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da Silva GC, Rossi CC, Rosa JN, Sanches NM, Cardoso DL, Li Y, Witney AA, Gould KA, Fontes PP, Callaghan AJ, Bossé JT, Langford PR, Bazzolli DMS. Identification of small RNAs associated with RNA chaperone Hfq reveals a new stress response regulator in Actinobacillus pleuropneumoniae. Front Microbiol 2022; 13:1017278. [PMID: 36267174 PMCID: PMC9577009 DOI: 10.3389/fmicb.2022.1017278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/09/2022] [Indexed: 11/16/2022] Open
Abstract
The RNA chaperone Hfq promotes the association of small RNAs (sRNAs) with cognate mRNAs, controlling the expression of bacterial phenotype. Actinobacillus pleuropneumoniae hfq mutants strains are attenuated for virulence in pigs, impaired in the ability to form biofilms, and more susceptible to stress, but knowledge of the extent of sRNA involvement is limited. Here, using A. pleuropneumoniae strain MIDG2331 (serovar 8), 14 sRNAs were identified by co-immunoprecipitation with Hfq and the expression of eight, identified as trans-acting sRNAs, were confirmed by Northern blotting. We focused on one of these sRNAs, named Rna01, containing a putative promoter for RpoE (stress regulon) recognition. Knockout mutants of rna01 and a double knockout mutant of rna01 and hfq, both had decreased biofilm formation and hemolytic activity, attenuation for virulence in Galleria mellonella, altered stress susceptibility, and an altered outer membrane protein profile. Rna01 affected extracellular vesicle production, size and toxicity in G. mellonella. qRT-PCR analysis of rna01 and putative cognate mRNA targets indicated that Rna01 is associated with the extracytoplasmic stress response. This work increases our understanding of the multilayered and complex nature of the influence of Hfq-dependent sRNAs on the physiology and virulence of A. pleuropneumoniae.
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Affiliation(s)
- Giarlã Cunha da Silva
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Ciro César Rossi
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Jéssica Nogueira Rosa
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Newton Moreno Sanches
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Daniela Lopes Cardoso
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Yanwen Li
- Section of Pediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Adam A. Witney
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | - Kate A. Gould
- Institute for Infection and Immunity, St. George’s, University of London, London, United Kingdom
| | | | - Anastasia J. Callaghan
- School of Biological Sciences and Institute of Biological and Biomedical Sciences, University of Portsmouth, Portsmouth, United Kingdom
| | - Janine Thérèse Bossé
- Section of Pediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Paul Richard Langford
- Section of Pediatric Infectious Disease, Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Denise Mara Soares Bazzolli
- Laboratório de Genética Molecular de Bactérias, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária—Bioagro, Universidade Federal de Viçosa, Viçosa, Brazil
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Mewalal R, Yin H, Hu R, Jawdy S, Vion P, Tuskan GA, Le Tacon F, Labbé JL, Yang X. Identification of Populus Small RNAs Responsive to Mutualistic Interactions With Mycorrhizal Fungi, Laccaria bicolor and Rhizophagus irregularis. Front Microbiol 2019; 10:515. [PMID: 30936859 PMCID: PMC6431645 DOI: 10.3389/fmicb.2019.00515] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 02/28/2019] [Indexed: 12/02/2022] Open
Abstract
Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, (1) within the genomic regions lacking annotated genes in the Populus genome and (2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments. Root colonization by either fungus was more effective in P. trichocarpa than in P. deltoides, thus the relatively few differentially-expressed miRNAs predicted in P. deltoides might reflect the extent of the symbiosis. Finally, we predicted several genes targets for the plant miRNAs identified here, including potential fungal gene targets. Our findings shed light on additional molecular tiers with a role in Populus-fungal mutualistic associations and provides a set of potential molecular targets for future enhancement.
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Affiliation(s)
- Ritesh Mewalal
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, China
| | - Rongbin Hu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Patrice Vion
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, VandIJuvre-lès-Nancy, France
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - François Le Tacon
- INRA, UMR 1136 INRA-University of Lorraine, Interactions Arbres/Microorganismes, Laboratory of Excellence ARBRE, INRA-Nancy, VandIJuvre-lès-Nancy, France
| | - Jessy L. Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Kranz A, Vogel A, Degner U, Kiefler I, Bott M, Usadel B, Polen T. High precision genome sequencing of engineered Gluconobacter oxydans 621H by combining long nanopore and short accurate Illumina reads. J Biotechnol 2017; 258:197-205. [PMID: 28433722 DOI: 10.1016/j.jbiotec.2017.04.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Revised: 04/14/2017] [Accepted: 04/15/2017] [Indexed: 02/08/2023]
Abstract
State of the art and novel high-throughput DNA sequencing technologies enable fascinating opportunities and applications in the life sciences including microbial genomics. Short high-quality read data already enable not only microbial genome sequencing, yet can be inadequately to solve problems in genome assemblies and for the analysis of structural variants, especially in engineered microbial cell factories. Single-molecule real-time sequencing technologies generating long reads promise to solve such assembly problems. In our study, we wanted to increase the average read length of long nanopore reads with R9 chemistry and conducted a hybrid approach for the analysis of structural variants to check the genome stability of a recombinant Gluconobacter oxydans 621H strain (IK003.1) engineered for improved growth. Therefore we combined accurate Illumina sequencing technology and low-cost single-molecule nanopore sequencing using the MinION® device from Oxford Nanopore. In our hybrid approach with a modified library protocol we could increase the average size of nanopore 2D reads to about 18.9kb. Combining the long MinION nanopore reads with the high quality short Illumina reads enabled the assembly of the engineered chromosome into a single contig and comprehensive detection and clarification of 7 structural variants including all three known genetically engineered modifications. We found the genome of IK003.1 was stable over 70 generations of strain handling including 28h of process time in a bioreactor. The long read data revealed a novel 1420 bp transposon-flanked and ORF-containing sequence which was hitherto unknown in the G. oxydans 621H reference. Further analysis and genome sequencing showed that this region is already present in G. oxydans 621H wild-type strains. Our data of G. oxydans 621H wild-type DNA from different resources also revealed in 73 annotated coding sequences about 91 uniform nucleotide differences including InDels. Together, our results contribute to an improved high quality genome reference for G. oxydans 621H which is available via ENA accession PRJEB18739.
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Affiliation(s)
- Angela Kranz
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Alexander Vogel
- IBMG: Institute for Biology I, RWTH Aachen University, Worringer Weg 2, 52074 Aachen, Germany; IBG-2 Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ursula Degner
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Ines Kiefler
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Michael Bott
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Björn Usadel
- IBMG: Institute for Biology I, RWTH Aachen University, Worringer Weg 2, 52074 Aachen, Germany; IBG-2 Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; The Bioeconomy Science Center (BioSC), c/o Forschungszentrum Jülich GmbH, 52425 Jülich, Germany.
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Firrman J, Liu L, Zhang L, Arango Argoty G, Wang M, Tomasula P, Kobori M, Pontious S, Xiao W. The effect of quercetin on genetic expression of the commensal gut microbes Bifidobacterium catenulatum, Enterococcus caccae and Ruminococcus gauvreauii. Anaerobe 2016; 42:130-141. [PMID: 27742572 DOI: 10.1016/j.anaerobe.2016.10.004] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/07/2016] [Accepted: 10/10/2016] [Indexed: 11/27/2022]
Abstract
Quercetin is one of the most abundant polyphenols found in fruits and vegetables. The ability of the gut microbiota to metabolize quercetin has been previously documented; however, the effect that quercetin may have on commensal gut microbes remains unclear. In the present study, the effects of quercetin on the commensal gut microbes Ruminococcus gauvreauii, Bifidobacterium catenulatum and Enterococcus caccae were determined through evaluation of growth patterns and cell morphology, and analysis of genetic expression profiles between quercetin treated and non-treated groups using Single Molecule RNA sequencing via Helicos technology. Results of this study revealed that phenotypically, quercetin did not prevent growth of Ruminococcus gauvreauii, mildly suppressed growth of Bifidobacterium catenulatum, and moderately inhibited growth of Enterococcus caccae. Genetic analysis revealed that in response to quercetin, Ruminococcus gauvreauii down regulated genes responsible for protein folding, purine synthesis and metabolism. Bifidobacterium catenulatum increased expression of the ABC transport pathway and decreased metabolic pathways and cell wall synthesis. Enterococcus caccae upregulated genes responsible for energy production and metabolism, and downregulated pathways of stress response, translation and sugar transport. For the first time, the effect of quercetin on the growth and genetic expression of three different commensal gut bacteria was documented. The data provides insight into the interactions between genetic regulation and growth. This is also a unique demonstration of how RNA single molecule sequencing can be used to study the gut microbiota.
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Affiliation(s)
- Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA, 19038, USA.
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Liqing Zhang
- Virginia Tech College of Engineering, Department of Computer Science, 1425 S Main St., Blacksburg, VA, 24061, USA
| | - Gustavo Arango Argoty
- Virginia Tech College of Engineering, Department of Computer Science, 1425 S Main St., Blacksburg, VA, 24061, USA
| | - Minqian Wang
- Rutgers University, Department of Food Science, 65 Dudley Road, New Brunswick, NJ, 08901, USA
| | - Peggy Tomasula
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 600 E Mermaid Lane, Wyndmoor, PA, 19038, USA
| | - Masuko Kobori
- Food Research Institute, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8642, Japan
| | - Sherri Pontious
- Department of Microbiology and Immunology, Temple University School of Medicine, 3400 North Broad Street, Philadelphia, USA
| | - Weidong Xiao
- Department of Microbiology and Immunology, Temple University School of Medicine, 3400 North Broad Street, Philadelphia, USA
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