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Hosseini SB, Azizi M, Nojoumi SA, Valizadeh V. An up-to-date review of biomedical applications of serratiopeptidase and its biobetter derivatives as a multi-potential metalloprotease. Arch Microbiol 2024; 206:180. [PMID: 38502196 DOI: 10.1007/s00203-024-03889-6] [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: 12/23/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 03/21/2024]
Abstract
Serratiopeptidase is a bacterial metalloprotease used in a variety of medical applications. The multidimensional properties of serratiopeptidase make it noticeable as a miraculous enzyme. Anti-coagulant, anti-inflammatory and anti-biofilm activity of serratiopeptidase making it useful in reducing pain and swelling associated with various conditions including arthritis, diabetes, cancer, swelling, pain and also thrombolytic disorders. It breaks down fibrin, thins the fluids formed during inflammation and due to its anti-biofilm activity, can be used in the combination of antibiotics to reduce development of antibiotic resistance. However, some drawbacks like sensitivity to environmental conditions and low penetration into cells due to its large size have limited its usage as a potent pharmaceutical agent. To overcome such limitations, improved versions of the enzyme were introduced using protein engineering in our previous studies. Novel functional serratiopeptidases with shorter length and higher stability have seemingly created a hope for using this enzyme as a more effective therapeutic enzyme. This review explains the structural properties and functional aspects of serratiopeptidase, its main characteristics and properties, pre-clinical and clinical applications of the enzyme, improved qualities of the modified forms, different formulations of the enzyme, and the potential future developments.
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Affiliation(s)
- Seyedeh Bahareh Hosseini
- New Technologies Research Group, Nanobiotechnology Department, Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Azizi
- Department of Molecular Medicine, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Ali Nojoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Vahideh Valizadeh
- New Technologies Research Group, Nanobiotechnology Department, Pasteur Institute of Iran, Tehran, Iran.
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Mousavi SM, Archangi B, Zamani I. Antibacterial Properties of Bacteriocin Purified from Serratia marcescens and Computerized Assessment of its Interaction with Antigen 43 in Escherichia coli. ARCHIVES OF RAZI INSTITUTE 2023; 78:1738-1745. [PMID: 38828162 PMCID: PMC11139391 DOI: 10.32592/ari.2023.78.6.2694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/06/2023] [Indexed: 06/05/2024]
Abstract
Bacteriocins are a kind of antimicrobial peptides that kill or inhibit the growth of bacterial strains. The purpose of this study was to investigate the antibacterial effect of Serratia marcescens on several pathogenic bacterial strains. Bacteriocin produced by S. marcescens was purified by chromatography with Sephadex G-75 column, and its antibacterial effect on gram-negative bacteria, including Escherichia coli ATCC 700928, Pseudomonas aeruginosa PTCC 1707, S. marcescens PTCC 1621, Vibrio fischeri PTCC 1693, and Vibrio harveyi PTCC 1755, were evaluated by the disk diffusion method. The structure of bacteriocin was determined by nuclear magnetic resonance spectroscopy. The interaction of bacteriocin with the antigen 43 (Ag43) of E. coli was evaluated by the molecular docking method. Bacteriocin extracted from bacterial isolates had antibacterial activity on E. coli strains but not on other studied strains. Bioinformatics analysis also showed bacteriocin docking with Ag43 with an energy of -159.968 kJ/mol. Natural compounds, such as bacteriocin, can be an alternative to common chemical compounds and antibiotics. To reach a definite conclusion in this regard, there is a need for further research and understanding of their mechanism of action.
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Affiliation(s)
- S M Mousavi
- Department of Marine Biotechnology, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | - B Archangi
- Department of Marine Biotechnology, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | - I Zamani
- Department of Marine Biotechnology, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
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Zhao X, Xu D, Xia W, Hu M, Peng X, Liu X, Ran T, Wang W. Multicopy expression of sigma factor RpoH reduces prodigiosin biosynthesis in Serratia marcescens FS14. Antonie Van Leeuwenhoek 2023; 116:1197-1208. [PMID: 37728826 DOI: 10.1007/s10482-023-01875-4] [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: 05/22/2022] [Accepted: 08/22/2023] [Indexed: 09/21/2023]
Abstract
Regulation of prodigiosin biosynthesis is received wide attention due to the antimicrobial, immunosuppressive and anticancer activities of prodigiosin. Here, we constructed a transposon mutant library in S. marcescens FS14 to identify genes involved in the regulation of prodigiosin biosynthesis. 62 strains with apparently different colors were obtained. Identification of the transposon insertion sites revealed that they are classified into three groups: the coding region of cyaA and two component system eepS/R and the promoter region of rpoH. Since the effect of cyaA and eepS/R genes on prodigiosin was extensively investigated in Serratia marcescens, we chose the mutant of rpoH for further investigation. Further deletion mutation of rpoH gene showed no effect on prodigiosin production suggesting that the effect on prodigiosin production caused by transposon insertion is not due to the deletion of RpoH. We further demonstrated that multicopy expression of RpoH reduced prodigiosin biosynthesis indicating that transposon insertion caused RpoH enhanced expression. Previous results indicate that RpoS is the sigma factor for transcription of pig gene cluster in FS14, to test whether the enhanced expression of RpoH prevents prodigiosin by competing with RpoS, we found that multicopy expression of RpoS could alleviate the prodigiosin production inhibition by enhanced RpoH. We proposed that multicopy expressed RpoH competes with RpoS for core RNA polymerase (RNAP) resulting in decreased transcription of pig gene cluster and prodigiosin production reduction. We also demonstrated that RpoH is not directly involved in prodigiosin biosynthesis. Our results suggest that manipulating the transcription level of sigma factors may be applied to regulate the production of secondary metabolites.
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Affiliation(s)
- Xuezheng Zhao
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Xu
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Wenxiao Xia
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Menghua Hu
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Xuede Peng
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Xia Liu
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China.
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences,, Nanjing Agricultural University, Nanjing, China.
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Shikov AE, Merkushova AV, Savina IA, Nizhnikov AA, Antonets KS. The man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome. Front Microbiol 2023; 14:1211999. [PMID: 38029097 PMCID: PMC10656689 DOI: 10.3389/fmicb.2023.1211999] [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: 04/25/2023] [Accepted: 08/21/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors. Methods We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants. Results According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants. In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively. Discussion In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.
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Affiliation(s)
- Anton E. Shikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Anastasiya V. Merkushova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Iuliia A. Savina
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology, St. Petersburg, Russia
- Faculty of Biology, St. Petersburg State University, St. Petersburg, Russia
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Baráti-Deák B, Da Costa Arruda GC, Perjéssy J, Klupács A, Zalán Z, Mohácsi-Farkas C, Belák Á. Inhibition of Foodborne Pathogenic Bacteria by Excreted Metabolites of Serratia marcescens Strains Isolated from a Dairy-Producing Environment. Microorganisms 2023; 11:microorganisms11020403. [PMID: 36838368 PMCID: PMC9959323 DOI: 10.3390/microorganisms11020403] [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: 12/29/2022] [Revised: 02/01/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023] Open
Abstract
Serratia marcescens strains from a dairy-producing environment were tested for their inhibitory effect on Listeria monocytogenes, Salmonella Hartford, Yersinia enterocolitica and Escherichia coli. Inhibition of foodborne pathogens was observed in the case of a non-pigmented Serratia strain, while the pigment-producing isolate was able to inhibit only Y. enterocolitica. The co-culturing study in tryptone soya broth (TSB) and milk showed that the growth of Salmonella was inhibited in the first 24 h, but later the pathogen could grow in the presence of the Serratia strain even if its cell concentration was 1000 times higher than that of Salmonella. However, we found that (1) concentrated cell-free supernatants had stronger inhibitory activity, which confirms the extracellular nature of the antagonistic compound(s). We proved that (2) protease and chitinase enzymes can take part in this mechanism, but they are not the main inhibitory compounds. The presence of prodigiosin was observed only in the case of the pigmented strain; thus, (3) we hypothesized that prodigiosin does not take part in the inhibition of the pathogens. However, (4) the combined effect of different extracellular metabolites might be attributed to the inhibitory property. Application of concentrated S. marcescens cell-free supernatant can be an effective antibacterial strategy in the food industry, mainly in the form of a bio-disinfectant on surfaces of food-processing areas.
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Affiliation(s)
- Bernadett Baráti-Deák
- Department of Food Microbiology, Hygiene and Safety, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, H-1118 Budapest, Hungary
| | - Giseli Cristina Da Costa Arruda
- Department of Food Microbiology, Hygiene and Safety, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, H-1118 Budapest, Hungary
| | - Judit Perjéssy
- Department of Nutrition, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út, 14-16, H-1118 Budapest, Hungary
| | - Adél Klupács
- Department of Nutrition, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út, 14-16, H-1118 Budapest, Hungary
| | - Zsolt Zalán
- Department of Bioengineering and Fermentation Technology, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Ménesi út 45, H-1118 Budapest, Hungary
| | - Csilla Mohácsi-Farkas
- Department of Food Microbiology, Hygiene and Safety, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, H-1118 Budapest, Hungary
| | - Ágnes Belák
- Department of Food Microbiology, Hygiene and Safety, Institute of Food Science and Technology, Hungarian University of Agriculture and Life Sciences, Somlói út 14-16, H-1118 Budapest, Hungary
- Correspondence: ; Tel.: +36-1-305-7360
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Genetic Determinants of Antagonistic Interactions and the Response of New Endophytic Strain Serratia quinivorans KP32 to Fungal Phytopathogens. Int J Mol Sci 2022; 23:ijms232415561. [PMID: 36555201 PMCID: PMC9779691 DOI: 10.3390/ijms232415561] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
Fungal phytopathogens are challenging to control due to their penetration into plant tissues. Therefore, plant-colonizing bacteria could serve as an excellent weapon in fighting fungal infections. In this study, we aim to determine the biocontrol potential of the new endophytic strain Serratia quinivorans KP32, isolated from the roots of Petroselinum crispum L.; identify the related mechanisms; and understand the basis of its antagonistic interaction with taxonomically diverse fungi at the molecular level. The KP32 strain presented biological activity against Rhizoctonia solani, Colletotrichum dematium, Fusarium avenaceum, and Sclerotinia sclerotiorum, and its ability to inhibit the growth of the phytopathogens was found to be mediated by a broad spectrum of biocontrol features, such as the production of a number of lytic enzymes (amylases, chitinases, and proteases), siderophores, volatile organic and inorganic compounds, salicylic acid, and N-acyl-homoserine lactones. The higher expression of chitinase (chiA) and genes involved in the biosynthesis of hydrogen cyanide (hcnC), enterobactin (entB), and acetoin (budA) in bacteria exposed to fungal filtrates confirmed that these factors could act in combination, leading to a synergistic inhibitory effect of the strain against phytopathogens. We also confirm the active movement, self-aggregation, exopolysaccharide production, and biofilm formation abilities of the KP32 strain, which are essential for effective plant colonization. Its biological activity and colonization potential indicate that KP32 holds tremendous potential for use as an active biopesticide and plant growth promoter.
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Histometric and morphological damage caused by Serratia marcescens to the tick Rhipicephalus microplus (Acari: Ixodidae). Arch Microbiol 2022; 204:677. [DOI: 10.1007/s00203-022-03275-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 11/02/2022]
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Nones S, Sousa E, Holighaus G. Symbiotic Fungi of an Ambrosia Beetle Alter the Volatile Bouquet of Cork Oak Seedlings. PHYTOPATHOLOGY 2022; 112:1965-1978. [PMID: 35357159 DOI: 10.1094/phyto-08-21-0345-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
In Portugal, fungal symbionts of the ambrosia beetle Platypus cylindrus affect tree vigor of cork oak (Quercus suber) and are linked with the cork oak decline process. Fungal symbionts play crucial roles in the life history of bark and ambrosia beetles and recent work indicates complex interactions on the fungal and plant metabolic level. Colonized trees may respond with an array of currently unknown volatile metabolites being indicative of such interactions, acting as infochemicals with their environment. In this study, we examined volatile organic compounds (VOCs) of cork oak seedlings wound inoculated with strains of three fungal associates of P. cylindrus (Raffaelea montetyi, R. quercina, and Ceratocystiopsis sp. nov.) over a 45-day period by means of thermodesorption gas chromatography-mass spectrometry techniques. Fungal strains induced largely quantitative but species-specific changes among the 58 VOCs characterized. Overall, monoterpenes-the major volatiles of cork oak foliage-were significantly reduced, possibly a result of fungal biotransformation. Acetophenone, sulcatone, and nonanal-volatiles known for mediating ambrosia beetle behavior-increased in response to fungal inoculation. Qualitative VOC profiles of excised tissue of wood lesions (21 VOCs) and pure fungal cultures (60 VOCs) showed little overlap with seedling VOCs, indicating their plant-derived but fungal-induced origin. This chemoecological study expands on the limited knowledge of VOCs as infochemicals emitted from oak trees threatened by oak decline in relation to beetle-vectored ophiostomatoid fungi. It opens new avenues of research to clarify mutualistic or pathogenic aspects of these complex symbiotic interactions and develop new control strategies for P. cylindrus, including its mycobiota.
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Affiliation(s)
- Stefano Nones
- Agrarian and Forestry Systems and Vegetal Health Unit, National Institute for Agricultural and Veterinary Research (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
- Institute of Chemical and Biological Technology António Xavier, NOVA University of Lisbon, Av. da República, 2780-157 Oeiras, Portugal
| | - Edmundo Sousa
- Agrarian and Forestry Systems and Vegetal Health Unit, National Institute for Agricultural and Veterinary Research (INIAV, I.P.), Av. da República, Quinta do Marquês, 2780-159 Oeiras, Portugal
- GREEN-IT Bioresources for Sustainability, ITQB NOVA, Av. da República, 2780-157 Oeiras, Portugal
| | - Gerrit Holighaus
- Department of Forest Zoology and Forest Conservation, Büsgen Institute, Georg-August-University Göttingen, Büsgenweg 3, 37077 Göttingen, Germany
- Northwest German Forest Research Institute, Department of Forest Protection, Grätzelstraße 2, 37079 Göttingen, Germany
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Gupta V, Shekhawat SS, Kulshreshtha NM, Gupta AB. A systematic review on chlorine tolerance among bacteria and standardization of their assessment protocol in wastewater. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2022; 86:261-291. [PMID: 35906907 DOI: 10.2166/wst.2022.206] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Though chlorine is a cost-effective disinfectant for water and wastewaters, the bacteria surviving after chlorination pose serious public health and environmental problems. This review critically assesses the mechanism of chlorine disinfection as described by various researchers; factors affecting chlorination efficacy; and the re-growth potential of microbial contaminations in treated wastewater post chlorination to arrive at meaningful doses for ensuring health safety. Literature analysis shows procedural inconsistencies in the assessment of chlorine tolerant bacteria, making it extremely difficult to compare the tolerance characteristics of different reported tolerant bacteria. A comparison of logarithmic reduction after chlorination and the concentration-time values for prominent pathogens led to the generation of a standard protocol for the assessment of chlorine tolerance. The factors that need to be critically monitored include applied chlorine doses, contact time, determination of chlorine demands of the medium, and the consideration of bacterial counts immediately after chlorination and in post chlorinated samples (regrowth). The protocol devised here appropriately assesses the chlorine-tolerant bacteria and urges the scientific community to report the regrowth characteristics as well. This would increase the confidence in data interpretation that can provide a better understanding of chlorine tolerance in bacteria and aid in formulating strategies for effective chlorination.
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Affiliation(s)
- Vinayak Gupta
- Alumnus, Department of Civil and Environmental Engineering, National University of Singapore, Singapore; School of Environment and Society, Tokyo Institute of Technology, Tokyo, Japan
| | - Sandeep Singh Shekhawat
- Department of Civil Engineering, Malaviya National Institute of Technology, Jaipur, India E-mail: ; School of Life and Basic Sciences, SIILAS Campus, Jaipur National University Jaipur, India
| | - Niha Mohan Kulshreshtha
- Department of Civil Engineering, Malaviya National Institute of Technology, Jaipur, India E-mail:
| | - Akhilendra Bhushan Gupta
- Department of Civil Engineering, Malaviya National Institute of Technology, Jaipur, India E-mail:
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Genomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil. Sci Rep 2022; 12:8439. [PMID: 35589928 PMCID: PMC9120033 DOI: 10.1038/s41598-022-12435-7] [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: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 01/08/2023] Open
Abstract
Contamination of soil by antibiotics and heavy metals originating from hospital facilities has emerged as a major cause for the development of resistant microbes. We collected soil samples surrounding a hospital effluent and measured the resistance of bacterial isolates against multiple antibiotics and heavy metals. One strain BMCSI 3 was found to be sensitive to all tested antibiotics. However, it was resistant to many heavy metals and metalloids like cadmium, chromium, copper, mercury, arsenic, and others. This strain was motile and potentially spore-forming. Whole-genome shotgun assembly of BMCSI 3 produced 4.95 Mb genome with 4,638 protein-coding genes. The taxonomic and phylogenetic analysis revealed it, to be a Bordetella petrii strain. Multiple genomic islands carrying mobile genetic elements; coding for heavy metal resistant genes, response regulators or transcription factors, transporters, and multi-drug efflux pumps were identified from the genome. A comparative genomic analysis of BMCSI 3 with annotated genomes of other free-living B. petrii revealed the presence of multiple transposable elements and several genes involved in stress response and metabolism. This study provides insights into how genomic reorganization and plasticity results in evolution of heavy metals resistance by acquiring genes from its natural environment.
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Qiu S, Xu D, Xu M, Zhou H, Sun N, Zhang L, Zhao M, He J, Ran T, Sun B, Wang W. Crystal structures of PigF, an O-methyltransferase involved in the prodigiosin synthetic pathway, reveal an induced-fit substrate-recognition mechanism. IUCRJ 2022; 9:316-327. [PMID: 35371495 PMCID: PMC8895007 DOI: 10.1107/s2052252521011696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 11/04/2021] [Indexed: 06/14/2023]
Abstract
Prodigiosin, a red linear tripyrrole pigment, is a typical secondary metabolite with numerous biological functions, such as anticancer, antibacterial and immunosuppressant activities, and is synthesized through a bifurcated biosynthesis pathway from 4-methoxy-2,2'-bipyrrole-5-carbaldehyde (MBC) and 2-methyl-3-n-amylpyrrole (MAP). The last step in the biosynthetic pathway of MBC is catalysed by PigF, which transfers a methyl group to 4-hydroxy-2,20-bipyrrole-5-carbaldehyde (HBC) to form the final product MBC. However, the catalytic mechanism of PigF is still elusive. In this study, crystal structures of apo PigF and S-adenosylhomocysteine (SAH)-bound PigF were determined. PigF forms a homodimer and each monomer consists of two domains: a C-terminal catalytic domain and an N-terminal dimerization domain. Apo PigF adopts an open conformation, while the structure of the complex with the product SAH adopts a closed conformation. The binding of SAH induces dramatic conformational changes of PigF, suggesting an induced-fit substrate-binding mechanism. Further structural comparison suggests that this induced-fit substrate-recognition mechanism may generally exist in O-methyltransferases. Docking and mutation studies identified three key residues (His98, His247 and Asp248) that are crucial for enzyme activity. The essential function of His247 and Asp248 and structure analysis suggests that both residues are involved in activation of the HBC substrate of PigF. The invariance of Asp248 in PigF further confirmed its essential role. The invariance and essential role of His98 in PigF suggests that it is involved in correctly positioning the substrate. This study provides new insight into the catalytic mechanism of PigF, reveals an induced-fit substrate-recognition model for PigF and broadens the understanding of O-methyltransferases.
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Affiliation(s)
- Shenshen Qiu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Dongqing Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Mengxue Xu
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Huan Zhou
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Ning Sun
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Li Zhang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Mengmeng Zhao
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Jianhua He
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Tingting Ran
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
| | - Bo Sun
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201204, People’s Republic of China
| | - Weiwu Wang
- Department of Microbiology, College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, People’s Republic of China
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Castro-Saines E, Hernandez-Ortiz R, Lagunes-Quintanilla R, Peña-Chora G. Characterization of a strain of Serratia sp. with ixodicide activity against the cattle tick Rhipicephalus microplus. EXPERIMENTAL & APPLIED ACAROLOGY 2021; 85:101-111. [PMID: 34559350 DOI: 10.1007/s10493-021-00640-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 06/22/2021] [Indexed: 06/13/2023]
Abstract
Cattle ticks are considered the most important ectoparasite in the livestock industry. Rhipicephalus microplus causes economic losses both through direct feeding on livestock and through disease transmission. Reports of the failure of chemical ixodicides to control this tick have led to a search for control alternatives, such as bacteria with ixodicide activity. The objective of this work was to select a bacterial strain with ixodicide activity against R. microplus. In total, 83 bacterial strains were isolated from soil and dead R. microplus specimens, and all strains were evaluated against larvae in a screening test. Bacteria with ixodicide activity were evaluated in larvae and engorged adult female ticks. The larvae were challenged using the larval immersion test (LIT) with 20 µg/mL total protein. The median lethal concentration (LC50) for larvae was obtained by using nine total protein concentrations. Engorged adult female ticks were challenged using the adult immersion test (AIT) with six protein concentrations. We evaluated adult mortality on day 10, oviposition rate on day 14 and hatching rate on day 40 after challenge. Only one bacterial strain (EC-35) showed ixodicide activity against larvae and adult R. microplus. The highest larval mortality, 52.3%, occurred with a total protein concentration of 40 μg/mL, and the LC50 was 13.9 µg/mL of protein. In adults, a total protein concentration of 10 µg/mL had the highest mortality (55%), oviposition inhibition (50.9%) and reproductive potential inhibition (52.5%). However, there was no significant effect on hatching. The 16S rRNA gene sequence showed 99% identity of EC-35 with Serratia sp.
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Affiliation(s)
- Edgar Castro-Saines
- Facultad de Ciencias Agropecuarias, Universidad Autónoma del Estado de Morelos, Avenida Universidad, 1001, Colonia Chamilpa, CP 62209, Cuernavaca, Morelos, Mexico
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Carretera Federal Cuernavaca-Cuautla 8534, Colonia Progreso, CP 62550, Jiutepec, Morelos, Mexico
| | - Ruben Hernandez-Ortiz
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Carretera Federal Cuernavaca-Cuautla 8534, Colonia Progreso, CP 62550, Jiutepec, Morelos, Mexico
| | - Rodolfo Lagunes-Quintanilla
- Centro Nacional de Investigación Disciplinaria en Salud Animal e Inocuidad, Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, Carretera Federal Cuernavaca-Cuautla 8534, Colonia Progreso, CP 62550, Jiutepec, Morelos, Mexico
| | - Guadalupe Peña-Chora
- Centro de Investigaciones Biológicas, Universidad Autónoma del Estado de Morelos, Avenida Universidad, 1001, Colonia Chamilpa, CP 62209, Cuernavaca, Morelos, Mexico.
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Yang B, Chu F, Li H, Wang W, Ran T, Xu D. RpoS Activates the Prodigionsin Production by Activating the Transcription of the RpoS-Dependent Pig Gene Cluster in Serratia marcescens FS14. Indian J Microbiol 2021; 61:355-363. [PMID: 34295001 DOI: 10.1007/s12088-021-00952-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/01/2021] [Indexed: 01/14/2023] Open
Abstract
RpoS, an alternative sigma factor of RNA polymerase, regulates the expression of a great deal of genes involved in stationary-phase survival and stress response. To identify the function of RpoS homologue in Serratia marcescens FS14, in-frame deletion mutant of rpoS was constructed. It was found that RpoS activates the biosynthesis of prodigiosin in FS14 which is just opposite to what was observed in Serratia sp. ATCC 39006. We also demonstrated that RpoS positively regulates the prodigiosin production by activating the transcription of pig cluster in FS14, and the transcription of pig cluster is RpoS-dependent. Further study showed that the differences in the promoters of pig clusters in FS14 and 39006 lead to the different selection of the sigma factors and result in the different regulation mechanisms. The -10 element and the spacer region between -10 and -35 elements of the pig cluster in FS14 are vital for the RpoS recognition in FS14. Supplementary Information The online version contains supplementary material available at 10.1007/s12088-021-00952-4.
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Affiliation(s)
- Baoling Yang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Fenglian Chu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Haixia Li
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Weiwu Wang
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tingting Ran
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Dongqing Xu
- Key Laboratory of Agricultural and Environmental Microbiology, Ministry of Agriculture, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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Li X, Tan X, Zhang J, Zhang J. Complete Genome Sequences of One Prodigiosin-Producing Serratia marcescens Strain ZPG19. Front Bioeng Biotechnol 2021; 9:665077. [PMID: 34046401 PMCID: PMC8144439 DOI: 10.3389/fbioe.2021.665077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/06/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Xue Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Xinfeng Tan
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Jing Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Jie Zhang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
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Choi SY, Lim S, Yoon KH, Lee JI, Mitchell RJ. Biotechnological Activities and Applications of Bacterial Pigments Violacein and Prodigiosin. J Biol Eng 2021; 15:10. [PMID: 33706806 PMCID: PMC7948353 DOI: 10.1186/s13036-021-00262-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 03/03/2021] [Indexed: 12/14/2022] Open
Abstract
In this review, we discuss violacein and prodigiosin, two chromogenic bacterial secondary metabolites that have diverse biological activities. Although both compounds were "discovered" more than seven decades ago, interest into their biological applications has grown in the last two decades, particularly driven by their antimicrobial and anticancer properties. These topics will be discussed in the first half of this review. The latter half delves into the current efforts of groups to produce these two compounds. This includes in both their native bacterial hosts and heterogeneously in other bacterial hosts, including discussing some of the caveats related to the yields reported in the literature, and some of the synthetic biology techniques employed in this pursuit.
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Affiliation(s)
- Seong Yeol Choi
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Sungbin Lim
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea
| | - Kyoung-Hye Yoon
- Department of Physiology, Mitohormesis Research Center, Yonsei University Wonju College of Medicine, Wonju, Gangwon-do, South Korea.
| | - Jin I Lee
- Division of Biological Science and Technology, College of Science and Technology, Yonsei University, Mirae Campus, Wonju, Gangwon-do, South Korea.
| | - Robert J Mitchell
- School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, South Korea.
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Genome Sequences of Serratia Strains Revealed Common Genes in Both Serratomolides Gene Clusters. BIOLOGY 2020; 9:biology9120482. [PMID: 33419369 PMCID: PMC7767323 DOI: 10.3390/biology9120482] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 12/04/2020] [Accepted: 12/17/2020] [Indexed: 02/07/2023]
Abstract
Simple Summary Biosurfactants are amphiphilic molecules produced by microorganisms with a hydrophilic and a hydrophobic group, able to reduce surface tension. These molecules are largely used in the environmental, food, pharmaceutical, medical, and cleaning industries, among others. Serratia strains are ubiquitous microorganisms with the ability to produce biosurfactants, such as serrawettins. These extracellular lipopeptides are described as biocides against many bacteria and fungi. This work used comparative genomics to determine the distribution and organization of the serrawettins W1 and W2 biosynthetic gene clusters in all the 84 publicly available genomes of the Serratia genus. Here, the serrawettin W1 gene clusters’ organization is reported for the first time. The serrawettin W1 biosynthetic gene swrW and serrawettin W2 biosynthetic gene swrA were present in 17 and 11 Serratia genomes, respectively. The same genes in the biosynthetic clusters frame the swrW and swrA biosynthetic genes. This work identified four genes common to all serrawettin gene clusters, highlighting their key potential in the serrawettins biosynthetic process. Abstract Serratia strains are ubiquitous microorganisms with the ability to produce serratomolides, such as serrawettins. These extracellular lipopeptides are described as biocides against many bacteria and fungi and may have a nematicidal activity against phytopathogenic nematodes. Serrawettins W1 and W2 from different strains have different structures that might be correlated with distinct genomic organizations. This work used comparative genomics to determine the distribution and the organization of the serrawettins biosynthetic gene clusters in all the 84 publicly available genomes of the Serratia genus. The serrawettin W1 and W2 gene clusters’ organization was established using antiSMASH software and compared with single and short data previously described for YD25TSerratia. Here, the serrawettin W1 gene clusters’ organization is reported for the first time. The serrawettin W1 biosynthetic gene swrW was present in 17 Serratia genomes. Eighty different coding sequence (CDS) were assigned to the W1 gene cluster, 13 being common to all clusters. The serrawettin W2 swrA gene was present in 11 Serratia genomes. The W2 gene clusters included 68 CDS with 24 present in all the clusters. The genomic analysis showed the swrA gene constitutes five modules, four with three domains and one with four domains, while the swrW gene constitutes one module with four domains. This work identified four genes common to all serrawettin gene clusters, highlighting their essential potential in the serrawettins biosynthetic process.
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Hazarika DJ, Gautom T, Parveen A, Goswami G, Barooah M, Modi MK, Boro RC. Mechanism of interaction of an endofungal bacterium Serratia marcescens D1 with its host and non-host fungi. PLoS One 2020; 15:e0224051. [PMID: 32320394 PMCID: PMC7176118 DOI: 10.1371/journal.pone.0224051] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 03/07/2020] [Indexed: 01/17/2023] Open
Abstract
Association of bacteria with fungi is a major area of research in infection biology, however, very few strains of bacteria have been reported that can invade and reside within fungal hyphae. Here, we report the characterization of an endofungal bacterium Serratia marcescens D1 from Mucor irregularis SS7 hyphae. Upon re-inoculation, colonization of the endobacterium S. marcescens D1 in the hyphae of Mucor irregularis SS7 was demonstrated using stereo microscopy. However, S. marcescens D1 failed to invade into the hyphae of the tested Ascomycetes (except Fusarium oxysporum) and Basidiomycetes. Remarkably, Serratia marcescens D1 could invade and spread over the culture of F. oxysporum that resulted in mycelial death. Prodigiosin, the red pigment produced by the Serratia marcescens D1, helps the bacterium to invade fungal hyphae as revealed by the increasing permeability in fungal cell membrane. On the other hand, genes encoding the type VI secretion system (T6SS) assembly protein TssJ and an outer membrane associated murein lipoprotein also showed significant up-regulation during the interaction process, suggesting the involvement of T6SS in the invasion process.
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Affiliation(s)
- Dibya Jyoti Hazarika
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Trishnamoni Gautom
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Assma Parveen
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Gunajit Goswami
- DBT-North East Centre for Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Madhumita Barooah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
| | - Robin Chandra Boro
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, India
- * E-mail:
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18
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Fitness costs of the cultivable symbiont Serratia symbiotica and its phenotypic consequences to aphids in presence of environmental stressors. Evol Ecol 2019. [DOI: 10.1007/s10682-019-10012-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Abstract
Serratia marcescens is a Gram-negative nosocomial pathogen causing various hospital-acquired infections. Here, we describe the complete genome sequence of S. marcescens myophage Moabite. The genome of Moabite is 273,933 bp long, with 337 predicted coding sequences and two tRNA genes, and it shares its highest amino acid identity with Serratia phage 2050HW. Serratia marcescens is a Gram-negative nosocomial pathogen causing various hospital-acquired infections. Here, we describe the complete genome sequence of S. marcescens myophage Moabite. The genome of Moabite is 273,933 bp long, with 337 predicted coding sequences and two tRNA genes, and it shares its highest amino acid identity with Serratia phage 2050HW.
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20
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Brothers KM, Callaghan JD, Stella NA, Bachinsky JM, AlHigaylan M, Lehner KL, Franks JM, Lathrop KL, Collins E, Schmitt DM, Horzempa J, Shanks RMQ. Blowing epithelial cell bubbles with GumB: ShlA-family pore-forming toxins induce blebbing and rapid cellular death in corneal epithelial cells. PLoS Pathog 2019; 15:e1007825. [PMID: 31220184 PMCID: PMC6586354 DOI: 10.1371/journal.ppat.1007825] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/07/2019] [Indexed: 12/18/2022] Open
Abstract
Medical devices, such as contact lenses, bring bacteria in direct contact with human cells. Consequences of these host-pathogen interactions include the alteration of mammalian cell surface architecture and induction of cellular death that renders tissues more susceptible to infection. Gram-negative bacteria known to induce cellular blebbing by mammalian cells, Pseudomonas and Vibrio species, do so through a type III secretion system-dependent mechanism. This study demonstrates that a subset of bacteria from the Enterobacteriaceae bacterial family induce cellular death and membrane blebs in a variety of cell types via a type V secretion-system dependent mechanism. Here, we report that ShlA-family cytolysins from Proteus mirabilis and Serratia marcescens were required to induce membrane blebbling and cell death. Blebbing and cellular death were blocked by an antioxidant and RIP-1 and MLKL inhibitors, implicating necroptosis in the observed phenotypes. Additional genetic studies determined that an IgaA family stress-response protein, GumB, was necessary to induce blebs. Data supported a model where GumB and shlBA are in a regulatory circuit through the Rcs stress response phosphorelay system required for bleb formation and pathogenesis in an invertebrate model of infection and proliferation in a phagocytic cell line. This study introduces GumB as a regulator of S. marcescens host-pathogen interactions and demonstrates a common type V secretion system-dependent mechanism by which bacteria elicit surface morphological changes on mammalian cells. This type V secretion-system mechanism likely contributes bacterial damage to the corneal epithelial layer, and enables access to deeper parts of the tissue that are more susceptible to infection.
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Affiliation(s)
- Kimberly M. Brothers
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
- Charles T. Campbell Laboratory of Ophthalmic Microbiology
| | - Jake D. Callaghan
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
- Charles T. Campbell Laboratory of Ophthalmic Microbiology
| | - Nicholas A. Stella
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
- Charles T. Campbell Laboratory of Ophthalmic Microbiology
| | - Julianna M. Bachinsky
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
- Charles T. Campbell Laboratory of Ophthalmic Microbiology
| | - Mohammed AlHigaylan
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
- Charles T. Campbell Laboratory of Ophthalmic Microbiology
| | - Kara L. Lehner
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
- Charles T. Campbell Laboratory of Ophthalmic Microbiology
| | - Jonathan M. Franks
- Center for Biological Imaging, University of Pittsburgh, Pittsburgh, PA United States of America
| | - Kira L. Lathrop
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
| | - Elliot Collins
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, WV United States of America
| | - Deanna M. Schmitt
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, WV United States of America
| | - Joseph Horzempa
- Department of Natural Sciences and Mathematics, West Liberty University, West Liberty, WV United States of America
| | - Robert M. Q. Shanks
- Department of Ophthalmology, University of Pittsburgh, Pittsburgh, PA United States of America
- Charles T. Campbell Laboratory of Ophthalmic Microbiology
- * E-mail:
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21
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Ravindran A, Sunderrajan S, Pennathur G. Phylogenetic Studies on the Prodigiosin Biosynthetic Operon. Curr Microbiol 2019; 76:597-606. [DOI: 10.1007/s00284-019-01665-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 03/01/2019] [Indexed: 11/30/2022]
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Genomic analysis of carbon dioxide sequestering bacterium for exopolysaccharides production. Sci Rep 2019; 9:4270. [PMID: 30862945 PMCID: PMC6414628 DOI: 10.1038/s41598-019-41052-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 02/20/2019] [Indexed: 02/05/2023] Open
Abstract
In the present study, genomic analysis of a previously reported carbon dioxide (CO2) sequestering bacterium Serratia sp. ISTD04 was performed along with exopolysaccharide (EPS) production. Genomic analysis identified key and accessory enzymes responsible for CO2 sequestration. EPS synthesis genes were discovered in the genome and identified 8 putative clusters responsible for lipopolysaccharide, stewartan, emulsan, polysaccharide B, capsular polysaccharide and fatty acid-saccharide production. The production of EPS was found to be 0.88 ± 0.08, 1.25 ± 0.13 and 1.44 ± 0.10 g L−1 on glucose, bicarbonate (NaHCO3) and NaHCO3 plus glucose respectively at pH 7.8. After optimizing process parameters, the EPS production increased more than 3 folds. The morphology of strain and elemental composition of EPS was characterized by SEM-EDX. The functional groups, monomer composition, linkage analysis and structure of purified EPS was characterized by FTIR, GC-MS and 1H and 13C NMR. Glucose, galactose, mannose and glucosamine are the monomers detected in the EPS. EPS was further applied for bioflocculation (kaolin test) and dye removal. The EPS showed 68% ± 0.9 flocculating activity and decolorized cationic dye acridine orange (80%) and crystal violet (95%). The results highlight CO2 sequestration and EPS production potential of Serratia sp. ISTD04 that can be harnessed in future.
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Direct pathway cloning of the sodorifen biosynthetic gene cluster and recombinant generation of its product in E. coli. Microb Cell Fact 2019; 18:32. [PMID: 30732610 PMCID: PMC6366047 DOI: 10.1186/s12934-019-1080-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/30/2019] [Indexed: 01/15/2023] Open
Abstract
Background Serratia plymuthica WS3236 was selected for whole genome sequencing based on preliminary genetic and chemical screening indicating the presence of multiple natural product pathways. This led to the identification of a putative sodorifen biosynthetic gene cluster (BGC). The natural product sodorifen is a volatile organic compound (VOC) with an unusual polymethylated hydrocarbon bicyclic structure (C16H26) produced by selected strains of S. plymuthica. The BGC encoding sodorifen consists of four genes, two of which (sodA, sodB) are homologs of genes encoding enzymes of the non-mevalonate pathway and are thought to enhance the amounts of available farnesyl pyrophosphate (FPP), the precursor of sodorifen. Proceeding from FPP, only two enzymes are necessary to produce sodorifen: an S-adenosyl methionine dependent methyltransferase (SodC) with additional cyclisation activity and a terpene-cyclase (SodD). Previous analysis of S. plymuthica found sodorifen production titers are generally low and vary significantly among different producer strains. This precludes studies on the still elusive biological function of this structurally and biosynthetically fascinating bacterial terpene. Results Sequencing and mining of the S. plymuthica WS3236 genome revealed the presence of 38 BGCs according to antiSMASH analysis, including a putative sodorifen BGC. Further genome mining for sodorifen and sodorifen-like BGCs throughout bacteria was performed using SodC and SodD as queries and identified a total of 28 sod-like gene clusters. Using direct pathway cloning (DiPaC) we intercepted the 4.6 kb candidate sodorifen BGC from S. plymuthica WS3236 (sodA–D) and transformed it into Escherichia coli BL21. Heterologous expression under the control of the tetracycline inducible PtetO promoter firmly linked this BGC to sodorifen production. By utilizing this newly established expression system, we increased the production yields by approximately 26-fold when compared to the native producer. In addition, sodorifen was easily isolated in high purity by simple head-space sampling. Conclusions Genome mining of all available genomes within the NCBI and JGI IMG databases led to the identification of a wealth of sod-like pathways which may be responsible for producing a range of structurally unknown sodorifen analogs. Introduction of the S. plymuthica WS3236 sodorifen BGC into the fast-growing heterologous expression host E. coli with a very low VOC background led to a significant increase in both sodorifen product yield and purity compared to the native producer. By providing a reliable, high-level production system, this study sets the stage for future investigations of the biological role and function of sodorifen and for functionally unlocking the bioinformatically identified putative sod-like pathways. Electronic supplementary material The online version of this article (10.1186/s12934-019-1080-6) contains supplementary material, which is available to authorized users.
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24
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da Mota FF, Castro DP, Vieira CS, Gumiel M, de Albuquerque JP, Carels N, Azambuja P. In vitro Trypanocidal Activity, Genomic Analysis of Isolates, and in vivo Transcription of Type VI Secretion System of Serratia marcescens Belonging to the Microbiota of Rhodnius prolixus Digestive Tract. Front Microbiol 2019; 9:3205. [PMID: 30733713 PMCID: PMC6353840 DOI: 10.3389/fmicb.2018.03205] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/11/2018] [Indexed: 11/13/2022] Open
Abstract
Serratia marcescens is a bacterium with the ability to colonize several niches, including some eukaryotic hosts. S. marcescens have been recently found in the gut of hematophagous insects that act as parasite vectors, such as Anopheles, Rhodnius, and Triatoma. While some S. marcescens strains have been reported as symbiotic or pathogenic to other insects, the role of S. marcescens populations from the gut microbiota of Rhodnius prolixus, a vector of Chagas’ disease, remains unknown. Bacterial colonies from R. prolixus gut were isolated on BHI agar. After BOX-PCR fingerprinting, the genomic sequences of two isolates RPA1 and RPH1 were compared to others S. marcescens from the NCBI database in other to estimate their evolutionary divergence. The in vitro trypanolytic activity of these two bacterial isolates against Trypanosoma cruzi (DM28c clone and Y strain) was assessed by microscopy. In addition, the gene expression of type VI secretion system (T6SS) was detected in vivo by RT-PCR. Comparative genomics of RPA1 and RPH1 revealed, besides plasmid presence and genomic islands, genes related to motility, attachment, and quorum sensing in both genomes while genes for urea hydrolysis and type II secretion system (T2SS) were found only in the RPA1 genome. The in vitro trypanolytic activity of both S. marcescens strains was stronger in their stationary phases of growth than in their exponential ones, with 65–70 and 85–90% of epimastigotes (Dm28c clone and Y strain, respectively) being lysed after incubation with RPA1 or RPH1 in stationary phase. Although T6SS transcripts were detected in guts up to 40 days after feeding (DAF), R. prolixus morbidity or mortality did not appear to be affected. In this report, we made available two trypanolytic S. marcescens strains from R. prolixus gut to the scientific community together with their genomic sequences. Here, we describe their genomic features with the purpose of bringing new insights into the S. marcescens adaptations for colonization of the specific niche of triatomine guts. This study provides the basis for a better understanding of the role of S. marcescens in the microbiota of R. prolixus gut as a potential antagonist of T. cruzi in this complex system.
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Affiliation(s)
- Fabio Faria da Mota
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil
| | - Daniele Pereira Castro
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil.,Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Cecilia Stahl Vieira
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Marcia Gumiel
- Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
| | - Julia Peixoto de Albuquerque
- Laboratório de Enteropatógenos, Microbiologia Veterinária e de Alimentos, Departamento de Microbiologia e Parasitologia, Instituto Biomédico, Universidade Federal Fluminense (MIP/UFF), Rio de Janeiro, Brazil
| | - Nicolas Carels
- Laboratório de Modelagem de Sistemas Biológicos, National Institute for Science and Technology on Innovation in Neglected Diseases (INCT-IDN), Centro de Desenvolvimento Tecnológico em Saúde, Fundação Oswaldo Cruz (CDTS/FIOCRUZ), Rio de Janeiro, Brazil
| | - Patricia Azambuja
- Instituto Nacional de Ciência e Tecnologia em Entomologia Molecular (INCT-EM), Rio de Janeiro, Brazil.,Laboratório de Bioquímica e Fisiologia de Insetos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (IOC/FIOCRUZ), Rio de Janeiro, Brazil
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Yip CH, Yarkoni O, Ajioka J, Wan KL, Nathan S. Recent advancements in high-level synthesis of the promising clinical drug, prodigiosin. Appl Microbiol Biotechnol 2019; 103:1667-1680. [PMID: 30637495 DOI: 10.1007/s00253-018-09611-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 12/27/2018] [Accepted: 12/28/2018] [Indexed: 12/19/2022]
Abstract
Prodigiosin, a red linear tripyrrole pigment and a member of the prodiginine family, is normally secreted by the human pathogen Serratia marcescens as a secondary metabolite. Studies on prodigiosin have received renewed attention as a result of reported immunosuppressive, antimicrobial and anticancer properties. High-level synthesis of prodigiosin and the bioengineering of strains to synthesise useful prodiginine derivatives have also been a subject of investigation. To exploit the potential use of prodigiosin as a clinical drug targeting bacteria or as a dye for textiles, high-level synthesis of prodigiosin is a prerequisite. This review presents an overview on the biosynthesis of prodigiosin from its natural host Serratia marcescens and through recombinant approaches as well as highlighting the beneficial properties of prodigiosin. We also discuss the prospect of adopting a synthetic biology approach for safe and cost-effective production of prodigiosin in a more industrially compliant surrogate host.
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Affiliation(s)
- Chee-Hoo Yip
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Orr Yarkoni
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - James Ajioka
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QP, UK
| | - Kiew-Lian Wan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia
| | - Sheila Nathan
- School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM, Bangi, Selangor, Malaysia.
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Matteoli FP, Passarelli-Araujo H, Reis RJA, da Rocha LO, de Souza EM, Aravind L, Olivares FL, Venancio TM. Genome sequencing and assessment of plant growth-promoting properties of a Serratia marcescens strain isolated from vermicompost. BMC Genomics 2018; 19:750. [PMID: 30326830 PMCID: PMC6192313 DOI: 10.1186/s12864-018-5130-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/27/2018] [Indexed: 01/11/2023] Open
Abstract
Background Plant-bacteria associations have been extensively studied for their potential in increasing crop productivity in a sustainable manner. Serratia marcescens is a species of Enterobacteriaceae found in a wide range of environments, including soil. Results Here we describe the genome sequencing and assessment of plant growth-promoting abilities of S. marcescens UENF-22GI, a strain isolated from mature cattle manure vermicompost. In vitro, S. marcescens UENF-22GI is able to solubilize P and Zn, to produce indole compounds (likely IAA), to colonize hyphae and counter the growth of two phytopathogenic fungi. Inoculation of maize with this strain remarkably increased seedling growth and biomass under greenhouse conditions. The S. marcescens UENF-22GI genome has 5 Mb, assembled in 17 scaffolds comprising 4662 genes (4528 are protein-coding). No plasmids were identified. S. marcescens UENF-22GI is phylogenetically placed within a clade comprised almost exclusively of non-clinical strains. We identified genes and operons that are likely responsible for the interesting plant-growth promoting features that were experimentally described. The S. marcescens UENF-22GI genome harbors a horizontally-transferred genomic island involved in antibiotic production, antibiotic resistance, and anti-phage defense via a novel ADP-ribosyltransferase-like protein and possible modification of DNA by a deazapurine base, which likely contributes to its competitiveness against other bacteria. Conclusions Collectively, our results suggest that S. marcescens UENF-22GI is a strong candidate to be used in the enrichment of substrates for plant growth promotion or as part of bioinoculants for agriculture. Electronic supplementary material The online version of this article (10.1186/s12864-018-5130-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Filipe P Matteoli
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Régis Josué A Reis
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Letícia O da Rocha
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil
| | - Emanuel M de Souza
- Departamento de Bioquímica e Biologia Molecular, Núcleo de Fixação Biológica de Nitrogênio, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Fabio L Olivares
- Núcleo de Desenvolvimento de Insumos Biológicos para a Agricultura (NUDIBA), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Rio de Janeiro, Brazil.
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Devi AR, Sharma GD, Majumdar PB, Pandey P. A multispecies consortium of bacteria having plant growth promotion and antifungal activities, for the management of Fusarium wilt complex disease in potato (Solanum tuberosum L.). BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2018. [DOI: 10.1016/j.bcab.2018.10.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Crystal structures of the kinase domain of PpkA, a key regulatory component of T6SS, reveal a general inhibitory mechanism. Biochem J 2018; 475:2209-2224. [DOI: 10.1042/bcj20180077] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/01/2018] [Accepted: 06/01/2018] [Indexed: 11/17/2022]
Abstract
The type VI secretion system (T6SS) is a versatile and widespread export system found in many Gram-negative bacteria that delivers effector proteins into target cells. The functions of T6SSs are tightly regulated by diverse mechanisms at multiple levels, including post-translational modification through threonine phosphorylation via the Ser/Thr protein kinase (STPK) PpkA. Here, we identified that PpkA is essential for T6SS secretion in Serratia marcescens since its deletion eliminated the secretion of haemolysin co-regulated protein, while the periplasmic and transmembrane portion of PpkA was found to be disposable for T6SS secretion. We further determined the crystal structure of the kinase domain of PpkA (PpkA-294). The structure of PpkA-294 was determined in its apo form to a 1.6 Å resolution as well as in complex with ATP to a 1.41 Å resolution and with an ATP analogue AMP-PCP to a 1.45 Å resolution. The residues in the activation loop of PpkA-294 were fully determined, and the N-terminus of the loop was folded into an unprecedented inhibitory helix, revealing that the PpkA kinase domain was in an auto-inhibitory state. The ternary MgATP–PpkA-294 complex was also inactive with nucleotide ribose and phosphates in unexpected and unproductive conformations. The αC-helix in the inactive PpkA-294 adopted a conformation towards the active site but with the conserved glutamate in the helix rotated away, which we suggest to be a general conformation for all STPK kinases in the inactive form. Structural comparison of PpkA with its eukaryotic homologues reinforced the universal regulation mechanism of protein kinases.
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Sandner-Miranda L, Vinuesa P, Cravioto A, Morales-Espinosa R. The Genomic Basis of Intrinsic and Acquired Antibiotic Resistance in the Genus Serratia. Front Microbiol 2018; 9:828. [PMID: 29867787 PMCID: PMC5958200 DOI: 10.3389/fmicb.2018.00828] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 04/11/2018] [Indexed: 12/18/2022] Open
Abstract
Serratia marcescens, a member of the Enterobacteriaceae family, was long thought to be a non-pathogenic bacterium prevalent in environmental habitats. Together with other members of this genus, it has emerged in recent years as an opportunistic nosocomial pathogen causing various types of infections. One important feature of pathogens belonging to this genus is their intrinsic and acquired resistance to a variety of antibiotic families, including β-lactam, aminoglycosides, quinolones and polypeptide antibiotics. The aim of this study was to elucidate which genes participate in the intrinsic and acquired antibiotic resistance of this genus in order to determine the Serratia genus resistome. We performed phylogenomic and comparative genomic analyses using 32 Serratia spp. genomes deposited in the NCBI GenBank from strains isolated from different ecological niches and different lifestyles. S. marcescens strain SmUNAM836, which was previously isolated from a Mexican adult with obstructive pulmonary disease, was included in this study. The results show that most of the antibiotic resistance genes (ARGs) were found on the chromosome, and to a lesser degree, on plasmids and transposons acquired through horizontal gene transfer. Four strains contained the gyrA point mutation in codon Ser83 that confers quinolone resistance. Pathogenic and environmental isolates presented a high number of ARGs, especially genes associated with efflux systems. Pathogenic strains, specifically nosocomial strains, presented more acquired resistance genes than environmental isolates. We may conclude that the environment provides a natural reservoir for antibiotic resistance, which has been underestimated in the medical field.
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Affiliation(s)
- Luisa Sandner-Miranda
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Pablo Vinuesa
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alejandro Cravioto
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Differential roles for ArcA and ArcB homologues in swarming motility in Serratia marcescens FS14. Antonie van Leeuwenhoek 2017; 111:609-617. [DOI: 10.1007/s10482-017-0981-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 11/10/2017] [Indexed: 12/30/2022]
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Douriet-Gámez NR, Maldonado-Mendoza IE, Ibarra-Laclette E, Blom J, Calderón-Vázquez CL. Genomic Analysis of Bacillus sp. Strain B25, a Biocontrol Agent of Maize Pathogen Fusarium verticillioides. Curr Microbiol 2017; 75:247-255. [DOI: 10.1007/s00284-017-1372-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 10/10/2017] [Indexed: 11/24/2022]
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Chen S, Blom J, Walker ED. Genomic, Physiologic, and Symbiotic Characterization of Serratia marcescens Strains Isolated from the Mosquito Anopheles stephensi. Front Microbiol 2017; 8:1483. [PMID: 28861046 PMCID: PMC5561391 DOI: 10.3389/fmicb.2017.01483] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/24/2017] [Indexed: 11/14/2022] Open
Abstract
Strains of Serratia marcescens, originally isolated from the gut lumen of adult female Anopheles stephensi mosquitoes, established persistent infection at high rates in adult A. stephensi whether fed to larvae or in the sugar meal to adults. By contrast, the congener S. fonticola originating from Aedes triseriatus had lower infection in A. stephensi, suggesting co-adaptation of Serratia strains in different species of host mosquitoes. Coinfection at high infection rate in adult A. stephensi resulted after feeding S. marcescens and Elizabethkingia anophelis in the sugar meal, but when fed together to larvae, infection rates with E. anophelis were much higher than were S. marcescens in adult A. stephensi, suggesting a suppression effect of coinfection across life stages. A primary isolate of S. marcescens was resistant to all tested antibiotics, showed high survival in the mosquito gut, and produced alpha-hemolysins which contributed to lysis of erythrocytes ingested with the blood meal. Genomes of two primary isolates from A. stephensi, designated S. marcescens ano1 and ano2, were sequenced and compared to other Serratia symbionts associated with insects, nematodes and plants. Serratia marcescens ano1 and ano2 had predicted virulence factors possibly involved in attacking parasites and/or causing opportunistic infection in mosquito hosts. S. marcescens ano1 and ano2 possessed multiple mechanisms for antagonism against other microorganisms, including production of bacteriocins and multi-antibiotic resistance determinants. These genes contributing to potential anti-malaria activity including serralysins, hemolysins and chitinases are only found in some Serratia species. It is interesting that genome sequences in S. marcescens ano1 and ano2 are distinctly different from those in Serratia sp. Ag1 and Ag2 which were isolated from Anopheles gambiae. Compared to Serratia sp. Ag1 and Ag2, S. marcescens ano1 and ano2 have more rRNAs and many important genes involved in commensal and anti-parasite traits.
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Affiliation(s)
- Shicheng Chen
- Department of Microbiology and Molecular Genetics, Michigan State UniversityEast Lansing, MI, United States
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-UniversityGiessen, Germany
| | - Edward D. Walker
- Department of Microbiology and Molecular Genetics, Michigan State UniversityEast Lansing, MI, United States
- Department of Entomology, Michigan State UniversityEast Lansing, MI, United States
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McMullen JG, McQuade R, Ogier JC, Pagès S, Gaudriault S, Patricia Stock S. Variable virulence phenotype of Xenorhabdus bovienii (γ-Proteobacteria: Enterobacteriaceae) in the absence of their vector hosts. MICROBIOLOGY-SGM 2017; 163:510-522. [PMID: 28430102 DOI: 10.1099/mic.0.000449] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Xenorhabdus bovienii bacteria have a dual lifestyle: they are mutualistic symbionts to many species of Steinernema nematodes and are pathogens to a wide array of insects. Previous studies have shown that virulence of X.bovienii-Steinernema spp. pairs decreases when the nematodes associate with non-cognate bacterial strains. However, the virulence of the X. bovienii strains alone has not been fully investigated. In this study, we characterized the virulence of nine X. bovienii strains in Galleria mellonella and Spodoptera littoralis and performed a comparative genomic analysis to correlate observed phenotypes with strain genotypes. Two X. bovienii strains were found to be highly virulent against the tested insect hosts, while three strains displayed attenuated insect virulence. Comparative genomic analyses revealed the presence of several clusters present only in virulent strains, including a predicted type VI secretion system (T6SS). We performed intra-species-competition assays, and showed that the virulent T6SS+ strains generally outcompeted the less virulent T6SS- strains. Thus, we speculate that the T6SS in X. bovienii may be another addition to the arsenal of antibacterial mechanisms expressed by these bacteria in an insect, where it could potentially play three key roles: (1) competition against the insect host microbiota; (2) protection of the insect cadaver from necrotrophic microbial competitors; and (3) outcompeting other Xenorhabdus species and/or strains when co-infections occur.
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Affiliation(s)
- John G McMullen
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
| | - Rebecca McQuade
- Postdoctoral Excellence in Research and Teaching (PERT) Fellow, Center for Insect Science, University of Arizona, Tucson, AZ, USA
| | | | - Sylvie Pagès
- DGIMI, INRA, Université de Montpellier, Montpellier, France
| | | | - S Patricia Stock
- Department of Entomology, University of Arizona, Forbes Bldg. Room 410, 1140 E. South Campus Dr, Tucson, AZ, 85750, USA.,School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, USA
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Crystal structure of MBP-PigG fusion protein and the essential function of PigG in the prodigiosin biosynthetic pathway in Serratia marcescens FS14. Int J Biol Macromol 2017; 99:394-400. [PMID: 28258005 DOI: 10.1016/j.ijbiomac.2017.02.088] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 11/23/2022]
Abstract
Prodigiosin, a tripyrrole red pigment is synthesized by Serratia and some other microbes through a bifurcated biosynthesis pathway; MBC (4-methoxy-2,2'-bipyrrole-5-carbaldehyde) and MAP (2-methyl-3-n-amyl-pyrrole) are synthesized separately and then condensed by PigC to form prodigiosin. PigI, PigG and PigA have been shown to be involved in the first steps of MBC biosynthesis (proline incorporation). The crystal structure of PigG was resolved to elucidate its function and mechanism. PigG, an acyl carrier protein (ACP), features the ACP architecture:, a helical bundle fold containing three major helices and a minor distorted helix together with a conserved "S" motif. An in-frame deletion mutation of the pigG gene abolished the synthesis of prodigiosin in Serratia marcescens FS14. The production of prodigiosin was fully restored by complementation of intact pigG; however the S36A mutant was not able to restore function in the in-frame deletion pigG mutant, indicating that PigG and the conserved serine residue (S36) of PigG are essential for the synthesis of prodigiosin.
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Su C, Liu Y, Sun Y, Li Z. Complete genome sequence of Serratia sp. YD25 (KCTC 42987) presenting strong antagonistic activities to various pathogenic fungi and bacteria. J Biotechnol 2017; 245:9-13. [DOI: 10.1016/j.jbiotec.2017.01.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 01/25/2017] [Accepted: 01/25/2017] [Indexed: 11/28/2022]
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Khan AR, Park GS, Asaf S, Hong SJ, Jung BK, Shin JH. Complete genome analysis of Serratia marcescens RSC-14: A plant growth-promoting bacterium that alleviates cadmium stress in host plants. PLoS One 2017; 12:e0171534. [PMID: 28187139 PMCID: PMC5302809 DOI: 10.1371/journal.pone.0171534] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2016] [Accepted: 01/22/2017] [Indexed: 11/28/2022] Open
Abstract
Serratia marcescens RSC-14 is a Gram-negative bacterium that was previously isolated from the surface-sterilized roots of the Cd-hyperaccumulator Solanum nigrum. The strain stimulates plant growth and alleviates Cd stress in host plants. To investigate the genetic basis for these traits, the complete genome of RSC-14 was obtained by single-molecule real-time sequencing. The genome of S. marcescens RSC-14 comprised a 5.12-Mbp-long circular chromosome containing 4,593 predicted protein-coding genes, 22 rRNA genes, 88 tRNA genes, and 41 pseudogenes. It contained genes with potential functions in plant growth promotion, including genes involved in indole-3-acetic acid (IAA) biosynthesis, acetoin synthesis, and phosphate solubilization. Moreover, annotation using NCBI and Rapid Annotation using Subsystem Technology identified several genes that encode antioxidant enzymes as well as genes involved in antioxidant production, supporting the observed resistance towards heavy metals, such as Cd. The presence of IAA pathway-related genes and oxidative stress-responsive enzyme genes may explain the plant growth-promoting potential and Cd tolerance, respectively. This is the first report of a complete genome sequence of Cd-tolerant S. marcescens and its plant growth promotion pathway. The whole-genome analysis of this strain clarified the genetic basis underlying its phenotypic and biochemical characteristics, underpinning the beneficial interactions between RSC-14 and plants.
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Affiliation(s)
- Abdur Rahim Khan
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, United States of America
| | - Gun-Seok Park
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sajjad Asaf
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Sung-Jun Hong
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Byung Kwon Jung
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, Republic of Korea
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Wu D, Li P, Zhou J, Gao M, Lou X, Ran T, Wu S, Wang W, Xu D. Identification of a toxic serralysin family protease with unique thermostable property from S. marcescens FS14. Int J Biol Macromol 2016; 93:98-106. [DOI: 10.1016/j.ijbiomac.2016.08.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/12/2016] [Accepted: 08/13/2016] [Indexed: 11/17/2022]
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Su C, Xiang Z, Liu Y, Zhao X, Sun Y, Li Z, Li L, Chang F, Chen T, Wen X, Zhou Y, Zhao F. Analysis of the genomic sequences and metabolites of Serratia surfactantfaciens sp. nov. YD25 T that simultaneously produces prodigiosin and serrawettin W2. BMC Genomics 2016; 17:865. [PMID: 27809759 PMCID: PMC5094094 DOI: 10.1186/s12864-016-3171-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 10/18/2016] [Indexed: 12/27/2022] Open
Abstract
Background Gram-negative bacteria of the genus Serratia are potential producers of many useful secondary metabolites, such as prodigiosin and serrawettins, which have potential applications in environmental bioremediation or in the pharmaceutical industry. Several Serratia strains produce prodigiosin and serrawettin W1 as the main bioactive compounds, and the biosynthetic pathways are co-regulated by quorum sensing (QS). In contrast, the Serratia strain, which can simultaneously produce prodigiosin and serrawettin W2, has not been reported. This study focused on analyzing the genomic sequence of Serratia sp. strain YD25T isolated from rhizosphere soil under continuously planted burley tobacco collected from Yongding, Fujian province, China, which is unique in producing both prodigiosin and serrawettin W2. Results A hybrid polyketide synthases (PKS)-non-ribosomal peptide synthetases (NRPS) gene cluster putatively involved in biosynthesis of antimicrobial serrawettin W2 was identified in the genome of YD25T, and its biosynthesis pathway was proposed. We found potent antimicrobial activity of serrawettin W2 purified from YD25T against various pathogenic bacteria and fungi as well as antitumor activity against Hela cells. Subsequently, comparative genomic analyses were performed among a total of 133 Serratia species. The prodigiosin biosynthesis gene cluster in YD25T belongs to the type I pig cluster, which is the main form of pig-encoding genes existing in most of the pigmented Serratia species. In addition, a complete autoinducer-2 (AI-2) system (including luxS, lsrBACDEF, lsrGK, and lsrR) as a conserved bacterial operator is found in the genome of Serratia sp. strain YD25T. Phylogenetic analysis based on concatenated Lsr and LuxS proteins revealed that YD25T formed an independent branch and was clearly distant from the strains that solely produce either prodigiosin or serrawettin W2. The Fe (III) ion reduction assay confirmed that strain YD25T could produce an AI-2 signal molecule. Phylogenetic analysis using the genomic sequence of YD25T combined with phylogenetic and phenotypic analyses support this strain as a member of a novel and previously uncharacterized Serratia species. Conclusion Genomic sequence and metabolite analysis of Serratia surfactantfaciens YD25T indicate that this strain can be further explored for the production of useful metabolites. Unveiling the genomic sequence of S. surfactantfaciens YD25T benefits the usage of this unique strain as a model system for studying the biosynthesis regulation of both prodigiosin and serrawettin W2 by the QS system. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3171-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chun Su
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Zhaoju Xiang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Yibo Liu
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Xinqing Zhao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200000, China
| | - Yan Sun
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.
| | - Zhi Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China.
| | - Lijun Li
- College of Food and Biological Engineering, Jimei University, Xiamen, 361000, China
| | - Fan Chang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Tianjun Chen
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Xinrong Wen
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Yidan Zhou
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
| | - Furong Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, People's Republic of China
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Lamacchia M, Dyrka W, Breton A, Saupe SJ, Paoletti M. Overlapping Podospora anserina Transcriptional Responses to Bacterial and Fungal Non Self Indicate a Multilayered Innate Immune Response. Front Microbiol 2016; 7:471. [PMID: 27148175 PMCID: PMC4835503 DOI: 10.3389/fmicb.2016.00471] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/21/2016] [Indexed: 11/13/2022] Open
Abstract
Recognition and response to non self is essential to development and survival of all organisms. It can occur between individuals of the same species or between different organisms. Fungi are established models for conspecific non self recognition in the form of vegetative incompatibility (VI), a genetically controlled process initiating a programmed cell death (PCD) leading to the rejection of a fusion cell between genetically different isolates of the same species. In Podospora anserina VI is controlled by members of the hnwd gene family encoding for proteins analogous to NOD Like Receptors (NLR) immune receptors in eukaryotes. It was hypothesized that the hnwd controlled VI reaction was derived from the fungal innate immune response. Here we analyze the P. anserina transcriptional responses to two bacterial species, Serratia fonticola to which P. anserina survives and S. marcescens to which P. anserina succumbs, and compare these to the transcriptional response induced under VI conditions. Transcriptional responses to both bacteria largely overlap, however the number of genes regulated and magnitude of regulation is more important when P. anserina survives. Transcriptional responses to bacteria also overlap with the VI reaction for both up or down regulated gene sets. Genes up regulated tend to be clustered in the genome, and display limited phylogenetic distribution. In all three responses we observed genes related to autophagy to be up-regulated. Autophagy contributes to the fungal survival in all three conditions. Genes encoding for secondary metabolites and histidine kinase signaling are also up regulated in all three conditions. Transcriptional responses also display differences. Genes involved in response to oxidative stress, or encoding small secreted proteins are essentially expressed in response to bacteria, while genes encoding NLR proteins are expressed during VI. Most functions encoded in response to bacteria favor survival of the fungus while most functions up regulated during VI would lead to cell death. These differences are discussed in the frame of a multilayered response to non self in fungi.
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Affiliation(s)
- Marina Lamacchia
- Institut de Biologie et Génétique Cellulaire, UMR 5095, Centre National de la Recherche Scientifique et Université de Bordeaux Bordeaux, France
| | - Witold Dyrka
- Equipe MAGNOME, INRIA, Université de Bordeaux, Centre National de la Recherche ScientifiqueTalence, France; Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of TechnologyWroclaw, Poland
| | - Annick Breton
- Institut de Biologie et Génétique Cellulaire, UMR 5095, Centre National de la Recherche Scientifique et Université de Bordeaux Bordeaux, France
| | - Sven J Saupe
- Institut de Biologie et Génétique Cellulaire, UMR 5095, Centre National de la Recherche Scientifique et Université de Bordeaux Bordeaux, France
| | - Mathieu Paoletti
- Institut de Biologie et Génétique Cellulaire, UMR 5095, Centre National de la Recherche Scientifique et Université de Bordeaux Bordeaux, France
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