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Lin L, Tao M, He WM, Wu QH, Huang HK, Murero AK, Shao XL, Wang LM, Qian GL. Identification of non-canonical antagonistic bacteria via interspecies contact-dependent killing. PEST MANAGEMENT SCIENCE 2024; 80:3997-4005. [PMID: 38527976 DOI: 10.1002/ps.8103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 01/18/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Canonical biocontrol bacteria were considered to inhibit pathogenic bacteria mainly by secreting antibiotic metabolites or enzymes. Recent studies revealed that some biocontrol bacteria can inhibit pathogenic bacteria through contact-dependent killing (CDK) mediated by contact-dependent secretion systems. The CDK was independent of antibiotic metabolites and often ignored in normal biocontrol activity assay. RESULTS In this study, we aimed to use a pathogen enrichment strategy to isolate non-canonical bacteria with CDK ability. Rhizosphere soil samples from Chinese cabbage showing soft rot symptom were collected and Pectobacterium carotovorum subsp. carotovorum (Pcc), the pathogen of cabbage soft rot, were added into these samples to enrich bacteria which attached on Pcc cells. By co-culture with Pcc, four bacteria strains (named as PcE1, PcE8, PcE12 and PcE13) showing antibacterial activity were isolated from Chinese cabbage rhizosphere. These four bacteria strains showed CDK abilities to different pathogenic bacteria of horticultural plants. Among them, PcE1 was identified as Chryseobacterium cucumeris. Genome sequencing showed that PcE1 genome encoded a type VI secretion system (T6SS) gene cluster. By heterologous expression, four predicted T6SS effectors of PcE1 showed antibacterial activity to Escherichia coli. CONCLUSION Overall, this study isolated four bacteria strains with CDK activity to various horticultural plant pathogens, and revealed possible involvement of T6SS of Chryseobacterium cucumeris in antibacterial activity. These results provide valuable insight for potential application of CDK activity in biocontrol bacteria. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Long Lin
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Min Tao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Wei-Mei He
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Qian-Hua Wu
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Hao-Kai Huang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Aprodisia Kavutu Murero
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiao-Long Shao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Li-Min Wang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Guo-Liang Qian
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
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Petrova O, Semenova E, Parfirova O, Tsers I, Gogoleva N, Gogolev Y, Nikolaichik Y, Gorshkov V. RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum. Int J Mol Sci 2023; 24:17348. [PMID: 38139177 PMCID: PMC10743746 DOI: 10.3390/ijms242417348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/04/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
The alternative sigma factor RpoS is considered to be one of the major regulators providing stress resistance and cross-protection in bacteria. In phytopathogenic bacteria, the effects of RpoS have not been analyzed with regard to cross-protection, and genes whose expression is directly or indirectly controlled by RpoS have not been determined at the whole-transcriptome level. Our study aimed to determine RpoS-regulated genes and phenotypes in the phytopathogenic bacterium Pectobacterium atrosepticum. Knockout of the rpoS gene in P. atrosepticum affected the long-term starvation response, cross-protection, and virulence toward plants with enhanced immune status. The whole-transcriptome profiles of the wild-type P. atrosepticum strain and its ΔrpoS mutant were compared under different experimental conditions, and functional gene groups whose expression was affected by RpoS were determined. The RpoS promoter motif was inferred within the promoter regions of the genes affected by rpoS deletion, and the P. atrosepticum RpoS regulon was predicted. Based on RpoS-controlled phenotypes, transcriptome profiles, and RpoS regulon composition, the regulatory role of RpoS in P. atrosepticum is discussed.
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Affiliation(s)
- Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Elizaveta Semenova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Ivan Tsers
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
| | - Yevgeny Nikolaichik
- Department of Molecular Biology, Belarusian State University, 220030 Minsk, Belarus;
| | - Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center “Kazan Scientific Center of the Russian Academy of Sciences”, 420111 Kazan, Russia; (O.P.); (E.S.); (O.P.); (I.T.); (N.G.); (Y.G.)
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
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Wang B, Zhang Z, Xu F, Yang Z, Li Z, Shen D, Wang L, Wu H, Li T, Yan Q, Wei Q, Shao X, Qian G. Soil bacterium manipulates antifungal weapons by sensing intracellular type IVA secretion system effectors of a competitor. THE ISME JOURNAL 2023; 17:2232-2246. [PMID: 37838821 PMCID: PMC10689834 DOI: 10.1038/s41396-023-01533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Soil beneficial bacteria can effectively inhibit bacterial pathogens by assembling contact-dependent killing weapons, such as the type IVA secretion system (T4ASS). It's not clear whether these antibacterial weapons are involved in biotrophic microbial interactions in soil. Here we showed that an antifungal antibiotic 2,4-DAPG production of the soil bacterium, Pseudomonas protegens can be triggered by another soil bacterium, Lysobacter enzymogenes, via T4ASS by co-culturing on agar plates to mimic cell-to-cell contact. We demonstrated that the induced 2,4-DAPG production of P. protegens is achieved by intracellular detection of the T4ASS effector protein Le1519 translocated from L. enzymogenes. We defined Le1519 as LtaE (Lysobacter T4E triggering antifungal effects), which specifically stimulates the expression of 2,4-DAPG biosynthesis genes in P. protegens, thereby protecting soybean seedlings from infection by the fungus Rhizoctonia solani. We further found that LtaE directly bound to PhlF, a pathway-specific transcriptional repressor of the 2,4-DAPG biosynthesis, then activated the 2,4-DAPG production. Our results highlight a novel pattern of microbial interspecies and interkingdom interactions, providing a unique case for expanding the diversity of soil microbial interactions.
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Affiliation(s)
- Bingxin Wang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Zeyu Zhang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Fugui Xu
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Zixiang Yang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Zihan Li
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Danyu Shen
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Limin Wang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Huijun Wu
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Tao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Qi Wei
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaolong Shao
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Guoliang Qian
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China.
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Li J, Chen R, Yang R, Wei X, Xie H, Shi Y, Xie X, Chai A, Fan T, Li B, Li L. Rapid Detection and Quantification of Viable Cells of Pectobacterium brasiliense Using Propidium Monoazide Combined with Real-Time PCR. Microorganisms 2023; 11:2808. [PMID: 38004819 PMCID: PMC10673545 DOI: 10.3390/microorganisms11112808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 11/26/2023] Open
Abstract
Pectobacterium brasiliense (Pbr) has caused significant economic losses in major vegetable production areas in Northern China by causing bacterial soft rot in cash crops such as potatoes and cucumbers. This study aimed to establish a PMA-qPCR detection method for Pbr by screening specific and sensitive primers based on the glu gene and the conserved region of the 23S rRNA gene. Based on the optimized PMA pretreatment conditions, a standard curve was designed and constructed for PMA-qPCR detection (y = -3.391x + 36.28; R2 = 0.99). The amplification efficiency reached 97%, and the lowest detection limit of viable cells was approximately 2 × 102 CFU·mL-1. The feasibility of the PMA-qPCR method was confirmed through a manually simulated viable/dead cell assay under various concentrations. The analysis of potato tubers and cucumber seeds revealed that nine naturally collected seed samples contained a range from 102 to 104 CFU·g-1 viable Pbr bacteria. Furthermore, the system effectively identified changes in the number of pathogenic bacteria in cucumber and potato leaves affected by soft rot throughout the disease period. Overall, the detection and prevention of bacterial soft rot caused by Pbr is crucial.
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Affiliation(s)
- Junhui Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Ruxing Chen
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Ruwei Yang
- Comprehensive Experimental Farm, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China;
| | - Xinchen Wei
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Hua Xie
- Beijing Agro-Biotechnology Research Center, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China;
| | - Yanxia Shi
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Xuewen Xie
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Ali Chai
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Tengfei Fan
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Baoju Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
| | - Lei Li
- State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (J.L.); (R.C.); (X.W.); (Y.S.); (X.X.); (A.C.); (T.F.)
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Leesombun A, Sungpradit S, Sariya L, Taowan J, Boonmasawai S. Transcriptional Profiling of the Effect of Coleus amboinicus L. Essential Oil against Salmonella Typhimurium Biofilm Formation. Antibiotics (Basel) 2023; 12:1598. [PMID: 37998800 PMCID: PMC10668763 DOI: 10.3390/antibiotics12111598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Salmonella enterica serovar Typhimurium cause infections primarily through foodborne transmission and remains a significant public health concern. The biofilm formation of this bacteria also contributes to their multidrug-resistant nature. Essential oils from medicinal plants are considered potential alternatives to conventional antibiotics. Therefore, this study assessed the antimicrobial and antibiofilm activities of Coleus amboinicus essential oil (EO-CA) against S. Typhimurium ATCC 14028. Seventeen chemical compounds of EO-CA were identified, and carvacrol (38.26%) was found to be the main constituent. The minimum inhibitory concentration (MIC) of EO-CA for S. Typhimurium planktonic growth was 1024 µg/mL while the minimum bactericidal concentration was 1024 µg/mL. EO-CA at sub-MIC (≥1/16× MIC) exhibited antibiofilm activity against the prebiofilm formation of S. Typhimurium at 24 h. Furthermore, EO-CA (≥1/4× MIC) inhibited postbiofilm formation at 24 and 48 h (p < 0.05). Transcriptional profiling revealed that the EO-CA-treated group at 1/2× MIC had 375 differentially expressed genes (DEGs), 106 of which were upregulated and 269 were downregulated. Five significantly downregulated virulent DEGs responsible for motility (flhD, fljB, and fimD), curli fimbriae (csgD), and invasion (hilA) were screened via quantitative reverse transcription PCR (qRT-PCR). This study suggests the potential of EO-CA as an effective antimicrobial agent for combating planktonic and biofilm formation of Salmonella.
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Affiliation(s)
- Arpron Leesombun
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (A.L.); (S.S.)
| | - Sivapong Sungpradit
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (A.L.); (S.S.)
| | - Ladawan Sariya
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (L.S.); (J.T.)
| | - Jarupha Taowan
- The Monitoring and Surveillance Center for Zoonotic Diseases in Wildlife and Exotic Animals (MoZWE), Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (L.S.); (J.T.)
| | - Sookruetai Boonmasawai
- Department of Pre-Clinic and Applied Animal Science, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom 73170, Thailand; (A.L.); (S.S.)
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Chen C, Che S, Dong Z, Sui J, Tian Y, Su Y, Zhang M, Sun W, Fan J, Xie J, Xie H. A genome-wide association study reveals that epistasis underlies the pathogenicity of Pectobacterium. Microbiol Spectr 2023; 11:e0176423. [PMID: 37712699 PMCID: PMC10580964 DOI: 10.1128/spectrum.01764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023] Open
Abstract
Pectobacterium spp. are important bacterial pathogens that cause soft rot symptoms in various crops. However, their mechanism of pathogenicity requires clarity to help control their infections. Here, genome-wide association studies (GWAS) were conducted by integrating genomic data and measurements of two phenotypes (virulence and cellulase activity) for 120 various Pectobacterium strains in order to identify the genetic basis of their pathogenicity. An artificial intelligence-based software program was developed to automatically measure lesion areas on Chinese cabbage, thereby facilitating accurate and rapid data collection for virulence phenotypes for use in GWAS analysis. The analysis discovered 428 and 158 loci significantly associated with Pectobacterium virulence (lesion area) and cellulase activity, respectively. In addition, 1,229 and 586 epistasis loci pairs were identified for the virulence and cellulase activity phenotypes, respectively. Among them, the AraC transcriptional regulator exerted epistasis effects with another three nutrient transport-related genes in pairs contributing to the virulence phenotype, and their epistatic effects were experimentally confirmed for one pair with knockout mutants of each single gene and double gene. This study consequently provides valuable insights into the genetic mechanism underlying Pectobacterium spp. pathogenicity. IMPORTANCE Plant diseases and pests are responsible for the loss of up to 40% of food crops, and annual economic losses caused by plant diseases reach more than $220 billion. Fighting against plant diseases requires an understanding of the pathogenic mechanisms of pathogens. This study adopted an advanced approach using population genomics integrated with virulence-related phenotype data to investigate the genetic basis of Pectobacterium spp., which causes serious crop losses worldwide. An automated software program based on artificial intelligence was developed to measure the virulence phenotype (lesion area), which greatly facilitated this research. The analysis predicted key genomic loci that were highly associated with virulence phenotypes, exhibited epistasis effects, and were further confirmed as critical for virulence with mutant gene deletion experiments. The present study provides new insights into the genetic determinants associated with Pectobacterium pathogenicity and provides a valuable new software resource that can be adapted to improve plant infection measurements.
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Affiliation(s)
- Changlong Chen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Shu Che
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Zhou Dong
- EVision Technology (Beijing) Co. Ltd, Beijing, China
| | - Jiayi Sui
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yu Tian
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Yanyan Su
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Meng Zhang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wangwang Sun
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Jiaqin Fan
- Department of Plant Pathology, Nanjing Agricultural University, Nanjing, China
| | - Jianbo Xie
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Hua Xie
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
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Fekete FJ, Marotta NJ, Liu X, Weinert EE. An O 2-sensing diguanylate cyclase broadly affects the aerobic transcriptome in the phytopathogen Pectobacterium carotovorum. Front Microbiol 2023; 14:1134742. [PMID: 37485529 PMCID: PMC10360401 DOI: 10.3389/fmicb.2023.1134742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 06/26/2023] [Indexed: 07/25/2023] Open
Abstract
Pectobacterium carotovorum is an important plant pathogen responsible for the destruction of crops through bacterial soft rot, which is modulated by oxygen (O2) concentration. A soluble globin coupled sensor protein, Pcc DgcO (also referred to as PccGCS) is one way through which P. carotovorum senses oxygen. DgcO contains a diguanylate cyclase output domain producing c-di-GMP. Synthesis of the bacterial second messenger c-di-GMP is increased upon oxygen binding to the sensory globin domain. This work seeks to understand regulation of function by DgcO at the transcript level. RNA sequencing and differential expression analysis revealed that the deletion of DgcO only affects transcript levels in cells grown under aerobic conditions. Differential expression analysis showed that DgcO deletion alters transcript levels for metal transporters. These results, followed by inductively coupled plasma-mass spectrometry showing decreased concentrations of six biologically relevant metals upon DgcO deletion, provide evidence that a globin coupled sensor can affect cellular metal content. These findings improve the understanding of the transcript level control of O2-dependent phenotypes in an important phytopathogen and establish a basis for further studies on c-di-GMP-dependent functions in P. carotovorum.
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Affiliation(s)
- Florian J. Fekete
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, United States
| | - Nick J. Marotta
- Graduate Program in Molecular, Cellular, and Integrative Biosciences, Penn State University, University Park, PA, United States
| | - Xuanyu Liu
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, United States
| | - Emily E. Weinert
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, United States
- Department of Chemistry, Penn State University, University Park, PA, United States
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Chen C, Cui S, Guan J, Su Y, Liang X, Tian Y, Xie H. Investigation of the Role of a Zinc Uptake Regulator (Zur) in the Virulence of Pectobacterium odoriferum. Int J Mol Sci 2023; 24:9991. [PMID: 37373138 DOI: 10.3390/ijms24129991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Pectobacterium spp. infect many horticultural crops worldwide and lead to serious crop losses. Zinc-uptake-regulator (Zur) proteins are present widely in prokaryotes and play an important role in pathogenicity. To uncover the role of Zur in P. odoriferum, we constructed mutant (ΔZur) and overexpression [Po (Zur)] strains of a Zur, and a virulence assay showed that the Po (Zur) was of significantly lower virulence, while the ΔZur displayed significantly increased virulence on Chinese cabbage compared to their respective control strains, wild-type P. odoriferum (Po WT) and P. odoriferum harboring an empty vector (Po (EV)) (p < 0.05). The growth curves of the ΔZur and Po (Zur) showed no obvious differences from those of the control strains. Comparative transcriptome analysis showed that Zur overexpression in P. odoriferum induced differentially expressed genes (DEGs) related to flagellum and cell motility, while mutating Zur resulted in DEGs mainly corresponding to divalent-metal-ion transport and membrane transport. Phenotypic experiments on the Po (Zur) showed that flagellum numbers and cell motility were reduced in comparison with the control, while those of the ΔZur did not change. Collectively, these results show that the Zur negatively regulates the virulence of P. odoriferum and might function via a dual mechanism dependent on dose.
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Affiliation(s)
- Changlong Chen
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Shuang Cui
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jiantao Guan
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yanyan Su
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Xucong Liang
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Yu Tian
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Hua Xie
- Institute of Biotechnology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
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Development of a Bacteriophage Cocktail against Pectobacterium carotovorum Subsp. carotovorum and Its Effects on Pectobacterium Virulence. Appl Environ Microbiol 2022; 88:e0076122. [PMID: 36165651 PMCID: PMC9552609 DOI: 10.1128/aem.00761-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Pectobacterium carotovorum subsp. carotovorum is a necrotrophic plant pathogen that secretes plant cell wall-degrading enzymes (PCWDEs) that cause soft rot disease in various crops. Bacteriophages have been under consideration as harmless antibacterial agents to replace antibiotics and copper-based pesticides. However, the emergence of bacteriophage resistance is one of the main concerns that should be resolved for practical phage applications. In this study, we developed a phage cocktail with three lytic phages that recognize colanic acid (phage POP12) or flagella (phages POP15 and POP17) as phage receptors to minimize phage resistance. The phage cocktail effectively suppressed the emergence of phage-resistant P. carotovorum subsp. carotovorum compared with single phages in in vitro challenge assays. The application of the phage cocktail to napa cabbage (Brassica rapa subsp. pekinensis) resulted in significant growth retardation of P. carotovorum subsp. carotovorum (P < 0.05) and prevented the symptoms of soft rot disease. Furthermore, phage cocktail treatments of young napa cabbage leaves in a greenhouse environment indicated effective prevention of soft rot disease compared to that in the nonphage negative control. We isolated 15 phage-resistant mutants after a phage cocktail treatment to assess the virulence-associated phenotypes compared to those of wild-type (WT) strain Pcc27. All mutants showed reduced production of four different PCWDEs, leading to lower levels of tissue softening. Ten of the 15 phage-resistant mutants additionally exhibited decreased swimming motility. Taken together, these results show that the phage cocktail developed here, which targets two different types of phage receptors, provides an effective strategy for controlling P. carotovorum subsp. carotovorum in agricultural products, with a potential ability to attenuate P. carotovorum subsp. carotovorum virulence. IMPORTANCE Pectobacterium carotovorum subsp. carotovorum is a phytopathogen that causes soft rot disease in various crops by producing plant cell wall-degrading enzymes (PCWDEs). Although antibiotics and copper-based pesticides have been extensively applied to inhibit P. carotovorum subsp. carotovorum, the emergence of antibiotic-resistant bacteria and demand for harmless antimicrobial products have emphasized the necessity of finding alternative therapeutic strategies. To address this problem, we developed a phage cocktail consisting of three P. carotovorum subsp. carotovorum-specific phages that recognize colanic acids and flagella of P. carotovorum subsp. carotovorum. The phage cocktail treatments significantly decreased P. carotovorum subsp. carotovorum populations, as well as soft rot symptoms in napa cabbage. Simultaneously, they resulted in virulence attenuation in phage-resistant P. carotovorum subsp. carotovorum, which was represented by decreased PCWDE production and decreased flagellum-mediated swimming motility. These results suggested that preparations of phage cocktails targeting multiple receptors would be an effective approach to biocontrol of P. carotovorum subsp. carotovorum in crops.
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Effects of Natural Rheum tanguticum on the Cell Wall Integrity of Resistant Phytopathogenic Pectobacterium carotovorum subsp. Carotovorum. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165291. [PMID: 36014529 PMCID: PMC9414576 DOI: 10.3390/molecules27165291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 12/02/2022]
Abstract
The abuse of agricultural antibiotics has led to the emergence of drug-resistant phytopathogens. Rifampicin and streptomycin and streptomycin resistance Pectobacterium carotovorum subsp. carotovorum (PccS1) was obtained from pathological plants in a previous experiment. Rheum tanguticum, derived from the Chinese plateau area, exhibits excellent antibacterial activity against PccS1, yet the action mode has not been fully understood. In present text, the cell wall integrity of the PccS1 was tested by the variation of the cellular proteins, SDS polyacrylamide gel electrophoresis (SDS-PAGE), scanning electron microscopy (SEM) and Fourier transform infrared spectrophotometer (FTIR) characteristics. Label-free quantitative proteomics was further used to identify the DEPs in the pathogen response to treatment with Rheum tanguticum Maxim. ex Balf. extract (abbreviated as RTMBE). Based on the bioinformatics analysis of these different expressed proteins (DEPs), RTMBE mainly inhibited some key protein expressions of beta-Lactam resistance, a two-component system and phosphotransferase system. Most of these membrane proteins were extraordinarily suppressed, which was also consistent with the morphological tests. In addition, from the downregulated flagellar motility related proteins, it was also speculated that RTMBE played an essential antibacterial role by affecting the swimming motility of the cells. The results indicated that Rheum tanguticum can be used to attenuate the virulence of the drug-resistant phytopathogenic bacteria.
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Arif M, Czajkowski R, Chapman TA. Editorial: Genome-Wide Analyses of Pectobacterium and Dickeya Species. FRONTIERS IN PLANT SCIENCE 2022; 13:855262. [PMID: 35317016 PMCID: PMC8934395 DOI: 10.3389/fpls.2022.855262] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Affiliation(s)
- Mohammad Arif
- Department of Plant and Environmental Protection Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Robert Czajkowski
- Laboratory of Biologically Active Compounds, Intercollegiate Faculty of Biotechnology UG and MUG, University of Gdansk, Gdańsk, Poland
| | - Toni A. Chapman
- Biosecurity and Food Safety, NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute (EMAI), Menangle, NSW, Australia
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Lu Q, Yan F, Liu Y, Li Q, Yang M, Liu P. Comparative Genomic Analyses Reveal Functional Insights Into Key Determinants of the Pathogenesis of Pectobacterium actinidiae in Kiwifruit. PHYTOPATHOLOGY 2021; 111:789-798. [PMID: 33245255 DOI: 10.1094/phyto-07-20-0287-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Gram-negative bacterial species Pectobacterium actinidiae causes summer canker in kiwifruit plants. However, little is known about its virulence factors and mechanisms of genetic adaptation. We aimed to identify the key determinants that control the virulence of P. actinidiae in kiwifruit by genomic and functional analyses. Analysis of four P. actinidiae isolates indicated low genetic variability with an average of 98.7% genome-level sequence similarity and 82% shared protein-coding gene content. Phylogenetic analysis, based on both bulk single nucleotide polymorphisms (SNPs) and single-copy genes, revealed that P. actinidiae strains cluster into a single clade, which is closely related to the clades of P. odoriferum (species with a completely different host range). Through comparison between these two clades of strains, 746 unique core orthologs/genes were clustered in the clades of P. actinidiae, especially key virulence determinants involved in the biosynthesis of secretion systems (type III, IV, and VI), iron, flagellar structure, and the quorum-sensing system. Our results provide insights into the pathogenomics underlying the genetic diversification and evolution of pathogenicity in P. actinidiae species.
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Affiliation(s)
- Qi Lu
- School of Horticulture, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Fuhua Yan
- Lishui Academy of Agricultural and Forestry Sciences, Lishui 323000, People's Republic of China
| | - Yuanyuan Liu
- School of Horticulture, Anhui Agricultural University, Hefei 230036, People's Republic of China
| | - Qiaohong Li
- Kiwifruit Breeding and Utilization Key Laboratory, Sichuan Provincial Academy of Natural Resource Sciences, Chengdu 610015, People's Republic of China
| | - Meng Yang
- School of Horticulture, Hebei Agricultural University, Baoding 071001, People's Republic of China
| | - Pu Liu
- School of Horticulture, Anhui Agricultural University, Hefei 230036, People's Republic of China
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Paulson AR, O’Callaghan M, Zhang XX, Rainey PB, Hurst MRH. In vivo transcriptome analysis provides insights into host-dependent expression of virulence factors by Yersinia entomophaga MH96, during infection of Galleria mellonella. G3 (BETHESDA, MD.) 2021; 11:jkaa024. [PMID: 33561230 PMCID: PMC7849909 DOI: 10.1093/g3journal/jkaa024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/19/2020] [Indexed: 12/31/2022]
Abstract
The function of microbes can be inferred from knowledge of genes specifically expressed in natural environments. Here, we report the in vivo transcriptome of the entomopathogenic bacterium Yersinia entomophaga MH96, captured during initial, septicemic, and pre-cadaveric stages of intrahemocoelic infection in Galleria mellonella. A total of 1285 genes were significantly upregulated by MH96 during infection; 829 genes responded to in vivo conditions during at least one stage of infection, 289 responded during two stages of infection, and 167 transcripts responded throughout all three stages of infection compared to in vitro conditions at equivalent cell densities. Genes upregulated during the earliest infection stage included components of the insecticidal toxin complex Yen-TC (chi1, chi2, and yenC1), genes for rearrangement hotspot element containing protein yenC3, cytolethal distending toxin cdtAB, and vegetative insecticidal toxin vip2. Genes more highly expressed throughout the infection cycle included the putative heat-stable enterotoxin yenT and three adhesins (usher-chaperone fimbria, filamentous hemagglutinin, and an AidA-like secreted adhesin). Clustering and functional enrichment of gene expression data also revealed expression of genes encoding type III and VI secretion system-associated effectors. Together these data provide insight into the pathobiology of MH96 and serve as an important resource supporting efforts to identify novel insecticidal agents.
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Affiliation(s)
- Amber R Paulson
- Forage Science, AgResearch Ltd., Lincoln 8140, New Zealand
- New Zealand Institute for Advanced Study, Massey University, Auckland 0745, New Zealand
- Department of Biology, Queen’s University, Kingston, ON K7L 3N6, Canada
| | | | - Xue-Xian Zhang
- School of Natural and Computational Sciences, Massey University, Auckland 0745, New Zealand
| | - Paul B Rainey
- New Zealand Institute for Advanced Study, Massey University, Auckland 0745, New Zealand
- Laboratoire de Génétique de l’Evolution CBI, ESPCI Paris, Université PSL, CNRS, Paris 75005, France
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Mark R H Hurst
- Forage Science, AgResearch Ltd., Lincoln 8140, New Zealand
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Tsers I, Gorshkov V, Gogoleva N, Parfirova O, Petrova O, Gogolev Y. Plant Soft Rot Development and Regulation from the Viewpoint of Transcriptomic Profiling. PLANTS 2020; 9:plants9091176. [PMID: 32927917 PMCID: PMC7570247 DOI: 10.3390/plants9091176] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/05/2020] [Accepted: 09/07/2020] [Indexed: 02/07/2023]
Abstract
Soft rot caused by Pectobacterium species is a devastating plant disease poorly characterized in terms of host plant responses. In this study, changes in the transcriptome of tobacco plants after infection with Pectobacterium atrosepticum (Pba) were analyzed using RNA-Seq. To draw a comprehensive and nontrivially itemized picture of physiological events in Pba-infected plants and to reveal novel potential molecular "players" in plant-Pba interactions, an original functional gene classification was performed. The classifications present in various databases were merged, enriched by "missed" genes, and divided into subcategories. Particular changes in plant cell wall-related processes, perturbations in hormonal and other regulatory systems, and alterations in primary, secondary, and redox metabolism were elucidated in terms of gene expression. Special attention was paid to the prediction of transcription factors (TFs) involved in the disease's development. Herewith, gene expression was analyzed within the predicted TF regulons assembled at the whole-genome level based on the presence of particular cis-regulatory elements (CREs) in gene promoters. Several TFs, whose regulons were enriched by differentially expressed genes, were considered to be potential master regulators of Pba-induced plant responses. Differential regulation of genes belonging to a particular multigene family and encoding cognate proteins was explained by the presence/absence of the particular CRE in gene promoters.
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Affiliation(s)
- Ivan Tsers
- Laboratory of plant infectious diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia;
| | - Vladimir Gorshkov
- Laboratory of plant infectious diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia;
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (N.G.); (O.P.); (O.P.); (Y.G.)
- Correspondence:
| | - Natalia Gogoleva
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (N.G.); (O.P.); (O.P.); (Y.G.)
| | - Olga Parfirova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (N.G.); (O.P.); (O.P.); (Y.G.)
| | - Olga Petrova
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (N.G.); (O.P.); (O.P.); (Y.G.)
| | - Yuri Gogolev
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, 420111 Kazan, Russia; (N.G.); (O.P.); (O.P.); (Y.G.)
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