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Yang HW, Thapa R, Johnson K, DuPont ST, Khan A, Zhao Y. Examination of Large Chromosomal Inversions in the Genome of Erwinia amylovora Strains Reveals Worldwide Distribution and North America-Specific Types. PHYTOPATHOLOGY 2023; 113:2174-2186. [PMID: 36935376 DOI: 10.1094/phyto-01-23-0004-sa] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Erwinia amylovora is a relatively homogeneous species with low genetic diversity at the nucleotide level. However, phenotypic differences and genomic structural variations among E. amylovora strains have been documented. In this study, we identified 10 large chromosomal inversion (LCI) types in the Spiraeoideae-infecting (SI) E. amylovora strains by combining whole genome sequencing and PCR-based molecular markers. It was found that LCIs were mainly caused by homologous recombination events among seven rRNA operons (rrns) in SI E. amylovora strains. Although ribotyping results identified inter- and intra-variations in the internal transcribed spacer (ITS1 and ITS2) regions among rrns, LCIs tend to occur between rrns transcribed in the opposite directions and with the same tRNA content (tRNA-Glu or tRNA-Ile/Ala) in ITS1. Based on the LCI types, physical/estimated replichore imbalance (PRI/ERI) was examined and calculated. Among the 117 SI strains evaluated, the LCI types of Ea1189, CFBP1430, and Ea273 were the most common, with ERI values at 1.31, 7.87, and 4.47°, respectively. These three LCI types had worldwide distribution, whereas the remaining seven LCI types were restricted to North America (or certain regions of the United States). Our results indicated ongoing chromosomal recombination events in the SI E. amylovora population and showed that LCI events are mostly symmetrical, keeping the ERI less than 15°. These findings provide initial evidence about the prevalence of certain LCI types in E. amylovora strains, how LCI occurs, and its potential evolutionary advantage and history, which might help track the movement of the pathogen.
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Affiliation(s)
- Ho-Wen Yang
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
| | - Ranjita Thapa
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Kenneth Johnson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | | | - Awais Khan
- School of Integrative Plant Science Plant Pathology and Plant-Microbe Biology, Cornell University, Geneva, NY 14456
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802
- Department of Plant Pathology, WSU-IAREC, Prosser, WA 99350
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Yuan X, Eldred LI, Sundin GW. Exopolysaccharides amylovoran and levan contribute to sliding motility in the fire blight pathogen Erwinia amylovora. Environ Microbiol 2022; 24:4738-4754. [PMID: 36054324 PMCID: PMC9826367 DOI: 10.1111/1462-2920.16193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 08/31/2022] [Indexed: 01/11/2023]
Abstract
Erwinia amylovora, the causative agent of fire blight, uses flagella-based motilities to translocate to host plant natural openings; however, little is known about how this bacterium migrates systemically in the apoplast. Here, we reveal a novel surface motility mechanism, defined as sliding, in E. amylovora. Deletion of flagella assembly genes did not affect this movement, whereas deletion of biosynthesis genes for the exopolysaccharides (EPSs) amylovoran and levan resulted in non-sliding phenotypes. Since EPS production generates osmotic pressure that potentially powers sliding, we validated this mechanism by demonstrating that water potential positively contributes to sliding. In addition, no sliding was observed when the water potential of the surface was lower than -0.5 MPa. Sliding is a passive motility mechanism. We further show that the force of gravity plays a critical role in directing E. amylovora sliding on unconfined surfaces but has a negligible effect when cells are sliding in confined microcapillaries, in which EPS-dependent osmotic pressure acts as the main force. Although amylovoran and levan are both required for sliding, we demonstrate that they exhibit different roles in bacterial communities. In summary, our study provides fundamental knowledge for a better understanding of mechanisms that drive bacterial sliding motility.
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Affiliation(s)
- Xiaochen Yuan
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - Lauren I. Eldred
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
| | - George W. Sundin
- Department of Plant, Soil, and Microbial SciencesMichigan State UniversityEast LansingMichiganUSA
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Yuan X, Hulin MT, Sundin GW. Effectors, chaperones, and harpins of the Type III secretion system in the fire blight pathogen Erwinia amylovora: a review. JOURNAL OF PLANT PATHOLOGY 2021; 103:25-39. [PMID: 0 DOI: 10.1007/s42161-020-00623-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/23/2020] [Indexed: 05/20/2023]
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Ma R, Lai J, Chen X, Wang L, Yang Y, Wei S, Jiao N, Zhang R. A Novel Phage Infecting Alteromonas Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs. mSphere 2021; 6:e0045421. [PMID: 34106770 PMCID: PMC8265664 DOI: 10.1128/msphere.00454-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages play critical roles in impacting microbial community succession both ecologically and evolutionarily. Although the majority of phage genetic diversity has been increasingly unveiled, phages infecting members of the ecologically important genus Alteromonas remain poorly understood. Here, we present a comprehensive analysis of a newly isolated alterophage, vB_AcoS-R7M (R7M), to characterize its life cycle traits, genomic features, and putative evolutionary origin. R7M harbors abundant genes identified as host-like auxiliary metabolic genes facilitating viral propagation. Genomic analysis suggested that R7M is distinct from currently known alterophages. Interestingly, R7M was found to share a set of similar characteristics with a number of siphophages infecting diverse aquatic opportunistic copiotrophs. We therefore proposed the creation of one new subfamily (Queuovirinae) to group with these evolutionarily related phages. Notably, tail genes were less likely to be shared among them, and baseplate-related genes varied the most. In-depth analyses indicated that R7M has replaced its distal tail with a Rhodobacter capsulatus gene transfer agent (RcGTA)-like baseplate and further acquired a putative receptor interaction site targeting Alteromonas. These findings suggest that horizontal exchanges of viral tail adsorption apparatuses are widespread and vital for phages to hunt new hosts and to adapt to new niches. IMPORTANCE The evolution and ecology of phages infecting members of Alteromonas, a marine opportunistic genus that is widely distributed and of great ecological significance, remain poorly understood. The present study integrates physiological and genomic evidence to characterize the properties and putative phage-host interactions of a newly isolated Alteromonas phage, vB_AcoS-R7M (R7M). A taxonomic study reveals close evolutionary relationships among R7M and a number of siphophages infecting various aquatic copiotrophs. Their similar head morphology and overall genetic framework suggest their putative common ancestry and the grouping of a new viral subfamily. However, their major difference lies in the viral tail adsorption apparatuses and the horizontal exchanges of which possibly account for variations in host specificity. These findings outline an evolutionary scenario for the emergence of diverse viral lineages of a shared genetic pool and give insights into the genetics and ecology of viral host jumps.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Jiayong Lai
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yahui Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Song JY, Yun YH, Kim GD, Kim SH, Lee SJ, Kim JF. Genome Analysis of Erwinia amylovora Strains Responsible for a Fire Blight Outbreak in Korea. PLANT DISEASE 2021; 105:1143-1152. [PMID: 32931384 DOI: 10.1094/pdis-06-20-1329-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Erwinia amylovora is a plant-pathogenic bacterium that causes fire blight disease in Rosaceae plants. Since fire blight is highly contagious and results in serious losses once introduced, it is regulated as a quarantine disease. Recently, for the first time in East Asia, fire blight emerged in Korea with strains of E. amylovora being isolated from lesions of infected trees. Five of those strains were selected and subjected to whole-genome shotgun sequencing. Each strain had two circular replicons, a 3.8-Mb chromosome and a 28-kb plasmid. The genome sequences were compared with those of other E. amylovora strains isolated from different hosts or geographical regions. Genome synteny was analyzed and sequence variations including nucleotide substitutions, inversions, insertions, and deletions were detected. Analysis of the population genomic structure revealed that the five strains form a distinct structural group. Phylogenomic analysis was performed to infer the evolutionary relationships among E. amylovora strains, which indicated that the Korean isolates, all descended from a common ancestor, are closely related to a lineage of North American strains. These results provide useful information for understanding the genomic dynamics of E. amylovora strains including those in Korea, developing genetic markers for surveillance of the pathogen or diagnosis of the disease, and eventually developing measures to eradicate it.
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Affiliation(s)
- Ju Yeon Song
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
| | - Yeo Hong Yun
- Department of Microbiology and Institute for Biodiversity, Dankook University, Dongnam-gu, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Gi-Don Kim
- Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Seong Hwan Kim
- Department of Microbiology and Institute for Biodiversity, Dankook University, Dongnam-gu, Cheonan-si, Chungcheongnam-do 31116, Republic of Korea
| | - Seong-Jin Lee
- Animal and Plant Quarantine Agency, Gimcheon-si, Gyeongsangbuk-do 39660, Republic of Korea
| | - Jihyun F Kim
- Department of Systems Biology, Division of Life Sciences, and Institute for Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
- Strategic Initiative for Microbiomes in Agriculture and Food, Yonsei University, Seodaemun-gu, Seoul 03722, Republic of Korea
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Akremi I, Holtappels D, Brabra W, Jlidi M, Hadj Ibrahim A, Ben Ali M, Fortuna K, Ahmed M, Meerbeek BV, Rhouma A, Lavigne R, Ben Ali M, Wagemans J. First Report of Filamentous Phages Isolated from Tunisian Orchards to Control Erwinia amylovora. Microorganisms 2020; 8:microorganisms8111762. [PMID: 33182526 PMCID: PMC7697814 DOI: 10.3390/microorganisms8111762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 10/20/2020] [Accepted: 10/22/2020] [Indexed: 01/28/2023] Open
Abstract
Newly discovered Erwinia amylovora phages PEar1, PEar2, PEar4 and PEar6 were isolated from three different orchards in North Tunisia to study their potential as biocontrol agents. Illumina sequencing revealed that the PEar viruses carry a single-strand DNA genome between 6608 and 6801 nucleotides and belong to the Inoviridae, making them the first described filamentous phages of E. amylovora. Interestingly, phage-infected cells show a decreased swimming and swarming motility and a cocktail of the four phages can significantly reduce infection of E. amylovora in a pear bioassay, potentially making them suitable candidates for phage biocontrol.
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Affiliation(s)
- Ismahen Akremi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Dominique Holtappels
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Wided Brabra
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Mouna Jlidi
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
| | - Adel Hadj Ibrahim
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
| | - Manel Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Kiandro Fortuna
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Mohammed Ahmed
- Biomaterials Research Group (BIOMAT), Department of Oral Sciences, KU Leuven, Kapucijnenvoer 7-Block A Box 7001, 3000 Leuven, Belgium; (M.A.); (B.V.M.)
- Department of Dental Biomaterials, Tanta University, Biomedical Campus, 32511 Tanta, Gharbia Governorate, Egypt
| | - Bart Van Meerbeek
- Biomaterials Research Group (BIOMAT), Department of Oral Sciences, KU Leuven, Kapucijnenvoer 7-Block A Box 7001, 3000 Leuven, Belgium; (M.A.); (B.V.M.)
| | - Ali Rhouma
- Laboratory of Integrated Olive Production, Olive Tree Institute, BP208 Marhajene City, Tunis 1082, Tunisia;
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
| | - Mamdouh Ben Ali
- Laboratory of Microbial Biotechnology, Enzymatics and Biomolecules (LBMEB), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia; (I.A.); (W.B.); (M.J.); (A.H.I.); (M.B.A.); (M.B.A.)
- Astrum Biotech, Business Incubator, Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour km 6, P.O. Box 1177, Sfax 3018, Tunisia
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21-Box 2462, 3001 Leuven, Belgium; (D.H.); (K.F.); (R.L.)
- Correspondence: ; Tel.: +32-1637-4622
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Van de Vondel J, Lambrecht MA, Delcour JA. Osborne extractability and chromatographic separation of protein from quinoa (Chenopodium quinoa Willd.) wholemeal. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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8
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Xu J, Li X, Kang G, Bai L, Wang P, Huang H. Isolation and Characterization of AbTJ, an Acinetobacter baumannii Phage, and Functional Identification of Its Receptor-Binding Modules. Viruses 2020; 12:v12020205. [PMID: 32059512 PMCID: PMC7077233 DOI: 10.3390/v12020205] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 12/29/2022] Open
Abstract
A. baumannii is an opportunistic pathogen and a major cause of various community-acquired infections. Strains of this species can be resistant to multiple antimicrobial agents, leaving limited therapeutic options, also lacking in methods for accurate and prompt diagnosis. In this context, AbTJ, a novel phage that infects A. baumannii MDR-TJ, was isolated and characterized, together with its two tail fiber proteins. Morphological analysis revealed that it belongs to Podoviridae family. Its host range, growth characteristics, stability under various conditions, and genomic sequence, were systematically investigated. Bioinformatic analysis showed that AbTJ consists of a circular, double-stranded 42670-bp DNA molecule which contains 62 putative open reading frames (ORFs). Genome comparison revealed that the phage AbTJ is related to the Acinetobacter phage Ab105-1phi (No. KT588074). Tail fiber protein (TFPs) gp52 and gp53 were then identified and confirmed as species-specific proteins. By using a combination of bioluminescent methods and magnetic beads, these TFPs exhibit excellent specificity to detect A. baumannii. The findings of this study can be used to help control opportunistic infections and to provide pathogen-binding modules for further construction of engineered bacteria of diagnosis and treatment.
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Affiliation(s)
- Jingzhi Xu
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Xiaobo Li
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin 300392, China
| | - Guangbo Kang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Liang Bai
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Ping Wang
- Tianjin Modern Innovative TCM Technology Co. Ltd., Tianjin 300392, China
- Correspondence: (P.W.); (H.H.); Tel.: +86-22-6031-8081 (P.W.); +86-22-2740-3389 (H.H.)
| | - He Huang
- Department of Biochemical Engineering, School of Chemical Engineering & Technology, Tianjin University, Tianjin 300350, China; (J.X.); (X.L.); (G.K.); (L.B.)
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Correspondence: (P.W.); (H.H.); Tel.: +86-22-6031-8081 (P.W.); +86-22-2740-3389 (H.H.)
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9
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Leathers TD, Saunders LP, Bowman MJ, Price NPJ, Bischoff KM, Rich JO, Skory CD, Nunnally MS. Inhibition of Erwinia amylovora by Bacillus nakamurai. Curr Microbiol 2020; 77:875-881. [PMID: 31938805 DOI: 10.1007/s00284-019-01845-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 12/11/2019] [Indexed: 11/29/2022]
Abstract
A variety of potential inhibitors were tested for the first time for the suppression of Erwinia amylovora, the causal agent of fire blight in apples and pears. Strain variability was evident in susceptibility to inhibitors among five independently isolated virulent strains of E. amylovora. However, most strains were susceptible to culture supernatants from strains of Bacillus spp., and particularly to the recently described species B. nakamurai. Minimal inhibitory concentrations (MICs) were 5-20% (vol/vol) of culture supernatant from B. nakamurai against all five strains of E. amylovora. Although Bacillus species have been previously reported to produce lipopeptide inhibitors of E. amylovora, matrix-assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) and column chromatography indicated that the inhibitor from B. nakamurai was not a lipopeptide, but rather a novel inhibitor.
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Affiliation(s)
- Timothy D Leathers
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA.
| | - Lauren P Saunders
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA
| | - Michael J Bowman
- Bioenergy Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA
| | - Neil P J Price
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA
| | - Kenneth M Bischoff
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA
| | - Joseph O Rich
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA
| | - Christopher D Skory
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA
| | - Melinda S Nunnally
- Renewable Product Technology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, U.S. Department of Agriculture, 1815 North University Street, Peoria, IL, 61604, USA
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10
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Feyereisen M, Mahony J, Neve H, Franz CMAP, Noben JP, O’Sullivan T, Boer V, van Sinderen D. Biodiversity and Classification of Phages Infecting Lactobacillus brevis. Front Microbiol 2019; 10:2396. [PMID: 31681247 PMCID: PMC6805780 DOI: 10.3389/fmicb.2019.02396] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/03/2019] [Indexed: 11/13/2022] Open
Abstract
Lactobacillus brevis is a lactic acid bacterium that is known as a food and beverage spoilage organism, and more specifically as a beer-spoiler. Phages of L. brevis have been described, but very limited data is available regarding temperate phages of L. brevis. Temperate phages may exert benefits to the host, while they may also be employed to combat beer spoilage. The current study reports on the incidence of prophage sequences present in nineteen distinct L. brevis genomes. Prophage induction was evaluated using mitomycin C exposure followed by genome targeted-PCR, electron microscopy and structural proteome analysis. The morphological and genome sequence analyses revealed significant diversity among L. brevis prophages, which appear to be dominated by members of the Myoviridae phage family. Based on this analysis, we propose a classification of L. brevis phages into five groups.
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Affiliation(s)
| | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Horst Neve
- Department Microbiology and Biotechnology, Federal Research Centre of Nutrition and Food, Max Rubner-Institut, Kiel, Germany
| | - Charles M. A. P. Franz
- Department Microbiology and Biotechnology, Federal Research Centre of Nutrition and Food, Max Rubner-Institut, Kiel, Germany
| | - Jean-Paul Noben
- Department Physiology Biochemistry and Immunology, Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Tadhg O’Sullivan
- HEINEKEN Global Innovation and Research, Heineken Supply Chain B.V, Zoeterwoude, Netherlands
| | - Viktor Boer
- HEINEKEN Global Innovation and Research, Heineken Supply Chain B.V, Zoeterwoude, Netherlands
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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11
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Van der Maelen E, Rezaei MN, Struyf N, Proost P, Verstrepen KJ, Courtin CM. Identification of a Wheat Thaumatin-like Protein That Inhibits Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:10423-10431. [PMID: 31487168 DOI: 10.1021/acs.jafc.9b03432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Plants often produce antifungal peptides and proteins in response to infection. Also wheat, which is the main ingredient of bread dough, contains such components. Here, we show that while some industrial strains of the baker's yeast Saccharomyces cerevisiae can efficiently ferment dough, some other strains show much lower fermentation capacities because they are sensitive to a specific wheat protein. We purified and identified what turned out to be a thaumatin-like protein through a combination of activity-guided fractionation, cation exchange chromatography, reversed-phase HPLC, and LC-MS/MS. Recombinant expression of the corresponding gene and testing the activity confirmed the inhibitory activity of the protein.
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Affiliation(s)
- Eva Van der Maelen
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , B-3001 Leuven , Belgium
| | - Mohammad N Rezaei
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , B-3001 Leuven , Belgium
| | - Nore Struyf
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , B-3001 Leuven , Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Rega Institute for Medical Research , KU Leuven , Herestraat 49 , B-3000 Leuven , Belgium
| | - Kevin J Verstrepen
- VIB - KU Leuven Laboratory for Systems Biology & CMPG Laboratory for Genetics and Genomics, VIB - KU Leuven Center for Microbiology, Bio-Incubator , Gaston Geenslaan 1 , B-3001 Leuven , Belgium
| | - Christophe M Courtin
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe) , KU Leuven , Kasteelpark Arenberg 20 , B-3001 Leuven , Belgium
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12
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The Leucine-Responsive Regulatory Protein Lrp Participates in Virulence Regulation Downstream of Small RNA ArcZ in Erwinia amylovora. mBio 2019; 10:mBio.00757-19. [PMID: 31138749 PMCID: PMC6538786 DOI: 10.1128/mbio.00757-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Fire blight disease continues to plague the commercial production of apples and pears despite more than a century of research into disease epidemiology and disease control. The causative agent of fire blight, Erwinia amylovora coordinates turning on or off specific virulence-associated traits at the appropriate time during disease development. The development of novel control strategies requires an in-depth understanding of E. amylovora regulatory mechanisms, including regulatory control of virulence-associated traits. This study investigates how the small RNA ArcZ regulates motility at the transcriptional level and identifies the transcription factor Lrp as a novel participant in the regulation of several virulence-associated traits. We report that ArcZ and Lrp together affect key virulence-associated traits through integration of transcriptional and posttranscriptional mechanisms. Further understanding of the topology of virulence regulatory networks can uncover weak points that can subsequently be exploited to control E. amylovora. Erwinia amylovora causes the devastating fire blight disease of apple and pear trees. During systemic infection of host trees, pathogen cells must rapidly respond to changes in their environment as they move through different host tissues that present distinct challenges and sources of nutrition. Growing evidence indicates that small RNAs (sRNAs) play an important role in disease progression as posttranscriptional regulators. The sRNA ArcZ positively regulates the motility phenotype and transcription of flagellar genes in E. amylovora Ea1189 yet is a direct repressor of translation of the flagellar master regulator, FlhD. We utilized transposon mutagenesis to conduct a forward genetic screen and identified suppressor mutations that increase motility in the Ea1189ΔarcZ mutant background. This enabled us to determine that the mechanism of transcriptional activation of the flhDC mRNA by ArcZ is mediated by the leucine-responsive regulatory protein, Lrp. We show that Lrp contributes to expression of virulence and several virulence-associated traits, including production of the exopolysaccharide amylovoran, levansucrase activity, and biofilm formation. We further show that Lrp is regulated posttranscriptionally by ArcZ through destabilization of lrp mRNA. Thus, ArcZ regulation of FlhDC directly and indirectly through Lrp forms an incoherent feed-forward loop that regulates levansucrase activity and motility as outputs. This work identifies Lrp as a novel participant in virulence regulation in E. amylovora and places it in the context of a virulence-associated regulatory network.
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13
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Feyereisen M, Mahony J, Lugli GA, Ventura M, Neve H, Franz CMAP, Noben JP, O'Sullivan T, Sinderen DV. Isolation and Characterization of Lactobacillus brevis Phages. Viruses 2019; 11:v11050393. [PMID: 31035495 PMCID: PMC6563214 DOI: 10.3390/v11050393] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/23/2019] [Accepted: 04/24/2019] [Indexed: 11/22/2022] Open
Abstract
Lactobacillus brevis has been widely used in industry for fermentation purposes. However, it is also associated with the spoilage of foods and beverages, in particular, beer. There is an increasing demand for natural food preservation methods, and in this context, bacteriophages possess the potential to control such spoilage bacteria. Just a few studies on phages infecting Lactobacillus brevis have been performed to date and in the present study, we report the isolation and characterization of five virulent phages capable of infecting Lb. brevis strains. The analysis reveals a high diversity among the isolates, with members belonging to both, the Myoviridae and Siphoviridae families. One isolate, designated phage 3-521, possesses a genome of 140.8 kb, thus representing the largest Lb. brevis phage genome sequenced to date. While the isolated phages do not propagate on Lb. brevis beer-spoiling strains, phages showed activity against these strains, impairing the growth of some Lb. brevis strains. The results highlight the potential of bacteriophage-based treatments as an effective approach to prevent bacterial spoilage of beer.
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Affiliation(s)
- Marine Feyereisen
- School of Microbiology, University College of Cork, T12 YT20 Cork, Ireland.
| | - Jennifer Mahony
- School of Microbiology, University College of Cork, T12 YT20 Cork, Ireland.
- APC Microbiome Ireland, University College of Cork, T12 YT20 Cork, Ireland.
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, 43124, Parma, Italy.
| | - Horst Neve
- Department Microbiology and Biotechnology, Federal Research Centre of Nutrition and Food, Max Rubner-Institut, 24103, Kiel, Germany.
| | - Charles M A P Franz
- Department Microbiology and Biotechnology, Federal Research Centre of Nutrition and Food, Max Rubner-Institut, 24103, Kiel, Germany.
| | - Jean-Paul Noben
- Department Physiology Biochemistry and Immunology, Biomedical Research Institute, Hasselt University, B-3590 Diepenbeek, Belgium.
| | - Tadhg O'Sullivan
- HEINEKEN Global Innovation and Research, Heineken Supply Chain B.V, 2382 Zoeterwoude, The Netherlands.
| | - Douwe van Sinderen
- School of Microbiology, University College of Cork, T12 YT20 Cork, Ireland.
- APC Microbiome Ireland, University College of Cork, T12 YT20 Cork, Ireland.
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14
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Schachterle JK, Zeng Q, Sundin GW. Three Hfq-dependent small RNAs regulate flagellar motility in the fire blight pathogen Erwinia amylovora. Mol Microbiol 2019; 111:1476-1492. [PMID: 30821016 DOI: 10.1111/mmi.14232] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2019] [Indexed: 12/13/2022]
Abstract
Erwinia amylovora, the causative agent of fire blight disease of apple and pear trees, causes disease on flowers by invading natural openings at the base of the floral cup. To reach these openings, the bacteria use flagellar motility to swim from stigma tips to the hypanthium and through nectar. We have previously shown that the Hfq-dependent sRNAs ArcZ, OmrAB and RmaA regulate swimming motility in E. amylovora. Here, we tested these three sRNAs to determine at what regulatory level they exert their effects and to what extent they can complement each other. We found that ArcZ and OmrAB repress the flagellar master regulator flhD post-transcriptionally. We also found that ArcZ and RmaA positively regulate flhD at the transcriptional level. The role of ArcZ as an activator of flagellar motility appears to be unique to E. amylovora and may have recently evolved. Our results suggest that the Hfq-dependent sRNAs ArcZ, OmrAB and RmaA play an integral role in regulation of flagellar motility by acting primarily on the master regulator, FlhD, but also through additional factors.
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Affiliation(s)
- Jeffrey K Schachterle
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Quan Zeng
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA.,Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - George W Sundin
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, USA
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15
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Hayes S, Duhoo Y, Neve H, Murphy J, Noben JP, Franz CMAP, Cambillau C, Mahony J, Nauta A, van Sinderen D. Identification of Dual Receptor Binding Protein Systems in Lactococcal 936 Group Phages. Viruses 2018; 10:v10120668. [PMID: 30486343 PMCID: PMC6315561 DOI: 10.3390/v10120668] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 01/14/2023] Open
Abstract
Siphoviridae of the lactococcal 936 group are the most commonly encountered bacteriophages in the dairy processing environment. The 936 group phages possess a discrete baseplate at the tip of their tail—a complex harbouring the Receptor Binding Protein (RBP) which is responsible for host recognition and attachment. The baseplate-encoding region is highly conserved amongst 936 phages, with 112 of 115 publicly available phages exhibiting complete synteny. Here, we detail the three exceptions (Phi4.2, Phi4R15L, and Phi4R16L), which differ from this genomic architecture in possessing an apparent second RBP-encoding gene upstream of the “classical” rbp gene. The newly identified RBP possesses an elongated neck region relative to currently defined 936 phage RBPs and is genetically distinct from defined 936 group RBPs. Through detailed characterisation of the representative phage Phi4.2 using a wide range of complementary techniques, we demonstrated that the above-mentioned three phages possess a complex and atypical baseplate structure. Furthermore, the presence of both RBPs in the tail tip of the mature virion was confirmed, while the anticipated host-binding capabilities of both proteins were also verified.
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Affiliation(s)
- Stephen Hayes
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland.
| | - Yoan Duhoo
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France.
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - James Murphy
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland.
| | - Jean-Paul Noben
- Biomedical Research Institute, Hasselt University, 3500 Diepenbeek, Belgium.
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany.
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, 13288 Marseille, France.
- Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, 13288 Marseille, France.
| | - Jennifer Mahony
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland.
| | - Arjen Nauta
- FrieslandCampina, 3818 Amersfoort, The Netherlands.
| | - Douwe van Sinderen
- School of Microbiology & APC Microbiome Ireland, University College Cork, Western Road, Cork T12 YT20, Ireland.
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16
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Fire blight host-pathogen interaction: proteome profiles of Erwinia amylovora infecting apple rootstocks. Sci Rep 2018; 8:11689. [PMID: 30076380 PMCID: PMC6076297 DOI: 10.1038/s41598-018-30064-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 07/24/2018] [Indexed: 11/09/2022] Open
Abstract
Fire blight, caused by the enterobacterium Erwinia amylovora, is a destructive disease, which can affect most members of the Rosaceae family. Since no significant genomic differences have been found by others to explain differences in virulence, we used here a gel-based proteomic approach to elucidate mechanisms and key players that allow the pathogen to survive, grow and multiply inside its host. Therefore, two strains with proven difference in virulence were grown under controlled conditions in vitro as well as in planta (infected apple rootstocks). Proteomic analysis including 2DE and mass spectrometry revealed that proteins involved in transcription regulation were more abundant in the in planta condition for both strains. In addition, genes involved in RNA processing were upregulated in planta for the highly virulent strain PFB5. Moreover, the upregulation of structural components of the F0F1-ATP synthase are major findings, giving important information on the infection strategy of this devastating pathogen. Overall, this research provides the first proteomic profile of E. amylovora during infection of apple rootstocks and insights into the response of the pathogen in interaction with its host.
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17
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Klee SM, Mostafa I, Chen S, Dufresne C, Lehman BL, Sinn JP, Peter KA, McNellis TW. An Erwinia amylovora yjeK mutant exhibits reduced virulence, increased chemical sensitivity and numerous environmentally dependent proteomic alterations. MOLECULAR PLANT PATHOLOGY 2018; 19:1667-1678. [PMID: 29232043 PMCID: PMC6638024 DOI: 10.1111/mpp.12650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/04/2017] [Accepted: 12/05/2017] [Indexed: 05/02/2023]
Abstract
The Gram-negative bacterium Erwinia amylovora causes fire blight, an economically important disease of apples and pears. Elongation factor P (EF-P) is a highly conserved protein that stimulates the formation of the first peptide bond of certain proteins and facilitates the translation of certain proteins, including those with polyproline motifs. YjeK and YjeA are two enzymes involved in the essential post-translational β-lysylation of EF-P at a conserved lysine residue, K34. EF-P, YjeA and YjeK have been shown to be essential for the full virulence of Escherichia coli, Salmonella species and Agrobacterium tumefaciens, with efp, yjeA and yjeK mutants having highly similar phenotypes. Here, we identified an E. amylovora yjeK::Tn5 transposon mutant with decreased virulence in apple fruit and trees. The yjeK::Tn5 mutant also showed pleiotropic phenotypes, including reduced growth in rich medium, lower extracellular polysaccharide production, reduced swimming motility and increased chemical sensitivity compared with the wild-type, whilst maintaining wild-type level growth in minimal medium. All yjeK::Tn5 mutant phenotypes were complemented in trans with a plasmid bearing a wild-type copy of yjeK. Comprehensive, quantitative proteomics analyses revealed numerous, environmentally dependent changes in the prevalence of a wide range of proteins, in higher abundance and lower abundance, in yjeK::Tn5 compared with the wild-type, and many of these alterations could be linked to yjeK::Tn5 mutant phenotypes. The environmental dependence of the yjeK::Tn5 mutant proteomic alterations suggests that YjeK could be required for aspects of the environmentally dependent regulation of protein translation. YjeK activity may be critical to overcoming stress, including the challenging host environment faced by invading pathogenic bacteria.
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Affiliation(s)
- Sara M. Klee
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
- Graduate Program in Plant PathologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
| | - Islam Mostafa
- Department of BiologyUniversity of FloridaGainesvilleFL 32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFL 32611USA
- Department of Pharmacognosy, Faculty of PharmacyZagazig UniversityZagazig 44519Egypt
| | - Sixue Chen
- Department of BiologyUniversity of FloridaGainesvilleFL 32611USA
- Genetics InstituteUniversity of FloridaGainesvilleFL 32611USA
- Plant Molecular and Cellular Biology ProgramUniversity of FloridaGainesvilleFL 32611USA
- Interdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFL 32611USA
| | | | - brian L. Lehman
- The Pennsylvania State University Fruit Research and Extension CenterBiglervillePA 17307USA
| | - Judith P. Sinn
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
| | - Kari A. Peter
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
- The Pennsylvania State University Fruit Research and Extension CenterBiglervillePA 17307USA
| | - Timothy W. McNellis
- Department of Plant Pathology & Environmental MicrobiologyThe Pennsylvania State UniversityUniversity ParkPA 16802USA
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18
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Puławska J, Kałużna M, Warabieda W, Mikiciński A. Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars - susceptible and resistant to fire blight. BMC Genomics 2017; 18:868. [PMID: 29132313 PMCID: PMC5683332 DOI: 10.1186/s12864-017-4251-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 10/31/2017] [Indexed: 12/23/2022] Open
Abstract
Background Erwinia amylovora is generally considered to be a homogeneous species in terms of phenotypic and genetic features. However, strains show variation in their virulence, particularly on hosts with different susceptibility to fire blight. We applied the RNA-seq technique to elucidate transcriptome-level changes of the lowly virulent E. amylovora 650 strain during infection of shoots of susceptible (Idared) and resistant (Free Redstar) apple cultivars. Results The highest number of differentially expressed E. amylovora genes between the two apple genotypes was observed at 24 h after inoculation. Six days after inoculation, only a few bacterial genes were differentially expressed in the susceptible and resistant apple cultivars. The analysis of differentially expressed gene functions showed that generally, higher expression of genes related to stress response and defence against toxic compounds was observed in Free Redstar. Also in this cultivar, higher expression of flagellar genes (FlaI), which are recognized as PAMP (pathogen-associated molecular pattern) by the innate immune systems of plants, was noted. Additionally, several genes that have not yet been proven to play a role in the pathogenic abilities of E. amylovora were found to be differentially expressed in the two apple cultivars. Conclusions This RNA-seq analysis generated a novel dataset describing the transcriptional response of the lowly virulent strain of E. amylovora in susceptible and resistant apple cultivar. Most genes were regulated in the same way in both apple cultivars, but there were also some cultivar-specific responses suggesting that the environment in Free Redstar is more stressful for bacteria what can be the reason of their inability to infect of this cultivar. Among genes with the highest fold change in expression between experimental combinations or with the highest transcript abundance, there are many genes without ascribed functions, which have never been tested for their role in pathogenicity. Overall, this study provides the first transcriptional profile by RNA-seq of E. amylovora during infection of a host plant and insights into the transcriptional response of this pathogen in the environments of susceptible and resistant apple plants. Electronic supplementary material The online version of this article (10.1186/s12864-017-4251-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joanna Puławska
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland.
| | - Monika Kałużna
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | - Wojciech Warabieda
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
| | - Artur Mikiciński
- Research Institute of Horticulture, ul. Konstytucji 3 Maja 1/3, 96-100, Skierniewice, Poland
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19
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Santander RD, Biosca EG. Erwinia amylovora psychrotrophic adaptations: evidence of pathogenic potential and survival at temperate and low environmental temperatures. PeerJ 2017; 5:e3931. [PMID: 29085749 PMCID: PMC5660878 DOI: 10.7717/peerj.3931] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 09/26/2017] [Indexed: 12/12/2022] Open
Abstract
The fire blight pathogen Erwinia amylovora can be considered a psychrotrophic bacterial species since it can grow at temperatures ranging from 4 °C to 37 °C, with an optimum of 28 °C. In many plant pathogens the expression of virulence determinants is restricted to a certain range of temperatures. In the case of E. amylovora, temperatures above 18 °C are required for blossom blight epidemics under field conditions. Moreover, this bacterium is able to infect a variety of host tissues/organs apart from flowers, but it is still unknown how environmental temperatures, especially those below 18 °C, affect the pathogen ability to cause fire blight disease symptoms in such tissues/organs. There is also scarce information on how temperatures below 18 °C affect the E. amylovora starvation-survival responses, which might determine its persistence in the environment and probably contribute to the seasonal development of fire blight disease, as occurs in other pathogens. To characterize the virulence and survival of E. amylovora at temperate and low temperatures, we evaluated the effect of three temperatures (4 °C, 14 °C, 28 °C) on symptom development, and on different parameters linked to starvation and virulence. E. amylovora was pathogenic at the three assayed temperatures, with a slow-down of symptom development correlating with colder temperatures and slower growth rates. Siderophore secretion and motility also decreased in parallel to incubation temperatures. However, production of the exopolysaccharides amylovoran and levan was enhanced at 4 °C and 14 °C, respectively. Similarly, biofilm formation, and oxidative stress resistance were improved at 14 °C, with this temperature also favoring the maintenance of culturability, together with a reduction in cell size and the acquisition of rounded shapes in E. amylovora cells subjected to long-term starvation. However, starvation at 28 °C and 4 °C induced an enhanced viable but nonculturable (VBNC) response (to a lesser extent at 4 °C). This work reveals E. amylovora as a highly adaptable pathogen that retains its pathogenic potential even at the minimal growth temperatures, with an improved exopolysaccharide synthesis, biofilm formation or oxidative stress resistance at 14 °C, with respect to the optimal growth temperature (28 °C). Finally, our results also demonstrate the thermal modulation of starvation responses in E. amylovora, suggesting that the starvation-survival and the VBNC states are part of its life cycle. These results confirm the particular psychrotrophic adaptations of E. amylovora, revealing its pathogenic potential and survival at temperate and low environmental temperatures, which have probably contributed to its successful spread to countries with different climates. This knowledge might improve integrated control measures against fire blight.
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Affiliation(s)
- Ricardo D. Santander
- Department of Microbiology and Ecology, Universitat de València, Burjassot, Spain
| | - Elena G. Biosca
- Department of Microbiology and Ecology, Universitat de València, Burjassot, Spain
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20
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Validation of reference genes for the normalization of the RT-qPCR gene expression of virulence genes of Erwinia amylovora in apple shoots. Sci Rep 2017; 7:2034. [PMID: 28515453 PMCID: PMC5435713 DOI: 10.1038/s41598-017-02078-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 04/05/2017] [Indexed: 01/11/2023] Open
Abstract
To study the expression of pathogenicity-related genes in Erwinia amylovora, seven candidate reference genes (ffh, glyA, gyrA, proC, pykA, recA, rpoB) were selected and validated with the following five different mathematic algorithms: geNorm, NormFinder, BestKeeper, the delta CT method and the RefFinder web-based tool. An overall comprehensive ranking output from each of the selected software programs revealed that proC and recA, followed by ffh and pykA, were the most stably expressed genes and can be recommended for the normalization of RT-qPCR data. A combination of the three reference genes, proC, recA and ffh, allowed for the accurate expression analysis of amsB and hrpN genes and the calculation of their fold change in E. amylovora after its infection of susceptible and resistant apple cultivars. To the best of our knowledge, this is the first study presenting a list of the most suitable reference genes for use in the relative quantification of target gene expression in E. amylovora in planta, selected on the basis of a multi-algorithm analysis.
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21
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Hayes S, Murphy J, Mahony J, Lugli GA, Ventura M, Noben JP, Franz CMAP, Neve H, Nauta A, Van Sinderen D. Biocidal Inactivation of Lactococcus lactis Bacteriophages: Efficacy and Targets of Commonly Used Sanitizers. Front Microbiol 2017; 8:107. [PMID: 28210242 PMCID: PMC5288689 DOI: 10.3389/fmicb.2017.00107] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/16/2017] [Indexed: 02/02/2023] Open
Abstract
Lactococcus lactis strains, being intensely used in the dairy industry, are particularly vulnerable to members of the so-called 936 group of phages. Sanitization and disinfection using purpose-made biocidal solutions is a critical step in controlling phage contamination in such dairy processing plants. The susceptibility of 36 936 group phages to biocidal treatments was examined using 14 biocides and commercially available sanitizers. The targets of a number of these biocides were investigated by means of electron microscopic and proteomic analyses. The results from this study highlight significant variations in phage resistance to biocides among 936 phages. Furthermore, rather than possessing resistance to specific biocides or biocide types, biocide-resistant phages tend to possess a broad tolerance to multiple classes of antimicrobial compounds.
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Affiliation(s)
- Stephen Hayes
- School of Microbiology, University College Cork Cork, Ireland
| | - James Murphy
- School of Microbiology, University College Cork Cork, Ireland
| | - Jennifer Mahony
- School of Microbiology, University College CorkCork, Ireland; APC Microbiome Institute, University College CorkCork, Ireland
| | - Gabriele A Lugli
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Life Sciences, University of Parma Parma, Italy
| | - Jean-Paul Noben
- Biomedical Research Institute, Hasselt University Diepenbeek, Belgium
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Germany
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut Kiel, Germany
| | | | - Douwe Van Sinderen
- School of Microbiology, University College CorkCork, Ireland; APC Microbiome Institute, University College CorkCork, Ireland
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22
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Holtappels M, Noben JP, Valcke R. Virulence of Erwinia amylovora, a prevalent apple pathogen: Outer membrane proteins and type III secreted effectors increase fitness and compromise plant defenses. Proteomics 2016; 16:2377-90. [PMID: 27345300 DOI: 10.1002/pmic.201500513] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 06/15/2016] [Accepted: 06/23/2016] [Indexed: 01/30/2023]
Abstract
Until now, no data are available on the outer membrane (OM) proteome of Erwinia amylovora, a Gram-negative plant pathogen, causing fire blight in most of the members of the Rosaceae family. Since the OM forms the interface between the bacterial cell and its environment it is in direct contact with the host. Additionally, the type III secretion system, embedded in the OM, is a pathogenicity factor of E. amylovora. To assess the influence of the OM composition and the secretion behavior on virulence, a 2D-DIGE analysis and gene expression profiling were performed on a high and lower virulent strain, both in vitro and in planta. Proteome data showed an increase in flagellin for the lower virulent strain in vitro, whereas, in planta several interesting proteins were identified as being differently expressed between both the strains. Further, gene expression of nearly all type III secreted effectors was elevated for the higher virulent strain, both in vitro and in planta. As a first, we report that several characteristics of virulence can be assigned to the OM proteome. Moreover, we demonstrate that secreted proteins prove to be the important factors determining differences in virulence between the strains, otherwise regarded as homogeneous on a genome level.
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Affiliation(s)
- Michelle Holtappels
- Molecular and Physical Plant Physiology, Faculty of Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jean-Paul Noben
- School of Life Sciences, Biomedical Research Institute, Hasselt University and Transnational University Limburg, Hasselt, Belgium
| | - Roland Valcke
- Molecular and Physical Plant Physiology, Faculty of Sciences, Hasselt University, Diepenbeek, Belgium.
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Yılmaz Ş, Victor B, Hulstaert N, Vandermarliere E, Barsnes H, Degroeve S, Gupta S, Sticker A, Gabriël S, Dorny P, Palmblad M, Martens L. A Pipeline for Differential Proteomics in Unsequenced Species. J Proteome Res 2016; 15:1963-70. [DOI: 10.1021/acs.jproteome.6b00140] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Şule Yılmaz
- Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Bjorn Victor
- Veterinary
Helminthology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Niels Hulstaert
- Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Elien Vandermarliere
- Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Harald Barsnes
- Proteomics
Unit (PROBE), Department of Biomedicine, University of Bergen, Jonas Liesvei 91, N-5009 Bergen, Norway
| | - Sven Degroeve
- Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Surya Gupta
- Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, B-9052 Ghent, Belgium
| | - Adriaan Sticker
- Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, B-9052 Ghent, Belgium
- Department
of Applied Mathematics, Computer Science, and Statistics, Ghent University, B-9000 Ghent, Belgium
| | - Sarah Gabriël
- Veterinary
Helminthology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Pierre Dorny
- Veterinary
Helminthology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Magnus Palmblad
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Lennart Martens
- Medical Biotechnology Center, VIB, Albert Baertsoenkaai 3, Ghent B-9000, Belgium
- Department
of Biochemistry, Ghent University, Albert Baertsoenkaai 3, B-9000 Ghent, Belgium
- Bioinformatics
Institute Ghent, Ghent University, B-9052 Ghent, Belgium
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Holtappels M, Vrancken K, Noben J, Remans T, Schoofs H, Deckers T, Valcke R. The in planta proteome of wild type strains of the fire blight pathogen, Erwinia amylovora. J Proteomics 2016; 139:1-12. [DOI: 10.1016/j.jprot.2016.02.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/13/2016] [Accepted: 02/17/2016] [Indexed: 12/20/2022]
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