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Bozhüyük KAJ, Präve L, Kegler C, Schenk L, Kaiser S, Schelhas C, Shi YN, Kuttenlochner W, Schreiber M, Kandler J, Alanjary M, Mohiuddin TM, Groll M, Hochberg GKA, Bode HB. Evolution-inspired engineering of nonribosomal peptide synthetases. Science 2024; 383:eadg4320. [PMID: 38513038 DOI: 10.1126/science.adg4320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/09/2024] [Indexed: 03/23/2024]
Abstract
Many clinically used drugs are derived from or inspired by bacterial natural products that often are produced through nonribosomal peptide synthetases (NRPSs), megasynthetases that activate and join individual amino acids in an assembly line fashion. In this work, we describe a detailed phylogenetic analysis of several bacterial NRPSs that led to the identification of yet undescribed recombination sites within the thiolation (T) domain that can be used for NRPS engineering. We then developed an evolution-inspired "eXchange Unit between T domains" (XUT) approach, which allows the assembly of NRPS fragments over a broad range of GC contents, protein similarities, and extender unit specificities, as demonstrated for the specific production of a proteasome inhibitor designed and assembled from five different NRPS fragments.
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Affiliation(s)
- Kenan A J Bozhüyük
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Myria Biosciences AG, Tech Park Basel, Hochbergstrasse 60C, 4057 Basel, Switzerland
| | - Leonard Präve
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Carsten Kegler
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Leonie Schenk
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Sebastian Kaiser
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Christian Schelhas
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
| | - Yan-Ni Shi
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Wolfgang Kuttenlochner
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Max Schreiber
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Joshua Kandler
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Mohammad Alanjary
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
| | - T M Mohiuddin
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
| | - Michael Groll
- Chair of Biochemistry, Center for Protein Assemblies, Technical University of Munich, Ernst-Otto-Fischer-Straße 8, 85748 Garching, Germany
| | - Georg K A Hochberg
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
| | - Helge B Bode
- Max Planck Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043 Marburg, Germany
- Molecular Biotechnology, Department of Biosciences, Goethe-University Frankfurt, 60438 Frankfurt, Germany
- Center for Synthetic Microbiology (SYNMIKRO), Phillips University Marburg, 35043 Marburg, Germany
- Department of Chemistry, Phillips University Marburg, 35043 Marburg, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG) & Senckenberg Gesellschaft für Naturforschung, 60325 Frankfurt, Germany
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2
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De Anda-Mora KL, Tavares-Carreón F, Alvarez C, Barahona S, Becerril-García MA, Treviño-Rangel RJ, García-Contreras R, Andrade A. Increased Proteolytic Activity of Serratia marcescens Clinical Isolate HU1848 Is Associated with Higher eepR Expression. Pol J Microbiol 2024; 73:11-20. [PMID: 38437469 PMCID: PMC10911700 DOI: 10.33073/pjm-2024-002] [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: 09/22/2023] [Accepted: 12/14/2023] [Indexed: 03/06/2024] Open
Abstract
Serratia marcescens is a global opportunistic pathogen. In vitro cytotoxicity of this bacterium is mainly related to metalloprotease serralysin (PrtS) activity. Proteolytic capability varies among the different isolates. Here, we characterized protease production and transcriptional regulators at 37°C of two S. marcescens isolates from bronchial expectorations, HU1848 and SmUNAM836. As a reference strain the insect pathogen S. marcescens Db10 was included. Zymography of supernatant cultures revealed a single (SmUNAM836) or double proteolytic zones (HU1848 and Db10). Mass spectrometry confirmed the identity of PrtS and the serralysin-like protease SlpB from supernatant samples. Elevated proteolytic activity and prtS expression were evidenced in the HU1848 strain through azocasein degradation and qRT-PCR, respectively. Evaluation of transcriptional regulators revealed higher eepR expression in HU1848, whereas cpxR and hexS transcriptional levels were similar between studied strains. Higher eepR expression in HU1848 was further confirmed through an in vivo transcriptional assay. Moreover, two putative CpxR binding motifs were identified within the eepR regulatory region. EMSA validated the interaction of CpxR with both motifs. The evaluation of eepR transcription in a cpxR deletion strain indicated that CpxR negatively regulates eepR. Sequence conservation suggests that regulation of eepR by CpxR is common along S. marcescens species. Overall, our data incorporates CpxR to the complex regulatory mechanisms governing eepR expression and associates the increased proteolytic activity of the HU1848 strain with higher eepR transcription. Based on the global impact of EepR in secondary metabolites production, our work contributes to understanding virulence factors variances across S. marcescens isolates.
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Affiliation(s)
- Karla L. De Anda-Mora
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Faviola Tavares-Carreón
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Carlos Alvarez
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Samantha Barahona
- Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Miguel A. Becerril-García
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Rogelio J. Treviño-Rangel
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Rodolfo García-Contreras
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Angel Andrade
- Departamento de Microbiología, Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey, Mexico
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3
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Zhang Y, Gu X, Huang C, Zhou J, Shi J, Zhao L. Temperature-regulated metabolites of Serratiamarcescens inhibited reproduction of pinewood nematode Bursaphelenchus xylophilus. iScience 2023; 26:107082. [PMID: 37416473 PMCID: PMC10320214 DOI: 10.1016/j.isci.2023.107082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/08/2023] [Accepted: 06/06/2023] [Indexed: 07/08/2023] Open
Abstract
The pinewood nematode Bursaphelenchus xylophilus is an invasive and destructive pathogen in forestry. Serratia marcescens AHPC29 was previously found to have nematicidal activity on B. xylophilus. The effect of AHPC29 growth temperature on B. xylophilus inhibition is unknown. Here we show that AHPC29 cultured at 15°C or 25°C, but not 37°C, inhibited B. xylophilus reproduction. Metabolomic analysis found 31 up-regulated metabolites as potential effective substances in this temperature-related difference, with five of them were tested to be effective in inhibiting B. xylophilus reproduction. Among the five metabolites, salsolinol was further verified in bacterial cultures with effective inhibition concentrations. This study found the inhibition of S. marcescens AHPC29 on B. xylophilus reproduction was temperature regulated and the differently expressed metabolites salsolinol played roles in this temperature-regulated effect, which implies the capability of S. marcescens and its metabolites as promising new agents for the management of B. xylophilus.
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Affiliation(s)
- Yanfen Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoting Gu
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenying Huang
- Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Jiao Zhou
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Juan Shi
- Sino-France Joint Laboratory for Invasive Forest Pests in Eurasia, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Lilin Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
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4
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Bruneaux M, Ashrafi R, Kronholm I, Laanto E, Örmälä‐Tiznado A, Galarza JA, Zihan C, Kubendran Sumathi M, Ketola T. The effect of a temperature-sensitive prophage on the evolution of virulence in an opportunistic bacterial pathogen. Mol Ecol 2022; 31:5402-5418. [PMID: 35917247 PMCID: PMC9826266 DOI: 10.1111/mec.16638] [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: 03/01/2022] [Revised: 07/14/2022] [Accepted: 07/21/2022] [Indexed: 01/11/2023]
Abstract
Viruses are key actors of ecosystems and have major impacts on global biogeochemical cycles. Prophages deserve particular attention as they are ubiquitous in bacterial genomes and can enter a lytic cycle when triggered by environmental conditions. We explored how temperature affects the interactions between prophages and other biological levels using an opportunistic pathogen, the bacterium Serratia marcescens, which harbours several prophages and that had undergone an evolution experiment under several temperature regimes. We found that the release of one of the prophages was temperature-sensitive and malleable to evolutionary changes. We further discovered that the virulence of the bacterium in an insect model also evolved and was positively correlated with phage release rates. We determined through analysis of genetic and epigenetic data that changes in the bacterial outer cell wall structure possibly explain this phenomenon. We hypothezise that the temperature-dependent phage release rate acted as a selection pressure on S. marcescens and that it resulted in modified bacterial virulence in the insect host. Our study system illustrates how viruses can mediate the influence of abiotic environmental changes to other biological levels and thus be involved in ecosystem feedback loops.
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Affiliation(s)
- Matthieu Bruneaux
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Roghaieh Ashrafi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Ilkka Kronholm
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Elina Laanto
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental SciencesUniversity of HelsinkiHelsinkiFinland
| | | | - Juan A. Galarza
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Chen Zihan
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Shenzhen Research InstituteThe Chinese University of Hong KongShenzhenChina
| | - Mruthyunjay Kubendran Sumathi
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland,Department of Ecology and Evolutionary BiologyUniversity of ArizonaTucsonArizonaUSA
| | - Tarmo Ketola
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
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5
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Enhanced Prodigiosin Production in Serratia marcescens JNB5-1 by Introduction of a Polynucleotide Fragment into the pigN 3' Untranslated Region and Disulfide Bonds into O-Methyl Transferase (PigF). Appl Environ Microbiol 2021; 87:e0054321. [PMID: 34232745 DOI: 10.1128/aem.00543-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In Serratia marcescens JNB5-1, prodigiosin was highly produced at 30°C, but it was noticeably repressed at ≥37°C. Our initial results demonstrated that both the production and the stability of the O-methyl transferase (PigF) and oxidoreductase (PigN) involved in the prodigiosin pathway in S. marcescens JNB5-1 sharply decreased at ≥37°C. Therefore, in this study, we improved mRNA stability and protein production using de novo polynucleotide fragments (PNFs) and the introduction of disulfide bonds, respectively, and observed their effects on prodigiosin production. Our results demonstrate that adding PNFs at the 3' untranslated regions of pigF and pigN significantly improved the mRNA half-lives of these genes, leading to an increase in the transcript and expression levels. Subsequently, the introduction of disulfide bonds in pigF improved the thermal stability, pH stability, and copper ion resistance of PigF. Finally, shake flask fermentation showed that the prodigiosin titer with the engineered S. marcescens was increased by 61.38% from 5.36 to 8.65 g/liter compared to the JNB5-1 strain at 30°C and, significantly, the prodigiosin yield increased 2.05-fold from 0.38 to 0.78 g/liter at 37°C. In this study, we revealed that the introduction of PNFs and disulfide bonds greatly improved the expression and stability of pigF and pigN, hence efficiently enhancing prodigiosin production with S. marcescens at 30 and 37°C. IMPORTANCE This study highlights a promising strategy to improve mRNA/enzyme stability and to increase production using de novo PNF libraries and the introduction of disulfide bonds into the protein. PNFs could increase the half-life of target gene mRNA and effectively prevent its degradation. Moreover, PNFs could increase the relative intensity of target genes without affecting the expression of other genes; as a result, it could alleviate the cellular burden compared to other regulatory elements such as promoters. In addition, we obtained a PigF variant with improved activity and stability by the introduction of disulfide bonds into PigF. Collectively, we demonstrate here a novel approach for improving mRNA/enzyme stability using PNFs, which results in enhanced prodigiosin production in S. marcescens at 30°C.
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6
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Comparative transcriptome analysis reveals metabolic regulation of prodigiosin in Serratia marcescens. ACTA ACUST UNITED AC 2021. [DOI: 10.1007/s43393-021-00028-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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7
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Kryukov VY, Kosman E, Tomilova O, Polenogova O, Rotskaya U, Tyurin M, Alikina T, Yaroslavtseva O, Kabilov M, Glupov V. Interplay between Fungal Infection and Bacterial Associates in the Wax Moth Galleria mellonella under Different Temperature Conditions. J Fungi (Basel) 2020; 6:E170. [PMID: 32927906 PMCID: PMC7558722 DOI: 10.3390/jof6030170] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 12/22/2022] Open
Abstract
Various insect bacterial associates are involved in pathogeneses caused by entomopathogenic fungi. The outcome of infection (fungal growth or decomposition) may depend on environmental factors such as temperature. The aim of this study was to analyze the bacterial communities and immune response of Galleria mellonella larvae injected with Cordyceps militaris and incubated at 15 °C and 25 °C. We examined changes in the bacterial CFUs, bacterial communities (Illumina MiSeq 16S rRNA gene sequencing) and expression of immune, apoptosis, ROS and stress-related genes (qPCR) in larval tissues in response to fungal infection at the mentioned temperatures. Increased survival of larvae after C. militaris injection was observed at 25 °C, although more frequent episodes of spontaneous bacteriosis were observed at this temperature compared to 15 °C. We revealed an increase in the abundance of enterococci and enterobacteria in the midgut and hemolymph in response to infection at 25 °C, which was not observed at 15 °C. Antifungal peptide genes showed the highest expression at 25 °C, while antibacterial peptides and inhibitor of apoptosis genes were strongly expressed at 15 °C. Cultivable bacteria significantly suppressed the growth of C. militaris. We suggest that fungi such as C. militaris may need low temperatures to avoid competition with host bacterial associates.
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Affiliation(s)
- Vadim Yu Kryukov
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
| | - Elena Kosman
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
| | - Oksana Tomilova
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
| | - Olga Polenogova
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
| | - Ulyana Rotskaya
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
| | - Maksim Tyurin
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
| | - Tatyana Alikina
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (T.A.); (M.K.)
| | - Olga Yaroslavtseva
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
| | - Marsel Kabilov
- Institute of Chemical Biology and Fundamental Medicine SB RAS, Lavrentiev av. 8, 630090 Novosibirsk, Russia; (T.A.); (M.K.)
| | - Viktor Glupov
- Institute of Systematics and Ecology of Animals SB RAS, Frunze str. 11, 630091 Novosibirsk, Russia; (E.K.); (O.T.); (O.P.); (U.R.); (M.T.); (O.Y.); (V.G.)
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8
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Azizoglu U, Jouzani GS, Yilmaz N, Baz E, Ozkok D. Genetically modified entomopathogenic bacteria, recent developments, benefits and impacts: A review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 734:139169. [PMID: 32460068 DOI: 10.1016/j.scitotenv.2020.139169] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/10/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023]
Abstract
Entomopathogenic bacteria (EPBs), insect pathogens that produce pest-specific toxins, are environmentally-friendly alternatives to chemical insecticides. However, the most important problem with EPBs application is their limited field stability. Moreover, environmental factors such as solar radiation, leaf temperature, and vapor pressure can affect the pathogenicity of these pathogens and their toxins. Scientists have conducted intensive research to overcome such problems. Genetic engineering has great potential for the development of new engineered entomopathogens with more resistance to adverse environmental factors. Genetically modified entomopathogenic bacteria (GM-EPBs) have many advantages over wild EPBs, such as higher pathogenicity, lower spraying requirements and longer-term persistence. Genetic manipulations have been mostly applied to members of the bacterial genera Bacillus, Lysinibacillus, Pseudomonas, Serratia, Photorhabdus and Xenorhabdus. Although many researchers have found that GM-EPBs can be used safely as plant protection bioproducts, limited attention has been paid to their potential ecological impacts. The main concerns about GM-EPBs and their products are their potential unintended effects on beneficial insects (predators, parasitoids, pollinators, etc.) and rhizospheric bacteria. This review address recent update on the significant role of GM-EPBs in biological control, examining them through different perspectives in an attempt to generate critical discussion and aid in the understanding of their potential ecological impacts.
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Affiliation(s)
- Ugur Azizoglu
- Department of Crop and Animal Production, Safiye Cikrikcioglu Vocational College, Kayseri University, Kayseri, Turkey.
| | - Gholamreza Salehi Jouzani
- Microbial Biotechnology Department, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Nihat Yilmaz
- Department of Crop and Animal Production, Safiye Cikrikcioglu Vocational College, Kayseri University, Kayseri, Turkey
| | - Ethem Baz
- Laboratory and Veterinary Health Department, Safiye Cikrikcioglu Vocational College, Kayseri University, Kayseri, Turkey
| | - Duran Ozkok
- Department of Crop and Animal Production, Safiye Cikrikcioglu Vocational College, Kayseri University, Kayseri, Turkey
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9
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Panjiar N, Mattam AJ, Jose S, Gandham S, Velankar HR. Valorization of xylose-rich hydrolysate from rice straw, an agroresidue, through biosurfactant production by the soil bacterium Serratia nematodiphila. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 729:138933. [PMID: 32371209 DOI: 10.1016/j.scitotenv.2020.138933] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 05/26/2023]
Abstract
Biosurfactants, amphiphilic compounds that reduce interfacial tension in oil-aqueous mixtures, are used in the petroleum, pharmaceutical, food, and agriculture industries. Fermentative production of biosurfactants requires expensive sugar or lipid substrates. Lignocellulosic biomass is a relatively cheap and abundant agricultural residue that can be used as an alternative substrate. Currently, several million tonnes of rice and wheat straw are generated globally as agricultural residues, most of which is disposed by open-field burning thereby leading to severe environmental pollution. This study aimed to produce biosurfactants in xylose-rich hydrolysates generated from rice straw. The hydrolysate is also a byproduct of 2G biofuel processes that often goes underutilized. A soil bacterium capable of growing and producing biosurfactants in rice straw hydrolysates, which typically contain growth-inhibitory compounds such as furfural and hydroxymethyl furfural, was isolated. Interestingly, the organism, identified as Serratia nematodiphila, exhibited higher glycolipid formation (4.5 ± 0.6 gL-1) in xylose-rich hydrolysate than in glucose-rich enzymatic hydrolysate (3.1 ± 0.2 gL-1) despite the higher bacterial cell density observed with the latter. The biosurfactants were thermostable and possessed promising emulsifying property and anti-microbial activity against bacteria and yeast. Further optimization of C:N resulted in a 2.8-fold increase in glycolipid production from xylose-rich hydrolysates. This study demonstrates the production of glycolipid biosurfactants from lignocellulosic biomass, a low-cost substrate and offers a plausible strategy for the management of these residues. Further, it also provides insights into the generation of additional high-value compounds in a bioethanol biorefinery to improve its commercial feasibility.
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Affiliation(s)
- Neha Panjiar
- Hindustan Petroleum Green R&D Centre, KIADB Industrial Area, Tarabanahalli, Devanagonthi, Hoskote, Bengaluru 560067, India
| | - Anu Jose Mattam
- Hindustan Petroleum Green R&D Centre, KIADB Industrial Area, Tarabanahalli, Devanagonthi, Hoskote, Bengaluru 560067, India
| | - Steffi Jose
- Hindustan Petroleum Green R&D Centre, KIADB Industrial Area, Tarabanahalli, Devanagonthi, Hoskote, Bengaluru 560067, India
| | - Sriganesh Gandham
- Hindustan Petroleum Green R&D Centre, KIADB Industrial Area, Tarabanahalli, Devanagonthi, Hoskote, Bengaluru 560067, India
| | - Harshad Ravindra Velankar
- Hindustan Petroleum Green R&D Centre, KIADB Industrial Area, Tarabanahalli, Devanagonthi, Hoskote, Bengaluru 560067, India.
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10
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Zhang Y, Shang R, Zhang J, Li J, Zhu G, Yao M, Sun J, Shen Z. Isolation and identification of two Serratia marcescens strains from silkworm, Bombyx mori. Antonie van Leeuwenhoek 2020; 113:1313-1321. [PMID: 32607923 DOI: 10.1007/s10482-020-01442-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 06/22/2020] [Indexed: 10/24/2022]
Abstract
Bacterial septicemia commonly occurs and usually cause huge losses in sericulture industry. Here, two pathogenic bacterial strains were isolated from dead silkworm and named as ZJ-1 and ZJ-2. Phenotypic and genotypic analysis results revealed that both of these two strains are closely related to Serratia marcescens (S. marcescens). The morphological as well as physiological and biochemical characteristics of ZJ-1 were accordant with S. marcescens mentioned in Bergey's manual of determinative bacteriology, whereas ZJ-2 showed some discrepancies such as the utilization of malonate and starch, fermentation of maltose and sucrose, and tests of urease, etc. Surprisingly, ZJ-2 could produce red pigment at high temperature (37°) but ZJ-1 could not. Besides, by analyzing the lethal concentration 50 (LC50) of ZJ-1 and ZJ-2, it was found that the virulence of ZJ-2 was lower than that of ZJ-1. These results revealed that ZJ-1 and ZJ-2 were two different strains of S. marcescens and that ZJ-2 was expected to be a safe (low-toxicity) and efficient strain for the production of red pigment. Nonetheless, further research in molecular level is needed to understand the regulation mechanism of pigment production and infection of ZJ-2.
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Affiliation(s)
- Yiling Zhang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China.,The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212021, China.,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang, 212021, China.,Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163, China
| | - Ruisha Shang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China
| | - Jiao Zhang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China
| | - Junhao Li
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China
| | - Guanyu Zhu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China
| | - Mingshuai Yao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China
| | - Jiancheng Sun
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China
| | - Zhongyuan Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 212021, China. .,The Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, 212021, China. .,Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agriculture and Rural Affairs, Zhenjiang, 212021, China.
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11
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Gilbert R, Torres M, Clemens R, Hateley S, Hosamani R, Wade W, Bhattacharya S. Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model. NPJ Microgravity 2020; 6:4. [PMID: 32047838 PMCID: PMC7000411 DOI: 10.1038/s41526-019-0091-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 11/21/2019] [Indexed: 12/14/2022] Open
Abstract
While it has been shown that astronauts suffer immune disorders after spaceflight, the underlying causes are still poorly understood and there are many variables to consider when investigating the immune system in a complex environment. Additionally, there is growing evidence that suggests that not only is the immune system being altered, but the pathogens that infect the host are significantly influenced by spaceflight and ground-based spaceflight conditions. In this study, we demonstrate that Serratia marcescens (strain Db11) was significantly more lethal to Drosophila melanogaster after growth on the International Space Station than ground-based controls, but the increased virulence phenotype of S. marcescens did not persist after the bacterial cultures were passaged on the ground. Increased virulence was also observed in bacteria that were grown in simulated microgravity conditions on the ground using the rotating wall vessel. Increased virulence of the space-flown bacteria was similar in magnitude between wild-type flies and those that were mutants for the well-characterized immune pathways Imd and Toll, suggesting that changes to the host immune system after infection are likely not a major factor contributing towards increased susceptibility of ground-reared flies infected with space-flown bacteria. Characterization of the bacteria shows that at later timepoints spaceflight bacteria grew at a greater rate than ground controls in vitro, and in the host. These results suggest complex physiological changes occurring in pathogenic bacteria in space environments, and there may be novel mechanisms mediating these physiological effects that need to be characterized.
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Affiliation(s)
- Rachel Gilbert
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA USA
| | - Medaya Torres
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
| | - Rachel Clemens
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
| | - Shannon Hateley
- 3Department of Molecular and Cell Biology, University of California, Berkeley, CA USA
| | - Ravikumar Hosamani
- NASA Postdoctoral Program, Universities Space Research Association, NASA Ames Research Center, Moffett Field, CA USA
| | - William Wade
- 2FILMSS/Bionetics, NASA Ames Research Center, Moffett Field, CA USA
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12
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Sánchez-Cruz R, Tpia Vázquez I, Batista-García RA, Méndez-Santiago EW, Sánchez-Carbente MDR, Leija A, Lira-Ruan V, Hernández G, Wong-Villarreal A, Folch-Mallol JL. Isolation and characterization of endophytes from nodules of Mimosa pudica with biotechnological potential. Microbiol Res 2018; 218:76-86. [PMID: 30454661 DOI: 10.1016/j.micres.2018.09.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 09/20/2018] [Accepted: 09/28/2018] [Indexed: 02/04/2023]
Abstract
Legumes establish symbiotic relationships with different microorganisms, which could function as plant growth promotion microorganisms (PGPM). The finding of new PGPM strains is important to increase plant production avoiding or diminishing the use of industrial fertilizers. Thus, in this work we evaluated the plant growth promotion traits of ten strains isolated from Mimosa pudica root nodules. According to the 16S rDNA sequence, the microorganisms were identified as Enterobacter sp. and Serratia sp. To the best of our knowledge this is the first report describing and endophytic interaction between Mimosa pudica and Enterobacter sp. These strains have some plant growth promoting traits such as phosphate solubilization, auxin production and cellulase and chitinase activity. Strains identified as Serratia sp. inhibited the growth of the phytopathogenic fungi Fusarium sp., and Alternaria solani and the oomycete Phytophthora capsici. According to their biochemical characteristics, three strains were selected to test their plant growth promoting activity in a medium with an insoluble phosphate source. These bacteria show low specificity for their hosts as endophytes, since they were able to colonize two very different legumes: Phaseolus vulgaris and M. pudica. Seedlings of P. vulgaris were inoculated and grown for fifteen days. Enterobacter sp. NOD1 and NOD10, promoted growth as reflected by an increase in shoot height as well as an increase in the size and emergence of the first two trifolia. We could localize NOD5 as an endophyte in roots in P. vulgaris by transforming the strain with a Green Fluorescent Protein carrying plasmid. Experiments of co-inoculation with different Rhizobium etli strains allowed us to discard that NOD5 can fix nitrogen in the nodules formed by a R. etli Fix- strain. The isolates described in this work show biotechnological potential for plant growth promoting activity and production of indoleacetic acid and siderophores.
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Affiliation(s)
- Ricardo Sánchez-Cruz
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Irán Tpia Vázquez
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Ramón Alberto Batista-García
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | | | | | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Verónica Lira-Ruan
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico
| | - Gerogina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | - Jorge Luis Folch-Mallol
- Centro de Investigación en Biotecnología, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, Mexico.
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CpxR-Dependent Thermoregulation of Serratia marcescens PrtA Metalloprotease Expression and Its Contribution to Bacterial Biofilm Formation. J Bacteriol 2018; 200:JB.00006-18. [PMID: 29378892 DOI: 10.1128/jb.00006-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 01/20/2018] [Indexed: 12/19/2022] Open
Abstract
PrtA is the major secreted metalloprotease of Serratia marcescens Previous reports implicate PrtA in the pathogenic capacity of this bacterium. PrtA is also clinically used as a potent analgesic and anti-inflammatory drug, and its catalytic properties attract industrial interest. Comparatively, there is scarce knowledge about the mechanisms that physiologically govern PrtA expression in Serratia In this work, we demonstrate that PrtA production is derepressed when the bacterial growth temperature decreases from 37°C to 30°C. We show that this thermoregulation occurs at the transcriptional level. We determined that upstream of prtA, there is a conserved motif that is directly recognized by the CpxR transcriptional regulator. This feature is found along Serratia strains irrespective of their isolation source, suggesting an evolutionary conservation of CpxR-dependent regulation of PrtA expression. We found that in S. marcescens, the CpxAR system is more active at 37°C than at 30°C. In good agreement with these results, in a cpxR mutant background, prtA is derepressed at 37°C, while overexpression of the NlpE lipoprotein, a well-known CpxAR-inducing condition, inhibits PrtA expression, suggesting that the levels of the activated form of CpxR are increased at 37°C over those at 30°C. In addition, we establish that PrtA is involved in the ability of S. marcescens to develop biofilm. In accordance, CpxR influences the biofilm phenotype only when bacteria are grown at 37°C. In sum, our findings shed light on regulatory mechanisms that fine-tune PrtA expression and reveal a novel role for PrtA in the lifestyle of S. marcescensIMPORTANCE We demonstrate that S. marcescens metalloprotease PrtA expression is transcriptionally thermoregulated. While strongly activated below 30°C, its expression is downregulated at 37°C. We found that in S. marcescens, the CpxAR signal transduction system, which responds to envelope stress and bacterial surface adhesion, is activated at 37°C and able to downregulate PrtA expression by direct interaction of CpxR with a binding motif located upstream of the prtA gene. Moreover, we reveal that PrtA expression favors the ability of S. marcescens to develop biofilm, irrespective of the bacterial growth temperature. In this context, thermoregulation along with a highly conserved CpxR-dependent modulation mechanism gives clues about the relevance of PrtA as a factor implicated in the persistence of S. marcescens on abiotic surfaces and in bacterial host colonization capacity.
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Inactivation of the Major Hemolysin Gene Influences Expression of the Nonribosomal Peptide Synthetase Gene swrA in the Insect Pathogen Serratia sp. Strain SCBI. J Bacteriol 2017; 199:JB.00333-17. [PMID: 28784817 DOI: 10.1128/jb.00333-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 08/03/2017] [Indexed: 11/20/2022] Open
Abstract
Hemolysins are important virulence factors for many bacterial pathogens, including Serratia marcescens The role of the major hemolysin gene in the insect pathogen Serratia sp. strain SCBI was investigated using both forward and reverse-genetics approaches. Introduction of the major hemolysin gene into Escherichia coli resulted in a gain of both virulence and hemolytic activity. Inactivation of this hemolysin in Serratia sp. SCBI resulted in a loss of hemolysis but did not attenuate insecticidal activity. Unexpectedly, inactivation of the hemolysin gene in Serratia sp. SCBI resulted in significantly increased motility and increased antimicrobial activity. Reverse transcription-quantitative PCR (qRT-PCR) analysis of mutants with a disrupted hemolysin gene showed a dramatic increase in mRNA levels of a nonribosomal peptide synthetase gene, swrA, which produces the surfactant serrawettin W2. Mutation of the swrA gene in Serratia sp. SCBI resulted in highly varied antibiotic activity, motility, virulence, and hemolysis phenotypes that were dependent on the site of disruption within this 17.75-kb gene. When introduced into E. coli, swrA increases rates of motility and confers antimicrobial activity. While it is unclear how inactivation of the major hemolysin gene influences the expression of swrA, these results suggest that swrA plays an important role in motility and antimicrobial activity in Serratia sp. SCBI.IMPORTANCE The opportunistic Gram-negative bacteria of the genus Serratia are widespread in the environment and can cause human illness. A comparative genomics analysis between Serratia marcescens and a new Serratia species from South Africa, termed Serratia sp. strain SCBI, shows that these two organisms are closely related but differ in pathogenesis. S. marcescens kills Caenorhabditis nematodes, while Serratia sp. SCBI is not harmful and forms a beneficial association with them. This distinction presented the opportunity to investigate potential differences in regulation of common virulence mechanisms between these two species. With the emergence of antibiotic-resistant microorganisms, there is a widespread need to understand the regulation of pathogenesis. The significance of this study is the presentation of evidence for cross-pathway regulation of virulence factors and how the elimination of one mechanism may be compensated for by the upregulation of others.
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15
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Characterization of putative virulence factors of Serratia marcescens strain SEN for pathogenesis in Spodoptera litura. J Invertebr Pathol 2017; 143:115-123. [DOI: 10.1016/j.jip.2016.12.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/09/2016] [Accepted: 12/12/2016] [Indexed: 12/20/2022]
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16
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Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria. PLoS One 2016; 11:e0167752. [PMID: 28002470 PMCID: PMC5176276 DOI: 10.1371/journal.pone.0167752] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Accepted: 11/18/2016] [Indexed: 11/19/2022] Open
Abstract
Global loss of honey bee colonies is threatening the human food supply. Diverse pathogens reduce honey bee hardiness needed to sustain colonies, especially in winter. We isolated a free-living Gram negative bacillus from hemolymph of worker honey bees (Apis mellifera) found separated from winter clusters. In some hives, greater than 90% of the dying bees detached from the winter cluster were found to contain this bacterium in their hemolymph. Throughout the year, the same organism was rarely found in bees engaged in normal hive activities, but was detected in about half of Varroa destructor mites obtained from colonies that housed the septic bees. Flow cytometry of hemolymph from septic bees showed a significant reduction of plasmatocytes and other types of hemocytes. Interpretation of the16S rRNA sequence of the bacterium indicated that it belongs to the Serratia genus of Gram-negative Gammaproteobacteria, which has not previously been implicated as a pathogen of adult honey bees. Complete genome sequence analysis of the bacterium supported its classification as a novel strain of Serratia marcescens, which was designated as S. marcescens strain sicaria (Ss1). When compared with other strains of S. marcescens, Ss1 demonstrated several phenotypic and genetic differences, including 65 genes not previously found in other Serratia genomes. Some of the unique genes we identified in Ss1 were related to those from bacterial insect pathogens and commensals. Recovery of this organism extends a complex pathosphere of agents which may contribute to failure of honey bee colonies.
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Tetz G, Tetz V, Vecherkovskaya M. Genomic characterization and assessment of the virulence and antibiotic resistance of the novel species Paenibacillus sp. strain VT-400, a potentially pathogenic bacterium in the oral cavity of patients with hematological malignancies. Gut Pathog 2016; 8:6. [PMID: 26900405 PMCID: PMC4761199 DOI: 10.1186/s13099-016-0089-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 02/10/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Paenibacillus sp. strain VT-400, a novel spore-forming bacterium, was isolated from patients with hematological malignancies. METHODS Paenibacillus sp. strain VT-400 was isolated from the saliva of four children with acute lymphoblastic leukemia. The genome was annotated using RAST and the NCBI Prokaryotic Genome Annotation Pipeline to characterize features of antibiotic resistance and virulence factors. Susceptibility to antibiotics was determined by the Kirby-Bauer disc diffusion method. We used a mouse model of pneumonia to study virulence in vivo. Mice were challenged with 7.5 log10-9.5 log10 CFU, and survival was monitored over 7 days. Bacterial load was measured in the lungs and spleen of surviving mice 48 h post-infection to reveal bacterial invasion and dissemination. RESULTS Whole-genome sequencing revealed a large number of virulence factors such as hemolysin D and CD4+ T cell-stimulating antigen. Furthermore, the strain harbors numerous antibiotic resistance genes, including small multidrug resistance proteins, which have never been previously found in the Paenibacillus genus. We then compared the presence of antibiotic resistance genes against results from antibiotic susceptibility testing. Paenibacillus sp. strain VT-400 was found to be resistant to macrolides such as erythromycin and azithromycin, as well as to chloramphenicol and trimethoprim-sulphamethoxazole. Finally, the isolate caused mortality in mice infected with ≥8.5 log10 CFU. CONCLUSIONS Based on our results and on the available literature, there is yet no strong evidence that shows Paenibacillus species as an opportunistic pathogen in immunocompromised patients. However, the presence of spore-forming bacteria with virulence and antibiotic resistance genes in such patients warrants special attention because infections caused by spore-forming bacteria are poorly treatable.
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Affiliation(s)
- George Tetz
- Institute of Human Microbiology, LLC, 303 5th Avenue, Suite 2012, New York, NY 10016 USA
| | - Victor Tetz
- First State I. P. Pavlov Medical University, Lev Tolstoy Str. 6/8, Saint Petersburg, Russia 197022
| | - Maria Vecherkovskaya
- First State I. P. Pavlov Medical University, Lev Tolstoy Str. 6/8, Saint Petersburg, Russia 197022
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18
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Abebe-Akele F, Tisa LS, Cooper VS, Hatcher PJ, Abebe E, Thomas WK. Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae. BMC Genomics 2015; 16:531. [PMID: 26187596 PMCID: PMC4506600 DOI: 10.1186/s12864-015-1697-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Accepted: 06/12/2015] [Indexed: 12/21/2022] Open
Abstract
Background Entomopathogenic associations between nematodes in the genera Steinernema and Heterorhabdus with their cognate bacteria from the bacterial genera Xenorhabdus and Photorhabdus, respectively, are extensively studied for their potential as biological control agents against invasive insect species. These two highly coevolved associations were results of convergent evolution. Given the natural abundance of bacteria, nematodes and insects, it is surprising that only these two associations with no intermediate forms are widely studied in the entomopathogenic context. Discovering analogous systems involving novel bacterial and nematode species would shed light on the evolutionary processes involved in the transition from free living organisms to obligatory partners in entomopathogenicity. Results We report the complete genome sequence of a new member of the enterobacterial genus Serratia that forms a putative entomopathogenic complex with Caenorhabditis briggsae. Analysis of the 5.04 MB chromosomal genome predicts 4599 protein coding genes, seven sets of ribosomal RNA genes, 84 tRNA genes and a 64.8 KB plasmid encoding 74 genes. Comparative genomic analysis with three of the previously sequenced Serratia species, S. marcescens DB11 and S. proteamaculans 568, and Serratia sp. AS12, revealed that these four representatives of the genus share a core set of ~3100 genes and extensive structural conservation. The newly identified species shares a more recent common ancestor with S. marcescens with 99 % sequence identity in rDNA sequence and orthology across 85.6 % of predicted genes. Of the 39 genes/operons implicated in the virulence, symbiosis, recolonization, immune evasion and bioconversion, 21 (53.8 %) were present in Serratia while 33 (84.6 %) and 35 (89 %) were present in Xenorhabdus and Photorhabdus EPN bacteria respectively. Conclusion The majority of unique sequences in Serratia sp. SCBI (South African Caenorhabditis briggsae Isolate) are found in ~29 genomic islands of 5 to 65 genes and are enriched in putative functions that are biologically relevant to an entomopathogenic lifestyle, including non-ribosomal peptide synthetases, bacteriocins, fimbrial biogenesis, ushering proteins, toxins, secondary metabolite secretion and multiple drug resistance/efflux systems. By revealing the early stages of adaptation to this lifestyle, the Serratia sp. SCBI genome underscores the fact that in EPN formation the composite end result – killing, bioconversion, cadaver protection and recolonization- can be achieved by dissimilar mechanisms. This genome sequence will enable further study of the evolution of entomopathogenic nematode-bacteria complexes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1697-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Feseha Abebe-Akele
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA. .,Hubbard Center for Genome Studies, 444 Gregg Hall, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA.
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Vaughn S Cooper
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
| | - Philip J Hatcher
- Department of Computer Science, University of New Hampshire, Durham, NH, USA
| | - Eyualem Abebe
- Department of Biology, Elizabeth City State University, 1704 Weeksville Road, Jenkins Science Center 421, Elizabeth City, NC, 27909, USA
| | - W Kelley Thomas
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, USA.,Hubbard Center for Genome Studies, 444 Gregg Hall, University of New Hampshire, 35 Colovos Road, Durham, NH, 03824, USA
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Infection dynamic of symbiotic bacteria in the pea aphid Acyrthosiphon pisum gut and host immune response at the early steps in the infection process. PLoS One 2015; 10:e0122099. [PMID: 25811863 PMCID: PMC4374939 DOI: 10.1371/journal.pone.0122099] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 02/22/2015] [Indexed: 12/20/2022] Open
Abstract
In addition to its obligatory symbiont Buchnera aphidicola, the pea aphid Acyrthosiphon pisum can harbor several facultative bacterial symbionts which can be mutualistic in the context of various ecological interactions. Belonging to a genus where many members have been described as pathogen in invertebrates, Serratia symbiotica is one of the most common facultative partners found in aphids. The recent discovery of strains able to grow outside their host allowed us to simulate environmental acquisition of symbiotic bacteria by aphids. Here, we performed an experiment to characterize the A. pisum response to the ingestion of the free-living S. symbiotica CWBI-2.3T in comparison to the ingestion of the pathogenic Serratia marcescens Db11 at the early steps in the infection process. We found that, while S. marcescens Db11 killed the aphids within a few days, S. symbiotica CWBI-2.3T did not affect host survival and colonized the whole digestive tract within a few days. Gene expression analysis of immune genes suggests that S. symbiotica CWBI-2.3T did not trigger an immune reaction, while S. marcescens Db11 did, and supports the hypothesis of a fine-tuning of the host immune response set-up for fighting pathogens while maintaining mutualistic partners. Our results also suggest that the lysosomal system and the JNK pathway are possibly involved in the regulation of invasive bacteria in aphids and that the activation of the JNK pathway is IMD-independent in the pea aphid.
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Tsaplina O, Bozhokina E, Mardanova A, Khaitlina S. Virulence factors contributing to invasive activities of Serratia grimesii and Serratia proteamaculans. Arch Microbiol 2015; 197:481-8. [DOI: 10.1007/s00203-014-1079-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 12/26/2014] [Accepted: 12/30/2014] [Indexed: 11/28/2022]
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Kwak Y, Khan AR, Shin JH. Genome sequence of Serratia nematodiphila DSM 21420T, a symbiotic bacterium from entomopathogenic nematode. J Biotechnol 2014; 193:1-2. [PMID: 25444874 DOI: 10.1016/j.jbiotec.2014.11.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 11/03/2014] [Indexed: 01/12/2023]
Abstract
Serratia nematodiphila DSM 21420(T) (=CGMCC 1.6853(T), DZ0503SBS1(T)), isolated from the intestine of Heterorhabditidoides chongmingensis, has been known to have symbiotic-pathogenic life cycle, on the multilateral relationships with entomopathogenic nematode and insect pest. In order to better understanding of this rare feature in Serratia species, we present here the genome sequence of S. nematodiphila DSM 21420(T) with the significance of first genome sequence in this species.
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Affiliation(s)
- Yunyoung Kwak
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Abdur Rahim Khan
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea
| | - Jae-Ho Shin
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 702-701, Republic of Korea.
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Petersen LM, Tisa LS. Molecular characterization of protease activity in Serratia sp. strain SCBI and its importance in cytotoxicity and virulence. J Bacteriol 2014; 196:3923-36. [PMID: 25182493 PMCID: PMC4248818 DOI: 10.1128/jb.01908-14] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 08/26/2014] [Indexed: 01/19/2023] Open
Abstract
A newly recognized Serratia species, termed South African Caenorhabditis briggsae isolate (SCBI), is both a mutualist of the nematode Caenorhabditis briggsae KT0001 and a pathogen of lepidopteran insects. Serratia sp. strain SCBI displays high proteolytic activity, and because secreted proteases are known virulence factors for many pathogens, the purpose of this study was to identify genes essential for extracellular protease activity in Serratia sp. strain SCBI and to determine what role proteases play in insect pathogenesis and cytotoxicity. A bank of 2,100 transposon mutants was generated, and six SCBI mutants with defective proteolytic activity were identified. These mutants were also defective in cytotoxicity. The mutants were found defective in genes encoding the following proteins: alkaline metalloprotease secretion protein AprE, a BglB family transcriptional antiterminator, an inosine/xanthosine triphosphatase, GidA, a methyl-accepting chemotaxis protein, and a PIN domain protein. Gene expression analysis on these six mutants showed significant downregulation in mRNA levels of several different types of predicted protease genes. In addition, transcriptome sequencing (RNA-seq) analysis provided insight into how inactivation of AprE, GidA, and a PIN domain protein influences motility and virulence, as well as protease activity. Using quantitative reverse transcription-PCR (qRT-PCR) to further characterize expression of predicted protease genes in wild-type Serratia sp. SCBI, the highest mRNA levels for the alkaline metalloprotease genes (termed prtA1 to prtA4) occurred following the death of an insect host, while two serine protease and two metalloprotease genes had their highest mRNA levels during active infection. Overall, these results indicate that proteolytic activity is essential for cytotoxicity in Serratia sp. SCBI and that its regulation appears to be highly complex.
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Affiliation(s)
- Lauren M Petersen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
| | - Louis S Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA
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Mikonranta L, Mappes J, Kaukoniitty M, Freitak D. Insect immunity: oral exposure to a bacterial pathogen elicits free radical response and protects from a recurring infection. Front Zool 2014; 11:23. [PMID: 24602309 PMCID: PMC3975449 DOI: 10.1186/1742-9994-11-23] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 03/03/2014] [Indexed: 12/04/2022] Open
Abstract
Background Previous exposure to a pathogen can help organisms cope with recurring infection. This is widely recognised in vertebrates, but increasing occasions are also being reported in invertebrates where this phenomenon is referred to as immune priming. However, the mechanisms that allow acquired pathogen resistance in insects remain largely unknown. Results We studied the priming of bacterial resistance in the larvae of the tiger moth, Parasemia plantaginis using two gram-negative bacteria, a pathogenic Serratia marcescens and a non-pathogenic control, Escherichia coli. A sublethal oral dose of S. marcescens provided the larvae with effective protection against an otherwise lethal septic infection with the same pathogen five days later. At the same time, we assessed three anti-bacterial defence mechanisms from the larvae that had been primarily exposed to the bacteria via contaminated host plant. Results showed that S. marcescens had induced a higher amount of reactive oxygen species (ROS) in the larval haemolymph, possibly protecting the host from the recurring infection. Conclusions Our study supports the growing evidence of immune priming in insects. It shows that activation of the protective mechanism requires a specific induction, rather than a sheer exposure to any gram-negative bacteria. The findings indicate that systemic pathogen recognition happens via the gut, and suggest that persistent loitering of immune elicitors or anti-microbial molecules are a possible mechanism for the observed prophylaxis. The self-harming effects of ROS molecules are well known, which indicates a potential cost of increased resistance. Together these findings could have important implications on the ecological and epidemiological processes affecting insect and pathogen populations.
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Affiliation(s)
- Lauri Mikonranta
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, University of Jyväskylä, P,O, Box 35, Jyväskylä FI-40014, Finland.
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Petersen LM, Tisa LS. Friend or foe? A review of the mechanisms that driveSerratiatowards diverse lifestyles. Can J Microbiol 2013; 59:627-40. [DOI: 10.1139/cjm-2013-0343] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Found widespread around the globe, Serratia are Gram-negative bacteria capable of thriving in a diverse number of environments that include water, soil, and the digestive tracts of various animals. Known for their ability to produce a myriad of extracellular enzymes, these bacteria also produce various secondary metabolites that directly contribute to their survival. While the effects Serratia species have on other organisms range from parasitic to symbiotic, what these bacteria have in common is their ability to resist attack, respond appropriately to environmental conditions, and outcompete other microorganisms when colonizing their respective niche. This review highlights the mechanisms utilized by Serratia species that drive their ubiquitous nature, with emphasis on the latest findings. Also discussed is how secreted compounds drive these bacteria towards pathogenic, mutualistic, and antagonistic associations.
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Affiliation(s)
- Lauren M. Petersen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
| | - Louis S. Tisa
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, 46 College Road, Durham, NH 03824-2617, USA
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