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Knights HE, Ramachandran VK, Jorrin B, Ledermann R, Parsons JD, Aroney STN, Poole PS. Rhizobium determinants of rhizosphere persistence and root colonization. ISME J 2024; 18:wrae072. [PMID: 38690786 DOI: 10.1093/ismejo/wrae072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/16/2024] [Accepted: 04/23/2024] [Indexed: 05/03/2024]
Abstract
Bacterial persistence in the rhizosphere and colonization of root niches are critical for the establishment of many beneficial plant-bacteria interactions including those between Rhizobium leguminosarum and its host legumes. Despite this, most studies on R. leguminosarum have focused on its symbiotic lifestyle as an endosymbiont in root nodules. Here, we use random barcode transposon sequencing to assay gene contributions of R. leguminosarum during competitive growth in the rhizosphere and colonization of various plant species. This facilitated the identification of 189 genes commonly required for growth in diverse plant rhizospheres, mutation of 111 of which also affected subsequent root colonization (rhizosphere progressive), and a further 119 genes necessary for colonization. Common determinants reveal a need to synthesize essential compounds (amino acids, ribonucleotides, and cofactors), adapt metabolic function, respond to external stimuli, and withstand various stresses (such as changes in osmolarity). Additionally, chemotaxis and flagella-mediated motility are prerequisites for root colonization. Many genes showed plant-specific dependencies highlighting significant adaptation to different plant species. This work provides a greater understanding of factors promoting rhizosphere fitness and root colonization in plant-beneficial bacteria, facilitating their exploitation for agricultural benefit.
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Affiliation(s)
- Hayley E Knights
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | | | - Beatriz Jorrin
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Raphael Ledermann
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Jack D Parsons
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Samuel T N Aroney
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
| | - Philip S Poole
- Department of Biology, University of Oxford, Oxford OX1 3RB, United Kingdom
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Bassano I, Ramachandran VK, Khalifa MS, Lilley CJ, Brown MR, van Aerle R, Denise H, Rowe W, George A, Cairns E, Wierzbicki C, Pickwell ND, Carlile M, Holmes N, Payne A, Loose M, Burke TA, Paterson S, Wade MJ, Grimsley JMS. Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples. Microb Genom 2023; 9. [PMID: 37074153 DOI: 10.1099/mgen.0.000933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
Wastewater-based epidemiology has been used extensively throughout the COVID-19 (coronavirus disease 19) pandemic to detect and monitor the spread and prevalence of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) and its variants. It has proven an excellent, complementary tool to clinical sequencing, supporting the insights gained and helping to make informed public-health decisions. Consequently, many groups globally have developed bioinformatics pipelines to analyse sequencing data from wastewater. Accurate calling of mutations is critical in this process and in the assignment of circulating variants; yet, to date, the performance of variant-calling algorithms in wastewater samples has not been investigated. To address this, we compared the performance of six variant callers (VarScan, iVar, GATK, FreeBayes, LoFreq and BCFtools), used widely in bioinformatics pipelines, on 19 synthetic samples with known ratios of three different SARS-CoV-2 variants of concern (VOCs) (Alpha, Beta and Delta), as well as 13 wastewater samples collected in London between the 15th and 18th December 2021. We used the fundamental parameters of recall (sensitivity) and precision (specificity) to confirm the presence of mutational profiles defining specific variants across the six variant callers. Our results show that BCFtools, FreeBayes and VarScan found the expected variants with higher precision and recall than GATK or iVar, although the latter identified more expected defining mutations than other callers. LoFreq gave the least reliable results due to the high number of false-positive mutations detected, resulting in lower precision. Similar results were obtained for both the synthetic and wastewater samples.
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Affiliation(s)
- Irene Bassano
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- Department of Infectious Disease, Imperial College London, London SW7 2AZ, UK
| | - Vinoy K Ramachandran
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - Mohammad S Khalifa
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- Division of Biosciences, College of Health, Medicine and Life Sciences, Brunel University, London UB8 3PH, UK
| | - Chris J Lilley
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - Mathew R Brown
- School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - Ronny van Aerle
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Clyst Honiton EX5 2FN, UK
| | - Hubert Denise
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - William Rowe
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
| | - Airey George
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Edward Cairns
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Claudia Wierzbicki
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Natalie D Pickwell
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Matthew Carlile
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Nadine Holmes
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Alexander Payne
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Matthew Loose
- DeepSeq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Terry A Burke
- NERC Environmental Omics Facility, Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Steve Paterson
- Centre for Genomic Research and NERC Environmental Omics Facility, Institute of Infection, Veterinary and Ecological Sciences (IVES), University of Liverpool, Liverpool L69 7ZB, UK
| | - Matthew J Wade
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
- School of Engineering, Newcastle University, Newcastle-upon-Tyne NE1 7RU, UK
| | - Jasmine M S Grimsley
- Analytics & Data Science Directorate, UK Health Security Agency, London SW1P 3JR, UK
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Webb IUC, Xu J, Sánchez-Cañizares C, Karunakaran R, Ramachandran VK, Rutten PJ, East AK, Huang WE, Watmough NJ, Poole PS. Regulation and Characterization of Mutants of fixABCX in Rhizobium leguminosarum. Mol Plant Microbe Interact 2021; 34:1167-1180. [PMID: 34110256 DOI: 10.1094/mpmi-02-21-0037-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Symbiosis between Rhizobium leguminosarum and Pisum sativum requires tight control of redox balance in order to maintain respiration under the microaerobic conditions required for nitrogenase while still producing the eight electrons and sixteen molecules of ATP needed for nitrogen fixation. FixABCX, a cluster of electron transfer flavoproteins essential for nitrogen fixation, is encoded on the Sym plasmid (pRL10), immediately upstream of nifA, which encodes the general transcriptional regulator of nitrogen fixation. There is a symbiotically regulated NifA-dependent promoter upstream of fixA (PnifA1), as well as an additional basal constitutive promoter driving background expression of nifA (PnifA2). These were confirmed by 5'-end mapping of transcription start sites using differential RNA-seq. Complementation of polar fixAB and fixX mutants (Fix- strains) confirmed expression of nifA from PnifA1 in symbiosis. Electron microscopy combined with single-cell Raman microspectroscopy characterization of fixAB mutants revealed previously unknown heterogeneity in bacteroid morphology within a single nodule. Two morphotypes of mutant fixAB bacteroids were observed. One was larger than wild-type bacteroids and contained high levels of polyhydroxy-3-butyrate, a complex energy/reductant storage product. A second bacteroid phenotype was morphologically and compositionally different and resembled wild-type infection thread cells. From these two characteristic fixAB mutant bacteroid morphotypes, inferences can be drawn on the metabolism of wild-type nitrogen-fixing bacteroids.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Isabel U C Webb
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Jiabao Xu
- Department of Engineering, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K
| | | | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
| | - Vinoy K Ramachandran
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Paul J Rutten
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Alison K East
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
| | - Wei E Huang
- Department of Engineering, University of Oxford, Parks Road, Oxford OX1 3PJ, U.K
| | - Nicholas J Watmough
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, Norfolk NR4 7TJ, U.K
| | - Philip S Poole
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, U.K
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, U.K
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Jorrin B, Maluk M, Atoliya N, Kumar SC, Chalasani D, Tkacz A, Singh P, Basu A, Pullabhotla SVSRN, Kumar M, Mohanty SR, East AK, Ramachandran VK, James EK, Podile AR, Saxena AK, Rao DLN, Poole PS. Genomic Diversity of Pigeon Pea ( Cajanus cajan L. Millsp.) Endosymbionts in India and Selection of Potential Strains for Use as Agricultural Inoculants. Front Plant Sci 2021; 12:680981. [PMID: 34557206 PMCID: PMC8453007 DOI: 10.3389/fpls.2021.680981] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/06/2021] [Indexed: 05/27/2023]
Abstract
Pigeon pea (Cajanus cajan L. Millsp. ) is a legume crop resilient to climate change due to its tolerance to drought. It is grown by millions of resource-poor farmers in semiarid and tropical subregions of Asia and Africa and is a major contributor to their nutritional food security. Pigeon pea is the sixth most important legume in the world, with India contributing more than 70% of the total production and harbouring a wide variety of cultivars. Nevertheless, the low yield of pigeon pea grown under dry land conditions and its yield instability need to be improved. This may be done by enhancing crop nodulation and, hence, biological nitrogen fixation (BNF) by supplying effective symbiotic rhizobia through the application of "elite" inoculants. Therefore, the main aim in this study was the isolation and genomic analysis of effective rhizobial strains potentially adapted to drought conditions. Accordingly, pigeon pea endosymbionts were isolated from different soil types in Southern, Central, and Northern India. After functional characterisation of the isolated strains in terms of their ability to nodulate and promote the growth of pigeon pea, 19 were selected for full genome sequencing, along with eight commercial inoculant strains obtained from the ICRISAT culture collection. The phylogenomic analysis [Average nucleotide identity MUMmer (ANIm)] revealed that the pigeon pea endosymbionts were members of the genera Bradyrhizobium and Ensifer. Based on nodC phylogeny and nod cluster synteny, Bradyrhizobium yuanmingense was revealed as the most common endosymbiont, harbouring nod genes similar to those of Bradyrhizobium cajani and Bradyrhizobium zhanjiangense. This symbiont type (e.g., strain BRP05 from Madhya Pradesh) also outperformed all other strains tested on pigeon pea, with the notable exception of an Ensifer alkalisoli strain from North India (NBAIM29). The results provide the basis for the development of pigeon pea inoculants to increase the yield of this legume through the use of effective nitrogen-fixing rhizobia, tailored for the different agroclimatic regions of India.
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Affiliation(s)
- Beatriz Jorrin
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Marta Maluk
- The James Hutton Institute, Dundee, United Kingdom
| | | | - Shiv Charan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Danteswari Chalasani
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Andrzej Tkacz
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Prachi Singh
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - Anirban Basu
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Sarma VSRN Pullabhotla
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Murugan Kumar
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | | | - Alison K. East
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | | | | | - Appa Rao Podile
- Department of Plant Sciences, School of Life Science, University of Hyderabad, Hyderabad, India
| | - Anil Kumar Saxena
- ICAR-National Bureau of Agriculturally Important Microorganisms, Mau, India
| | - DLN Rao
- ICAR-Indian Institute of Soil Science, Bhopal, India
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
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5
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Rubia MI, Ramachandran VK, Arrese-Igor C, Larrainzar E, Poole PS. A novel biosensor to monitor proline in pea root exudates and nodules under osmotic stress and recovery. Plant Soil 2020; 452:413-422. [PMID: 32713966 PMCID: PMC7371648 DOI: 10.1007/s11104-020-04577-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND AIMS Plant and bacteria are able to synthesise proline, which acts as a compound to counteract the negative effects of osmotic stresses. Most methodologies rely on the extraction of compounds using destructive methods. This work describes a new proline biosensor that allows the monitoring of proline levels in a non-invasive manner in root exudates and nodules of legume plants. METHODS The proline biosensor was constructed by cloning the promoter region of pRL120553, a gene with high levels of induction in the presence of proline, in front of the lux cassette in Rhizobium leguminosarum bv. viciae. RESULTS Free-living assays show that the proline biosensor is sensitive and specific for proline. Proline was detected in both root exudates and nodules of pea plants. The luminescence detected in bacteroids did not show variations during osmotic stress treatments, but significantly increased during recovery. CONCLUSIONS This biosensor is a useful tool for the in vivo monitoring of proline levels in root exudates and bacteroids of symbiotic root nodules, and it contributes to our understanding of the metabolic exchange occurring in nodules under abiotic stress conditions.
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Affiliation(s)
- María I. Rubia
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, Campus Arrosadia, Pamplona, 31006 Spain
| | | | - Cesar Arrese-Igor
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, Campus Arrosadia, Pamplona, 31006 Spain
| | - Estíbaliz Larrainzar
- Institute for Multidisciplinary Research in Applied Biology-IMAB, Universidad Pública de Navarra, Campus Arrosadia, Pamplona, 31006 Spain
| | - Philip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB UK
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Haskett TL, Terpolilli JJ, Ramachandran VK, Verdonk CJ, Poole PS, O’Hara GW, Ramsay JP. Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements. PLoS Genet 2018; 14:e1007292. [PMID: 29565971 PMCID: PMC5882170 DOI: 10.1371/journal.pgen.1007292] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 04/03/2018] [Accepted: 03/06/2018] [Indexed: 12/14/2022] Open
Abstract
Tripartite integrative and conjugative elements (ICE3) are a novel form of ICE that exist as three separate DNA regions integrated within the genomes of Mesorhizobium spp. Prior to conjugative transfer the three ICE3 regions of M. ciceri WSM1271 ICEMcSym1271 combine and excise to form a single circular element. This assembly requires three coordinated recombination events involving three site-specific recombinases IntS, IntG and IntM. Here, we demonstrate that three excisionases–or recombination directionality factors—RdfS, RdfG and RdfM are required for ICE3 excision. Transcriptome sequencing revealed that expression of ICE3 transfer and conjugation genes was induced by quorum sensing. Quorum sensing activated expression of rdfS, and in turn RdfS stimulated transcription of both rdfG and rdfM. Therefore, RdfS acts as a “master controller” of ICE3 assembly and excision. The dependence of all three excisive reactions on RdfS ensures that ICE3 excision occurs via a stepwise sequence of recombination events that avoids splitting the chromosome into a non-viable configuration. These discoveries expose a surprisingly simple control system guiding molecular assembly of these novel and complex mobile genetic elements and highlight the diverse and critical functions of excisionase proteins in control of horizontal gene transfer. Bacteria evolve and adapt quickly through the horizontal transfer of DNA. A major mechanism facilitating this transfer is conjugation. Conjugative DNA elements that integrate into the chromosome are termed ‘Integrative and Conjugative Elements’ (ICE). We recently discovered a unique form of ICE that undergoes a complex series of recombination events with the host chromosome to split itself into three separate parts. This tripartite ICE must also precisely order its recombination when leaving the current host to avoid splitting the host chromosome and the ICE into non-viable parts. In this work, we show that the tripartite ICEs use chemical cell-cell communication to stimulate recombination and that recombination events are specifically ordered through cascaded transcriptional activation of small DNA-binding proteins called recombination directionality factors. Despite the inherent complexity of tripartite ICEs this work exposes a surprisingly simple system to stimulate their precise and ordered molecular assembly prior to horizontal transfer.
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Affiliation(s)
- Timothy L. Haskett
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
- * E-mail:
| | - Jason J. Terpolilli
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | | | - Callum J. Verdonk
- School of Pharmacy and Biomedical Sciences and the Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
| | - Phillip S. Poole
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - Graham W. O’Hara
- Centre for Rhizobium Studies, School of Veterinary and Life Sciences, Murdoch University, Perth, WA, Australia
| | - Joshua P. Ramsay
- School of Pharmacy and Biomedical Sciences and the Curtin Health Innovation Research Institute, Curtin University, Perth, WA, Australia
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Rice CJ, Ramachandran VK, Shearer N, Thompson A. Transcriptional and Post-Transcriptional Modulation of SPI1 and SPI2 Expression by ppGpp, RpoS and DksA in Salmonella enterica sv Typhimurium. PLoS One 2015; 10:e0127523. [PMID: 26039089 PMCID: PMC4454661 DOI: 10.1371/journal.pone.0127523] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/16/2015] [Indexed: 12/02/2022] Open
Abstract
The expression of genes within Salmonella Pathogenicity Islands 1 and 2 (SPI1, SPI2) is required to facilitate invasion and intracellular replication respectively of S. Typhimurium in host cell lines. Control of their expression is complex and occurs via a variety of factors operating at transcriptional and post-transcriptional levels in response to the environmental stimuli found within the host. Several of the factors that modulate SPI1 and SPI2 expression are involved in the redistribution or modification of RNA polymerase (RNAP) specificity. These factors include the bacterial alarmone, ppGpp, the alternative sigma factor, RpoS, and the RNAP accessory protein, DksA. In this report we show not only how these three factors modulate SPI1 and SPI2 expression but also how they contribute to the 'phased' expression of SPI1 and SPI2 during progress through late-log and stationary phase in aerobic rich broth culture conditions. In addition, we demonstrate that the expression of at least one SPI1-encoded protein, SipC is subject to DksA-dependent post-transcriptional control.
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Affiliation(s)
| | | | - Neil Shearer
- Institute of Food Research, Norwich, NR4 7UA, United Kingdom
| | - Arthur Thompson
- Institute of Food Research, Norwich, NR4 7UA, United Kingdom
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Handley RA, Mulholland F, Reuter M, Ramachandran VK, Musk H, Clissold L, Le Brun NE, van Vliet AHM. PerR controls oxidative stress defence and aerotolerance but not motility-associated phenotypes of Campylobacter jejuni. Microbiology (Reading) 2015; 161:1524-36. [PMID: 25968890 DOI: 10.1099/mic.0.000109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The foodborne bacterial pathogen Campylobacter jejuni is an obligate microaerophile that is exposed to atmospheric oxygen during transmission through the food chain. Survival under aerobic conditions requires the concerted control of oxidative stress systems, which in C. jejuni are intimately connected with iron metabolism via the PerR and Fur regulatory proteins. Here, we have characterized the roles of C. jejuni PerR in oxidative stress and motility phenotypes, and its regulon at the level of transcription, protein expression and promoter interactions. Insertional inactivation of perR in the C. jejuni reference strains NCTC 11168, 81-176 and 81116 did not result in any growth deficiencies, but strongly increased survival in atmospheric oxygen conditions, and allowed growth around filter discs infused with up to 30 % H2O2 (8.8 M). Expression of catalase, alkyl hydroperoxide reductase, thioredoxin reductase and the Rrc desulforubrerythrin was increased in the perR mutant, and this was mediated at the transcriptional level as shown by electrophoretic mobility shift assays of the katA, ahpC and trxB promoters using purified PerR. Differential RNA-sequencing analysis of a fur perR mutant allowed the identification of eight previously unknown transcription start sites of genes controlled by Fur and/or PerR. Finally, inactivation of perR in C. jejuni did not result in reduced motility, and did not reduce killing of Galleria melonella wax moth larvae. In conclusion, PerR plays an important role in controlling oxidative stress resistance and aerobic survival of C. jejuni, but this role does not extend into control of motility and associated phenotypes.
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Affiliation(s)
- Rebecca A Handley
- 1 Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK 2 Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Francis Mulholland
- 1 Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | - Mark Reuter
- 1 Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
| | | | - Heather Musk
- 4 The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Leah Clissold
- 4 The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK
| | - Nick E Le Brun
- 2 Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Arnoud H M van Vliet
- 1 Gut Health and Food Safety Programme, Institute of Food Research, Norwich Research Park, Norwich NR4 7UA, UK
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9
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Bowden SD, Hopper-Chidlaw AC, Rice CJ, Ramachandran VK, Kelly DJ, Thompson A. Nutritional and metabolic requirements for the infection of HeLa cells by Salmonella enterica serovar Typhimurium. PLoS One 2014; 9:e96266. [PMID: 24797930 PMCID: PMC4010460 DOI: 10.1371/journal.pone.0096266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 04/07/2014] [Indexed: 12/04/2022] Open
Abstract
Salmonella is the causative agent of a spectrum of human and animal diseases ranging from gastroenteritis to typhoid fever. It is a food - and water - borne pathogen and infects via ingestion followed by invasion of intestinal epithelial cells and phagocytic cells. In this study we employed a mutational approach to define the nutrients and metabolic pathways required by Salmonella enterica serovar Typhimurium during infection of a human epithelial cell line (HeLa). We deleted the key glycolytic genes, pfkA and pfkB to show that S. Typhimurium utilizes glycolysis for replication within HeLa cells; however, glycolysis was not absolutely essential for intracellular replication. Using S. Typhimurium strains deleted for genes encoding components of the phosphotransferase system and glucose transport, we show that glucose is a major substrate required for the intracellular replication of S. Typhimurium in HeLa cells. We also deleted genes encoding enzymes involved in the utilization of gluconeogenic substrates and the glyoxylate shunt and show that neither of these pathways were required for intracellular replication of S. Typhimurium within HeLa cells.
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Affiliation(s)
- Steven D. Bowden
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
| | | | | | - Vinoy K. Ramachandran
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- Department of Plant Sciences, University of Oxford, Oxford, United Kingdom
| | - David J. Kelly
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom
| | - Arthur Thompson
- Institute of Food Research, Norwich Research Park, Colney, Norwich, United Kingdom
- * E-mail:
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10
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Ramachandran VK, Shearer N, Thompson A. The primary transcriptome of Salmonella enterica Serovar Typhimurium and its dependence on ppGpp during late stationary phase. PLoS One 2014; 9:e92690. [PMID: 24664308 PMCID: PMC3963941 DOI: 10.1371/journal.pone.0092690] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 02/24/2014] [Indexed: 12/01/2022] Open
Abstract
We have used differential RNA-seq (dRNA-seq) to characterise the transcriptomic architecture of S. Typhimurium SL1344, and its dependence on the bacterial alarmone, guanosine tetraphosphate (ppGpp) during late stationary phase, (LSP). Under LSP conditions we were able to identify the transcriptional start sites (TSSs) for 53% of the S. Typhimurium open reading frames (ORFs) and discovered 282 candidate non-coding RNAs (ncRNAs). The mapping of LSP TSSs enabled a detailed comparison with a previous dRNA-seq study of the early stationary phase (ESP) transcriptional architecture of S. Typhimurium SL1344 and its dependence on ppGpp. For the purposes of this study, LSP was defined as an aerobic LB culture grown to a later optical density reading (OD600 = 3.6) compared to ESP (OD600 = 2.3). The precise nucleotide positions of the majority of S. Typhimurium TSSs at LSP agreed closely with those identified at ESP. However, the identification of TSSs at different positions, or where additional or fewer TSSs were found at LSP compared to ESP enabled the genome-wide categorisation of growth phase dependent changes in promoter structure, the first time such an analysis has been done on this scale. Comparison of the ppGpp-dependency LSP and ESP TSSs for mRNAs and ncRNAs revealed a similar breadth of ppGpp-activation and repression. However, we note several ncRNAs previously shown to be involved in virulence were highly ppGpp-dependent at LSP. Finally, although SPI1 was expressed at ESP, we found SPI1 was not as highly expressed at LSP, instead we observed elevated expression of SPI2 encoded genes. We therefore also report an analysis of SPI2 transcriptional architecture at LSP resulting in localisation of SsrB binding sites and identification of a previously unreported SPI2 TSS. We also show that ppGpp is required for nearly all of SPI2 expression at LSP as well as for expression of SPI1 at ESP.
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Affiliation(s)
| | - Neil Shearer
- Institute of Food Research, Norwich, United Kingdom
| | - Arthur Thompson
- Institute of Food Research, Norwich, United Kingdom
- * E-mail:
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Ramachandran VK, Shearer N, Jacob JJ, Sharma CM, Thompson A. The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella Typhimurium during invasion gene expression. BMC Genomics 2012; 13:25. [PMID: 22251276 PMCID: PMC3293720 DOI: 10.1186/1471-2164-13-25] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 01/17/2012] [Indexed: 11/26/2022] Open
Abstract
Background Invasion of intestinal epithelial cells by Salmonella enterica serovar Typhimurium (S. Typhimurium) requires expression of the extracellular virulence gene expression programme (STEX), activation of which is dependent on the signalling molecule guanosine tetraphosphate (ppGpp). Recently, next-generation transcriptomics (RNA-seq) has revealed the unexpected complexity of bacterial transcriptomes and in this report we use differential RNA sequencing (dRNA-seq) to define the high-resolution transcriptomic architecture of wild-type S. Typhimurium and a ppGpp null strain under growth conditions which model STEX. In doing so we show that ppGpp plays a much wider role in regulating the S. Typhimurium STEX primary transcriptome than previously recognised. Results Here we report the precise mapping of transcriptional start sites (TSSs) for 78% of the S. Typhimurium open reading frames (ORFs). The TSS mapping enabled a genome-wide promoter analysis resulting in the prediction of 169 alternative sigma factor binding sites, and the prediction of the structure of 625 operons. We also report the discovery of 55 new candidate small RNAs (sRNAs) and 302 candidate antisense RNAs (asRNAs). We discovered 32 ppGpp-dependent alternative TSSs and determined the extent and level of ppGpp-dependent coding and non-coding transcription. We found that 34% and 20% of coding and non-coding RNA transcription respectively was ppGpp-dependent under these growth conditions, adding a further dimension to the role of this remarkable small regulatory molecule in enabling rapid adaptation to the infective environment. Conclusions The transcriptional architecture of S. Typhimurium and finer definition of the key role ppGpp plays in regulating Salmonella coding and non-coding transcription should promote the understanding of gene regulation in this important food borne pathogen and act as a resource for future research.
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Affiliation(s)
- Vinoy K Ramachandran
- Institute of Food Research, Norwich, UK, University of Würzburg, Josef-Schneider-Str, 2/Bau D15, 97080 Würzburg, Germany
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Ramachandran VK, East AK, Karunakaran R, Downie JA, Poole PS. Adaptation of Rhizobium leguminosarum to pea, alfalfa and sugar beet rhizospheres investigated by comparative transcriptomics. Genome Biol 2011; 12:R106. [PMID: 22018401 PMCID: PMC3333776 DOI: 10.1186/gb-2011-12-10-r106] [Citation(s) in RCA: 109] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 09/19/2011] [Accepted: 10/21/2011] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The rhizosphere is the microbe-rich zone around plant roots and is a key determinant of the biosphere's productivity. Comparative transcriptomics was used to investigate general and plant-specific adaptations during rhizosphere colonization. Rhizobium leguminosarum biovar viciae was grown in the rhizospheres of pea (its legume nodulation host), alfalfa (a non-host legume) and sugar beet (non-legume). Gene expression data were compared to metabolic and transportome maps to understand adaptation to the rhizosphere. RESULTS Carbon metabolism was dominated by organic acids, with a strong bias towards aromatic amino acids, C1 and C2 compounds. This was confirmed by induction of the glyoxylate cycle required for C2 metabolism and gluconeogenesis in all rhizospheres. Gluconeogenesis is repressed in R. leguminosarum by sugars, suggesting that although numerous sugar and putative complex carbohydrate transport systems are induced in the rhizosphere, they are less important carbon sources than organic acids. A common core of rhizosphere-induced genes was identified, of which 66% are of unknown function. Many genes were induced in the rhizosphere of the legumes, but not sugar beet, and several were plant specific. The plasmid pRL8 can be considered pea rhizosphere specific, enabling adaptation of R. leguminosarum to its host. Mutation of many of the up-regulated genes reduced competitiveness for pea rhizosphere colonization, while two genes specifically up-regulated in the pea rhizosphere reduced colonization of the pea but not alfalfa rhizosphere. CONCLUSIONS Comparative transcriptome analysis has enabled differentiation between factors conserved across plants for rhizosphere colonization as well as identification of exquisite specific adaptation to host plants.
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Affiliation(s)
| | - Alison K East
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - J Allan Downie
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Philip S Poole
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
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Bowden SD, Ramachandran VK, Knudsen GM, Hinton JCD, Thompson A. An incomplete TCA cycle increases survival of Salmonella Typhimurium during infection of resting and activated murine macrophages. PLoS One 2010; 5:e13871. [PMID: 21079785 PMCID: PMC2975626 DOI: 10.1371/journal.pone.0013871] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2009] [Accepted: 10/14/2010] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In comparison to the comprehensive analyses performed on virulence gene expression, regulation and action, the intracellular metabolism of Salmonella during infection is a relatively under-studied area. We investigated the role of the tricarboxylic acid (TCA) cycle in the intracellular replication of Salmonella Typhimurium in resting and activated macrophages, epithelial cells, and during infection of mice. METHODOLOGY/PRINCIPAL FINDINGS We constructed deletion mutations of 5 TCA cycle genes in S. Typhimurium including gltA, mdh, sdhCDAB, sucAB, and sucCD. We found that the mutants exhibited increased net intracellular replication in resting and activated murine macrophages compared to the wild-type. In contrast, an epithelial cell infection model showed that the S. Typhimurium ΔsucCD and ΔgltA strains had reduced net intracellular replication compared to the wild-type. The glyoxylate shunt was not responsible for the net increased replication of the TCA cycle mutants within resting macrophages. We also confirmed that, in a murine infection model, the S. Typhimurium ΔsucAB and ΔsucCD strains are attenuated for virulence. CONCLUSIONS/SIGNIFICANCE Our results suggest that disruption of the TCA cycle increases the ability of S. Typhimurium to survive within resting and activated murine macrophages. In contrast, epithelial cells are non-phagocytic cells and unlike macrophages cannot mount an oxidative and nitrosative defence response against pathogens; our results show that in HeLa cells the S. Typhimurium TCA cycle mutant strains show reduced or no change in intracellular levels compared to the wild-type. The attenuation of the S. Typhimurium ΔsucAB and ΔsucCD mutants in mice, compared to their increased net intracellular replication in resting and activated macrophages suggest that Salmonella may encounter environments within the host where a complete TCA cycle is advantageous.
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Affiliation(s)
| | | | | | - Jay C. D. Hinton
- Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College, Dublin, Ireland
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Karunakaran R, Haag AF, East AK, Ramachandran VK, Prell J, James EK, Scocchi M, Ferguson GP, Poole PS. BacA is essential for bacteroid development in nodules of galegoid, but not phaseoloid, legumes. J Bacteriol 2010; 192:2920-8. [PMID: 20363949 PMCID: PMC2876491 DOI: 10.1128/jb.00020-10] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/22/2010] [Indexed: 01/01/2023] Open
Abstract
BacA is an integral membrane protein, the mutation of which leads to increased resistance to the antimicrobial peptides bleomycin and Bac7(1-35) and a greater sensitivity to SDS and vancomycin in Rhizobium leguminosarum bv. viciae, R. leguminosarum bv. phaseoli, and Rhizobium etli. The growth of Rhizobium strains on dicarboxylates as a sole carbon source was impaired in bacA mutants but was overcome by elevating the calcium level. While bacA mutants elicited indeterminate nodule formation on peas, which belong to the galegoid tribe of legumes, bacteria lysed after release from infection threads and mature bacteroids were not formed. Microarray analysis revealed almost no change in a bacA mutant of R. leguminosarum bv. viciae in free-living culture. In contrast, 45 genes were more-than 3-fold upregulated in a bacA mutant isolated from pea nodules. Almost half of these genes code for cell membrane components, suggesting that BacA is crucial to alterations that occur in the cell envelope during bacteroid development. In stark contrast, bacA mutants of R. leguminosarum bv. phaseoli and R. etli elicited the formation of normal determinate nodules on their bean host, which belongs to the phaseoloid tribe of legumes. Bacteroids from these nodules were indistinguishable from the wild type in morphology and nitrogen fixation. Thus, while bacA mutants of bacteria that infect galegoid or phaseoloid legumes have similar phenotypes in free-living culture, BacA is essential only for bacteroid development in indeterminate galegoid nodules.
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Affiliation(s)
- Ramakrishnan Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Andreas F. Haag
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Alison K. East
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Vinoy K. Ramachandran
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Jurgen Prell
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Euan K. James
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Marco Scocchi
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Gail P. Ferguson
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Philip S. Poole
- Department of Molecular Microbiology, John Innes Centre, Colney Lane, Norwich, NR4 7UH, United Kingdom, Division of Applied Medicine, School of Medicine & Dentistry, Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, AB25 2ZD, United Kingdom, School of Biological Sciences, University of Reading, Reading, RG6 6AJ, United Kingdom, EPI Division, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, United Kingdom, Department of Life Sciences, University of Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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Karunakaran R, Ramachandran VK, Seaman JC, East AK, Mouhsine B, Mauchline TH, Prell J, Skeffington A, Poole PS. Transcriptomic analysis of Rhizobium leguminosarum biovar viciae in symbiosis with host plants Pisum sativum and Vicia cracca. J Bacteriol 2009; 191:4002-14. [PMID: 19376875 PMCID: PMC2698398 DOI: 10.1128/jb.00165-09] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2009] [Accepted: 04/03/2009] [Indexed: 01/20/2023] Open
Abstract
Rhizobium leguminosarum bv. viciae forms nitrogen-fixing nodules on several legumes, including pea (Pisum sativum) and vetch (Vicia cracca), and has been widely used as a model to study nodule biochemistry. To understand the complex biochemical and developmental changes undergone by R. leguminosarum bv. viciae during bacteroid development, microarray experiments were first performed with cultured bacteria grown on a variety of carbon substrates (glucose, pyruvate, succinate, inositol, acetate, and acetoacetate) and then compared to bacteroids. Bacteroid metabolism is essentially that of dicarboxylate-grown cells (i.e., induction of dicarboxylate transport, gluconeogenesis and alanine synthesis, and repression of sugar utilization). The decarboxylating arm of the tricarboxylic acid cycle is highly induced, as is gamma-aminobutyrate metabolism, particularly in bacteroids from early (7-day) nodules. To investigate bacteroid development, gene expression in bacteroids was analyzed at 7, 15, and 21 days postinoculation of peas. This revealed that bacterial rRNA isolated from pea, but not vetch, is extensively processed in mature bacteroids. In early development (7 days), there were large changes in the expression of regulators, exported and cell surface molecules, multidrug exporters, and heat and cold shock proteins. fix genes were induced early but continued to increase in mature bacteroids, while nif genes were induced strongly in older bacteroids. Mutation of 37 genes that were strongly upregulated in mature bacteroids revealed that none were essential for nitrogen fixation. However, screening of 3,072 mini-Tn5 mutants on peas revealed previously uncharacterized genes essential for nitrogen fixation. These encoded a potential magnesium transporter, an AAA domain protein, and proteins involved in cytochrome synthesis.
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Affiliation(s)
- R Karunakaran
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
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White JP, Prell J, Ramachandran VK, Poole PS. Characterization of a {gamma}-aminobutyric acid transport system of Rhizobium leguminosarum bv. viciae 3841. J Bacteriol 2009; 191:1547-55. [PMID: 19103927 PMCID: PMC2648222 DOI: 10.1128/jb.00926-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2008] [Accepted: 12/09/2008] [Indexed: 12/29/2022] Open
Abstract
Spontaneous mutants of Rhizobium leguminosarum bv. viciae 3841 were isolated that grow faster than the wild type on gamma-aminobutyric acid (GABA) as the sole carbon and nitrogen source. These strains (RU1736 and RU1816) have frameshift mutations (gtsR101 and gtsR102, respectively) in a GntR-type regulator (GtsR) that result in a high rate of constitutive GABA transport. Tn5 mutagenesis and quantitative reverse transcription-PCR showed that GstR regulates expression of a large operon (pRL100242 to pRL100252) on the Sym plasmid that is required for GABA uptake. An ABC transport system, GtsABCD (for GABA transport system) (pRL100248-51), of the spermidine/putrescine family is part of this operon. GtsA is a periplasmic binding protein, GtsB and GtsC are integral membrane proteins, and GtsD is an ATP-binding subunit. Expression of gtsABCD from a lacZ promoter confirmed that it alone is responsible for high rates of GABA transport, enabling rapid growth of strain 3841 on GABA. Gts transports open-chain compounds with four or five carbon atoms with carboxyl and amino groups at, or close to, opposite termini. However, aromatic compounds with similar spacing between carboxyl and amino groups are excellent inhibitors of GABA uptake so they may also be transported. In addition to the ABC transporter, the operon contains two putative mono-oxygenases, a putative hydrolase, a putative aldehyde dehydrogenase, and a succinate semialdehyde dehydrogenase. This suggests the operon may be involved in the transport and breakdown of a more complex precursor to GABA. Gts is not expressed in pea bacteroids, and gtsB mutants are unaltered in their symbiotic phenotype, suggesting that Bra is the only GABA transport system available for amino acid cycling.
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Affiliation(s)
- J P White
- University of Reading, United Kingdom
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