNA) and cDNA obtained following reverse transcription of RNA, makes gDNA an automatic target for qPCR primers. This could lead to aberrant gene expression quantification. This is why a rigorous treatment of bacterial RNA with DNase I is usually required to remove any traces of carryover gDNA. As bacterial RNA is known to be extremely labile, any procedure that affects RNA yield, such as DNase I treatment, can be logically assumed to also influence detection and quantification of gene transcripts, leading to either an underestimation or no detection at all. To address such problems, we have developed a novel and versatile TaqMan RT-qPCR compliant anchor sequence (MYT4) for quantifying bacterial gene transcripts without the need for DNase I treatment. Results A non-genomic anchor sequence, henceforth referred to as MYT4 was designed using a synthetic DNA sequence called myIC, previously shown to share no significant homology to any known accession in the GenBank database. The sequence characteristic of MYT4 was kept within the design parameters required for the TaqMan RT-qPCR platform. The specificity and robustness of the novel MYT4 sequence was validated on RNA extracted from the bacterium Pseudomonas sp. LBUM300, grown under liquid culture and spiked soil conditions. Two transcripts, namely hcnC and phlD, were quantified from these two experimental systems. Using the MYT4 anchor, no RT-qPCR signal was detected from non-DNase I treated RNA, while strong signals were obtained using conventional reverse primers and RT-qPCR, indicating the presence of carryover gDNA in the RNA, extracted from either liquid culture or soil. Serial treatment of the RNA samples with DNase I (required to achieve absolute gDNA elimination) resulted in 50-70% loss of RNA which, when submitted to conventional RT-qPCR, significantly altered the transcript numbers detected when compared to the MYT4-based approach. Conclusions Implementation of the versatile approach described in this study, which can be “retrofitted” to any existing TaqMan RT-qPCR system, should contribute to reducing the time and lowering the costs required to perform adequate bacterial RNA purification for downstream quantification of gene transcripts.
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Affiliation(s)
- Vijay J Gadkar
- Department of Biology, Université de Moncton, 18 Antonine-Maillet, Moncton, NB E1A 3E9, Canada
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128
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Abstract
In microbial ecology, high-resolution molecular approaches are essential for characterizing the vast organismal and functional diversity and understanding the interaction of microbial communities with biotic and abiotic environmental factors. Integrated omics, comprising genomics, transcriptomics, proteomics, and metabolomics allows conclusive links to be drawn between genetic potential and function. However, this requires truly systematic measurements. In this chapter, we first assess the levels of heterogeneity within mixed microbial communities, thereby demonstrating the need for analyzing biomolecular fractions obtained from a single and undivided sample to facilitate multi-omic analysis and meaningful data integration. Further, we describe a methodological workflow for the reproducible isolation of concomitant metabolites, RNA (optionally split into large and small RNA fractions), DNA, and proteins. Depending on the nature of the sample, the methodology comprises different (pre)processing and preservation steps. If possible, extracellular polar and nonpolar metabolites may first be extracted from cell supernatants using organic solvents. Cells are homogenized by cryomilling before small molecules are extracted with organic solvents. After cell lysis, nucleic acids and protein fractions are sequentially isolated using chromatographic spin columns. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological (biological wastewater treatment biomass), environmental (freshwater planktonic communities), and biomedical (human fecal sample) research interest. The methodological framework should be applicable to other microbial communities as well as other biological samples with a minimum of tailoring and represents an important first step in standardization for the emerging field of Molecular Eco-Systems Biology.
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129
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Quantification of yeast and bacterial gene transcripts in retail cheeses by reverse transcription-quantitative PCR. Appl Environ Microbiol 2012; 79:469-77. [PMID: 23124230 DOI: 10.1128/aem.02360-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The cheese microbiota contributes to a large extent to the development of the typical color, flavor, and texture of the final product. Its composition is not well defined in most cases and varies from one cheese to another. The aim of the present study was to establish procedures for gene transcript quantification in cheeses by reverse transcription-quantitative PCR. Total RNA was extracted from five smear-ripened cheeses purchased on the retail market, using a method that does not involve prior separation of microbial cells. 16S rRNA and malate:quinone oxidoreductase gene transcripts of Corynebacterium casei, Brevibacterium aurantiacum, and Arthrobacter arilaitensis and 26S rRNA and beta tubulin gene transcripts of Geotrichum candidum and Debaryomyces hansenii could be detected and quantified in most of the samples. Three types of normalization were applied: against total RNA, against the amount of cheese, and against a reference gene. For the first two types of normalization, differences of reverse transcription efficiencies from one sample to another were taken into account by analysis of exogenous control mRNA. No good correlation was found between the abundances of target mRNA or rRNA transcripts and the viable cell concentration of the corresponding species. However, in most cases, no mRNA transcripts were detected for species that did not belong to the dominant species. The applications of gene expression measurement in cheeses containing an undefined microbiota, as well as issues concerning the strategy of normalization and the assessment of amplification specificity, are discussed.
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130
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Die JV, Román B. RNA quality assessment: a view from plant qPCR studies. JOURNAL OF EXPERIMENTAL BOTANY 2012; 63:6069-77. [PMID: 23045609 DOI: 10.1093/jxb/ers276] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR) is probably the most common molecular technique used in transcriptome analyses today. The simplicity of the technology and associated protocols that generate results without the need to understand the underlying principles has made RT-qPCR the method of choice for RNA quantification. Rather than the 'gold standard technology' often used to describe it, the performance of RT-qPCR suffers from considerable pitfalls during general workflow. The inconsistency of conventional methods for the evaluation of RNA quality and its influence on qPCR performance as well as stability of reference genes is summarized and discussed here.
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Affiliation(s)
- Jose V Die
- Mejora Genética Vegetal, Instituto de Agricultura Sostenible, CSIC, 14080 Córdoba, Spain.
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131
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Arora G, Sajid A, Arulanandh MD, Singhal A, Mattoo AR, Pomerantsev AP, Leppla SH, Maiti S, Singh Y. Unveiling the novel dual specificity protein kinases in Bacillus anthracis: identification of the first prokaryotic dual specificity tyrosine phosphorylation-regulated kinase (DYRK)-like kinase. J Biol Chem 2012; 287:26749-63. [PMID: 22711536 PMCID: PMC3411013 DOI: 10.1074/jbc.m112.351304] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 06/14/2012] [Indexed: 12/23/2022] Open
Abstract
Dual specificity protein kinases (DSPKs) are unique enzymes that can execute multiple functions in the cell, which are otherwise performed exclusively by serine/threonine and tyrosine protein kinases. In this study, we have characterized the protein kinases Bas2152 (PrkD) and Bas2037 (PrkG) from Bacillus anthracis. Transcriptional analyses of these kinases showed that they are expressed in all phases of growth. In a serendipitous discovery, both kinases were found to be DSPKs. PrkD was found to be similar to the eukaryotic dual specificity Tyr phosphorylation-regulated kinase class of dual specificity kinases, which autophosphorylates on Ser, Thr, and Tyr residues and phosphorylates Ser and Thr residues on substrates. PrkG was found to be a bona fide dual specificity protein kinase that mediates autophosphorylation and substrate phosphorylation on Ser, Thr, and Tyr residues. The sites of phosphorylation in both of the kinases were identified through mass spectrometry. Phosphorylation on Tyr residues regulates the kinase activity of PrkD and PrkG. PrpC, the only known Ser/Thr protein phosphatase, was also found to possess dual specificity. Genistein, a known Tyr kinase inhibitor, was found to inhibit the activities of PrkD and PrkG and affect the growth of B. anthracis cells, indicating a possible role of these kinases in cell growth and development. In addition, the glycolytic enzyme pyruvate kinase was found to be phosphorylated by PrkD on Ser and Thr residues but not by PrkG. Thus, this study provides the first evidence of DSPKs in B. anthracis that belong to different classes and have different modes of regulation.
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Affiliation(s)
- Gunjan Arora
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Andaleeb Sajid
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Mary Diana Arulanandh
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Anshika Singhal
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Abid R. Mattoo
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Andrei P. Pomerantsev
- the Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892-3202
| | - Stephen H. Leppla
- the Laboratory of Parasitic Diseases, NIAID, National Institutes of Health, Bethesda, Maryland 20892-3202
| | - Souvik Maiti
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
| | - Yogendra Singh
- From the Council of Scientific and Industrial Research-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110007, India and
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Stead MB, Agrawal A, Bowden KE, Nasir R, Mohanty BK, Meagher RB, Kushner SR. RNAsnap™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria. Nucleic Acids Res 2012; 40:e156. [PMID: 22821568 PMCID: PMC3488207 DOI: 10.1093/nar/gks680] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
RNAsnap™ is a simple and novel method that recovers all intracellular RNA quantitatively (>99%), faster (<15 min) and less expensively (∼3 cents/sample) than any of the currently available RNA isolation methods. In fact, none of the bacterial RNA isolation methods, including the commercial kits, are effective in recovering all species of intracellular RNAs (76–5700 nt) with equal efficiency, which can lead to biased results in genome-wide studies involving microarray or RNAseq analysis. The RNAsnap™ procedure yields ∼60 µg of RNA from 108Escherichia coli cells that can be used directly for northern analysis without any further purification. Based on a comparative analysis of specific transcripts ranging in size from 76 to 5700 nt, the RNAsnap™ method provided the most accurate measure of the relative amounts of the various intracellular RNAs. Furthermore, the RNAsnap™ RNA was successfully used in enzymatic reactions such as RNA ligation, reverse transcription, primer extension and reverse transcriptase–polymerase chain reaction, following sodium acetate/ethanol precipitation. The RNAsnap™ method can be used to isolate RNA from a wide range of Gram-negative and Gram-positive bacteria as well as yeast.
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Affiliation(s)
- Mark B Stead
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
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Abstract
Mixed microbial communities are complex, dynamic and heterogeneous. It is therefore essential that biomolecular fractions obtained for high-throughput omic analyses are representative of single samples to facilitate meaningful data integration, analysis and modeling. We have developed a new methodological framework for the reproducible isolation of high-quality genomic DNA, large and small RNA, proteins, and polar and non-polar metabolites from single unique mixed microbial community samples. The methodology is based around reproducible cryogenic sample preservation and cell lysis. Metabolites are extracted first using organic solvents, followed by the sequential isolation of nucleic acids and proteins using chromatographic spin columns. The methodology was validated by comparison to traditional dedicated and simultaneous biomolecular isolation methods. To prove the broad applicability of the methodology, we applied it to microbial consortia of biotechnological, environmental and biomedical research interest. The developed methodological framework lays the foundation for standardized molecular eco-systematic studies on a range of different microbial communities in the future.
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134
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Dimou M, Zografou C, Venieraki A, Katinakis P. Biochemical characterization of two Azotobacter vinelandii FKBPs and analysis of their interaction with the small subunit of carbamoyl phosphate synthetase. Mol Biol Rep 2012; 39:10003-12. [DOI: 10.1007/s11033-012-1869-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 06/19/2012] [Indexed: 10/28/2022]
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Monteiro F, Genin S, van Dijk I, Valls M. A luminescent reporter evidences active expression of Ralstonia solanacearum type III secretion system genes throughout plant infection. MICROBIOLOGY-SGM 2012; 158:2107-2116. [PMID: 22609750 DOI: 10.1099/mic.0.058610-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Although much is known about the signals that trigger transcription of virulence genes in plant pathogens, their prevalence and timing during infection are still unknown. In this work, we address these questions by analysing expression of the main pathogenicity determinants in the bacterial pathogen Ralstonia solanacearum. We set up a quantitative, non-invasive luminescent reporter to monitor in planta transcription from single promoters in the bacterial chromosome. We show that the new reporter provides a real-time measure of promoter output in vivo - either after re-isolation of pathogens from infected plants or directly in situ - and confirm that the promoter controlling exopolysaccharide (EPS) synthesis is active in bacteria growing in the xylem. We also provide evidence that hrpB, the master regulator of type III secretion system (T3SS) genes, is transcribed in symptomatic plants. Quantitative RT-PCR assays demonstrate that hrpB and type III effector transcripts are abundant at late stages of plant infection, suggesting that their function is required throughout disease. Our results challenge the widespread view in R. solanacearum pathogenicity that the T3SS, and thus injection of effector proteins, is only active to manipulate plant defences at the first stages of infection, and that its expression is turned down when bacteria reach high cell densities and EPS synthesis starts.
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Affiliation(s)
- Freddy Monteiro
- Department Genètica, Universitat de Barcelona and Centre de Recerca Agrigenòmica (IRTA-CSIC-UAB-UB) Edifici CRAG, Campus UAB, 08193 Bellaterra, Catalonia, Spain
| | - Stéphane Genin
- INRA, CNRS - Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR 441/2594, 31326 Castanet Tolosan, France
| | - Irene van Dijk
- Department Genètica, Universitat de Barcelona and Centre de Recerca Agrigenòmica (IRTA-CSIC-UAB-UB) Edifici CRAG, Campus UAB, 08193 Bellaterra, Catalonia, Spain
| | - Marc Valls
- Department Genètica, Universitat de Barcelona and Centre de Recerca Agrigenòmica (IRTA-CSIC-UAB-UB) Edifici CRAG, Campus UAB, 08193 Bellaterra, Catalonia, Spain
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136
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Greenwald JW, Greenwald CJ, Philmus BJ, Begley TP, Gross DC. RNA-seq analysis reveals that an ECF σ factor, AcsS, regulates achromobactin biosynthesis in Pseudomonas syringae pv. syringae B728a. PLoS One 2012; 7:e34804. [PMID: 22529937 PMCID: PMC3329529 DOI: 10.1371/journal.pone.0034804] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 03/08/2012] [Indexed: 12/30/2022] Open
Abstract
Iron is an essential micronutrient for Pseudomonas syringae pv. syringae strain B728a and many other microorganisms; therefore, B728a has evolved methods of iron acquirement including the use of iron-chelating siderophores. In this study an extracytoplasmic function (ECF) sigma factor, AcsS, encoded within the achromobactin gene cluster is shown to be a major regulator of genes involved in the biosynthesis and secretion of this siderophore. However, production of achromobactin was not completely abrogated in the deletion mutant, implying that other regulators may be involved such as PvdS, the sigma factor that regulates pyoverdine biosynthesis. RNA-seq analysis identified 287 genes that are differentially expressed between the AcsS deletion mutant and the wild type strain. These genes are involved in iron response, secretion, extracellular polysaccharide production, and cell motility. Thus, the transcriptome analysis supports a role for AcsS in the regulation of achromobactin production and the potential activity of both AcsS and achromobactin in the plant-associated lifestyle of strain B728a.
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Affiliation(s)
- Jessica W. Greenwald
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Charles J. Greenwald
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
| | - Benjamin J. Philmus
- Department of Chemistry, Texas A&M University, College Station, Texas, United States of America
| | - Tadhg P. Begley
- Department of Chemistry, Texas A&M University, College Station, Texas, United States of America
| | - Dennis C. Gross
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
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138
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Rio-Alvarez I, Rodríguez-Herva JJ, Cuartas-Lanza R, Toth I, Pritchard L, Rodríguez-Palenzuela P, López-Solanilla E. Genome-wide analysis of the response of Dickeya dadantii 3937 to plant antimicrobial peptides. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:523-533. [PMID: 22204647 DOI: 10.1094/mpmi-09-11-0247] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Antimicrobial peptides constitute an important factor in the defense of plants against pathogens, and bacterial resistance to these peptides have previously been shown to be an important virulence factor in Dickeya dadantii, the causal agent of soft-rot disease of vegetables. In order to understand the bacterial response to antimicrobial peptides, a transcriptional microarray analysis was performed upon treatment with sub-lethal concentration of thionins, a widespread plant peptide. In all, 36 genes were found to be overexpressed, and were classified according to their deduced function as i) transcriptional regulators, ii) transport, and iii) modification of the bacterial membrane. One gene encoding a uricase was found to be repressed. The majority of these genes are known to be under the control of the PhoP/PhoQ system. Five genes representing the different functions induced were selected for further analysis. The results obtained indicate that the presence of antimicrobial peptides induces a complex response which includes peptide-specific elements and general stress-response elements contributing differentially to the virulence in different hosts.
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Affiliation(s)
- Isabel Rio-Alvarez
- Centro de Biotecnología y Genómica de Plantas (CBGP), Universidad Politécnica de Madrid-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Pozuelo de Alarcón, Madrid, Spain
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139
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Atshan SS, Shamsudin MN, Lung LTT, Ling KH, Sekawi Z, Pei CP, Ghaznavi-Rad E. Improved method for the isolation of RNA from bacteria refractory to disruption, including S. aureus producing biofilm. Gene 2012; 494:219-24. [DOI: 10.1016/j.gene.2011.12.010] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 11/24/2011] [Accepted: 12/06/2011] [Indexed: 11/24/2022]
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140
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Zaher HS, Green R. A primary role for release factor 3 in quality control during translation elongation in Escherichia coli. Cell 2011; 147:396-408. [PMID: 22000017 DOI: 10.1016/j.cell.2011.08.045] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2011] [Revised: 07/10/2011] [Accepted: 08/29/2011] [Indexed: 11/18/2022]
Abstract
Release factor 3 (RF3) is a GTPase found in a broad range of bacteria where it is thought to play a critical "recycling" role in translation by facilitating the removal of class 1 release factors (RF1 and RF2) from the ribosome following peptide release. More recently, RF3 was shown in vitro to stimulate a retrospective editing reaction on the bacterial ribosome wherein peptides carrying mistakes are prematurely terminated during protein synthesis. Here, we examine the role of RF3 in the bacterial cell and show that the deletion of this gene sensitizes cells to other perturbations that reduce the overall fidelity of protein synthesis. We further document substantial effects on mRNA stability and protein expression using reporter systems, native mRNAs and proteins. We conclude that RF3 plays a primary role in vivo in specifying the fidelity of protein synthesis thus impacting overall protein quantity and quality.
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Affiliation(s)
- Hani S Zaher
- Howard Hughes Medical Institute, Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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141
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Dimou M, Zografou C, Venieraki A, Katinakis P. Transcriptional and biochemical characterization of two Azotobacter vinelandii FKBP family members. J Microbiol 2011; 49:635-40. [DOI: 10.1007/s12275-011-0498-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 04/18/2011] [Indexed: 02/02/2023]
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142
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Marquez-Villavicencio MDP, Weber B, Witherell RA, Willis DK, Charkowski AO. The 3-hydroxy-2-butanone pathway is required for Pectobacterium carotovorum pathogenesis. PLoS One 2011; 6:e22974. [PMID: 21876734 PMCID: PMC3158072 DOI: 10.1371/journal.pone.0022974] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 07/05/2011] [Indexed: 11/19/2022] Open
Abstract
Pectobacterium species are necrotrophic bacterial pathogens that cause soft rot diseases in potatoes and several other crops worldwide. Gene expression data identified Pectobacterium carotovorum subsp. carotovorum budB, which encodes the α-acetolactate synthase enzyme in the 2,3-butanediol pathway, as more highly expressed in potato tubers than potato stems. This pathway is of interest because volatiles produced by the 2,3-butanediol pathway have been shown to act as plant growth promoting molecules, insect attractants, and, in other bacterial species, affect virulence and fitness. Disruption of the 2,3-butanediol pathway reduced virulence of P. c. subsp. carotovorum WPP14 on potato tubers and impaired alkalinization of growth medium and potato tubers under anaerobic conditions. Alkalinization of the milieu via this pathway may aid in plant cell maceration since Pectobacterium pectate lyases are most active at alkaline pH.
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Affiliation(s)
| | - Brooke Weber
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - R. Andrews Witherell
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - David K. Willis
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
- Vegetable Crops Research Unit, Agricultural Research Service, United States Department of Agriculture, Madison, Wisconsin, United States of America
| | - Amy O. Charkowski
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
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143
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Liu X, Yang F, Song T, Zeng A, Wang Q, Sun Z, Shen J. Effects of chitosan, O-carboxymethyl chitosan and N-[(2-hydroxy-3-N,N-dimethylhexadecyl ammonium)propyl]chitosan chloride on lipid metabolism enzymes and low-density-lipoprotein receptor in a murine diet-induced obesity. Carbohydr Polym 2011. [DOI: 10.1016/j.carbpol.2011.02.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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144
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McCullumsmith RE, Meador-Woodruff JH. Novel approaches to the study of postmortem brain in psychiatric illness: old limitations and new challenges. Biol Psychiatry 2011; 69:127-33. [PMID: 21094488 DOI: 10.1016/j.biopsych.2010.09.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2010] [Revised: 09/14/2010] [Accepted: 09/27/2010] [Indexed: 11/29/2022]
Abstract
Biological psychiatry has made significant advances through the development of postmortem studies, animal models, and studies with living humans. Although these approaches each have advantages and disadvantages, the postmortem field is undergoing a significant shift toward more complex and informative methodologies. In the first part of this review, we summarize the long-standing methodologic challenges facing this field. In the second part of the article, we discuss the innovative approaches being used for postmortem studies, including laser capture microdissection and subcellular fractionization. These techniques will permit scientists working in the postmortem field to ask and answer the largest possible questions, providing new targets for drug discovery and improved treatments for severe mental illness.
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Affiliation(s)
- Robert E McCullumsmith
- Department of Psychiatry and Behavioral Neurobiology, Universityof Alabama at Birmingham School of Medicine, Birmingham, Alabama 35294, USA.
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145
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Dimou M, Venieraki A, Liakopoulos G, Kouri ED, Tampakaki A, Katinakis P. Gene Expression and Biochemical Characterization of Azotobacter vinelandii Cyclophilins and Protein Interaction Studies of the Cytoplasmic Isoform with dnaK and lpxH. J Mol Microbiol Biotechnol 2011; 20:176-90. [DOI: 10.1159/000329486] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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146
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Dimou M, Venieraki A, Liakopoulos G, Katinakis P. Cloning, characterization and transcriptional analysis of two phosphate acetyltransferase isoforms from Azotobacter vinelandii. Mol Biol Rep 2010; 38:3653-63. [DOI: 10.1007/s11033-010-0478-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Accepted: 11/09/2010] [Indexed: 10/18/2022]
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147
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Colburn-Clifford JM, Scherf JM, Allen C. Ralstonia solanacearum Dps contributes to oxidative stress tolerance and to colonization of and virulence on tomato plants. Appl Environ Microbiol 2010; 76:7392-9. [PMID: 20870795 PMCID: PMC2976212 DOI: 10.1128/aem.01742-10] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Accepted: 09/14/2010] [Indexed: 02/06/2023] Open
Abstract
Ralstonia solanacearum, an economically important soilborne plant pathogen, infects host roots to cause bacterial wilt disease. However, little is known about this pathogen's behavior in the rhizosphere and early in pathogenesis. In response to root exudates from tomato, R. solanacearum strain UW551 upregulated a gene resembling Dps, a nonspecific DNA binding protein from starved cells that is critical for stress survival in other bacteria. An R. solanacearum dps mutant had increased hydrogen peroxide sensitivity and mutation rate under starvation. Furthermore, dps expression was positively regulated by the oxidative stress response regulator OxyR. These functional results are consistent with a Dps annotation. The dps mutant caused slightly delayed bacterial wilt disease in tomato after a naturalistic soil soak inoculation. However, the dps mutant had a more pronounced reduction in virulence when bacteria were inoculated directly into host stems, suggesting that Dps helps R. solanacearum adapt to conditions inside plants. Passage through a tomato plant conferred transient increased hydrogen peroxide tolerance on both wild-type and dps mutant strains, demonstrating that R. solanacearum acquires Dps-independent oxidative stress tolerance during adaptation to the host environment. The dps mutant strain was also reduced in adhesion to tomato roots and tomato stem colonization. These results indicate that Dps is important when cells are starved or in stationary phase and that Dps contributes quantitatively to host plant colonization and bacterial wilt virulence. They further suggest that R. solanacearum must overcome oxidative stress during the bacterial wilt disease cycle.
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Affiliation(s)
| | - Jacob M. Scherf
- University of Wisconsin—Madison Department of Plant Pathology, 1630 Linden Drive, Madison, Wisconsin 53706
| | - Caitilyn Allen
- University of Wisconsin—Madison Department of Plant Pathology, 1630 Linden Drive, Madison, Wisconsin 53706
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148
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Rump LV, Asamoah B, Gonzalez-Escalona N. Comparison of commercial RNA extraction kits for preparation of DNA-free total RNA from Salmonella cells. BMC Res Notes 2010; 3:211. [PMID: 20663210 PMCID: PMC3161365 DOI: 10.1186/1756-0500-3-211] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Accepted: 07/27/2010] [Indexed: 12/23/2022] Open
Abstract
Background The isolation of DNA-free RNA is a crucial step in the reverse transcription PCR (RT-PCR). Every RNA extraction procedure results in RNA samples contaminated with genomic DNA, which can cause false-positive outcomes in highly sensitive applications, including a recently developed quantitative real-time PCR (RT-qPCR) assay that targets invA mRNA for the detection of live Salmonella cells. The assay of this specific mRNA can be used to indicate the presence of live, as opposed to dead, cells of Salmonella enterica in a food matrix. Findings We evaluated the ability of five RNA extraction kits to produce RNA preparations from exponentially growing Salmonella cells. The acceptability of the preparations for use in downstream applications such as RT-qPCR was judged in terms of the total amount of RNA recovered, the integrity of the RNA molecules, and minimal content of DNA. The five kits produced RNA preparations that differed markedly in yield, integrity of the Salmonella RNA and the amount of contaminant DNA. The greatest RNA recovery was achieved with the MasterPure kit; however, the preparation contained high levels of genomic DNA. The UltraClean extraction kit gave a low level of RNA recovery with a poor level of integrity. The RNeasy Mini, RiboPure and PureLink extraction kits produced high-quality, DNA-free RNA suitable for Salmonella detection by RT-qPCR. Conclusions We showed that the RNeasy Mini and PureLink RNA extraction kits were the most suitable for the detection of Salmonella invA mRNA by RT-qPCR. The use of these two kits will greatly reduce the frequency of false-positive results and might allow fast RT-qPCR determination of invA mRNA produced by viable Salmonella in food samples.
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Affiliation(s)
- Lydia V Rump
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, 5100 Paint Branch Parkway, College Park, MD 20740, USA.
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149
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Jung M, Schaefer A, Steiner I, Kempkensteffen C, Stephan C, Erbersdobler A, Jung K. Robust microRNA stability in degraded RNA preparations from human tissue and cell samples. Clin Chem 2010; 56:998-1006. [PMID: 20378769 DOI: 10.1373/clinchem.2009.141580] [Citation(s) in RCA: 234] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND RNA integrity is the essential factor that determines the accuracy of mRNA transcript measurements obtained with quantitative real-time reverse-transcription PCR (RT-qPCR), but evidence is clearly lacking on whether this conclusion also applies to microRNAs (miRNAs). We evaluated this issue by comparative analysis of the dependence of miRNA and mRNA measurements on RNA integrity in renal and prostate samples, under both model and clinical conditions. METHODS Samples of total RNA isolated from human renal tissue and Caki-2 cells, as well as from prostate tissue and LNCaP cells, were incubated at 80 degrees C for 5-240 min. We subsequently determined the RNA integrity number (RIN) and used RT-qPCR to measure various miRNAs (miR-141, miR-155, miR-200c, and miR-210 in renal samples, and miR-96, miR-130b, miR-149, miR-205, and miR-222 in prostate samples). We similarly measured mRNAs encoded by CDH16 (cadherin 16, KSP-cadherin), PPIA [peptidylprolyl isomerase A (cycophilin A)], and TBP (TATA box binding protein) in renal samples, and HIF1A [hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor)], HPRT1 (hypoxanthine phosphoribosyltransferase 1), and KLK3 (kallikrein-related peptidase 3; also known as PSA) in prostate samples. Additionally, we quantified selected miRNAs and mRNAs in samples of RNAs with different RIN values that we isolated from clinical samples. The effect of RIN on the miRNA and mRNA data was assessed by linear regression analysis and group comparison. RESULTS The heat-incubation experiments of cell line and tissue RNAs showed that RIN values had negligible or no effect on miRNA results, whereas all mRNAs gradually decreased with decreasing RIN values. These findings were corroborated by our findings with clinical samples. CONCLUSIONS Our results suggest the stability of miRNAs to be generally robust, which makes feasible accurate miRNA measurements with RT-qPCR, even in degraded RNA preparations for which reliable mRNA analyses are commonly inapplicable.
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Affiliation(s)
- Monika Jung
- Department of Urology, University Hospital Charité, Berlin, Germany
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150
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Lorenz C, Gesell T, Zimmermann B, Schoeberl U, Bilusic I, Rajkowitsch L, Waldsich C, von Haeseler A, Schroeder R. Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts. Nucleic Acids Res 2010; 38:3794-808. [PMID: 20348540 PMCID: PMC2887942 DOI: 10.1093/nar/gkq032] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regulator protein Hfq as bait, because it can interact with a large number of RNAs, promoting their interaction. The enriched SELEX pool was subjected to deep sequencing, and 8865 sequences were mapped to the E. coli genome. These short sequences represent genomic Hfq-aptamers and are part of potential regulatory elements within RNA molecules. The motif 5′-AAYAAYAA-3′ was enriched in the selected RNAs and confers low-nanomolar affinity to Hfq. The motif was confirmed to bind Hfq by DMS footprinting. The Hfq aptamers are 4-fold more frequent on the antisense strand of protein coding genes than on the sense strand. They were enriched opposite to translation start sites or opposite to intervening sequences between ORFs in operons. These results expand the repertoire of Hfq targets and also suggest that Hfq might regulate the expression of a large number of genes via interaction with cis-antisense RNAs.
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Affiliation(s)
- C Lorenz
- Department of Biochemistry, Medical University of Vienna and University of Veterinary Medicine, Vienna, Austria
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