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Rose CJ, Hammerschmidt K, Pichugin Y, Rainey PB. Meta‐population structure and the evolutionary transition to multicellularity. Ecol Lett 2020; 23:1380-1390. [DOI: 10.1111/ele.13570] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 05/27/2020] [Accepted: 06/08/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Caroline J. Rose
- New Zealand Institute for Advanced StudyMassey University Auckland New Zealand
| | | | - Yuriy Pichugin
- New Zealand Institute for Advanced StudyMassey University Auckland New Zealand
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey University Auckland New Zealand
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52
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Grenga L, Little RH, Chandra G, Woodcock SD, Saalbach G, Morris RJ, Malone JG. Control of mRNA translation by dynamic ribosome modification. PLoS Genet 2020; 16:e1008837. [PMID: 32584816 PMCID: PMC7343187 DOI: 10.1371/journal.pgen.1008837] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 07/08/2020] [Accepted: 05/07/2020] [Indexed: 01/28/2023] Open
Abstract
Control of mRNA translation is a crucial regulatory mechanism used by bacteria to respond to their environment. In the soil bacterium Pseudomonas fluorescens, RimK modifies the C-terminus of ribosomal protein RpsF to influence important aspects of rhizosphere colonisation through proteome remodelling. In this study, we show that RimK activity is itself under complex, multifactorial control by the co-transcribed phosphodiesterase trigger enzyme (RimA) and a polyglutamate-specific protease (RimB). Furthermore, biochemical experimentation and mathematical modelling reveal a role for the nucleotide second messenger cyclic-di-GMP in coordinating these activities. Active ribosome regulation by RimK occurs by two main routes: indirectly, through changes in the abundance of the global translational regulator Hfq and directly, with translation of surface attachment factors, amino acid transporters and key secreted molecules linked specifically to RpsF modification. Our findings show that post-translational ribosomal modification functions as a rapid-response mechanism that tunes global gene translation in response to environmental signals.
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Affiliation(s)
- Lucia Grenga
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
| | | | - Govind Chandra
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | | | - Gerhard Saalbach
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | - Richard James Morris
- Computational and Systems Biology, John Innes Centre, Norwich, Norfolk, United Kingdom
| | - Jacob George Malone
- Molecular Microbiology, John Innes Centre, Norwich, Norfolk, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, Norfolk, United Kingdom
- * E-mail:
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Global Regulatory Roles of the Histidine-Responsive Transcriptional Repressor HutC in Pseudomonas fluorescens SBW25. J Bacteriol 2020; 202:JB.00792-19. [PMID: 32291279 DOI: 10.1128/jb.00792-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/04/2020] [Indexed: 12/19/2022] Open
Abstract
HutC is known as a transcriptional repressor specific for histidine utilization (hut) genes in Gram-negative bacteria, including Pseudomonas fluorescens SBW25. However, its precise mode of protein-DNA interactions hasn't been examined with purified HutC proteins. Here, we performed electrophoretic mobility shift assay (EMSA) and DNase I footprinting using His6-tagged HutC and biotin-labeled probe of the hut promoter (PhutU). Results revealed a complex pattern of HutC oligomerization, and the specific protein-DNA interaction is disrupted by urocanate, a histidine derivative, in a concentration-dependent manner. Next, we searched for putative HutC-binding sites in the SBW25 genome. This led to the identification of 143 candidate targets with a P value less than 10-4 HutC interaction with eight selected candidate sites was subsequently confirmed by EMSA analysis, including the type IV pilus assembly protein PilZ, phospholipase C (PlcC) for phosphatidylcholine hydrolyzation, and key regulators of cellular nitrogen metabolism (NtrBC and GlnE). Finally, an isogenic hutC deletion mutant was subjected to transcriptome sequencing (RNA-seq) analysis and phenotypic characterization. When bacteria were grown on succinate and histidine, hutC deletion caused upregulation of 794 genes and downregulation of 525 genes at a P value of <0.05 with a fold change cutoff of 2.0. The hutC mutant displayed an enhanced spreading motility and pyoverdine production in laboratory media, in addition to the previously reported growth defect on the surfaces of plants. Together, our data indicate that HutC plays global regulatory roles beyond histidine catabolism through low-affinity binding with operator sites located outside the hut locus.IMPORTANCE HutC in Pseudomonas is a representative member of the GntR/HutC family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate-binding domain. HutC is generally known to repress expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. Here, we first describe the detailed molecular interactions between HutC and its PhutU target site in a plant growth-promoting bacterium, P. fluorescens SBW25, and further show that HutC possesses specific DNA-binding activities with many targets in the SBW25 genome. Subsequent RNA-seq analysis and phenotypic assays revealed an unexpected global regulatory role of HutC for successful bacterial colonization in planta.
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Zhang X, Ritchie SR, Chang H, Arnold DL, Jackson RW, Rainey PB. Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland. Ecol Evol 2020; 10:5963-5975. [PMID: 32607204 PMCID: PMC7319117 DOI: 10.1002/ece3.6334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 01/02/2023] Open
Abstract
Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A 660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches.
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Affiliation(s)
- Xue‐Xian Zhang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- School of Natural and Computational SciencesMassey UniversityAucklandNew Zealand
| | - Stephen R. Ritchie
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Faculty of Medical and Health SciencesUniversity of AucklandAucklandNew Zealand
| | - Hao Chang
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
| | - Dawn L. Arnold
- Centre for Research in BioscienceUniversity of the West of EnglandBristolUK
| | - Robert W. Jackson
- School of Biosciences and Birmingham Institute of Forest ResearchUniversity of BirminghamBirminghamUK
| | - Paul B. Rainey
- New Zealand Institute for Advanced StudyMassey UniversityAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Laboratoire de Génétique de l'Evolution, Chemistry, Biology and Innovation (CBI)UMR8231ESPCI ParisCNRSPSL Research UniversityParisFrance
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55
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Egelkamp R, Friedrich I, Hertel R, Daniel R. From sequence to function: a new workflow for nitrilase identification. Appl Microbiol Biotechnol 2020; 104:4957-4970. [PMID: 32291488 PMCID: PMC7228900 DOI: 10.1007/s00253-020-10544-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2019] [Revised: 02/28/2020] [Accepted: 03/11/2020] [Indexed: 11/16/2022]
Abstract
Abstract Nitrilases are industrially important biocatalysts due to their ability to degrade nitriles to carboxylic acids and ammonia. In this study, a workflow for simple and fast recovery of nitrilase candidates from metagenomes is presented. For identification of active enzymes, a NADH-coupled high-throughput assay was established. Purification of enzymes could be omitted as the assay is based on crude extract containing the expressed putative nitrilases. In addition, long incubation times were avoided by combining nitrile and NADH conversion in a single reaction. This allowed the direct measurement of nitrile degradation and provided not only insights into substrate spectrum and specificity but also in degradation efficiency. The novel assay was used for investigation of candidate nitrilase-encoding genes. Seventy putative nitrilase-encoding gene and the corresponding deduced protein sequences identified during sequence-based screens of metagenomes derived from nitrile-treated microbial communities were analyzed. Subsequently, the assay was applied to 13 selected candidate genes and proteins. Six of the generated corresponding Escherichia coli clones produced nitrilases that showed activity and one unusual nitrilase was purified and analyzed. The activity of the novel arylacetonitrilase Nit09 exhibited a broad pH range and a high long-term stability. The enzyme showed high activity for arylacetonitriles with a KM of 1.29 mM and a Vmax of 13.85 U/mg protein for phenylacetonitrile. In conclusion, we provided a setup for simple and rapid analysis of putative nitrilase-encoding genes from sequence to function. The suitability was demonstrated by identification, isolation, and characterization of the arylacetonitrilase. Key points • A simple and fast high-throughput nitrilase screening was developed. • A set of putative nitrilases was successfully screened with the assay. • A novel arylacetonitrilase was identified, purified, and characterized in detail. Electronic supplementary material The online version of this article (10.1007/s00253-020-10544-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Richard Egelkamp
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Ines Friedrich
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Robert Hertel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Institute of Microbiology and Genetics, Georg-August-University of Göttingen, Grisebachstraße 8, 37077, Göttingen, Germany.
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56
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Khan N, Yeung E, Farris Y, Fansler SJ, Bernstein HC. A broad-host-range event detector: expanding and quantifying performance between Escherichia coli and Pseudomonas species. Synth Biol (Oxf) 2020. [DOI: 10.1093/synbio/ysaa002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
AbstractModern microbial biodesign relies on the principle that well-characterized genetic parts can be reused and reconfigured for different functions. However, this paradigm has only been successful in a limited set of hosts, mostly comprised from common lab strains of Escherichia coli. It is clear that new applications such as chemical sensing and event logging in complex environments will benefit from new host chassis. This study quantitatively compared how the same chemical event logger performed across four strains and three different microbial species. An integrase-based sensor and memory device was operated by two representative soil Pseudomonads—Pseudomonas fluorescens SBW25 and Pseudomonas putida DSM 291. Quantitative comparisons were made between these two non-traditional hosts and two benchmark E. coli chassis including the probiotic Nissle 1917 and common cloning strain DH5α. The performance of sensor and memory components changed according to each host, such that a clear chassis effect was observed and quantified. These results were obtained via fluorescence from reporter proteins that were transcriptionally fused to the integrase and downstream recombinant region and via data-driven kinetic models. The Pseudomonads proved to be acceptable chassis for the operation of this event logger, which outperformed the common E. coli DH5α in many ways. This study advances an emerging frontier in synthetic biology that aims to build broad-host-range devices and understand the context by which different species can execute programmable genetic operations.
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Affiliation(s)
- Nymul Khan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Enoch Yeung
- Department of Mechanical Engineering, University of California, Santa Barbara, CA, USA
| | - Yuliya Farris
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Sarah J Fansler
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Hans C Bernstein
- The Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT - The Arctic University of Norway, Tromsø, Norway
- The Arctic Centre for Sustainable Energy, UiT - The Arctic University of Norway, Tromsø, Norway
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57
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Jerdan R, Kuśmierska A, Petric M, Spiers AJ. Penetrating the air-liquid interface is the key to colonization and wrinkly spreader fitness. MICROBIOLOGY-SGM 2020; 165:1061-1074. [PMID: 31436522 DOI: 10.1099/mic.0.000844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In radiating populations of Pseudomonas fluorescens SBW25, adaptive wrinkly spreader (WS) mutants are able to gain access to the air-liquid (A-L) interface of static liquid microcosms and achieve a significant competitive fitness advantage over other non-biofilm-forming competitors. Aerotaxis and flagella-based swimming allows SBW25 cells to move into the high-O2 region located at the top of the liquid column and maintain their position by countering the effects of random cell diffusion, convection and disturbance (i.e. physical displacement). However, wild-type cells showed significantly lower levels of enrichment in this region compared to the archetypal WS, indicating that WS cells employ an additional mechanism to transfer to the A-L interface where displacement is no longer an issue and a biofilm can develop at the top of the liquid column. Preliminary experiments suggest that this might be achieved through the expression of an as yet unidentified surface active agent that is weakly associated with WS cells and alters liquid surface tension, as determined by quantitative tensiometry. The effect of physical displacement on the colonization of the high-O2 region and A-L interface was reduced through the addition of agar or polyethylene glycol to increase liquid viscosity, and under these conditions the competitive fitness of the WS was significantly reduced. These observations suggest that the ability to transfer to the A-L interface from the high-O2 region and remain there without further expenditure of energy (through, for example, the deployment of flagella) is a key evolutionary innovation of the WS, as it allows subsequent biofilm development and significant population increase, thereby affording these adaptive mutants a competitive fitness advantage over non-biofilm-forming competitors located within the liquid column.
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Affiliation(s)
- Robyn Jerdan
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kuśmierska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.,School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Marija Petric
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Andrew J Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
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58
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Huang X, Lin Y. Reconstruction and analysis of a three‐compartment genome‐scale metabolic model for
Pseudomonas fluorescens. Biotechnol Appl Biochem 2020; 67:133-139. [DOI: 10.1002/bab.1852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 11/05/2019] [Indexed: 01/25/2023]
Affiliation(s)
- Xiaoyan Huang
- Department of Chemical and Biological EngineeringUniversity of Saskatchewan Saskatoon Saskatchewan Canada
| | - Yen‐Han Lin
- Department of Chemical and Biological EngineeringUniversity of Saskatchewan Saskatoon Saskatchewan Canada
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59
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Noirot-Gros MF, Forrester S, Malato G, Larsen PE, Noirot P. CRISPR interference to interrogate genes that control biofilm formation in Pseudomonas fluorescens. Sci Rep 2019; 9:15954. [PMID: 31685917 PMCID: PMC6828691 DOI: 10.1038/s41598-019-52400-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 10/12/2019] [Indexed: 12/11/2022] Open
Abstract
Bacterial biofilm formation involves signaling and regulatory pathways that control the transition from motile to sessile lifestyle, production of extracellular polymeric matrix, and maturation of the biofilm 3D structure. Biofilms are extensively studied because of their importance in biomedical, ecological and industrial settings. Gene inactivation is a powerful approach for functional studies but it is often labor intensive, limiting systematic gene surveys to the most tractable bacterial hosts. Here, we adapted the CRISPR interference (CRISPRi) system for use in diverse strain isolates of P. fluorescens, SBW25, WH6 and Pf0-1. We found that CRISPRi is applicable to study complex phenotypes such as cell morphology, motility and biofilm formation over extended periods of time. In SBW25, CRISPRi-mediated silencing of genes encoding the GacA/S two-component system and regulatory proteins associated with the cylic di-GMP signaling messenger produced swarming and biofilm phenotypes similar to those obtained after gene inactivation. Combined with detailed confocal microscopy of biofilms, our study also revealed novel phenotypes associated with extracellular matrix biosynthesis as well as the potent inhibition of SBW25 biofilm formation mediated by the PFLU1114 operon. We conclude that CRISPRi is a reliable and scalable approach to investigate gene networks in the diverse P. fluorescens group.
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Affiliation(s)
| | - Sara Forrester
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
| | - Grace Malato
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
| | - Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States.,Department of Bioengineering, University of Illinois Chicago, Chicago, IL60607, United States
| | - Philippe Noirot
- Biosciences Division, Argonne National Laboratory, Lemont, IL60439, United States
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60
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Kutschera A, Schombel U, Wröbel M, Gisch N, Ranf S. Loss of wbpL disrupts O-polysaccharide synthesis and impairs virulence of plant-associated Pseudomonas strains. MOLECULAR PLANT PATHOLOGY 2019; 20:1535-1549. [PMID: 31559681 PMCID: PMC6804347 DOI: 10.1111/mpp.12864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Despite its importance for membrane stability and pathogenicity of mammalian pathogens, functions of the O-polysaccharide (OPS) of lipopolysaccharide (LPS) remain unclear in plant-associated bacteria. Genetic information about OPS biosynthesis in these bacteria is largely missing. Genome analysis of various plant-associated Pseudomonas strains revealed that one of the two known OPS biosynthesis clusters from Pseudomonas aeruginosa PAO1, the common polysaccharide antigen (CPA) gene cluster, is only conserved in some strains of the Pseudomonas fluorescens group. For the O-specific antigen (OSA) biosynthesis cluster, the putative genomic position could be identified, but orthologues of most functional important OSA biosynthesis enzymes could not be detected. Nevertheless, orthologues of the glycosyltransferase WbpL, required for initiation of CPA and OSA synthesis in P. aeruginosa PAO1, could be identified in the analysed Pseudomonas genomes. Knockout mutations of wbpL orthologues in Pseudomonas syringae pv. tomato DC3000 (Pst) and Pseudomonas cichorii ATCC10857/DSM50259 (Pci) resulted in strains lacking the OPS. Infection experiments of Arabidopsis thaliana plants revealed a reduced entry into the leaf apoplast after spray inoculation and a reduced apoplastic amplification of Pst ∆wbpL. Stab and spray inoculation of lettuce (Lactuca sativa) leaves with Pci ∆wbpL causes reduced infection symptoms compared to the wild-type strain. Furthermore, swarming motility was reduced in ∆wbpL mutants of Pst and Pci. This might be a possible reason for reduced bacterial titres after surface inoculation and reduced bacterial amplification in the plant. Our results imply that the presence of lipopolysaccharide OPS is required for efficient host colonization and full virulence of plant-pathogenic Pseudomonas bacteria.
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Affiliation(s)
- Alexander Kutschera
- Technical University of MunichPhytopathology, TUM School of Life Sciences Weihenstephan85354Freising‐WeihenstephanGermany
| | - Ursula Schombel
- Research Center Borstel, Leibniz Lung CenterDivision of Bioanalytical Chemistry, Priority Area InfectionsParkallee 1‐4023845BorstelGermany
| | - Michelle Wröbel
- Research Center Borstel, Leibniz Lung CenterDivision of Bioanalytical Chemistry, Priority Area InfectionsParkallee 1‐4023845BorstelGermany
| | - Nicolas Gisch
- Research Center Borstel, Leibniz Lung CenterDivision of Bioanalytical Chemistry, Priority Area InfectionsParkallee 1‐4023845BorstelGermany
| | - Stefanie Ranf
- Technical University of MunichPhytopathology, TUM School of Life Sciences Weihenstephan85354Freising‐WeihenstephanGermany
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Dutta S, Yu SM, Jeong SC, Lee YH. High-throughput analysis of genes involved in biocontrol performance of Pseudomonas fluorescens NBC275 against Gray mold. J Appl Microbiol 2019; 128:265-279. [PMID: 31574191 DOI: 10.1111/jam.14475] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/01/2019] [Accepted: 09/17/2019] [Indexed: 01/16/2023]
Abstract
AIMS Many physiological and microbial characteristics influence the biocontrol performance of the biological control agents (BCAs) in agricultural fields. To implement effective biocontrol, the contribution of specific genes, mechanisms and traits to the biocontrol performance of BCAs need to be characterized and explored in greater detail. METHODS AND RESULTS In this study, a transposon (Tn) mutant library using the BCA Pseudomonas fluorescens NBC275 (Pf275) was generated to explore genes and bacterial characteristics involved in antifungal activity and biocontrol performance. Among the Tn mutants, 205 strains showing variations in antifungal activity compared to wild-type (WT) were selected and further analysed for biocontrol efficacy against gray mold in pepper fruits. The genes involved in pyoverdine biosynthesis (pvdI and pvdD) and chitin-binding protein (gbpA) played essential roles in the antifungal activity and biocontrol capacity of Pf275. In addition, a mutation in phlD completely abolished the antifungal activity and significantly suppressed the biocontrol ability of the strain. Genes affecting antifungal activity of Pf275 significantly influenced swimming motility, which was identified as an important trait for the biocontrol ability of the bacterial strain. CONCLUSIONS Overall, our results suggest that antifungal compound production, siderophore biosynthesis and swimming motility synergistically contribute to Pf275 biocontrol performance. The utility of this library was demonstrated by identifying genes for antagonism and biocontrol ability in this BCA strain. The functional roles of many genes identified as contributing to antagonism and in vivo biocontrol activity require further study. SIGNIFICANCE AND IMPACT OF THIS STUDY Genes contributing to antifungal activity and biocontrol performance of P. fluorescens were identified and highlighted by Tn mutagenesis, which will give insight to improve the biocontrol performance of this BCA.
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Affiliation(s)
- S Dutta
- Division of Biotechnology, Chonbuk National University, Iksan-si, Jeollabuk-do, Republic of Korea
| | - S-M Yu
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, Republic of Korea
| | - S C Jeong
- Freshwater Bioresources Utilization Division, Nakdonggang National Institute of Biological Resources, Sangju-si, Gyeongsangbuk-do, Republic of Korea
| | - Y H Lee
- Division of Biotechnology, Chonbuk National University, Iksan-si, Jeollabuk-do, Republic of Korea.,Advanced Institute of Environment and Bioscience, Plant Medical Research Center, and Institute of Bio-industry, Chonbuk National University, Ikansi-si, Jeollabuk-do, Republic of Korea
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62
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Quintieri L, Zühlke D, Fanelli F, Caputo L, Liuzzi VC, Logrieco AF, Hirschfeld C, Becher D, Riedel K. Proteomic analysis of the food spoiler Pseudomonas fluorescens ITEM 17298 reveals the antibiofilm activity of the pepsin-digested bovine lactoferrin. Food Microbiol 2019; 82:177-193. [DOI: 10.1016/j.fm.2019.02.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 02/04/2019] [Accepted: 02/06/2019] [Indexed: 11/29/2022]
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63
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Bergeau D, Mazurier S, Barbey C, Merieau A, Chane A, Goux D, Bernard S, Driouich A, Lemanceau P, Vicré M, Latour X. Unusual extracellular appendages deployed by the model strain Pseudomonas fluorescens C7R12. PLoS One 2019; 14:e0221025. [PMID: 31461454 PMCID: PMC6713353 DOI: 10.1371/journal.pone.0221025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 07/30/2019] [Indexed: 01/22/2023] Open
Abstract
Pseudomonas fluorescens is considered to be a typical plant-associated saprophytic bacterium with no pathogenic potential. Indeed, some P. fluorescens strains are well-known rhizobacteria that promote plant growth by direct stimulation, by preventing the deleterious effects of pathogens, or both. Pseudomonas fluorescens C7R12 is a rhizosphere-competent strain that is effective as a biocontrol agent and promotes plant growth and arbuscular mycorrhization. This strain has been studied in detail, but no visual evidence has ever been obtained for extracellular structures potentially involved in its remarkable fitness and biocontrol performances. On transmission electron microscopy of negatively stained C7R12 cells, we observed the following appendages: multiple polar flagella, an inducible putative type three secretion system typical of phytopathogenic Pseudomonas syringae strains and densely bundled fimbria-like appendages forming a broad fractal-like dendritic network around single cells and microcolonies. The deployment of one or other of these elements on the bacterial surface depends on the composition and affinity for the water of the microenvironment. The existence, within this single strain, of machineries known to be involved in motility, chemotaxis, hypersensitive response, cellular adhesion and biofilm formation, may partly explain the strong interactions of strain C7R12 with plants and associated microflora in addition to the type three secretion system previously shown to be implied in mycorrhizae promotion.
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Affiliation(s)
- Dorian Bergeau
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)—Normandie Université - LMSM, Evreux, France
| | - Sylvie Mazurier
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Corinne Barbey
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)—Normandie Université - LMSM, Evreux, France
- Structure Fédérative de Recherche Normandie Végétale 4277 (NORVEGE), Normandie, France
| | - Annabelle Merieau
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)—Normandie Université - LMSM, Evreux, France
- Structure Fédérative de Recherche Normandie Végétale 4277 (NORVEGE), Normandie, France
| | - Andrea Chane
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)—Normandie Université - LMSM, Evreux, France
| | - Didier Goux
- Centre de Microscopie Appliquée à la biologie, SFR 4206 ICORE Université de Caen Normandie (CMAbio3), Caen, France
| | - Sophie Bernard
- Structure Fédérative de Recherche Normandie Végétale 4277 (NORVEGE), Normandie, France
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale—Normandie Université - EA 4358 Université de Rouen, Mont-Saint-Aignan, France
| | - Azeddine Driouich
- Structure Fédérative de Recherche Normandie Végétale 4277 (NORVEGE), Normandie, France
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale—Normandie Université - EA 4358 Université de Rouen, Mont-Saint-Aignan, France
| | - Philippe Lemanceau
- Agroécologie, AgroSup Dijon, INRA, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | - Maïté Vicré
- Structure Fédérative de Recherche Normandie Végétale 4277 (NORVEGE), Normandie, France
- Laboratoire de Glycobiologie et Matrice Extracellulaire Végétale—Normandie Université - EA 4358 Université de Rouen, Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratoire de Microbiologie Signaux et Microenvironnement (LMSM EA 4312)—Normandie Université - LMSM, Evreux, France
- Structure Fédérative de Recherche Normandie Végétale 4277 (NORVEGE), Normandie, France
- * E-mail:
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64
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Causes and Biophysical Consequences of Cellulose Production by Pseudomonas fluorescens SBW25 at the Air-Liquid Interface. J Bacteriol 2019; 201:JB.00110-19. [PMID: 31085696 PMCID: PMC6707908 DOI: 10.1128/jb.00110-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 04/29/2019] [Indexed: 12/20/2022] Open
Abstract
This work reveals a hitherto unrecognized behavior that manifests at the air-liquid interface that depends on production of cellulose and hints at undiscovered dimensions to bacterial life at surfaces. Additionally, the study links activation of known diguanylate cyclase-encoding pathways to cellulose expression and to signals encountered at the meniscus. Further significance stems from recognition of the consequences of fluid instabilities arising from surface production of cellulose for transport of water-soluble products over large distances. Cellulose-overproducing wrinkly spreader mutants of Pseudomonas fluorescens SBW25 have been the focus of much investigation, but conditions promoting the production of cellulose in ancestral strain SBW25 and its effects and consequences have escaped in-depth investigation through lack of an in vitro phenotype. Here, using a custom-built device, we reveal that in static broth microcosms, ancestral SBW25 encounters environmental signals at the air-liquid interface that activate, via three diguanylate cyclase-encoding pathways (Wsp, Aws, and Mws), production of cellulose. Secretion of the polymer at the meniscus leads to modification of the environment and growth of numerous microcolonies that extend from the surface. Accumulation of cellulose and associated microbial growth leads to Rayleigh-Taylor instability resulting in bioconvection and rapid transport of water-soluble products over tens of millimeters. Drawing upon data, we built a mathematical model that recapitulates experimental results and captures the interactions between biological, chemical and physical processes. IMPORTANCE This work reveals a hitherto unrecognized behavior that manifests at the air-liquid interface that depends on production of cellulose and hints at undiscovered dimensions to bacterial life at surfaces. Additionally, the study links activation of known diguanylate cyclase-encoding pathways to cellulose expression and to signals encountered at the meniscus. Further significance stems from recognition of the consequences of fluid instabilities arising from surface production of cellulose for transport of water-soluble products over large distances.
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65
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Whole-Genome Sequences of Pantoea agglomerans BL3, Pseudomonas fluorescens BL, and Pseudomonas stutzeri CM14, Isolated from Hops (Humulus lupulus). Microbiol Resour Announc 2019; 8:8/30/e00545-19. [PMID: 31346016 PMCID: PMC6658686 DOI: 10.1128/mra.00545-19] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pseudomonas stutzeri CM14, Pseudomonas fluorescens BL, and Pantoea agglomerans BL3 were isolated from Humulus lupulus cones. Here, we present the draft genome sequences of three bacteria that have been associated with hop plants. Pseudomonas stutzeri CM14, Pseudomonas fluorescens BL, and Pantoea agglomerans BL3 were isolated from Humulus lupulus cones. Here, we present the draft genome sequences of three bacteria that have been associated with hop plants.
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66
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Gallie J, Bertels F, Remigi P, Ferguson GC, Nestmann S, Rainey PB. Repeated Phenotypic Evolution by Different Genetic Routes in Pseudomonas fluorescens SBW25. Mol Biol Evol 2019; 36:1071-1085. [PMID: 30835268 PMCID: PMC6519391 DOI: 10.1093/molbev/msz040] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Repeated evolution of functionally similar phenotypes is observed throughout the tree of life. The extent to which the underlying genetics are conserved remains an area of considerable interest. Previously, we reported the evolution of colony switching in two independent lineages of Pseudomonas fluorescens SBW25. The phenotypic and genotypic bases of colony switching in the first lineage (Line 1) have been described elsewhere. Here, we deconstruct the evolution of colony switching in the second lineage (Line 6). We show that, as for Line 1, Line 6 colony switching results from an increase in the expression of a colanic acid-like polymer (CAP). At the genetic level, nine mutations occur in Line 6. Only one of these—a nonsynonymous point mutation in the housekeeping sigma factor rpoD—is required for colony switching. In contrast, the genetic basis of colony switching in Line 1 is a mutation in the metabolic gene carB. A molecular model has recently been proposed whereby the carB mutation increases capsulation by redressing the intracellular balance of positive (ribosomes) and negative (RsmAE/CsrA) regulators of a positive feedback loop in capsule expression. We show that Line 6 colony switching is consistent with this model; the rpoD mutation generates an increase in ribosomal gene expression, and ultimately an increase in CAP expression.
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Affiliation(s)
- Jenna Gallie
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.,New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand
| | - Frederic Bertels
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Philippe Remigi
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Laboratoire des Interactions Plantes-Microorganismes (LIPM), Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Gayle C Ferguson
- School of Natural and Computational Sciences, Massey University at Albany, Auckland, New Zealand
| | - Sylke Nestmann
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, Paris, France
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67
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Little RH, Woodcock SD, Campilongo R, Fung RKY, Heal R, Humphries L, Pacheco-Moreno A, Paulusch S, Stigliano E, Vikeli E, Ward D, Malone JG. Differential Regulation of Genes for Cyclic-di-GMP Metabolism Orchestrates Adaptive Changes During Rhizosphere Colonization by Pseudomonas fluorescens. Front Microbiol 2019; 10:1089. [PMID: 31156596 PMCID: PMC6531821 DOI: 10.3389/fmicb.2019.01089] [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: 02/14/2019] [Accepted: 04/30/2019] [Indexed: 12/02/2022] Open
Abstract
Bacteria belonging to the Pseudomonas genus are highly successful colonizers of the plant rhizosphere. The ability of different Pseudomonas species to live either commensal lifestyles or to act as agents of plant-growth promotion or disease is reflected in a large, highly flexible accessory genome. Nevertheless, adaptation to the plant environment involves a commonality of phenotypic outputs such as changes to motility, coupled with synthesis of nutrient uptake systems, stress-response molecules and adherence factors including exopolysaccharides. Cyclic-di-GMP (cdG) is a highly important second messenger involved in the integration of environmental signals with appropriate adaptive responses and is known to play a central role in mediating effective rhizosphere colonization. In this study, we examined the transcription of multiple, reportedly plant-upregulated cdG metabolism genes during colonization of the wheat rhizosphere by the plant-growth-promoting strain P. fluorescens SBW25. While transcription of the tested genes generally increased in the rhizosphere environment, we additionally observed a tightly orchestrated response to environmental cues, with a distinct transcriptional pattern seen for each gene throughout the colonization process. Extensive phenotypical analysis of deletion and overexpression strains was then conducted and used to propose cellular functions for individual cdG signaling genes. Finally, in-depth genetic analysis of an important rhizosphere colonization regulator revealed a link between cdG control of growth, motility and stress response, and the carbon sources available in the rhizosphere.
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Affiliation(s)
- Richard H Little
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Stuart D Woodcock
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Rosaria Campilongo
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Rowena K Y Fung
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Robert Heal
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Libby Humphries
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Alba Pacheco-Moreno
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | | | - Egidio Stigliano
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Eleni Vikeli
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Danny Ward
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom
| | - Jacob G Malone
- Department of Molecular Microbiology, John Innes Centre, Norwich, United Kingdom.,School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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68
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Marshall DC, Arruda BE, Silby MW. Alginate genes are required for optimal soil colonization and persistence by Pseudomonas fluorescens Pf0-1. Access Microbiol 2019; 1:e000021. [PMID: 32974516 PMCID: PMC7471777 DOI: 10.1099/acmi.0.000021] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas fluorescens strains are important candidates for use as biological control agents to reduce fungal diseases on crop plants. To understand the ecological success of these bacteria and for successful and stable biological control, determination of how these bacteria colonize and persist in soil environments is critical. Here we show that P. fluorescens Pf0-1 is negatively impacted by reduced water availability in soil, but adapts and persists. A pilot transcriptomic study of Pf0-1 colonizing moist and dehydrated soil was used to identify candidate genetic loci, which could play a role in the adaptation to dehydration. Genes predicted to specify alginate production were identified and chosen for functional evaluation. Using deletion mutants, predicted alginate biosynthesis genes were shown to be important for optimal colonization of moist soil, and necessary for adaptation to reduced water availability in dried soil. Our findings extend in vitro studies of water stress into a more natural system and suggest alginate may be an essential extracellular product for the lifestyle of P. fluorescens when growing in soil.
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Affiliation(s)
- Douglas C Marshall
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02747, USA
| | - Brianna E Arruda
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02747, USA
| | - Mark W Silby
- Department of Biology, University of Massachusetts Dartmouth, 285 Old Westport Road, North Dartmouth, MA 02747, USA
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69
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Subedi D, Kohli GS, Vijay AK, Willcox M, Rice SA. Accessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34. PLoS One 2019; 14:e0215038. [PMID: 30986237 PMCID: PMC6464166 DOI: 10.1371/journal.pone.0215038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.
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Affiliation(s)
- Dinesh Subedi
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
- * E-mail:
| | - Gurjeet Singh Kohli
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Ajay Kumar Vijay
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Mark Willcox
- School of Optometry and Vision Science, University of New South Wales, Sydney, Australia
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- The School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- The ithree Institute, The University of Technology Sydney, Sydney, New South Wales, Australia
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70
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Zhang Q, Amor K, Galer SJG, Thompson I, Porcelli D. Using stable isotope fractionation factors to identify Cr(VI) reduction pathways: Metal-mineral-microbe interactions. WATER RESEARCH 2019; 151:98-109. [PMID: 30594094 DOI: 10.1016/j.watres.2018.11.088] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/26/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
Microbes interact with metals and minerals in the environment altering their physical and chemical states, whilst in turn metals and minerals impact on microbial growth, activity and survival. The interactions between bacteria and dissolved chromium in the presence of iron minerals, and their impact on Cr isotope variations, were investigated. Cr(VI) reduction experiments were conducted with two bacteria, Pseudomonas fluorescens LB 300 and Shewanella oneidensis MR-1, in the presence of two iron oxide minerals, goethite and hematite. Both minerals were found to inhibit the rates of Cr(VI) reduction by Pseudomonas, but accelerated those of Shewanella. The Cr isotopic fractionation factors generated by Shewanella were independent of the presence of the minerals (ε = -2.3‰). For Pseudomonas, the ε value was the same in both the presence and absence of goethite (-3.3‰); although, it was much higher (ε = -4.3‰) in the presence of hematite. The presence of aqueous Fe(III) in solution had no detectable impact on either bacterial Cr reduction rates nor isotopic fractionation factors. The presence of aqueous Fe(II) induced rapid abiotic reduction of Cr(VI). The different effects that the presence of Fe minerals had on the Cr fractionation factors and reduction rates of the different bacterial species may be attributed to the way each bacteria attached to the minerals and their different reduction pathways. SEM images confirmed that Pseudomonas cells were much more tightly packed on the mineral surfaces than were Shewanella. The images also confirmed that Shewanella oneidensis MR-1 produced nanowires. The results suggest that the dominant Cr(VI) reduction pathway for Pseudomonas fluorescens LB 300 may have been through membrane-bound enzymes, whilst for Shewanella oneidensis MR-1 it was probably via extracellular electron transfer. Since different minerals impact differentially on bacterial Cr(VI) reduction and isotope fractionation, variations of mineralogies and the associated changes of bacterial communities should be taken into consideration when using Cr isotopes to quantify Cr redox behaviour in the environment.
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Affiliation(s)
- Qiong Zhang
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom.
| | - Ken Amor
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
| | - Stephen J G Galer
- Max Planck Institute for Chemistry, Climate Geochemistry Department, 55128, Mainz, Germany
| | - Ian Thompson
- Department of Engineering Science, University of Oxford, Oxford, United Kingdom
| | - Don Porcelli
- Department of Earth Sciences, University of Oxford, Oxford, United Kingdom
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71
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Zhang L, Wu Z, Wang X, Tan G, Song J. Insights into the Draft Genome Sequence of the Kiwifruit-Associated Pathogenic Isolate Pseudomonas fluorescens AHK-1. Curr Microbiol 2019; 76:552-557. [PMID: 30824950 DOI: 10.1007/s00284-019-01655-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
Pseudomonas fluorescens is a physiologically diverse species of bacteria present in many habitats, which possesses multifunctional traits that provide it with the capability to exhibit biological control activities, promote plant health or cause plant disease. Here, we present the draft genome sequence of the kiwifruit-associated pathogenic isolate AHK-1 of P. fluorescens, which was isolated from the diseased leaves of kiwifruit plants. The genome size of AHK-1 was found to be 7,035,786 bp, with a G + C content of 60.88%. It is predicted to contain a total of 6327 genes, of which 3998 were homologous to genes in the other two sequenced P. fluorescens isolates (SBW25 and GcM5-1A) and 946 were unique to AHK-1 based on comparative genomic analysis. Furthermore, we identified several candidate virulence factors in the genome of AHK-1, including the fliA gene encoding flagellar biosynthetic protein for biosynthesis, and the genes for components of type VI, III, and IV secretion systems. This genomic resource will serve as a reference for better understanding the genetics of pathogenic and non-pathogenic strains, and will help to elucidate the pathogenic mechanisms of P. fluorescens associated with plant disease.
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Affiliation(s)
- Lixin Zhang
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Zhiran Wu
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Xia Wang
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Genjia Tan
- Department of Plant Pathology, College of Plant Protection, Anhui Agricultural University, Hefei, 230036, China
| | - Jianghua Song
- College of Horticulture, Anhui Agricultural University, Hefei, 230036, China.
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72
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Conte E, Mende L, Grainge I, Colloms SD. A Mini-ISY100 Transposon Delivery System Effective in γ Proteobacteria. Front Microbiol 2019; 10:280. [PMID: 30873132 PMCID: PMC6400869 DOI: 10.3389/fmicb.2019.00280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 02/04/2019] [Indexed: 11/17/2022] Open
Abstract
Transposons are invaluable biological tools for the genetic manipulation of microorganisms. ISY100 from Synechocystis sp. PCC6803 is a member of the Tc1/mariner/IS630 superfamily, and is characterized by high transposition efficiency and a strong preference for TA target sequences. In this paper, we describe the design and application of a mini-ISY100 suicide vector for the in vivo creation of stable random transposon insertion libraries. The system was successfully applied in seven species belonging to four different orders of γ proteobacteria. In all cases, delivery using conjugation consistently showed the highest transposition efficiency compared to chemical transformation or electroporation. We determined the frequency of transposon insertions in all the species and proved the utility of the system by identifying genes involved in colony coloration in Shewanella oneidensis. The ease and the efficiency of the protocol developed here allow the creation of complete knock-out libraries in an extensive range of host microorganisms in less than a week with no requirement for preparatory modification.
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Affiliation(s)
- Emanuele Conte
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Linda Mende
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
| | - Ian Grainge
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, NSW, Australia
| | - Sean D Colloms
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
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73
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Jahanshah G, Yan Q, Gerhardt H, Pataj Z, Lämmerhofer M, Pianet I, Josten M, Sahl HG, Silby MW, Loper JE, Gross H. Discovery of the Cyclic Lipopeptide Gacamide A by Genome Mining and Repair of the Defective GacA Regulator in Pseudomonas fluorescens Pf0-1. JOURNAL OF NATURAL PRODUCTS 2019; 82:301-308. [PMID: 30666877 DOI: 10.1021/acs.jnatprod.8b00747] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Genome mining of the Gram-negative bacterium Pseudomonas fluorescens Pf0-1 showed that the strain possesses a silent NRPS-based biosynthetic gene cluster encoding a new lipopeptide; its activation required the repair of the global regulator system. In this paper, we describe the genomics-driven discovery and characterization of the associated secondary metabolite gacamide A, a lipodepsipeptide that forms a new family of Pseudomonas lipopeptides. The compound has a moderate, narrow-spectrum antibiotic activity and facilitates bacterial surface motility.
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Affiliation(s)
- Gahzaleh Jahanshah
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
| | - Qing Yan
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
| | - Heike Gerhardt
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Zoltán Pataj
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Michael Lämmerhofer
- Pharmaceutical Institute, Department of Pharmaceutical Analysis and Bioanalysis , University of Tübingen , 72076 Tübingen , Germany
- UMR 5060, IRAMAT-CRP2A, Esplanade des Antilles , F-33600 Pessac , France
| | - Isabelle Pianet
- CESAMO-ISM, UMR 5255, CNRS , Université Bordeaux I , 351 Cours de la Libération , F-33405 Talence , France
| | - Michaele Josten
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Hans-Georg Sahl
- Institute for Medical Microbiology, Immunology and Parasitology (IMMIP), Pharmaceutical Microbiology Unit , University of Bonn , 53115 Bonn , Germany
- German Centre for Infection Research (DZIF) , partner site Bonn-Cologne , 53115 Bonn , Germany
| | - Mark W Silby
- Department of Biology , University of Massachusetts Dartmouth , North Dartmouth , Massachusetts 02747 , United States
| | - Joyce E Loper
- Department of Botany and Plant Pathology , Oregon State University , Corvallis , Oregon 97331 , United States
- Agricultural Research Service , U.S. Department of Agriculture , Corvallis , Oregon 97331 , United States
| | - Harald Gross
- Pharmaceutical Institute, Department of Pharmaceutical Biology , University of Tübingen , 72076 Tübingen , Germany
- German Centre for Infection Research (DZIF) , partner site Tübingen , 72076 Tübingen , Germany
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74
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Connolly JA, Wilson A, Macioszek M, Song Z, Wang L, Mohammad HH, Yadav M, di Martino M, Miller CE, Hothersall J, Haines AS, Stephens ER, Crump MP, Willis CL, Simpson TJ, Winn PJ, Thomas CM. Defining the genes for the final steps in biosynthesis of the complex polyketide antibiotic mupirocin by Pseudomonas fluorescens NCIMB10586. Sci Rep 2019; 9:1542. [PMID: 30733464 PMCID: PMC6367315 DOI: 10.1038/s41598-018-38038-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 12/17/2018] [Indexed: 11/09/2022] Open
Abstract
The mupirocin trans-AT polyketide synthase pathway, provides a model system for manipulation of antibiotic biosynthesis. Its final phase involves removal of the tertiary hydroxyl group from pseudomonic acid B, PA-B, producing the fully active PA-A in a complex series of steps. To further clarify requirements for this conversion, we fed extracts containing PA-B to mutants of the producer strain singly deficient in each mup gene. This additionally identified mupM and mupN as required plus the sequence but not enzymic activity of mupL and ruled out need for other mup genes. A plasmid expressing mupLMNOPVCFU + macpE together with a derivative of the producer P. fluorescens strain NCIMB10586 lacking the mup cluster allowed conversion of PA-B to PA-A. MupN converts apo-mAcpE to holo-form while MupM is a mupirocin-resistant isoleucyl tRNA synthase, preventing self-poisoning. Surprisingly, the expression plasmid failed to allow the closely related P. fluorescens strain SBW25 to convert PA-B to PA-A.
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Affiliation(s)
- Jack A Connolly
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,School of Chemistry, University of St Andrews, BMS Building, North Haugh, St Andrews, KY16 9ST, UK
| | - Amber Wilson
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Malgorzata Macioszek
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Dr M. Macioszek, DOCS International Poland, ul. Grojecka 5, 02-019, Warszawa, Poland
| | - Zhongshu Song
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Luoyi Wang
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Hadi H Mohammad
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,College of Medicine, Kirkuk University, Kirkuk, Iraq
| | - Mukul Yadav
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Maura di Martino
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Ms M. di Martino, Dept Biology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Claire E Miller
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Dr C. E. Miller, The BioHub Birmingham, Birmingham Research Park, 97 Vincent Drive, Edgbaston, Birmingham, B15 2SQ, UK
| | - Joanne Hothersall
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Anthony S Haines
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Elton R Stephens
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Matthew P Crump
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Christine L Willis
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Thomas J Simpson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK
| | - Peter J Winn
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Christopher M Thomas
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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75
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Lind PA, Libby E, Herzog J, Rainey PB. Predicting mutational routes to new adaptive phenotypes. eLife 2019; 8:e38822. [PMID: 30616716 PMCID: PMC6324874 DOI: 10.7554/elife.38822] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 11/27/2018] [Indexed: 12/21/2022] Open
Abstract
Predicting evolutionary change poses numerous challenges. Here we take advantage of the model bacterium Pseudomonas fluorescens in which the genotype-to-phenotype map determining evolution of the adaptive 'wrinkly spreader' (WS) type is known. We present mathematical descriptions of three necessary regulatory pathways and use these to predict both the rate at which each mutational route is used and the expected mutational targets. To test predictions, mutation rates and targets were determined for each pathway. Unanticipated mutational hotspots caused experimental observations to depart from predictions but additional data led to refined models. A mismatch was observed between the spectra of WS-causing mutations obtained with and without selection due to low fitness of previously undetected WS-causing mutations. Our findings contribute toward the development of mechanistic models for forecasting evolution, highlight current limitations, and draw attention to challenges in predicting locus-specific mutational biases and fitness effects.
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Affiliation(s)
- Peter A Lind
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Molecular BiologyUmeå UniversityUmeåSweden
| | - Eric Libby
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Santa Fe InstituteNew MexicoUnited States
- Department of MathematicsUmeå UniversityUmeåSweden
| | - Jenny Herzog
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
| | - Paul B Rainey
- New Zealand Institute for Advanced StudyMassey University at AlbanyAucklandNew Zealand
- Department of Microbial Population BiologyMax Planck Institute for Evolutionary BiologyPlönGermany
- Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, ESPCI Paris-TechCNRS UMR 8231, PSL Research UniversityParisFrance
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76
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Shinde S, Zerbs S, Collart FR, Cumming JR, Noirot P, Larsen PE. Pseudomonas fluorescens increases mycorrhization and modulates expression of antifungal defense response genes in roots of aspen seedlings. BMC PLANT BIOLOGY 2019; 19:4. [PMID: 30606121 PMCID: PMC6318872 DOI: 10.1186/s12870-018-1610-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/20/2018] [Indexed: 05/22/2023]
Abstract
BACKGROUND Plants, fungi, and bacteria form complex, mutually-beneficial communities within the soil environment. In return for photosynthetically derived sugars in the form of exudates from plant roots, the microbial symbionts in these rhizosphere communities provide their host plants access to otherwise inaccessible nutrients in soils and help defend the plant against biotic and abiotic stresses. One role that bacteria may play in these communities is that of Mycorrhizal Helper Bacteria (MHB). MHB are bacteria that facilitate the interactions between plant roots and symbiotic mycorrhizal fungi and, while the effects of MHB on the formation of plant-fungal symbiosis and on plant health have been well documented, the specific molecular mechanisms by which MHB drive gene regulation in plant roots leading to these benefits remain largely uncharacterized. RESULTS Here, we investigate the effects of the bacterium Pseudomonas fluorescens SBW25 (SBW25) on aspen root transcriptome using a tripartite laboratory community comprised of Populus tremuloides (aspen) seedlings and the ectomycorrhizal fungus Laccaria bicolor (Laccaria). We show that SBW25 has MHB activity and promotes mycorrhization of aspen roots by Laccaria. Using transcriptomic analysis of aspen roots under multiple community compositions, we identify clusters of co-regulated genes associated with mycorrhization, the presence of SBW25, and MHB-associated functions, and we generate a combinatorial logic network that links causal relationships in observed patterns of gene expression in aspen seedling roots in a single Boolean circuit diagram. The predicted regulatory circuit is used to infer regulatory mechanisms associated with MHB activity. CONCLUSIONS In our laboratory conditions, SBW25 increases the ability of Laccaria to form ectomycorrhizal interactions with aspen seedling roots through the suppression of aspen root antifungal defense responses. Analysis of transcriptomic data identifies that potential molecular mechanisms in aspen roots that respond to MHB activity are proteins with homology to pollen recognition sensors. Pollen recognition sensors integrate multiple environmental signals to down-regulate pollenization-associated gene clusters, making proteins with homology to this system an excellent fit for a predicted mechanism that integrates information from the rhizosphere to down-regulate antifungal defense response genes in the root. These results provide a deeper understanding of aspen gene regulation in response to MHB and suggest additional, hypothesis-driven biological experiments to validate putative molecular mechanisms of MHB activity in the aspen-Laccaria ectomycorrhizal symbiosis.
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Affiliation(s)
- Shalaka Shinde
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
- Present address: Oil-Dri Innovation Center, 777 Forest Edge Rd., Vernon Hills, IL 60061 USA
| | - Sarah Zerbs
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
| | - Frank R. Collart
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
| | - Jonathan R. Cumming
- Department of Biology, West Virginia University, 53 Campus Dr, Morgantown, WV 26506 USA
| | - Philippe Noirot
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
| | - Peter E. Larsen
- Argonne National Laboratory, Biosciences Division, 9700 S. Cass Ave., Argonne, IL 60439 USA
- Department of Bioengineering, University of Illinois at Chicago, 851 South Morgan St., Chicago, IL 60612 USA
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77
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Biessy A, Novinscak A, Blom J, Léger G, Thomashow LS, Cazorla FM, Josic D, Filion M. Diversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp. Environ Microbiol 2018; 21:437-455. [PMID: 30421490 DOI: 10.1111/1462-2920.14476] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/02/2018] [Accepted: 11/06/2018] [Indexed: 12/24/2022]
Abstract
Plant-beneficial Pseudomonas spp. competitively colonize the rhizosphere and display plant-growth promotion and/or disease-suppression activities. Some strains within the P. fluorescens species complex produce phenazine derivatives, such as phenazine-1-carboxylic acid. These antimicrobial compounds are broadly inhibitory to numerous soil-dwelling plant pathogens and play a role in the ecological competence of phenazine-producing Pseudomonas spp. We assembled a collection encompassing 63 strains representative of the worldwide diversity of plant-beneficial phenazine-producing Pseudomonas spp. In this study, we report the sequencing of 58 complete genomes using PacBio RS II sequencing technology. Distributed among four subgroups within the P. fluorescens species complex, the diversity of our collection is reflected by the large pangenome which accounts for 25 413 protein-coding genes. We identified genes and clusters encoding for numerous phytobeneficial traits, including antibiotics, siderophores and cyclic lipopeptides biosynthesis, some of which were previously unknown in these microorganisms. Finally, we gained insight into the evolutionary history of the phenazine biosynthetic operon. Given its diverse genomic context, it is likely that this operon was relocated several times during Pseudomonas evolution. Our findings acknowledge the tremendous diversity of plant-beneficial phenazine-producing Pseudomonas spp., paving the way for comparative analyses to identify new genetic determinants involved in biocontrol, plant-growth promotion and rhizosphere competence.
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Affiliation(s)
- Adrien Biessy
- Department of Biology, Université de Moncton, Moncton, NB, Canada
| | - Amy Novinscak
- Department of Biology, Université de Moncton, Moncton, NB, Canada
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-Universität Giessen, Giessen, Germany
| | - Geneviève Léger
- Department of Biology, Université de Moncton, Moncton, NB, Canada
| | - Linda S Thomashow
- United States Department of Agriculture - Agricultural Research Service, Pullman, WA, USA
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, Málaga, Spain
| | - Dragana Josic
- Department of Microbiology, Institute of Soil Science, Belgrade, Serbia
| | - Martin Filion
- Department of Biology, Université de Moncton, Moncton, NB, Canada
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78
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Dual-stressor selection alters eco-evolutionary dynamics in experimental communities. Nat Ecol Evol 2018; 2:1974-1981. [DOI: 10.1038/s41559-018-0701-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 09/24/2018] [Indexed: 11/08/2022]
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79
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Abstract
Bacterial pathogens cause plant diseases that threaten the global food supply. To control diseases, it is important to understand how pathogenic bacteria evade plant defense and promote infection. We identify from the phytopathogen Pseudomonas syringae a small-molecule virulence factor—phevamine A. Both the chemical structure and mode of action of phevamine A are different from known bacterial phytotoxins. Phevamine A promotes bacterial growth by suppressing plant immune responses, including both early (the generation of reactive oxygen species) and late (the deposition of cell wall reinforcing callose in leaves and leaf cell death) markers. This work uncovers a widely distributed, small-molecule virulence factor and shows the power of a multidisciplinary approach to identify small molecules important for plant infection. Bacterial plant pathogens cause significant crop damage worldwide. They invade plant cells by producing a variety of virulence factors, including small-molecule toxins and phytohormone mimics. Virulence of the model pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) is regulated in part by the sigma factor HrpL. Our study of the HrpL regulon identified an uncharacterized, three-gene operon in Pto that is controlled by HrpL and related to the Erwinia hrp-associated systemic virulence (hsv) operon. Here, we demonstrate that the hsv operon contributes to the virulence of Pto on Arabidopsis thaliana and suppresses bacteria-induced immune responses. We show that the hsv-encoded enzymes in Pto synthesize a small molecule, phevamine A. This molecule consists of l-phenylalanine, l-valine, and a modified spermidine, and is different from known small molecules produced by phytopathogens. We show that phevamine A suppresses a potentiation effect of spermidine and l-arginine on the reactive oxygen species burst generated upon recognition of bacterial flagellin. The hsv operon is found in the genomes of divergent bacterial genera, including ∼37% of P. syringae genomes, suggesting that phevamine A is a widely distributed virulence factor in phytopathogens. Our work identifies a small-molecule virulence factor and reveals a mechanism by which bacterial pathogens overcome plant defense. This work highlights the power of omics approaches in identifying important small molecules in bacteria–host interactions.
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80
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Analysis of the genome sequence of plant beneficial strain Pseudomonas sp. RU47. J Biotechnol 2018; 281:183-192. [DOI: 10.1016/j.jbiotec.2018.07.023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 11/22/2022]
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81
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Wong NR, Liu X, Lloyd H, Colthart AM, Ferrazzoli AE, Cooper DL, Zhuang Y, Esquea P, Futcher J, Pochapsky TM, Matthews JM, Pochapsky TC. A new approach to understanding structure-function relationships in cytochromes P450 by targeting terpene metabolism in the wild. J Inorg Biochem 2018; 188:96-101. [PMID: 30170307 DOI: 10.1016/j.jinorgbio.2018.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 07/24/2018] [Accepted: 08/03/2018] [Indexed: 01/30/2023]
Abstract
A strategy for elucidating sequence determinants of function in the class of cytochrome P450 (CYP) enzymes that catalyze the first steps of terpene metabolism in wild microbiomes is described. Wild organisms that can use camphor, terpineol, pinene and limonene were isolated from soils rich in coniferous waste. Cell free extracts and growth beers were analyzed by gas chromatography/mass spectrometry to identify primary oxidative metabolites. For one organism, Pseudomonas nitroreducens TPJM, a cytochrome P450 (CYP108B1) isolated from cell free extracts was demonstrated to catalyze the oxidation of α-terpineol in assays combining the native ferredoxin and putidaredoxin reductase, and the resulting oxidation products identified by gas chromatography/mass spectrometry. Shotgun sequencing of PnTPJM identified four candidate P450 genes, including an apparently fragmentary gene with a high degree of homology with the known enzyme CYP108 (P450terp).
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Affiliation(s)
- Nathan R Wong
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Xinyue Liu
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Hannah Lloyd
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Allison M Colthart
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Alexander E Ferrazzoli
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Deani L Cooper
- Department of Biology, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Yihao Zhuang
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Phillix Esquea
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Jeffrey Futcher
- Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America
| | - Theodore M Pochapsky
- Malden Catholic High School, 90 Crystal St., Malden, MA 02148, United States of America
| | - Jeffrey M Matthews
- Malden Catholic High School, 90 Crystal St., Malden, MA 02148, United States of America
| | - Thomas C Pochapsky
- Department of Biochemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America; Department of Chemistry, Brandeis University, 415 South St., Waltham, MA 02454-9110, United States of America.
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82
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Roberts DC, Fleischer SJ, Sakamoto JM, Rasgon JL. Potential biological control of Erwinia tracheiphila by internal alimentary canal interactions in Acalymma vittatum with Pseudomonas fluorescens. J Appl Microbiol 2018; 125:1137-1146. [PMID: 29890026 DOI: 10.1111/jam.13950] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 05/01/2018] [Accepted: 05/19/2018] [Indexed: 11/27/2022]
Abstract
AIMS We aim to determine if Pseudomonas fluorescens is a viable biological control for Erwinia tracheiphila within the insect vector, Acalymma vittatum. METHODS AND RESULTS Pseudomonas fluorescens secreted fluorescein and inhibited growth of E. tracheiphila in disc diffusion assays. To determine if this antagonism was conserved within the insect vector, we performed in vivo assays by orally injecting beetles with bacterial treatments and fluorescent in situ hybridization to determine bacterial presence within the alimentary canal. CONCLUSIONS Pseudomonas fluorescens inhibited the growth of E. tracheiphila on a nutrient-limiting medium. In situ experiments demonstrated that P. fluorescens is maintained within the alimentary canal of the beetle for at least 4 days, and co-occurred with E. tracheiphila. When beetles were first presented with Pseudomonas and then challenged with E. tracheiphila, E. tracheiphila was not recovered via FISH after 4 days. These data suggest that P. fluorescens has potential as a biological control agent to limit E. tracheiphila within the insect vector. SIGNIFICANCE AND IMPACT OF THE STUDY This is a novel approach for controlling E. tracheiphila that has the potential to decrease reliance on insecticides, providing a safer environment for pollinators and growers.
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Affiliation(s)
- D C Roberts
- The Pennsylvania State University, University Park, PA, USA
| | - S J Fleischer
- The Pennsylvania State University, University Park, PA, USA
| | - J M Sakamoto
- The Pennsylvania State University, University Park, PA, USA
| | - J L Rasgon
- The Pennsylvania State University, University Park, PA, USA
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83
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Modeling the Pseudomonas Sulfur Regulome by Quantifying the Storage and Communication of Information. mSystems 2018; 3:mSystems00189-17. [PMID: 29946568 PMCID: PMC6009100 DOI: 10.1128/msystems.00189-17] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 06/03/2018] [Indexed: 12/11/2022] Open
Abstract
Bacteria sense and respond to their environments using a sophisticated array of sensors and regulatory networks to optimize their fitness and survival in a constantly changing environment. Understanding how these regulatory and sensory networks work will provide the capacity to predict bacterial behaviors and, potentially, to manipulate their interactions with an environment or host. Leveraging the information theory provides useful quantitative metrics for modeling the information processing capacity of bacterial regulatory networks. As our model accurately predicted gene expression profiles in a bacterial model system, we posit that the information theory-based approaches will be important to enhance our understanding of a wide variety of bacterial regulomes and our ability to engineer bacterial sensory and regulatory networks. Bacteria are not simply passive consumers of nutrients or merely steady-state systems. Rather, bacteria are active participants in their environments, collecting information from their surroundings and processing and using that information to adapt their behavior and optimize survival. The bacterial regulome is the set of physical interactions that link environmental information to the expression of genes by way of networks of sensors, transporters, signal cascades, and transcription factors. As bacteria cannot have one dedicated sensor and regulatory response system for every possible condition that they may encounter, the sensor systems must respond to a variety of overlapping stimuli and collate multiple forms of information to make “decisions” about the most appropriate response to a specific set of environmental conditions. Here, we analyze Pseudomonas fluorescens transcriptional responses to multiple sulfur nutrient sources to generate a predictive, computational model of the sulfur regulome. To model the regulome, we utilize a transmitter-channel-receiver scheme of information transfer and utilize principles from information theory to portray P. fluorescens as an informatics system. This approach enables us to exploit the well-established metrics associated with information theory to model the sulfur regulome. Our computational modeling analysis results in the accurate prediction of gene expression patterns in response to the specific sulfur nutrient environments and provides insights into the molecular mechanisms of Pseudomonas sensory capabilities and gene regulatory networks. In addition, modeling the bacterial regulome using the tools of information theory is a powerful and generalizable approach that will have multiple future applications to other bacterial regulomes. IMPORTANCE Bacteria sense and respond to their environments using a sophisticated array of sensors and regulatory networks to optimize their fitness and survival in a constantly changing environment. Understanding how these regulatory and sensory networks work will provide the capacity to predict bacterial behaviors and, potentially, to manipulate their interactions with an environment or host. Leveraging the information theory provides useful quantitative metrics for modeling the information processing capacity of bacterial regulatory networks. As our model accurately predicted gene expression profiles in a bacterial model system, we posit that the information theory-based approaches will be important to enhance our understanding of a wide variety of bacterial regulomes and our ability to engineer bacterial sensory and regulatory networks.
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84
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Quentin Y, Siguier P, Chandler M, Fichant G. Single-strand DNA processing: phylogenomics and sequence diversity of a superfamily of potential prokaryotic HuH endonucleases. BMC Genomics 2018; 19:475. [PMID: 29914351 PMCID: PMC6006769 DOI: 10.1186/s12864-018-4836-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022] Open
Abstract
Background Some mobile genetic elements target the lagging strand template during DNA replication. Bacterial examples are insertion sequences IS608 and ISDra2 (IS200/IS605 family members). They use obligatory single-stranded circular DNA intermediates for excision and insertion and encode a transposase, TnpAIS200, which recognizes subterminal secondary structures at the insertion sequence ends. Similar secondary structures, Repeated Extragenic Palindromes (REP), are present in many bacterial genomes. TnpAIS200-related proteins, TnpAREP, have been identified and could be responsible for REP sequence proliferation. These proteins share a conserved HuH/Tyrosine core domain responsible for catalysis and are involved in processes of ssDNA cleavage and ligation. Our goal is to characterize the diversity of these proteins collectively referred as the TnpAY1 family. Results A genome-wide analysis of sequences similar to TnpAIS200 and TnpAREP in prokaryotes revealed a large number of family members with a wide taxonomic distribution. These can be arranged into three distinct classes and 12 subclasses based on sequence similarity. One subclass includes sequences similar to TnpAIS200. Proteins from other subclasses are not associated with typical insertion sequence features. These are characterized by specific additional domains possibly involved in protein/DNA or protein/protein interactions. Their genes are found in more than 25% of species analyzed. They exhibit a patchy taxonomic distribution consistent with dissemination by horizontal gene transfers followed by loss. The tnpAREP genes of five subclasses are flanked by typical REP sequences in a REPtron-like arrangement. Four distinct REP types were characterized with a subclass specific distribution. Other subclasses are not associated with REP sequences but have a large conserved domain located in C-terminal end of their sequence. This unexpected diversity suggests that, while most likely involved in processing single-strand DNA, proteins from different subfamilies may play a number of different roles. Conclusions We established a detailed classification of TnpAY1 proteins, consolidated by the analysis of the conserved core domains and the characterization of additional domains. The data obtained illustrate the unexpected diversity of the TnpAY1 family and provide a strong framework for future evolutionary and functional studies. By their potential function in ssDNA editing, they may confer adaptive responses to host cell physiology and metabolism. Electronic supplementary material The online version of this article (10.1186/s12864-018-4836-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yves Quentin
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Patricia Siguier
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
| | - Mick Chandler
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France.
| | - Gwennaele Fichant
- Laboratoire de Microbiologie et Génétique Moléculaires, UMR5100, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, F-31062, Toulouse, France
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85
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Noirot-Gros MF, Shinde S, Larsen PE, Zerbs S, Korajczyk PJ, Kemner KM, Noirot PH. Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation. Front Microbiol 2018; 9:853. [PMID: 29774013 PMCID: PMC5943511 DOI: 10.3389/fmicb.2018.00853] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/13/2018] [Indexed: 12/20/2022] Open
Abstract
Rhizosphere-associated Pseudomonas fluorescens are known plant growth promoting (PGP) and mycorrhizal helper bacteria (MHB) of many plants and ectomycorrhizal fungi. We investigated the spatial and temporal dynamics of colonization of mycorrhizal and non-mycorrhizal Aspen seedlings roots by the P. fluorescens strains SBW25, WH6, Pf0-1, and the P. protegens strain Pf-5. Seedlings were grown in laboratory vertical plates systems, inoculated with a fluorescently labeled Pseudomonas strain, and root colonization was monitored over a period of 5 weeks. We observed unexpected diversity of bacterial assemblies on seedling roots that changed over time and were strongly affected by root mycorrhization. P. fluorescens SBW25 and WH6 stains developed highly structured biofilms with internal void spaces forming channels. On mycorrhizal roots bacteria appeared encased in a mucilaginous substance in which they aligned side by side in parallel arrangements. The different phenotypic classes of bacterial assemblies observed for the four Pseudomonas strains were summarized in a single model describing transitions between phenotypic classes. Our findings also reveal that bacterial assembly phenotypes are driven by interactions with mucilaginous materials present at roots.
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Affiliation(s)
| | - Shalaka Shinde
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter J Korajczyk
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Philippe H Noirot
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
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86
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Abstract
Lectin-like bacteriocins (LlpAs) are secreted by proteobacteria and selectively kill strains of their own or related species, and they are composed of two B-lectin domains with divergent sequences. In Pseudomonas spp., initial binding of these antibacterial proteins to cells is mediated by the carboxy-terminal domain through d-rhamnose residues present in the common polysaccharide antigen of their lipopolysaccharide, whereas the amino-terminal domain accounts for strain selectivity of killing. Here, we show that spontaneous LlpA-resistant mutants carry mutations in one of three surface-exposed moieties of the essential β-barrel outer membrane protein insertase BamA, the core component of the BAM complex. Polymorphism of this loop in different Pseudomonas groups is linked to LlpA susceptibility, and targeted cells all share the same signature motif in this loop. Since heterologous expression of such a bamA gene confers LlpA susceptibility upon a resistant strain, BamA represents the primary bacteriocin selectivity determinant in pseudomonads. Contrary to modular bacteriocins that require uptake via the Tol or Ton system, parasitism of BamA as an LlpA receptor advocates a novel bacteriocin killing mechanism initiated by impairment of the BAM machinery. Bacteria secrete a variety of molecules to eliminate microbial rivals. Bacteriocins are a pivotal group of peptides and proteins that assist in this fight, specifically killing related bacteria. In Gram-negative bacteria, these antibacterial proteins often comprise distinct domains for initial binding to a target cell’s surface and subsequent killing via enzymatic or pore-forming activity. Here, we show that lectin-like bacteriocins, a family of bacteriocins that lack the prototypical modular toxin architecture, also stand out by parasitizing BamA, the core component of the outer membrane protein assembly machinery. A particular surface-exposed loop of BamA, critical for its function, serves as a key discriminant for cellular recognition, and polymorphisms in this loop determine whether a strain is susceptible or immune to a particular bacteriocin. These findings suggest a novel mechanism of contact-dependent killing that does not require cellular uptake. The evolutionary advantage of piracy of an essential cellular compound is highlighted by the observation that contact-dependent growth inhibition, a distinct antagonistic system, can equally take advantage of this receptor.
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87
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Sun J, Wang Q, Jiang Y, Wen Z, Yang L, Wu J, Yang S. Genome editing and transcriptional repression in Pseudomonas putida KT2440 via the type II CRISPR system. Microb Cell Fact 2018. [PMID: 29534717 PMCID: PMC5851096 DOI: 10.1186/s12934-018-0887-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background The soil bacterium Pseudomonas putida KT2440 is a “generally recognized as safe”-certified strain with robust property and versatile metabolism. Thus, it is an ideal candidate for synthetic biology, biodegradation, and other biotechnology applications. The known genome editing approaches of Pseudomonas are suboptimal; thus, it is necessary to develop a high efficiency genome editing tool. Results In this study, we established a fast and convenient CRISPR–Cas9 method in P. putida KT2440. Gene deletion, gene insertion and gene replacement could be achieved within 5 days, and the mutation efficiency reached > 70%. Single nucleotide replacement could be realized, overcoming the limitations of protospacer adjacent motif sequences. We also applied nuclease-deficient Cas9 binding at three locations upstream of enhanced green fluorescent protein (eGFP) for transcriptional inhibition, and the expression intensity of eGFP reduced to 28.5, 29.4, and 72.1% of the control level, respectively. Furthermore, based on this CRISPR–Cas9 system, we also constructed a CRISPR–Cpf1 system, which we validated for genome editing in P. putida KT2440. Conclusions In this research, we established CRISPR based genome editing and regulation control systems in P. putida KT2440. These fast and efficient approaches will greatly facilitate the application of P. putida KT2440.![]() Electronic supplementary material The online version of this article (10.1186/s12934-018-0887-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jun Sun
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Qingzhuo Wang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yu Jiang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.,Shanghai Research and Development Center of Industrial Biotechnology, Shanghai, 201206, China
| | - Zhiqiang Wen
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, China.
| | - Sheng Yang
- Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. .,Shanghai Research and Development Center of Industrial Biotechnology, Shanghai, 201206, China. .,Jiangsu National Synergetic Innovation Center for Advanced Materials, SICAM, Nanjing, 210009, China.
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88
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Koza A, Kusmierska A, McLaughlin K, Moshynets O, Spiers AJ. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation. FEMS Microbiol Lett 2018; 364:3850210. [PMID: 28535292 DOI: 10.1093/femsle/fnx109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function.
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Affiliation(s)
- Anna Koza
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kusmierska
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Kimberley McLaughlin
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kiev 03143, Ukraine
| | - Andrew J Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
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89
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Sepulveda E, Lupas AN. Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation. Front Microbiol 2017; 8:2287. [PMID: 29250042 PMCID: PMC5715377 DOI: 10.3389/fmicb.2017.02287] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/06/2017] [Indexed: 01/18/2023] Open
Abstract
The CrbS/R system is a two-component signal transduction system that regulates acetate utilization in Vibrio cholerae, P. aeruginosa, and P. entomophila. CrbS is a hybrid histidine kinase that belongs to a recently identified family, in which the signaling domain is fused to an SLC5 solute symporter domain through aSTAC domain. Upon activation by CrbS, CrbR activates transcription of the acs gene, which encodes an acetyl-CoA synthase (ACS), and the actP gene, which encodes an acetate/solute symporter. In this work, we characterized the CrbS/R system in Pseudomonas fluorescens SBW25. Through the quantitative proteome analysis of different mutants, we were able to identify a new set of genes under its control, which play an important role during growth on acetate. These results led us to the identification of a conserved DNA motif in the putative promoter region of acetate-utilization genes in the Gammaproteobacteria that is essential for the CrbR-mediated transcriptional activation of genes under acetate-utilizing conditions. Finally, we took advantage of the existence of a second SLC5-containing two-component signal transduction system in P. fluorescens, CbrA/B, to demonstrate that the activation of the response regulator by the histidine kinase is not dependent on substrate transport through the SLC5 domain.
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Affiliation(s)
- Edgardo Sepulveda
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Andrei N Lupas
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
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90
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The current status on the taxonomy of Pseudomonas revisited: An update. INFECTION GENETICS AND EVOLUTION 2017; 57:106-116. [PMID: 29104095 DOI: 10.1016/j.meegid.2017.10.026] [Citation(s) in RCA: 131] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Revised: 10/28/2017] [Accepted: 10/30/2017] [Indexed: 12/20/2022]
Abstract
The genus Pseudomonas described in 1894 is one of the most diverse and ubiquitous bacterial genera which encompass species isolated worldwide. In the last years more than 70 new species have been described, which were isolated from different environments, including soil, water, sediments, air, animals, plants, fungi, algae, compost, human and animal related sources. Some of these species have been isolated in extreme environments, such as Antarctica or Atacama desert, and from contaminated water or soil. Also, some species recently described are plant or animal pathogens. In this review, we revised the current status of the taxonomy of genus Pseudomonas and the methodologies currently used for the description of novel species which includes, in addition to the classic ones, new methodologies such as MALDI-TOF MS, MLSA and genome analyses. The novel Pseudomonas species described in the last years are listed, together with the available genome sequences of the type strains of Pseudomonas species present in different databases.
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91
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Adaptive evolution by spontaneous domain fusion and protein relocalization. Nat Ecol Evol 2017; 1:1562-1568. [PMID: 29185504 DOI: 10.1038/s41559-017-0283-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 07/18/2017] [Indexed: 11/08/2022]
Abstract
Knowledge of adaptive processes encompasses understanding the emergence of new genes. Computational analyses of genomes suggest that new genes can arise by domain swapping; however, empirical evidence has been lacking. Here we describe a set of nine independent deletion mutations that arose during selection experiments with the bacterium Pseudomonas fluorescens in which the membrane-spanning domain of a fatty acid desaturase became translationally fused to a cytosolic di-guanylate cyclase, generating an adaptive 'wrinkly spreader' phenotype. Detailed genetic analysis of one gene fusion shows that the mutant phenotype is caused by relocalization of the di-guanylate cyclase domain to the cell membrane. The relative ease by which this new gene arose, along with its functional and regulatory effects, provides a glimpse of mutational events and their consequences that are likely to have a role in the evolution of new genes.
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92
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Hernández-Salmerón JE, Moreno-Hagelsieb G, Santoyo G. Genome Comparison of Pseudomonas fluorescens UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization. J Genomics 2017; 5:91-98. [PMID: 28943971 PMCID: PMC5607707 DOI: 10.7150/jgen.21588] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 08/18/2017] [Indexed: 12/18/2022] Open
Abstract
Pseudomonas fluorescens UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens.In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other P. fluorescens strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities. Our analyses found high variation in genome size and gene content among the eight Pseudomonas genomes analyzed (strains UM270, Pf0-1, A506, F113, SBW25, PICF-7, UK4 and UW4). A core genome of 3,039 coding DNA sequences (CDSs) was determined, with 599 CDSs present only in the UM270 genome. From these unique UM270 genes, a set of 192 CDSs was found to be involved in signaling, rhizosphere colonization and competence, highlighted as important traits to achieve an effective biocontrol and plant growth promotion.
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Affiliation(s)
- Julie E Hernández-Salmerón
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | | | - Gustavo Santoyo
- Instituto de Investigaciones Químico Biológicas, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
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93
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Complete Genome Sequences of Three Novel Pseudomonas fluorescens SBW25 Bacteriophages, Noxifer, Phabio, and Skulduggery. GENOME ANNOUNCEMENTS 2017; 5:5/31/e00725-17. [PMID: 28774980 PMCID: PMC5543642 DOI: 10.1128/genomea.00725-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Three novel bacteriophages, two of which are jumbophages, were isolated from compost in Auckland, New Zealand. Noxifer, Phabio, and Skulduggery are double-stranded DNA (dsDNA) phages with genome sizes of 278,136 bp (Noxifer), 309,157 bp (Phabio), and 62,978 bp (Skulduggery).
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94
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Bertels F, Gokhale CS, Traulsen A. Discovering Complete Quasispecies in Bacterial Genomes. Genetics 2017; 206:2149-2157. [PMID: 28630115 PMCID: PMC5560812 DOI: 10.1534/genetics.117.201160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/08/2017] [Indexed: 01/15/2023] Open
Abstract
Mobile genetic elements can be found in almost all genomes. Possibly the most common nonautonomous mobile genetic elements in bacteria are repetitive extragenic palindromic doublets forming hairpins (REPINs) that can occur hundreds of times within a genome. The sum of all REPINs in a genome can be viewed as an evolving population because REPINs replicate and mutate. In contrast to most other biological populations, we know the exact composition of the REPIN population and the sequence of each member of the population. Here, we model the evolution of REPINs as quasispecies. We fit our quasispecies model to 10 different REPIN populations from 10 different bacterial strains and estimate effective duplication rates. Our estimated duplication rates range from ∼5 × 10-9 to 15 × 10-9 duplications per bacterial generation per REPIN. The small range and the low level of the REPIN duplication rates suggest a universal trade-off between the survival of the REPIN population and the reduction of the mutational load for the host genome. The REPIN populations we investigated also possess features typical of other natural populations. One population shows hallmarks of a population that is going extinct, another population seems to be growing in size, and we also see an example of competition between two REPIN populations.
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Affiliation(s)
- Frederic Bertels
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Chaitanya S Gokhale
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
| | - Arne Traulsen
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany
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95
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Hall JPJ, Williams D, Paterson S, Harrison E, Brockhurst MA. Positive selection inhibits gene mobilisation and transfer in soil bacterial communities. Nat Ecol Evol 2017; 1:1348-1353. [PMID: 28890938 PMCID: PMC5584672 DOI: 10.1038/s41559-017-0250-3] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK. .,Department of Biology, University of York, York, YO10 5DD, UK.
| | - David Williams
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB, UK
| | - Steve Paterson
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Liverpool, L69 7ZB, UK
| | - Ellie Harrison
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, S10 2TN, UK.
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96
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Basso P, Wallet P, Elsen S, Soleilhac E, Henry T, Faudry E, Attrée I. Multiple Pseudomonas species secrete exolysin-like toxins and provoke Caspase-1-dependent macrophage death. Environ Microbiol 2017; 19:4045-4064. [PMID: 28654176 DOI: 10.1111/1462-2920.13841] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/02/2017] [Accepted: 06/19/2017] [Indexed: 12/19/2022]
Abstract
Pathogenic bacteria secrete protein toxins that provoke apoptosis or necrosis of eukaryotic cells. Here, we developed a live-imaging method, based on incorporation of a DNA-intercalating dye into membrane-damaged host cells, to study the kinetics of primary bone marrow-derived macrophages (BMDMs) mortality induced by opportunistic pathogen Pseudomonas aeruginosa expressing either Type III Secretion System (T3SS) toxins or the pore-forming toxin, Exolysin (ExlA). We found that ExlA promotes the activation of Caspase-1 and maturation of interleukin-1β. BMDMs deficient for Caspase-1 and Caspase-11 were resistant to ExlA-induced death. Furthermore, by using KO BMDMs, we determined that the upstream NLRP3/ASC complex leads to the Caspase-1 activation. We also demonstrated that Pseudomonas putida and Pseudomonas protegens and the Drosophila pathogen Pseudomonas entomophila, which naturally express ExlA-like toxins, are cytotoxic toward macrophages and provoke the same type of pro-inflammatory death as does ExlA+ P. aeruginosa. These results demonstrate that ExlA-like toxins of two-partner secretion systems from diverse Pseudomonas species activate the NLRP3 inflammasome and provoke inflammatory pyroptotic death of macrophages.
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Affiliation(s)
- Pauline Basso
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, France
| | - Pierre Wallet
- CIRI, Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, Lyon, F-69007, France
| | - Sylvie Elsen
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, France
| | - Emmanuelle Soleilhac
- CMBA Platform, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, CEA, INSERM; Genetics & Chemogenomics, France
| | - Thomas Henry
- CIRI, Centre International de Recherche en Infectiologie, INSERM, U1111, Université Claude Bernard Lyon 1, CNRS, UMR5308, École Normale Supérieure de Lyon, Univ Lyon, Lyon, F-69007, France
| | - Eric Faudry
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, France
| | - Ina Attrée
- CNRS-ERL5261, INSERM, U1036, CEA, Bacterial Pathogenesis and Cellular Responses, Biosciences and Biotechnology Institute of Grenoble, University Grenoble Alpes, France
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97
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Draft Genome Sequence of Pseudomonas koreensis CI12, a Bacillus cereus "Hitchhiker" from the Soybean Rhizosphere. GENOME ANNOUNCEMENTS 2017; 5:5/26/e00570-17. [PMID: 28663293 PMCID: PMC5638277 DOI: 10.1128/genomea.00570-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Pseudomonas koreensis CI12 was coisolated with Bacillus cereus from a root of a soybean plant grown in a field in Arlington, WI. Here, we report the draft genome sequence of P. koreensis CI12 obtained by Illumina sequencing.
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98
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Campilongo R, Fung RKY, Little RH, Grenga L, Trampari E, Pepe S, Chandra G, Stevenson CEM, Roncarati D, Malone JG. One ligand, two regulators and three binding sites: How KDPG controls primary carbon metabolism in Pseudomonas. PLoS Genet 2017; 13:e1006839. [PMID: 28658302 PMCID: PMC5489143 DOI: 10.1371/journal.pgen.1006839] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/26/2017] [Indexed: 12/04/2022] Open
Abstract
Effective regulation of primary carbon metabolism is critically important for bacteria to successfully adapt to different environments. We have identified an uncharacterised transcriptional regulator; RccR, that controls this process in response to carbon source availability. Disruption of rccR in the plant-associated microbe Pseudomonas fluorescens inhibits growth in defined media, and compromises its ability to colonise the wheat rhizosphere. Structurally, RccR is almost identical to the Entner-Doudoroff (ED) pathway regulator HexR, and both proteins are controlled by the same ED-intermediate; 2-keto-3-deoxy-6-phosphogluconate (KDPG). Despite these similarities, HexR and RccR control entirely different aspects of primary metabolism, with RccR regulating pyruvate metabolism (aceEF), the glyoxylate shunt (aceA, glcB, pntAA) and gluconeogenesis (pckA, gap). RccR displays complex and unusual regulatory behaviour; switching repression between the pyruvate metabolism and glyoxylate shunt/gluconeogenesis loci depending on the available carbon source. This regulatory complexity is enabled by two distinct pseudo-palindromic binding sites, differing only in the length of their linker regions, with KDPG binding increasing affinity for the 28 bp aceA binding site but decreasing affinity for the 15 bp aceE site. Thus, RccR is able to simultaneously suppress and activate gene expression in response to carbon source availability. Together, the RccR and HexR regulators enable the rapid coordination of multiple aspects of primary carbon metabolism, in response to levels of a single key intermediate. Here we show how Pseudomonas controls multiple different primary carbon metabolism pathways by sensing levels of KDPG, an Entner Doudoroff (ED) pathway intermediate. KDPG binds to two highly similar transcription factors; the ED regulator HexR and the previously uncharacterised protein RccR. RccR inversely controls the glyoxylate shunt, gluconeogenesis and pyruvate metabolism, suppressing the first two pathways as pyruvate metabolism genes are expressed, and vice versa. This complex regulation is enabled by two distinct RccR-binding consensus sequences in the RccR regulon promoters. KDPG binding simultaneously increases RccR affinity for the glyoxylate shunt and gluconeogenesis promoters, and releases repression of pyruvate metabolism. This elegant two-regulator circuit allows Pseudomonas to rapidly respond to carbon source availability by sensing a single key intermediate, KDPG.
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Affiliation(s)
- Rosaria Campilongo
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- Istituto Pasteur- Fondazione Cenci Bolognetti, Dipartimento di Biologia e Biotecnologie ‘‘C. Darwin”, Sapienza Universita`di Roma, Roma, Italy
| | - Rowena K. Y. Fung
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Richard H. Little
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Lucia Grenga
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Eleftheria Trampari
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Simona Pepe
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Davide Roncarati
- Alma Mater Studiorum - University of Bologna, Department of Pharmacy and Biotechnology – FaBiT, Bologna, Italy
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
- * E-mail:
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99
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Liu Y, Gokhale CS, Rainey PB, Zhang XX. Unravelling the complexity and redundancy of carbon catabolic repression in Pseudomonas fluorescens SBW25. Mol Microbiol 2017; 105:589-605. [PMID: 28557013 DOI: 10.1111/mmi.13720] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2017] [Indexed: 12/11/2022]
Abstract
The two-component system CbrAB is the principal regulator for cellular metabolic balance in Pseudomonas fluorescens SBW25 and is necessary for growth on many substrates including xylose. To understand the regulatory linkage between CbrAB and genes for xylose utilization (xut), we performed transposon mutagenesis of ΔcbrB to select for Xut+ suppressors. This led to identification of crc and hfq. Subsequent genetic and biochemical analysis showed that Crc and Hfq are key mediators of succinate-provoked carbon catabolite repression (CCR). Specifically, Crc/Hfq sequentially bind to mRNAs of both the transcriptional activator and structural genes involved in xylose catabolism. However, in the absence of succinate, repression is relieved through competitive binding by two ncRNAs, CrcY and CrcZ, whose expression is activated by CbrAB. These findings provoke a model for CCR in which it is assumed that crc and hfq are functionally complementary, whereas crcY and crcZ are genetically redundant. Inactivation of either crcY or crcZ produced no effects on bacterial fitness in laboratory media, however, results of mathematical modelling predict that the co-existence of crcY and crcZ requires separate functional identity. Finally, we provide empirical evidence that CCR is advantageous in nutrient-complex environments where preferred carbon sources are present at high concentrations but fluctuate in their availability.
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Affiliation(s)
- Yunhao Liu
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand.,New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand
| | - Chaitanya S Gokhale
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University at Albany, Auckland, 0745, New Zealand.,Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany.,Ecole Supérieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI ParisTech), CNRS UMR 8231, PSL Research University, 75231 Paris Cedex 05, France
| | - Xue-Xian Zhang
- Institute of Natural and Mathematical Sciences, Massey University at Albany, Auckland, 0745, New Zealand
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100
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Rani P, Mahato NK, Sharma A, Rao DLN, Kamra K, Lal R. Genome Mining and Predictive Functional Profiling of Acidophilic Rhizobacterium Pseudomonas fluorescens Pt14. Indian J Microbiol 2017; 57:155-161. [PMID: 28611492 DOI: 10.1007/s12088-017-0648-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2017] [Accepted: 04/05/2017] [Indexed: 12/01/2022] Open
Abstract
Pseudomonas fluorescens Pt14 is a non-pathogenic and acidophilic bacterium isolated from acidic soil (pH 4.65). Genome sequencing of strain Pt14 was performed using Single Molecule Real Time (SMRT) sequencing to get insights into unique existence of this strain in acidic environment. Complete genome sequence of this strain revealed a chromosome of 5,841,722 bp having 5354 CDSs and 88 RNAs. Phylogenomic reconstruction based on 16S rRNA gene, Average Nucleotide Identity (ANI) values and marker proteins revealed that strain Pt14 shared a common clade with P. fluorescens strain A506 and strain SS101. ANI value of strain Pt14 in relation to strain A506 was found 99.23% demonstrating a very close sub-species association at genome level. Further, orthology determination among these three phylogenetic neighbors revealed 4726 core proteins. Functional analysis elucidated significantly higher abundance of sulphur metabolism (>1×) which could be one of the reasons for the survival of strain Pt14 under acidic conditions (pH 4.65). Acidophilic bacteria have capability to oxidize sulphur into sulphuric acid which in turn can make the soil acidic and genome-wide analysis of P. fluorescens Pt14 demonstrated that this strain contributes towards making the soil acidic.
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Affiliation(s)
- Pooja Rani
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Nitish Kumar Mahato
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Anukriti Sharma
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
| | - Desiraju Lakshmi Narsimha Rao
- All India Network Project on Soil Biodiversity and Biofertilizers, Indian Institute of Soil Science, Bhopal, 462038 India
| | - Komal Kamra
- Ciliate Biology Laboratory, SGTB Khalsa College, University of Delhi, Delhi, 110007 India
| | - Rup Lal
- Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi, 110007 India
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