1
|
Fabian B, Foster C, Asher A, Hassan K, Paulsen I, Tetu S. Identifying the suite of genes central to swimming in the biocontrol bacterium Pseudomonas protegens Pf-5. Microb Genom 2024; 10:001212. [PMID: 38546328 PMCID: PMC11004494 DOI: 10.1099/mgen.0.001212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/20/2024] [Indexed: 04/12/2024] Open
Abstract
Swimming motility is a key bacterial trait, important to success in many niches. Biocontrol bacteria, such as Pseudomonas protegens Pf-5, are increasingly used in agriculture to control crop diseases, where motility is important for colonization of the plant rhizosphere. Swimming motility typically involves a suite of flagella and chemotaxis genes, but the specific gene set employed for both regulation and biogenesis can differ substantially between organisms. Here we used transposon-directed insertion site sequencing (TraDIS), a genome-wide approach, to identify 249 genes involved in P. protegens Pf-5 swimming motility. In addition to the expected flagella and chemotaxis, we also identified a suite of additional genes important for swimming, including genes related to peptidoglycan turnover, O-antigen biosynthesis, cell division, signal transduction, c-di-GMP turnover and phosphate transport, and 27 conserved hypothetical proteins. Gene knockout mutants and TraDIS data suggest that defects in the Pst phosphate transport system lead to enhanced swimming motility. Overall, this study expands our knowledge of pseudomonad motility and highlights the utility of a TraDIS-based approach for analysing the functions of thousands of genes. This work sets a foundation for understanding how swimming motility may be related to the inconsistency in biocontrol bacteria performance in the field.
Collapse
Affiliation(s)
- B.K. Fabian
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - C. Foster
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - A. Asher
- School of Natural Sciences, Macquarie University, Sydney, Australia
| | - K.A. Hassan
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
- School of Environmental and Life Sciences, University of Newcastle, Newcastle, Australia
| | - I.T. Paulsen
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| | - S.G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, Australia
| |
Collapse
|
2
|
Dong X, Wu S, Rao Z, Xiao Y, Long Y, Xie Z. Insight into the High-Efficiency Benzo(a)pyrene Degradation Ability of Pseudomonas benzopyrenica BaP3 and Its Application in the Complete Bioremediation of Benzo(a)pyrene. Int J Mol Sci 2023; 24:15323. [PMID: 37895002 PMCID: PMC10607497 DOI: 10.3390/ijms242015323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/11/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) are common carcinogens. Benzo(a)pyrene is one of the most difficult high-molecular-weight (HMW) PAHs to remove. Biodegradation has become an ideal method to eliminate PAH pollutants from the environment. The existing research is mostly limited to low-molecular-weight PAHs; there is little understanding of HMW PAHs, particularly benzo(a)pyrene. Research into the biodegradation of HMW PAHs contributes to the development of microbial metabolic mechanisms and also provides new systems for environmental treatments. Pseudomonas benzopyrenica BaP3 is a highly efficient benzo(a)pyrene-degrading strain that is isolated from soil samples, but its mechanism of degradation remains unknown. In this study, we aimed to clarify the high degradation efficiency mechanism of BaP3. The genes encoding Rhd1 and Rhd2 in strain BaP3 were characterized, and the results revealed that rhd1 was the critical factor for high degradation efficiency. Molecular docking and enzyme activity determinations confirmed this conclusion. A recombinant strain that could completely mineralize benzo(a)pyrene was also proposed for the first time. We explained the mechanism of the high-efficiency benzo(a)pyrene degradation ability of BaP3 to improve understanding of the degradation mechanism of highly toxic PAHs and to provide new solutions to practical applications via synthetic biology.
Collapse
Affiliation(s)
| | | | | | | | | | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (X.D.); (S.W.); (Z.R.); (Y.X.); (Y.L.)
| |
Collapse
|
3
|
Wang P, Xiao Y, Gao D, Long Y, Xie Z. The Gene paaZ of the Phenylacetic Acid (PAA) Catabolic Pathway Branching Point and ech outside the PAA Catabolon Gene Cluster Are Synergistically Involved in the Biosynthesis of the Iron Scavenger 7-Hydroxytropolone in Pseudomonas donghuensis HYS. Int J Mol Sci 2023; 24:12632. [PMID: 37628812 PMCID: PMC10454607 DOI: 10.3390/ijms241612632] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
The newly discovered iron scavenger 7-hydroxytropolone (7-HT) is secreted by Pseudomonas donghuensis HYS. In addition to possessing an iron-chelating ability, 7-HT has various other biological activities. However, 7-HT's biosynthetic pathway remains unclear. This study was the first to report that the phenylacetic acid (PAA) catabolon genes in cluster 2 are involved in the biosynthesis of 7-HT and that two genes, paaZ (orf13) and ech, are synergistically involved in the biosynthesis of 7-HT in P. donghuensis HYS. Firstly, gene knockout and a sole carbon experiment indicated that the genes orf17-21 (paaEDCBA) and orf26 (paaG) were involved in the biosynthesis of 7-HT and participated in the PAA catabolon pathway in P. donghuensis HYS; these genes were arranged in gene cluster 2 in P. donghuensis HYS. Interestingly, ORF13 was a homologous protein of PaaZ, but orf13 (paaZ) was not essential for the biosynthesis of 7-HT in P. donghuensis HYS. A genome-wide BLASTP search, including gene knockout, complemented assays, and site mutation, showed that the gene ech homologous to the ECH domain of orf13 (paaZ) is essential for the biosynthesis of 7-HT. Three key conserved residues of ech (Asp39, His44, and Gly62) were identified in P. donghuensis HYS. Furthermore, orf13 (paaZ) could not complement the role of ech in the production of 7-HT, and the single carbon experiment indicated that paaZ mainly participates in PAA catabolism. Overall, this study reveals a natural association between PAA catabolon and the biosynthesis of 7-HT in P. donghuensis HYS. These two genes have a synergistic effect and different functions: paaZ is mainly involved in the degradation of PAA, while ech is mainly related to the biosynthesis of 7-HT in P. donghuensis HYS. These findings complement our understanding of the mechanism of the biosynthesis of 7-HT in the genus Pseudomonas.
Collapse
Affiliation(s)
| | | | | | - Yan Long
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (P.W.); (Y.X.); (D.G.)
| | - Zhixiong Xie
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China; (P.W.); (Y.X.); (D.G.)
| |
Collapse
|
4
|
Teng S, Wu T, Gao D, Wu S, Xiao Y, Long Y, Xie Z. Insight into the Global Negative Regulation of Iron Scavenger 7-HT Biosynthesis by the SigW/RsiW System in Pseudomonas donghuensis HYS. Int J Mol Sci 2023; 24:ijms24021184. [PMID: 36674714 PMCID: PMC9861184 DOI: 10.3390/ijms24021184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 01/04/2023] [Accepted: 01/05/2023] [Indexed: 01/11/2023] Open
Abstract
7-Hydroxytropolone (7-HT) is a unique iron scavenger synthesized by Pseudomonas donghuensis HYS that has various biological activities in addition to functioning as a siderophore. P. donghuensis HYS is more pathogenic than P. aeruginosa toward Caenorhabditis elegans, an observation that is closely linked to the biosynthesis of 7-HT. The nonfluorescent siderophore (nfs) gene cluster is responsible for the orderly biosynthesis of 7-HT and represents a competitive advantage that contributes to the increased survival of P. donghuensis HYS; however, the regulatory mechanisms of 7-HT biosynthesis remain unclear. This study is the first to propose that the ECF σ factor has a regulatory effect on 7-HT biosynthesis. In total, 20 ECF σ factors were identified through genome-wide scanning, and their responses to extracellular ferrous ions were characterized. We found that SigW was both significantly upregulated under high-iron conditions and repressed by an adjacent anti-σ factor. RNA-Seq results suggest that the SigW/RsiW system is involved in iron metabolism and 7-HT biosynthesis. Combined with the siderophore phenotype, we also found that SigW could inhibit siderophore synthesis, and this inhibition can be relieved by RsiW. EMSA assays proved that SigW, when highly expressed, can directly bind to the promoter region of five operons of the nfs cluster to inhibit the transcription of the corresponding genes and consequently suppress 7-HT biosynthesis. In addition, SigW not only directly negatively regulates structural genes related to 7-HT synthesis but also inhibits the transcription of regulatory proteins, including of the Gac/Rsm cascade system. Taken together, our results highlight that the biosynthesis of 7-HT is negatively regulated by SigW and that the SigW/RsiW system is involved in mechanisms for the regulation of iron homeostasis in P. donghuensis HYS. As a result of this work, we identified a novel mechanism for the global negative regulation of 7-HT biosynthesis, complementing our understanding of the function of ECF σ factors in Pseudomonas.
Collapse
|
5
|
Ding AJ, Zhang WM, Tao J, Chen B, Liu XC, Dong Y, Ma HJ, Pan SD, He JB, Zeng WK. Salmonella enterica serovar Paratyphi A-induced immune response in Caenorhabditis elegans depends on MAPK pathways and DAF-16. Front Immunol 2023; 14:1118003. [PMID: 37122724 PMCID: PMC10132459 DOI: 10.3389/fimmu.2023.1118003] [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: 12/19/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
Salmonella enterica serovar Paratyphi A (S. Paratyphi A) is a pathogen that can cause enteric fever. According to the recent epidemic trends of typhoid fever, S. Paratyphi A has been the major important causative factor in paratyphoid fever. An effective vaccine for S. Paratyphi A has not been developed, which made it a tricky public health concern. Until now, how S. Paratyphi A interacts with organisms remain unknown. Here using lifespan assay, we found that S. Paratyphi A could infect Caenorhabditis elegans (C. elegans) at 25°C, and attenuate thermotolerance. The immune response of C. elegans was mediated by tir-1, nsy-1, sek-1, pmk-1, mpk-1, skn-1, daf-2 and daf-16, suggesting that S. Paratyphi A could regulate the MAPK and insulin pathways. Furthermore, we observed several phenotypical changes when C. elegans were fed S. Paratyphi A, including an accelerated decline in body movement, reduced the reproductive capacity, shortened spawning cycle, strong preference for OP50, arrested pharyngeal pumping and colonization of the intestinal lumen. The virulence of S. Paratyphi A requires living bacteria and is not mediated by secreting toxin. Using hydrogen peroxide analysis and quantitative RT-PCR, we discovered that S. Paratyphi A could increase oxidative stress and regulate the immune response in C. elegans. Our results sheds light on the infection mechanisms of S. Paratyphi A and lays a foundation for drugs and vaccine development.
Collapse
|
6
|
Hem S, Jarocki VM, Baker DJ, Charles IG, Drigo B, Aucote S, Donner E, Burnard D, Bauer MJ, Harris PNA, Wyrsch ER, Djordjevic SP. Genomic analysis of Elizabethkingia species from aquatic environments: Evidence for potential clinical transmission. CURRENT RESEARCH IN MICROBIAL SCIENCES 2022; 3:100083. [PMID: 34988536 PMCID: PMC8703026 DOI: 10.1016/j.crmicr.2021.100083] [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: 10/12/2021] [Revised: 11/18/2021] [Accepted: 11/22/2021] [Indexed: 12/12/2022] Open
Abstract
Identification of closely related (< 50 SNV) clinical and environmental aquatic Elizabethkingia anophelis isolates. Identification of a provisional novel species Elizabethkingia umaracha. Novel blaGOB and blaB carbapenemases and extended spectrum β-lactamase blaCME alleles identified in Elizabethkingia spp. Analysis of the global phylogeny and pangenome of Elizabethkingia spp. Identification of novel ICE elements carrying uncharacterised genetic cargo in 67 / 94 (71.3%) of the aquatic environments Elizabethkingia spp.
Elizabethkingia species are ubiquitous in aquatic environments, colonize water systems in healthcare settings and are emerging opportunistic pathogens with reports surfacing in 25 countries across six continents. Elizabethkingia infections are challenging to treat, and case fatality rates are high. Chromosomal blaB, blaGOB and blaCME genes encoding carbapenemases and cephalosporinases are unique to Elizabethkingia spp. and reports of concomitant resistance to aminoglycosides, fluoroquinolones and sulfamethoxazole-trimethoprim are known. Here, we characterized whole-genome sequences of 94 Elizabethkingia isolates carrying multiple wide-spectrum metallo-β-lactamase (blaBand blaGOB) and extended-spectrum serine‑β-lactamase (blaCME) genes from Australian aquatic environments and performed comparative phylogenomic analyses against national clinical and international strains. qPCR was performed to quantify the levels of Elizabethkingia species in the source environments. Antibiotic MIC testing revealed significant resistance to carbapenems and cephalosporins but susceptibility to fluoroquinolones, tetracyclines and trimethoprim-sulfamethoxazole. Phylogenetics show that three environmental E. anophelis isolates are closely related to E. anophelis from Australian clinical isolates (∼36 SNPs), and a new species, E. umeracha sp. novel, was discovered. Genomic signatures provide insight into potentially shared origins and a capacity to transfer mobile genetic elements with both national and international isolates.
Collapse
Affiliation(s)
- Sopheak Hem
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Veronica M Jarocki
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Dave J Baker
- Quadram Institute Bioscience, Norwich, United Kingdom
| | - Ian G Charles
- Quadram Institute Bioscience, Norwich, United Kingdom.,Norwich Medical School, Norwich Research Park, Colney Lane, Norwich NR4 7TJ, United Kingdom
| | - Barbara Drigo
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Sarah Aucote
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Erica Donner
- Future Industries Institute, University of South Australia, Adelaide, SA 5001, Australia
| | - Delaney Burnard
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
| | - Michelle J Bauer
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
| | - Patrick N A Harris
- University of Queensland Centre for Clinical Research, Royal Brisbane and Woman's Hospital, Building 71/918 Royal Brisbane and Women's Hospital Campus, Herston, QLD 4029, Australia
| | - Ethan R Wyrsch
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| | - Steven P Djordjevic
- iThree Institute, University of Technology Sydney, Ultimo, NSW 2007, Australia.,Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, PO Box 123, Broadway, NSW 2007, Australia
| |
Collapse
|