1
|
Abril AG, Calo-Mata P, Böhme K, Villa TG, Barros-Velázquez J, Sánchez-Pérez Á, Pazos M, Carrera M. Shotgun proteomic analyses of Pseudomonas species isolated from fish products. Food Chem 2024; 450:139342. [PMID: 38631198 DOI: 10.1016/j.foodchem.2024.139342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/25/2024] [Accepted: 04/09/2024] [Indexed: 04/19/2024]
Abstract
Numerous Pseudomonas species can infect aquatic animals, such as farmed rainbow trout, sea trout, sea bass, and sea bream, by causing disease or stress reactions. In aquaculture facilities, a number of Pseudomonas species have been isolated and identified as the main pathogens. The present study describes the characterization of 18 Pseudomonas strains, isolated from fish products using shotgun proteomics. The bacterial proteomes obtained were further analyzed to identify the main functional pathway proteins involved. In addition, this study revealed the presence of 1015 non-redundant peptides related to virulence factors. An additional 25 species-specific peptides were identified as putative Pseudomonas spp. biomarkers. The results constitute the largest dataset, described thus far for the rapid identification and characterization of Pseudomonas species present in edible fish; furthermore, these data can provide the basis for further research into the development of new therapies against these harmful pathogens.
Collapse
Affiliation(s)
- Ana G Abril
- Department of Food Technology, Marine Research Institute (IIM-CSIC), Spanish National Research Council (CSIC), 36208 Vigo, Spain; Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain.
| | - Pilar Calo-Mata
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain.
| | - Karola Böhme
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain
| | - Tomás G Villa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Santiago de Compostela, 15898 Santiago de Compostela, Spain
| | - Jorge Barros-Velázquez
- Department of Analytical Chemistry, Nutrition and Food Science, Food Technology Division, School of Veterinary Sciences, University of Santiago de Compostela, Campus Lugo, 27002 Lugo, Spain.
| | - Ángeles Sánchez-Pérez
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, NSW 2006, Australia
| | - Manuel Pazos
- Department of Food Technology, Marine Research Institute (IIM-CSIC), Spanish National Research Council (CSIC), 36208 Vigo, Spain.
| | - Mónica Carrera
- Department of Food Technology, Marine Research Institute (IIM-CSIC), Spanish National Research Council (CSIC), 36208 Vigo, Spain.
| |
Collapse
|
2
|
Florek LC, Lin X, Lin YC, Lin MH, Chakraborty A, Price-Whelan A, Tong L, Rahme L, Dietrich LE. The L-lactate dehydrogenases of Pseudomonas aeruginosa are conditionally regulated but both contribute to survival during macrophage infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586142. [PMID: 38562866 PMCID: PMC10983889 DOI: 10.1101/2024.03.21.586142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that thrives in environments associated with human activity, including soil and water altered by agriculture or pollution. Because L-lactate is a significant product of plant and animal metabolism, it is available to serve as a carbon source for P. aeruginosa in the diverse settings it inhabits. Here, we evaluate P. aeruginosa's production and use of its redundant L-lactate dehydrogenases, termed LldD and LldA. We confirm that the protein LldR represses lldD and identify a new transcription factor, called LldS, that activates lldA; these distinct regulators and the genomic contexts of lldD and lldA contribute to their differential expression. We demonstrate that the lldD and lldA genes are conditionally controlled in response to lactate isomers as well as to glycolate and - hydroxybutyrate, which, like lactate, are -hydroxycarboxylates. We also show that lldA is induced when iron availability is low. Our examination of lldD and lldA expression across depth in biofilms indicates a complex pattern that is consistent with the effects of glycolate production, iron availability, and cross-regulation on enzyme preference. Finally, macrophage infection assays revealed that both lldD and lldA contribute to persistence within host cells, underscoring the potential role of L-lactate as a carbon source during P. aeruginosa-eukaryote interactions. Together, these findings help us understand the metabolism of a key resource that may promote P. aeruginosa's success as a resident of contaminated environments and animal hosts.
Collapse
Affiliation(s)
- Lindsey C. Florek
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Xi Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Yu-Cheng Lin
- Department of Dentistry, National Yang Ming Chiao Tung University, Taipei, Taiwan 112
| | - Min-Han Lin
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Arijit Chakraborty
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
| | - Alexa Price-Whelan
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Laurence Rahme
- Department of Surgery, Massachusetts General Hospital, and Harvard Medical School, Boston, Massachusetts, USA
- Shriners Hospitals for Children Boston, Boston, Massachusetts, USA
- Department of Microbiology, Harvard Medical School, Boston, Massachusetts, USA
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY 10027
| |
Collapse
|
3
|
Hu Y, Xiao R, Wang Y, Li J, Guo C, Bai J, Zhang L, Zhang K, Jorquera MA, Manquian J, Pan W. Distribution of organophosphorus pesticides and its potential connection with probiotics in sediments of a shallow freshwater lake. JOURNAL OF CONTAMINANT HYDROLOGY 2024; 261:104306. [PMID: 38244424 DOI: 10.1016/j.jconhyd.2024.104306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 01/09/2024] [Accepted: 01/16/2024] [Indexed: 01/22/2024]
Abstract
Despite the serious health threats due to wide use of organophosphorus pesticides (OPPs) have been experimentally claimed to be remediated by probiotic microorganisms in various food and organism models, the interactions between OPPs and probiotics in the natural wetland ecosystem was rarely investigated. This study delves into the spatial and temporal distribution, contamination levels of OPPs in the Baiyangdian region, the diversity of probiotic communities in varying environmental contexts, and the potential connection with OPPs on these probiotics. In typical shallow lake wetland ecosystem-Baiyangdian lake in north China, eight OPPs were identified in the lake sediments, even though their detection rates were generally low. Malathion exhibited the highest average content among these pesticides (9.51 ng/g), followed by fenitrothion (6.70 ng/g). Conversely, chlorpyrifos had the lowest detection rate at only 2.14%. The region near Nanliu Zhuang (F10), significantly influenced by human activities, displayed the highest concentration of total OPPs (136.82 ng/g). A total of 145 probiotic species spanning 78 genera were identified in Baiyangdian sediments. Our analysis underscores the relations of environmental factors such as phosphatase activity, pH, and electrical conductivity (EC) with probiotic community. Notably, several high-abundance probiotics including Pseudomonas chlororaphis, Clostridium sp., Lactobacillus fermentum, and Pseudomonas putida, etc., which were reported to exhibit significant potential for the degradation of OPPs, showed strongly correlations with OPPs in the Baiyangdian lake sediments. The outcomes of this research offer valuable insights into the spatiotemporal dynamics of OPPs in natural large lake wetland and the probability of their in-situ residue bioremediation through the phosphatase pathway mediated by probiotic such as Lactic acid bacteria in soils/sediments contaminated with OPPs.
Collapse
Affiliation(s)
- Yanping Hu
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Rong Xiao
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China.
| | - Yaping Wang
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Junming Li
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Congling Guo
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Ling Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing 100875, China
| | - Kegang Zhang
- Department of Environmental Science and Engineering, North China Electric Power University, Baoding 071003, China
| | - Milko A Jorquera
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco 01145, Chile
| | - Javiera Manquian
- Department of Chemical Sciences and Natural Resources, University of La Frontera, Temuco 01145, Chile
| | - Wenbin Pan
- College of Environment & Safety Engineering, Fuzhou University, Fuzhou 350108, China
| |
Collapse
|
4
|
Nikolaidis M, Oliver SG, Amoutzias GD. pyPGCF: A Python Software for Phylogenomic Analysis, Species Demarcation, Identification of Core, and Fingerprint Proteins of Bacterial Genomes That Are Important for Plants. Methods Mol Biol 2024; 2788:139-155. [PMID: 38656512 DOI: 10.1007/978-1-0716-3782-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
This computational protocol describes how to use pyPGCF, a python software package that runs in the linux environment, in order to analyze bacterial genomes and perform: (i) phylogenomic analysis, (ii) species demarcation, (iii) identification of the core proteins of a bacterial genus and its individual species, (iv) identification of species-specific fingerprint proteins that are found in all strains of a species and, at the same time, are absent from all other species of the genus, (v) functional annotation of the core and fingerprint proteins with eggNOG, and (vi) identification of secondary metabolite biosynthetic gene clusters (smBGCs) with antiSMASH. This software has already been implemented to analyze bacterial genera and species that are important for plants (e.g., Pseudomonas, Bacillus, Streptomyces). In addition, we provide a test dataset and example commands showing how to analyze 165 genomes from 55 species of the genus Bacillus. The main advantages of pyPGCF are that: (i) it uses adjustable orthology cut-offs, (ii) it identifies species-specific fingerprints, and (iii) its computational cost scales linearly with the number of genomes being analyzed. Therefore, pyPGCF is able to deal with a very large number of bacterial genomes, in reasonable timescales, using widely available levels of computing power.
Collapse
Affiliation(s)
- Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Greece
| | - Stephen G Oliver
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Grigorios D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, Greece.
| |
Collapse
|
5
|
Bourdin T, Benoit MÈ, Bédard E, Prévost M, Quach C, Déziel E, Constant P. High-Throughput Short Sequence Typing Schemes for Pseudomonas aeruginosa and Stenotrophomonas maltophilia Pure Culture and Environmental DNA. Microorganisms 2023; 12:48. [PMID: 38257875 PMCID: PMC10819370 DOI: 10.3390/microorganisms12010048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Molecular typing techniques are utilized to determine genetic similarities between bacterial isolates. However, the use of environmental DNA profiling to assess epidemiologic links between patients and their environment has not been fully explored. This work reports the development and validation of two high-throughput short sequence typing (HiSST) schemes targeting the opportunistic pathogens Pseudomonas aeruginosa and Stenotrophomonas maltophilia, along with a modified SM2I selective medium for the specific isolation of S. maltophilia. These HiSST schemes are based on four discriminative loci for each species and demonstrate high discriminating power, comparable to pairwise whole-genome comparisons. Each scheme includes species-specific PCR primers for precise differentiation from closely related taxa, without the need for upstream culture-dependent methods. For example, the primers targeting the bvgS locus make it possible to distinguish P. aeruginosa from the very closely related Pseudomonas paraeruginosa sp. nov. The selected loci included in the schemes are adapted to massive parallel amplicon sequencing technology. An R-based script implemented in the DADA2 pipeline was assembled to facilitate HiSST analyses for efficient and accurate genotyping of P. aeruginosa and S. maltophilia. We demonstrate the performance of both schemes through in silico validations, assessments against reference culture collections, and a case study involving environmental samples.
Collapse
Affiliation(s)
- Thibault Bourdin
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Marie-Ève Benoit
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Emilie Bédard
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Michèle Prévost
- Department of Civil Engineering, Polytechnique Montréal, Montréal, QC H3T 1J4, Canada; (E.B.); (M.P.)
| | - Caroline Quach
- CHU Sainte-Justine Research Center, Montréal, QC H3T 1C5, Canada; (M.-È.B.); (C.Q.)
| | - Eric Déziel
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| | - Philippe Constant
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique, 531 Boulevard des Prairies, Laval, QC H7V 1B7, Canada;
| |
Collapse
|
6
|
Zamanzadeh-Nasrabadi SM, Mohammadiapanah F, Sarikhan S, Shariati V, Saghafi K, Hosseini-Mazinani M. Comprehensive genome analysis of Pseudomonas sp. SWRIQ11, a new plant growth-promoting bacterium that alleviates salinity stress in olive. 3 Biotech 2023; 13:347. [PMID: 37750167 PMCID: PMC10517913 DOI: 10.1007/s13205-023-03755-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 08/20/2023] [Indexed: 09/27/2023] Open
Abstract
The study presents the genome analysis of a new Pseudomonas sp. (SWRIQ11), which can alleviate salinity stress effects on growth of olive seedlings in greenhouse study. The strain SWRIQ11 can tolerate salinity up to 6%, produce siderophores, indole acetic acid (IAA), aminocyclopropane-1-carboxylate (ACC) deaminase, and has the phosphate-solubilizing capability. The SWRIQ11 genome contained an assembly size of 6,196,390 bp with a GC content of 60.1%. According to derived indices based on whole-genome sequences for species delineation, including tetra nucleotide usage patterns (TETRA), genome-to-genome distance (GGDC), and average nucleotide identity (ANI), Pseudomonas sp. SWRIQ11 can be considered a novel species candidate. The phylogenetic analysis revealed SWRIQ11 clusters with Pseudomonas tehranensis SWRI196 in the same clade. The SWRIQ11 genome was rich in genes related to stress sensing, signaling, and response, chaperones, motility, attachments, colonization, and enzymes for degrading plant-derived carbohydrates. Furthermore, the genes for production of exopolysaccharides, osmoprotectants, phytohormones, and ACC deaminase, ion homeostasis, nutrient acquisition, and antioxidant defenses were identified in the SWRIQ11 genome. The results of genome analysis (identification of more than 825 CDSs related to plant growth-promoting and stress-alleviating traits in the SWRIQ11 genome which is more than 15% of its total CDSs) are in accordance with laboratory and greenhouse experiments assigning the Pseudomonas sp. SWRIQ11 as a halotolerant plant growth-promoting bacterium (PGPB). This research highlights the potential safe application of this new PGPB species in agriculture as a potent biofertilizer.
Collapse
Affiliation(s)
- Seyyedeh Maryam Zamanzadeh-Nasrabadi
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455 Iran
| | - Fatemeh Mohammadiapanah
- Pharmaceutial Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455 Iran
| | - Sajjad Sarikhan
- Molecular Bank, Iranian Biological Resource Center (IBRC), ACECR, Tehran, Iran
| | - Vahid Shariati
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Kobra Saghafi
- Soil and Water Research Institute (SWRI), Karaj, Iran
| | - Mehdi Hosseini-Mazinani
- Agricultural Biotechnology Department, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| |
Collapse
|
7
|
Tsavea E, Tzika P, Katsivelou E, Adamopoulou A, Nikolaidis M, Amoutzias GD, Mossialos D. Impact of Mt. Olympus Honeys on Virulence Factors Implicated in Pathogenesis Exerted by Pseudomonas aeruginosa. Antibiotics (Basel) 2023; 12:998. [PMID: 37370317 DOI: 10.3390/antibiotics12060998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The aim of this study was to examine the impact of twenty honey samples, harvested in Mt. Olympus (Greece), on the virulence factors implicated in P. aeruginosa pathogenesis. Six key virulence factors (protease and elastase activity, pyocyanin and pyoverdine concentration, biofilm formation, and swimming motility) were selected in order to assess the effect of the tested honeys compared with Manuka honey. All tested honeys demonstrated a significant inhibition of protease and elastase activity compared with the control. Six and thirteen honeys exerted superior protease (no inhibition zone) and elastase (values lower than 55%) activity, respectively, compared with Manuka honey. Seventeen tested honeys exhibited reduced pyoverdine production compared with the control; all tested honeys, except for one, showed an inhibitory effect on pyocyanin production compared with the control. Regarding swimming motility, nine tested honeys demonstrated significantly higher inhibition compared with Manuka honey. Honey concentrations (6% v/v and 8% v/v) had the most profound impact, as they reduced biofilm formation to less than 20% compared with the control. Overall, our data demonstrate a significant inhibition of the virulence factors in the tested Mt. Olympus honeys, highlighting the strong antimicrobial activity against P. aeruginosa, an antibiotic-resistant pathogen of growing concern, which is implicated in severe nosocomial infections globally.
Collapse
Affiliation(s)
- Eleni Tsavea
- Laboratory of Microbial Biotechnology, Molecular Bacteriology-Virology, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| | - Paraskevi Tzika
- Laboratory of Microbial Biotechnology, Molecular Bacteriology-Virology, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| | - Eleni Katsivelou
- Laboratory of Microbial Biotechnology, Molecular Bacteriology-Virology, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| | - Anna Adamopoulou
- Laboratory of Microbial Biotechnology, Molecular Bacteriology-Virology, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| | - Marios Nikolaidis
- Bioinformatics Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| | - Grigorios D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| | - Dimitris Mossialos
- Laboratory of Microbial Biotechnology, Molecular Bacteriology-Virology, Department of Biochemistry & Biotechnology, School of Health Sciences, University of Thessaly, 41500 Larissa, Greece
| |
Collapse
|
8
|
Dell’Olmo E, Tiberini A, Sigillo L. Leguminous Seedborne Pathogens: Seed Health and Sustainable Crop Management. PLANTS (BASEL, SWITZERLAND) 2023; 12:2040. [PMID: 37653957 PMCID: PMC10221191 DOI: 10.3390/plants12102040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 09/02/2023]
Abstract
Pulses have gained popularity over the past few decades due to their use as a source of protein in food and their favorable impact on soil fertility. Despite being essential to modern agriculture, these species face a number of challenges, such as agronomic crop management and threats from plant seed pathogens. This review's goal is to gather information on the distribution, symptomatology, biology, and host range of seedborne pathogens. Important diagnostic techniques are also discussed as a part of a successful process of seed health certification. Additionally, strategies for sustainable control are provided. Altogether, the data collected are suggested as basic criteria to set up a conscious laboratory approach.
Collapse
Affiliation(s)
- Eliana Dell’Olmo
- Council for Agricultural Research and Economics, Research Center for Vegetable and Ornamental Crops (CREA-OF), Via Cavalleggeri 25, 84098 Pontecagnano Faiano, Italy
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification (CREA-DC), Via C. G. Bertero, 22, 00156 Rome, Italy
| | - Loredana Sigillo
- Council for Agricultural Research and Economics, Research Center for Vegetable and Ornamental Crops (CREA-OF), Via Cavalleggeri 25, 84098 Pontecagnano Faiano, Italy
| |
Collapse
|
9
|
Todorović I, Abrouk D, Kyselková M, Lavire C, Rey M, Raičević V, Jovičić-Petrović J, Moënne-Loccoz Y, Muller D. Two novel species isolated from wheat rhizospheres in Serbia: Pseudomonas serbica sp. nov. and Pseudomonas serboccidentalis sp. nov. Syst Appl Microbiol 2023; 46:126425. [PMID: 37146562 DOI: 10.1016/j.syapm.2023.126425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 04/08/2023] [Accepted: 04/23/2023] [Indexed: 05/07/2023]
Abstract
Pseudomonas strains IT-194P, IT-215P, IT-P366T and IT-P374T were isolated from the rhizospheres of wheat grown in soils sampled from different fields (some of them known to be disease-suppressive) located near Mionica, Serbia. Phylogenetic analysis of the 16S rRNA genes and of whole genome sequences showed that these strains belong to two potentially new species, one containing strains IT-P366T and IT-194P and clustering (whole genome analysis) next to P. umsongensis DSM16611T, and another species containing strains IT-P374T and IT-215P and clustering next to P. koreensis LMG21318T. Genome analysis confirmed the proposition of novel species, as ANI was below the threshold of 95% and dDDH below 70% for strains IT-P366T (compared with P. umsongensis DSM16611T) and IT-P374T (compared with P. koreensis LMG21318T). Unlike P. umsongensis DSM16611T, strains of P. serbica can grow on D-mannitol, but not on pectin, D-galacturonic acid, L-galactonic acid lactone and α-hydroxybutyric acid. In contrary to P. koreensis LMG21318T, strains of P. serboccidentalis can use sucrose, inosine and α-ketoglutaric acid (but not L-histidine) as carbon sources. Altogether, these results indicate the existence of two novel species for which we propose the names Pseudomonas serbica sp. nov., with the type strain IT-P366T (=CFBP 9060 T = LMG 32732 T = EML 1791 T) and Pseudomonas serboccidentalis sp. nov., with the type strain IT-P374T (=CFBP 9061 T = LMG 32734 T = EML 1792 T). Strains from this study presented a set of phytobeneficial functions modulating plant hormonal balance, plant nutrition and plant protection, suggesting a potential as Plant Growth-Promoting Rhizobacteria (PGPR).
Collapse
Affiliation(s)
- Irena Todorović
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France; University of Belgrade, Faculty of Agriculture, Department of Microbial Ecology, Nemanjina 6, 11080 Zemun, Belgrade, Serbia
| | - Danis Abrouk
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Martina Kyselková
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 14220, Prague 4, Czech Republic
| | - Céline Lavire
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Marjolaine Rey
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Vera Raičević
- University of Belgrade, Faculty of Agriculture, Department of Microbial Ecology, Nemanjina 6, 11080 Zemun, Belgrade, Serbia
| | - Jelena Jovičić-Petrović
- University of Belgrade, Faculty of Agriculture, Department of Microbial Ecology, Nemanjina 6, 11080 Zemun, Belgrade, Serbia
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 bd du 11 novembre 1918, F-69622 Villeurbanne, France
| |
Collapse
|
10
|
Seebach H, Radow G, Brunek M, Schulz F, Piotrowski M, Krämer U. Arabidopsis Nicotianamine Synthases (NAS) comprise a common core-NAS domain fused to a variable auto-inhibitory C-terminus. J Biol Chem 2023:104732. [PMID: 37086785 DOI: 10.1016/j.jbc.2023.104732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/07/2023] [Accepted: 04/12/2023] [Indexed: 04/24/2023] Open
Abstract
Nicotianamine Synthase (NAS) catalyzes the biosynthesis of the low-molecular-mass metal chelator nicotianamine (NA) from the 2-aminobutyrate moieties of three S-adenosylmethionine molecules. NA has central roles in metal nutrition and metal homeostasis of flowering plants. The enzymatic function of NAS remains poorly understood. Crystal structures are available of archaeal and bacterial NAS-like proteins that carry out simpler aminobutanoyl transferase reactions. Here we report amino acids essential for the activity of AtNAS1 based on structural modeling and site-directed mutagenesis. Using a newly developed enzyme-coupled continuous activity assay, we compare differing NAS proteins identified through multiple sequence alignments and phylogenetic analyses. In most NAS of dicotyledonous and monocotyledonous plants (class Ia and Ib), the core-NAS domain is fused to a variable C-terminal domain. Compared to fungal and moss NAS that comprise merely a core-NAS domain (class III), NA biosynthetic activities of the four paralogous Arabidopsis thaliana NAS proteins were far lower. C-terminally trimmed core-AtNAS variants exhibited strongly elevated activities. Of 320 amino acids of AtNAS1, twelve, 287-TRGCMFMPCNCS-298, accounted for the auto-inhibitory effect of the C-terminus, of which approximately one-third was attributed to N296 within a CNCS motif that is fully conserved in Arabidopsis. No detectable NA biosynthesis was mediated by two representative plant NAS proteins that naturally lack the C-terminal domain, class Ia Arabidopsis halleri NAS5, and Medicago truncatula NAS2 of class II which is found in dicots and diverged early during the evolution of flowering plants. Next we will address a possible post-translational release of auto-inhibition in class I NAS proteins.
Collapse
Affiliation(s)
- Hiroyuki Seebach
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Gabriel Radow
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Michael Brunek
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany
| | - Frank Schulz
- Chemistry and Biochemistry of Natural Products, Faculty of Chemistry and Biochemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Markus Piotrowski
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
| | - Ute Krämer
- Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, 44801 Bochum, Germany.
| |
Collapse
|
11
|
Rahman A, Sarker MT, Islam MA, Hossain MU, Hasan M, Susmi TF. Targeting Essential Hypothetical Proteins of Pseudomonas aeruginosa PAO1 for Mining of Novel Therapeutics: An In Silico Approach. BIOMED RESEARCH INTERNATIONAL 2023; 2023:1787485. [PMID: 37090194 PMCID: PMC10119676 DOI: 10.1155/2023/1787485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Revised: 01/24/2023] [Accepted: 02/06/2023] [Indexed: 04/25/2023]
Abstract
As an omnipresent opportunistic bacterium, Pseudomonas aeruginosa PAO1 is responsible for acute and chronic infection in immunocompromised individuals. Currently, this bacterium is on WHO's red list where new antibiotics are urgently required for the treatment. Finding essential genes and essential hypothetical proteins (EHP) can be crucial in identifying novel druggable targets and therapeutics. This study is aimed at characterizing these EHPs and analyzing subcellular and physiochemical properties, PPI network, nonhomologous analysis against humans, virulence factor and novel drug target prediction, and finally structural analysis of the identified target employing around 42 robust bioinformatics tools/databases, the output of which was evaluated using the ROC analysis. The study discovered 18 EHPs from 336 essential genes, with domain and functional annotation revealing that 50% of these proteins belong to the enzyme category. The majority are cytoplasmic and cytoplasmic membrane proteins, with half being stable proteins subjected to PPIs network analysis. The network contains 261 nodes and 269 edges for 9 proteins of interest, with 11 hubs containing at least three nodes each. Finally, a pipeline builder predicts 7 proteins with novel drug targets, 5 nonhomologous proteins against human proteome, human antitargets, and human gut flora, and 3 virulent proteins. Among these, homology modeling of NP_249450 and NP_251676 was done, and the Ramachandran plot analysis revealed that more than 94% of the residues were in the preferred region. By analyzing functional attributes and virulence characteristics, the findings of this study may facilitate the development of innovative antibacterial drug targets and drugs of Pseudomonas aeruginosa PAO1.
Collapse
Affiliation(s)
- Atikur Rahman
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md. Takim Sarker
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| | - Md Ashiqul Islam
- Department of Chemistry and Biochemistry, University of Windsor, Canada
| | - Mohammad Uzzal Hossain
- Bioinformatics Division, National Institute of Biotechnology, Ganakbari, Ashulia, Savar, Dhaka 1349, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Tasmina Ferdous Susmi
- Department of Genetic Engineering and Biotechnology, Faculty of Biological Science and Technology, Jashore University of Science and Technology, Jashore 7408, Bangladesh
| |
Collapse
|
12
|
Leveraging Scheme for Cross-Study Microbiome Machine Learning Prediction and Feature Evaluations. Bioengineering (Basel) 2023; 10:bioengineering10020231. [PMID: 36829725 PMCID: PMC9952031 DOI: 10.3390/bioengineering10020231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 02/11/2023] Open
Abstract
The microbiota has proved to be one of the critical factors for many diseases, and researchers have been using microbiome data for disease prediction. However, models trained on one independent microbiome study may not be easily applicable to other independent studies due to the high level of variability in microbiome data. In this study, we developed a method for improving the generalizability and interpretability of machine learning models for predicting three different diseases (colorectal cancer, Crohn's disease, and immunotherapy response) using nine independent microbiome datasets. Our method involves combining a smaller dataset with a larger dataset, and we found that using at least 25% of the target samples in the source data resulted in improved model performance. We determined random forest as our top model and employed feature selection to identify common and important taxa for disease prediction across the different studies. Our results suggest that this leveraging scheme is a promising approach for improving the accuracy and interpretability of machine learning models for predicting diseases based on microbiome data.
Collapse
|
13
|
Bjørge Thomassen GM, Krych L, Knøchel S, Mehli L. Bacterial community development and diversity during the first year of production in a new salmon processing plant. Food Microbiol 2023; 109:104138. [DOI: 10.1016/j.fm.2022.104138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 11/26/2022]
|
14
|
Campolo A, Pifer R, Shannon P, Crary M. Microbial Adherence to Contact Lenses and Pseudomonas aeruginosa as a Model Organism for Microbial Keratitis. Pathogens 2022; 11:1383. [PMID: 36422634 PMCID: PMC9695309 DOI: 10.3390/pathogens11111383] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/11/2022] [Accepted: 11/17/2022] [Indexed: 08/27/2023] Open
Abstract
Microbial keratitis (MK), the infection of the cornea, is a devastating disease and the fifth leading cause of blindness and visual impairment around the world. The overwhelming majority of MK cases are linked to contact lens wear combined with factors which promote infection such as corneal abrasion, an immunocompromised state, improper contact lens use, or failing to routinely disinfect lenses after wear. Contact lens-related MK involves the adherence of microorganisms to the contact lens. Therefore, this review discusses the information currently available regarding the disease pathophysiology, the common types of microorganisms causing MK, physical and organic mechanisms of adhesion, material properties which are involved in adhesion, and current antimicrobial strategies. This review also concludes that Pseudomonas aeruginosa is a model organism for the investigation of contact lens microbial adherence due to its prevalence in MK cases, its extremely robust adhesion, antimicrobial-resistant properties, and the severity of the disease it causes.
Collapse
|
15
|
Lu CH, Han TH, Jiang N, Gai XT, Cao ZH, Zou SY, Chen W, Ma JH, Lin ZL, Li J, Liao DZ, Zhang LQ, Jin Y, Xia ZY. Pseudomonas lijiangensis sp. nov., a novel phytopathogenic bacterium isolated from black spots of tobacco. Int J Syst Evol Microbiol 2022; 72. [DOI: 10.1099/ijsem.0.005591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Three Gram-stain-negative, motile, with amphilophotrichous flagella, and rod-shaped bacteria (LJ1, LJ2T and LJ3) were isolated from lower leaves with black spots on flue-cured tobacco in Yunnan, PR China. The results of phylogenetic analysis based on 16S rRNA gene sequences indicate that all the strains from tobacco were closely related to the type strains of the
Pseudomonas syringae
group within the
P. fluorescens
lineage and LJ2T has the highest sequence identities with
P. cichorii
DSM 50259T (99.92 %),
P. capsici
Pc19-1T (99.67 %) and
P. ovata
F51T (98.94 %) . The 16S rRNA gene sequence identities between LJ2T and other members of the genus
Pseudomonas
were below 98.50%. The average nucleotide identity by blast (ANIb) values between LJ2T and
P. cichorii
DSM 50259T,
P. capsici
Pc19-1T and
P. ovata
F51T were less than 95 %, and the in silico DNA–DNA hybridization (isDDH) values (yielded by formula 2) were less than 70 %. The major fatty acids were C16 : 1ω7c and/or C16 : 1ω6c (summed feature 3), C16 : 0 and C18 : 1ω7c and/or C18 : 1ω6c (summed feature 8). The polar lipids profile of LJ2T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, two unidentified phospholipids and one unidentified glycolipid. The predominant respiratory quinone was Q-9. The DNA G+C content of LJ2T was 58.4 mol%. On the basis of these data, we concluded that LJ2T represents a novel species of the genus
Pseudomonas
, for which the name Pseudomonas lijiangensis sp. nov. is proposed. The type strain of Pseudomonas lijiangensis sp. nov. is LJ2T (=CCTCC AB 2021465T=GDMCC 1.2884T=JCM 35177T).
Collapse
Affiliation(s)
- Can-Hua Lu
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Tian-Hua Han
- Lijiang Branch of Yunnan Tobacco Company, Lijiang 674100, PR China
| | - Ning Jiang
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Xiao-Tong Gai
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Zheng-Hua Cao
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Si-Yuan Zou
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Wei Chen
- Colledge of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Jun-Hong Ma
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Zhong-Long Lin
- China National Tobacco Corporation Yunnan Company, Kunming 650011, PR China
| | - Jie Li
- Kunming Branch of Yunnan Tobacco Company, Kunming 650051, PR China
| | - De-Zhi Liao
- Lijiang Branch of Yunnan Tobacco Company, Lijiang 674100, PR China
| | - Li-Qun Zhang
- Colledge of Plant Protection, China Agricultural University, Beijing 100193, PR China
| | - Yan Jin
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| | - Zhen-Yuan Xia
- Yunnan Academy of Tobacco Agricultural Sciences, Kunming 650021, PR China
| |
Collapse
|
16
|
A Comparative Analysis of the Core Proteomes within and among the Bacillus subtilis and Bacillus cereus Evolutionary Groups Reveals the Patterns of Lineage- and Species-Specific Adaptations. Microorganisms 2022; 10:microorganisms10091720. [PMID: 36144322 PMCID: PMC9505155 DOI: 10.3390/microorganisms10091720] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
By integrating phylogenomic and comparative analyses of 1104 high-quality genome sequences, we identify the core proteins and the lineage-specific fingerprint proteins of the various evolutionary clusters (clades/groups/species) of the Bacillus genus. As fingerprints, we denote those core proteins of a certain lineage that are present only in that particular lineage and absent in any other Bacillus lineage. Thus, these lineage-specific fingerprints are expected to be involved in particular adaptations of that lineage. Intriguingly, with a few notable exceptions, the majority of the Bacillus species demonstrate a rather low number of species-specific fingerprints, with the majority of them being of unknown function. Therefore, species-specific adaptations are mostly attributed to highly unstable (in evolutionary terms) accessory proteomes and possibly to changes at the gene regulation level. A series of comparative analyses consistently demonstrated that the progenitor of the Cereus Clade underwent an extensive genomic expansion of chromosomal protein-coding genes. In addition, the majority (76–82%) of the B. subtilis proteins that are essential or play a significant role in sporulation have close homologs in most species of both the Subtilis and the Cereus Clades. Finally, the identification of lineage-specific fingerprints by this study may allow for the future development of highly specific vaccines, therapeutic molecules, or rapid and low-cost molecular tests for species identification.
Collapse
|
17
|
Lai X, Niroula D, Burrows M, Wu X, Yan Q. Identification and Characterization of Bacteria-Derived Antibiotics for the Biological Control of Pea Aphanomyces Root Rot. Microorganisms 2022; 10:microorganisms10081596. [PMID: 36014014 PMCID: PMC9416638 DOI: 10.3390/microorganisms10081596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 07/30/2022] [Accepted: 08/04/2022] [Indexed: 11/24/2022] Open
Abstract
Antibiosis has been proposed to contribute to the beneficial bacteria-mediated biocontrol against pea Aphanomyces root rot caused by the oomycete pathogen Aphanomyces euteiches. However, the antibiotics required for disease suppression remain unknown. In this study, we found that the wild type strains of Pseudomonas protegens Pf-5 and Pseudomonas fluorescens 2P24, but not their mutants that lack 2,4-diacetylphloroglucinol, strongly inhibited A. euteiches on culture plates. Purified 2,4-diacetylphloroglucinol compound caused extensive hyphal branching and stunted hyphal growth of A. euteiches. Using a GFP-based transcriptional reporter assay, we found that expression of the 2,4-diacetylphloroglucinol biosynthesis gene phlAPf-5 is activated by germinating pea seeds. The 2,4-diacetylphloroglucinol producing Pf-5 derivative, but not its 2,4-diacetylphloroglucinol non-producing mutant, reduced disease severity caused by A. euteiches on pea plants in greenhouse conditions. This is the first report that 2,4-diacetylphloroglucinol produced by strains of Pseudomonas species plays an important role in the biocontrol of pea Aphanomyces root rot.
Collapse
Affiliation(s)
- Xiao Lai
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Dhirendra Niroula
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Mary Burrows
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | - Xiaogang Wu
- College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence: (X.W.); (Q.Y.)
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
- Correspondence: (X.W.); (Q.Y.)
| |
Collapse
|
18
|
Lou X, Wang R, Yan J, Li W, Liu R, Zhang Q, Bartlam M. Structural characterization of the novel stress response facilitator (SrfA) from Pseudomonas aeruginosa. Biochem Biophys Res Commun 2022; 625:147-153. [DOI: 10.1016/j.bbrc.2022.07.094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/26/2022]
|
19
|
The Notable Achievements and the Prospects of Bacterial Pathogen Genomics. Microorganisms 2022; 10:microorganisms10051040. [PMID: 35630482 PMCID: PMC9148168 DOI: 10.3390/microorganisms10051040] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/04/2022] [Accepted: 05/16/2022] [Indexed: 02/04/2023] Open
Abstract
Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.
Collapse
|
20
|
Molecular and Genomic Characterization of the Pseudomonas syringae Phylogroup 4: An Emerging Pathogen of Arabidopsis thaliana and Nicotiana benthamiana. Microorganisms 2022; 10:microorganisms10040707. [PMID: 35456758 PMCID: PMC9030749 DOI: 10.3390/microorganisms10040707] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 12/10/2022] Open
Abstract
Environmental fluctuations such as increased temperature, water availability, and air CO2 concentration triggered by climate change influence plant disease dynamics by affecting hosts, pathogens, and their interactions. Here, we describe a newly discovered Pseudomonas syringae strain found in a natural population of Arabidopsis thaliana collected from the southwest of France. This strain, called Psy RAYR-BL, is highly virulent on natural Arabidopsis accessions, Arabidopsis model accession Columbia 0, and tobacco plants. Despite the severe disease phenotype caused by the Psy RAYR-BL strain, we identified a reduced repertoire of putative Type III virulence effectors by genomic sequencing compared to P. syringae pv tomato (Pst) DC3000. Furthermore, hopBJ1Psy is found exclusively on the Psy RAYR-BL genome but not in the Pst DC3000 genome. The plant expression of HopBJ1Psy induces ROS accumulation and cell death. In addition, HopBJ1Psy participates as a virulence factor in this plant-pathogen interaction, likely explaining the severity of the disease symptoms. This research describes the characterization of a newly discovered plant pathogen strain and possible virulence mechanisms underlying the infection process shaped by natural and changing environmental conditions.
Collapse
|
21
|
Abstract
The widely distributed, essential redox factor pyrroloquinoline quinone (PQQ, methoxatin) (1) was discovered in the mid-1960s. The breadth and depth of its biological effects are steadily being revealed, and understanding its biosynthesis at the genomic level is a continuing process. In this review, aspects of the chemistry, biology, biosynthesis, and commercial production of 1 at the gene level, and some applications, are presented from discovery through to mid-2021.
Collapse
Affiliation(s)
- Geoffrey A Cordell
- Natural Products Inc., Evanston, Illinois 60202, United States.,Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, Florida 32610, United States
| | | |
Collapse
|
22
|
Karimov IF, Fedorova TO, Zherebyateva OO, Borisov SD, Mikhailova EA. Evaluation of Homoserine Lactone Production by Pseudomonas spp. Isolates. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721060072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
23
|
Ellison AR, Wilcockson D, Cable J. Circadian dynamics of the teleost skin immune-microbiome interface. MICROBIOME 2021; 9:222. [PMID: 34782020 PMCID: PMC8594171 DOI: 10.1186/s40168-021-01160-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 08/28/2021] [Indexed: 05/20/2023]
Abstract
BACKGROUND Circadian rhythms of host immune activity and their microbiomes are likely pivotal to health and disease resistance. The integration of chronotherapeutic approaches to disease mitigation in managed animals, however, is yet to be realised. In aquaculture, light manipulation is commonly used to enhance growth and control reproduction but may have unknown negative consequences for animal health. Infectious diseases are a major barrier to sustainable aquaculture and understanding the circadian dynamics of fish immunity and crosstalk with the microbiome is urgently needed. RESULTS Here, using rainbow trout (Oncorhynchus mykiss) as a model, we combine 16S rRNA metabarcoding, metagenomic sequencing and direct mRNA quantification methods to simultaneously characterise the circadian dynamics of skin clock and immune gene expression, and daily changes of skin microbiota. We demonstrate daily rhythms in fish skin immune expression and microbiomes, which are modulated by photoperiod and parasitic lice infection. We identify putative associations of host clock and immune gene profiles with microbial composition. Our results suggest circadian perturbation, that shifts the magnitude and timing of immune and microbiota activity, is detrimental to fish health. CONCLUSIONS The substantial circadian dynamics and fish host expression-microbiome relationships we find represent a valuable foundation for investigating the utility of chronotherapies in aquaculture, and more broadly contributes to our understanding of the role of microbiomes in circadian health of vertebrates. Video Abstract.
Collapse
Affiliation(s)
- Amy R Ellison
- School of Natural Sciences, Bangor University, Bangor, LL57 2DG, UK.
| | - David Wilcockson
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Aberystwyth, SY23 3DA, UK
| | - Jo Cable
- School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| |
Collapse
|
24
|
Liu Y, Zhou Y, Qiao J, Yu W, Pan X, Zhang T, Liu Y, Lu SE. Phenazine-1-carboxylic Acid Produced by Pseudomonas chlororaphis YL-1 Is Effective against Acidovorax citrulli. Microorganisms 2021; 9:microorganisms9102012. [PMID: 34683333 PMCID: PMC8541086 DOI: 10.3390/microorganisms9102012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 11/16/2022] Open
Abstract
The bacterial pathogen Acidovorax citrulli causes the destructive fruit blotch (BFB) on cucurbit plants. Pseudomonas chlororaphis YL-1 is a bacterial strain isolated from Mississippi soil and its genome harbors some antimicrobial-related gene clusters, such as phenazine, pyrrolnitrin, and pyoverdine. Here, we evaluated the antimicrobial activity of strain YL-1 as compared with its deficient mutants of antimicrobial-related genes, which were obtained using a sacB-based site-specific mutagenesis strategy. We found that only phenazine-deficient mutants ΔphzE and ΔphzF almost lost the inhibitory effects against A. citrulli in LB plates compared with the wild-type strain YL-1, and that the main antibacterial compound produced by strain YL-1 in LB medium was phenazine-1-carboxylic acid (PCA) based on the liquid chromatography-mass spectrometry (LC-MS) analysis. Gene expression analyses revealed that PCA enhanced the accumulation of reactive oxygen species (ROS) and increased the activity of catalase (CAT) in A. citrulli. The inhibition effect of PCA against A. citrulli was lowered by adding exogenous CAT. PCA significantly upregulated the transcript level of katB from 6 to 10 h, which encodes CAT that helps to protect the bacteria against oxidative stress. Collectively, the findings of this research suggest PCA is one of the key antimicrobial metabolites of bacterial strain YL-1, a promising biocontrol agent for disease management of BFB of cucurbit plants.
Collapse
Affiliation(s)
- Youzhou Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39759, USA
| | - Yaqiu Zhou
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
| | - Junqing Qiao
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
| | - Wenjie Yu
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (W.Y.); (T.Z.)
| | - Xiayan Pan
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
| | - Tingting Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; (W.Y.); (T.Z.)
| | - Yongfeng Liu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (Y.Z.); (J.Q.); (X.P.)
- Correspondence: (Y.L.); (S.-E.L.)
| | - Shi-En Lu
- Department of Biochemistry, Molecular Biology, Entomology and Plant Pathology, Mississippi State University, Starkville, MS 39759, USA
- Correspondence: (Y.L.); (S.-E.L.)
| |
Collapse
|
25
|
Schito AM, Piatti G, Caviglia D, Zuccari G, Zorzoli A, Marimpietri D, Alfei S. Bactericidal Activity of Non-Cytotoxic Cationic Nanoparticles against Clinically and Environmentally Relevant Pseudomonas spp. Isolates. Pharmaceutics 2021; 13:1411. [PMID: 34575487 PMCID: PMC8465415 DOI: 10.3390/pharmaceutics13091411] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/01/2021] [Accepted: 09/04/2021] [Indexed: 11/16/2022] Open
Abstract
Difficult-to-treat bacterial infections caused by resistant human and plant pathogens severely afflict hospitals, and concern the agri-food sectors. Bacteria from the Pseudomonadaceae family, such as P. aeruginosa, P. putida, P. fluorescens, and P. straminea, can be responsible for severe nosocomial infections in humans. P. fragi is the major cause of dairy and meat spoilage, while P. syringae can infect a wide range of economically important plant species, including tobacco, kiwi, and tomato. Therefore, a cationic water-soluble lysine dendrimer (G5-PDK) was tested on several species of Pseudomonas genus. Interestingly, G5-PDK demonstrated variable minimum inhibitory concentrations (MICs), depending on their pigment production, on Pseudomonas aeruginosa (1.6-> 6.4 µM), MICs = 3.2-6.4 µM on P. putida clinical isolates producing pyoverdine, and very low MICs (0.2-1.6 µM) on strains that produced non-pigmented colonies. Time-kill experiments established the rapid bactericidal activity of G5-PDK. In the cytotoxicity experiments on human keratinocytes, after 4 h of treatment with G5-PDK at concentrations 16-500 × MIC, more than 80% of viable cells were observed, and after 24 h, the selectivity indices were maintained above the maximum value reported as acceptable. Due to its proven bactericidal potency and low cytotoxicity, G5-PDK should be seriously considered to counteract clinically and environmentally relevant Pseudomonas isolates.
Collapse
Affiliation(s)
- Anna Maria Schito
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Viale Benedetto XV, 6, I-16132 Genova, Italy; (A.M.S.); (G.P.); (D.C.)
| | - Gabriella Piatti
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Viale Benedetto XV, 6, I-16132 Genova, Italy; (A.M.S.); (G.P.); (D.C.)
| | - Debora Caviglia
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Viale Benedetto XV, 6, I-16132 Genova, Italy; (A.M.S.); (G.P.); (D.C.)
| | - Guendalina Zuccari
- Department of Pharmacy, University of Genoa, Viale Cembrano, 16148 Genoa, Italy;
| | - Alessia Zorzoli
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (A.Z.); (D.M.)
| | - Danilo Marimpietri
- Stem Cell Laboratory and Cell Therapy Center, IRCCS Istituto Giannina Gaslini, Via Gerolamo Gaslini 5, 16147 Genova, Italy; (A.Z.); (D.M.)
| | - Silvana Alfei
- Department of Pharmacy, University of Genoa, Viale Cembrano, 16148 Genoa, Italy;
| |
Collapse
|
26
|
Saati-Santamaría Z, Peral-Aranega E, Velázquez E, Rivas R, García-Fraile P. Phylogenomic Analyses of the Genus Pseudomonas Lead to the Rearrangement of Several Species and the Definition of New Genera. BIOLOGY 2021; 10:782. [PMID: 34440014 PMCID: PMC8389581 DOI: 10.3390/biology10080782] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Revised: 08/03/2021] [Accepted: 08/11/2021] [Indexed: 11/17/2022]
Abstract
Pseudomonas is a large and diverse genus broadly distributed in nature. Its species play relevant roles in the biology of earth and living beings. Because of its ubiquity, the number of new species is continuously increasing although its taxonomic organization remains quite difficult to unravel. Nowadays the use of genomics is routinely employed for the analysis of bacterial systematics. In this work, we aimed to investigate the classification of species of the genus Pseudomonas on the basis of the analyses of the type strains whose genomes are currently available. Based on these analyses, we propose the creation of three new genera (Denitrificimonas gen nov. comb. nov., Neopseudomonas gen nov. comb. nov. and Parapseudomonas gen nov. comb. nov) to encompass several species currently included within the genus Pseudomonas and the reclassification of several species of this genus in already described taxa.
Collapse
Affiliation(s)
- Zaki Saati-Santamaría
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Ezequiel Peral-Aranega
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
| | - Encarna Velázquez
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Raúl Rivas
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| | - Paula García-Fraile
- Microbiology and Genetics Department, University of Salamanca, 37007 Salamanca, Spain; (E.P.-A.); (E.V.); (R.R.); (P.G.-F.)
- Institute for Agribiotechnology Research (CIALE), 37185 Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, University of Salamanca-IRNASA-CSIC, 37008 Salamanca, Spain
| |
Collapse
|
27
|
Fabia BU, Bingwa J, Park J, Hieu NM, Ahn JH. Utilizing the ABC Transporter for Growth Factor Production by fleQ Deletion Mutant of Pseudomonas fluorescens. Biomedicines 2021; 9:biomedicines9060679. [PMID: 34208522 PMCID: PMC8234862 DOI: 10.3390/biomedicines9060679] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/31/2021] [Accepted: 06/04/2021] [Indexed: 12/01/2022] Open
Abstract
Pseudomonas fluorescens, a gram-negative bacterium, has been proven to be a capable protein manufacturing factory (PMF). Utilizing its ATP-binding cassette (ABC) transporter, a type I secretion system, P. fluorescens has successfully produced recombinant proteins. However, besides the target proteins, P. fluorescens also secretes unnecessary background proteins that complicate protein purification and other downstream processes. One of the background proteins produced in large amounts is FliC, a flagellin protein. In this study, the master regulator of flagella gene expression, fleQ, was deleted from P. fluorescens Δtp, a lipase and protease double-deletion mutant, via targeted gene knockout. FleQ directs flagella synthesis, so the new strain, P. fluorescens ΔfleQ, does not produce flagella-related proteins. This not only simplifies purification but also makes P. fluorescens ΔfleQ an eco-friendly expression host because it will not survive outside a controlled environment. Six recombinant growth factors, namely, insulin-like growth factors I and II, beta-nerve growth factor, fibroblast growth factor 1, transforming growth factor beta, and tumor necrosis factor beta, prepared using our supercharging method, were successfully secreted by P. fluorescens ΔfleQ. Our findings demonstrate the potential of P. fluorescens ΔfleQ, combined with our supercharging process, as a PMF.
Collapse
Affiliation(s)
- Benedict-Uy Fabia
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (B.-U.F.); (J.B.); (N.-M.H.)
| | - Joshua Bingwa
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (B.-U.F.); (J.B.); (N.-M.H.)
| | - Jiyeon Park
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, Korea;
| | - Nguyen-Mihn Hieu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (B.-U.F.); (J.B.); (N.-M.H.)
| | - Jung-Hoon Ahn
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Korea; (B.-U.F.); (J.B.); (N.-M.H.)
- Department of Chemistry and Biology, Korea Science Academy of Korea Advanced Institute of Science and Technology, Busan 47162, Korea;
- Correspondence: ; Tel.: +82-51-606-2335
| |
Collapse
|
28
|
Shchapova E, Nazarova A, Vasilyeva U, Gurkov A, Ostyak A, Mutin A, Adelshin R, Belkova N, Timofeyev M. Cellular Immune Response of an Endemic Lake Baikal Amphipod to Indigenous Pseudomonas sp. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2021; 23:463-471. [PMID: 34076776 DOI: 10.1007/s10126-021-10039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Studies of invertebrates have shown that the internal environment of crustaceans is not always sterile in normal conditions, and in many species, it can be populated by microorganisms even in the absence of any visible pathological processes in the body. This observation raises the question of whether genetically modified indigenous hemolymph microorganisms can be used for biotechnological purposes inside the crustacean either as local producers of some compounds or as sensors to physiological parameters. In this study, we tested the ability of the bacteria isolated from the hemolymph of the amphipod Eulimnogammarus verrucosus to hide from the cellular immune response of the host as the most important feature for their potential long-term application in vivo. 16S rDNA amplicon sequencing revealed five common bacterial genera in all analyzed samples of the amphipod hemolymph, among which Pseudomonas is most easily subjected to genome modification and, thus, the most prospective for biotechnological application. Cultivation of Pseudomonas gave us a number of strains undoubtedly derived from the amphipod hemolymph, and one of them (belonging to the Pseudomonas fluorescens group) was chosen for further tests. The primary culture of amphipod hemocytes was used to analyze the immunogenicity of the strain and showed a pronounced reaction of the immune cells to a high amount of the bacteria within six hours. This result indicates that modulation of cellular immune response to metabolically active bacterial cells is not mandatory for the survival and wide distribution of these microorganisms in the hemolymph of numerous amphipod individuals.
Collapse
Affiliation(s)
| | | | | | - Anton Gurkov
- Irkutsk State University, Irkutsk, Russia
- Baikal Research Centre, Irkutsk, Russia
| | - Alexander Ostyak
- Irkutsk Anti-Plague Research Institute of Siberia and Far East, Irkutsk, Russia
| | | | - Renat Adelshin
- Irkutsk State University, Irkutsk, Russia
- Irkutsk Anti-Plague Research Institute of Siberia and Far East, Irkutsk, Russia
| | - Natalia Belkova
- Scientific Centre for Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Maxim Timofeyev
- Irkutsk State University, Irkutsk, Russia.
- Baikal Research Centre, Irkutsk, Russia.
| |
Collapse
|
29
|
Transcriptomic Analysis of Pseudomonas aeruginosa Response to Pine Honey via RNA Sequencing Indicates Multiple Mechanisms of Antibacterial Activity. Foods 2021; 10:foods10050936. [PMID: 33923242 PMCID: PMC8145095 DOI: 10.3390/foods10050936] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 12/12/2022] Open
Abstract
Pine honey is a unique type of honeydew honey produced exclusively in Eastern Mediterranean countries like Greece and Turkey. Although the antioxidant and anti-inflammatory properties of pine honey are well documented, few studies have investigated so far its antibacterial activity. This study investigates the antibacterial effects of pine honey against P. aeruginosa PA14 at the molecular level using a global transcriptome approach via RNA-sequencing. Pine honey treatment was applied at sub-inhibitory concentration and short exposure time (0.5× of minimum inhibitory concentration –MIC- for 45 min). Pine honey induced the differential expression (>two-fold change and p ≤ 0.05) of 463 genes, with 274 of them being down-regulated and 189 being up-regulated. Gene ontology (GO) analysis revealed that pine honey affected a wide range of biological processes (BP). The most affected down-regulated BP GO terms were oxidation-reduction process, transmembrane transport, proteolysis, signal transduction, biosynthetic process, phenazine biosynthetic process, bacterial chemotaxis, and antibiotic biosynthetic process. The up-regulated BP terms, affected by pine honey treatment, were those related to the regulation of DNA-templated transcription, siderophore transport, and phosphorylation. Pathway analysis revealed that pine honey treatment significantly affected two-component regulatory systems, ABC transporter systems, quorum sensing, bacterial chemotaxis, biofilm formation and SOS response. These data collectively indicate that multiple mechanisms of action are implicated in antibacterial activity exerted by pine honey against P. aeruginosa.
Collapse
|