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Erban T, Sopko B. Understanding bacterial pathogen diversity: A proteogenomic analysis and use of an array of genome assemblies to identify novel virulence factors of the honey bee bacterial pathogen Paenibacillus larvae. Proteomics 2024; 24:e2300280. [PMID: 38742951 DOI: 10.1002/pmic.202300280] [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: 07/13/2023] [Revised: 03/07/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024]
Abstract
Mass spectrometry proteomics data are typically evaluated against publicly available annotated sequences, but the proteogenomics approach is a useful alternative. A single genome is commonly utilized in custom proteomic and proteogenomic data analysis. We pose the question of whether utilizing numerous different genome assemblies in a search database would be beneficial. We reanalyzed raw data from the exoprotein fraction of four reference Enterobacterial Repetitive Intergenic Consensus (ERIC) I-IV genotypes of the honey bee bacterial pathogen Paenibacillus larvae and evaluated them against three reference databases (from NCBI-protein, RefSeq, and UniProt) together with an array of protein sequences generated by six-frame direct translation of 15 genome assemblies from GenBank. The wide search yielded 453 protein hits/groups, which UpSet analysis categorized into 50 groups based on the success of protein identification by the 18 database components. Nine hits that were not identified by a unique peptide were not considered for marker selection, which discarded the only protein that was not identified by the reference databases. We propose that the variability in successful identifications between genome assemblies is useful for marker mining. The results suggest that various strains of P. larvae can exhibit specific traits that set them apart from the established genotypes ERIC I-V.
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Affiliation(s)
- Tomas Erban
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
| | - Bruno Sopko
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
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2
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Shu HY, Chen CC, Ku HT, Wang CL, Wu KM, Weng HY, Liu ST, Chen CL, Chiu CH. Complete genome sequence of Bacillus halotolerans F29-3, a fengycin-producing strain. Microbiol Resour Announc 2024; 13:e0124623. [PMID: 38451104 PMCID: PMC11008187 DOI: 10.1128/mra.01246-23] [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: 12/20/2023] [Accepted: 02/11/2024] [Indexed: 03/08/2024] Open
Abstract
Bacillus halotolerans F29-3, a Gram-positive bacterium, is recognized for its synthesis of the antifungal substance fengycin. This announcement introduces the complete genome sequence and provides insights into the genetic products related to antibiotic secondary metabolites, including non-ribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and NRPS/PKS combination.
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Affiliation(s)
- Hung-Yu Shu
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Hsin-Tzu Ku
- Department of Bioscience Technology, Chang Jung Christian University, Tainan, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Keh-Ming Wu
- Bioinformatics Department, Welgene Biotech Co., Ltd., Taipei, Taiwan
| | - Hui-Ying Weng
- Biomedical Industry Ph.D. Program, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Shih-Tung Liu
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chyi-Liang Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Chang Gung Memorial Hospital, Taoyuan, Taiwan
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3
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Gutiérrez-García K, Whitaker MRL, Bustos-Díaz ED, Salzman S, Ramos-Aboites HE, Reitz ZL, Pierce NE, Cibrián-Jaramillo A, Barona-Gómez F. Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis. ISME COMMUNICATIONS 2023; 3:122. [PMID: 37993724 PMCID: PMC10665472 DOI: 10.1038/s43705-023-00323-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 10/17/2023] [Accepted: 10/25/2023] [Indexed: 11/24/2023]
Abstract
Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.
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Affiliation(s)
- Karina Gutiérrez-García
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - Melissa R L Whitaker
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA.
- Department of Biological Sciences, East Tennessee State University, Johnson City, TN, 37614, USA.
| | - Edder D Bustos-Díaz
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE, The Netherlands
| | - Shayla Salzman
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
- University of Georgia, Entomology Department, Athens, GA, 30602, USA
| | - Hilda E Ramos-Aboites
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
| | - Zachary L Reitz
- Bioinformatics Group, Wageningen University, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands
| | - Naomi E Pierce
- Museum of Comparative Zoology, Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford Street, Cambridge, MA, 02138, USA
| | - Angélica Cibrián-Jaramillo
- Ecological and Evolutionary Genomics Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México
- Naturalis Biodiversity Center, Darwinweg 2, 2333 CR, Leiden, The Netherlands
| | - Francisco Barona-Gómez
- Evolution of Metabolic Diversity Laboratory, Unidad de Genómica Avanzada (Langebio), Cinvestav-IPN, Km 9.6 Libramiento Irapuato - León, Irapuato, Guanajuato, 36824, México.
- Institute of Biology, Leiden University, Sylviusweg 72, Leiden, 2333 BE, The Netherlands.
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de Leon V, Orr K, Stelinski LL, Mandadi K, Ibanez-Carrasco F. Inoculation of Tomato With Plant Growth Promoting Rhizobacteria Affects the Tomato-Potato Psyllid-Candidatus Liberibacter Solanacearum Interactions. JOURNAL OF ECONOMIC ENTOMOLOGY 2023; 116:379-388. [PMID: 36723158 DOI: 10.1093/jee/toad006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Indexed: 05/30/2023]
Abstract
The Rio Grande Valley (RGV) in southern Texas is well-suited for vegetable production due to its relatively mild/warm weather conditions in the fall and winter. Consequently, insects inflict year-round, persistent damage to crops in the RGV and regions with similar climate. Bactericera cockerelli (Šulc) (Hemiptera: Triozidae), commonly known as the potato psyllid, is a known vector of Candidatus Liberibacter solanacearum (CLso) (Hyphomicrobiales: Rhizobiaceae), a fastidious phloem-limited bacterium associated to vein-greening in tomatoes and Zebra Chip in potatoes. Vector control is the primary approach of integrated pest management (IPM) strategies that aim to prevent plant diseases in commercial agricultural systems. However, resistance-selective pressures that decrease the effectiveness of chemical control (insecticide) applications over time are of increasing concern. Therefore, we explore an ecological approach to devising alternative IPM methodologies to manage the psyllid-transmitted CLso pathogen to supplement existing chemical products and application schedules without increasing resistance. In this study, our objective was to examine the effects of plant-growth promoting rhizobacteria (PGPR) on host-vector-pathogen interactions. Soil-drench applications of PGPRs to Solanum lycopersicum (Solanales: Solanaceae) seedlings revealed structural and possible physiological changes to the plant host and indirect changes on psyllid behavior: host plants had increased length and biomass of roots and exhibited delayed colonization by CLso, while psyllids displayed changes in parental (F0) psyllid behavior (orientation and oviposition) in response to treated hosts and in the sex ratio of their progeny (F1). Based on our results, we suggest that PGPR may have practical use in commercial tomato production.
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Affiliation(s)
- Victoria de Leon
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA
| | - Katharine Orr
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA
| | - Lukasz L Stelinski
- Department of Entomology and Nematology, Citrus Research and Education Center, University of Florida, Lake Alfred, FL, 33850, USA
| | - Kranthi Mandadi
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA
- Department of Plant Pathology & Microbiology, Texas A&M University, 496 Olsen Boulevard, College Station, TX, 77840, USA
- Institute for Advancing Health Through Agriculture, Texas A&M AgriLife, College Station, TX, USA
| | - Freddy Ibanez-Carrasco
- Texas A&M AgriLife Research and Extension Center, 2415 East US Highway 83, Weslaco, TX, 78596, USA
- Department of Entomology, Texas A&M University, Minnie Bell Heep Center, Suite 412, 2475 TAMU, 370 Olsen Boulevard, College Station, TX, 77843, USA
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Naranjo HD, Lebbe L, Cnockaert M, Lassalle F, Chin Too C, Willems A. Phylogenomics reveals insights into the functional evolution of the genus Agrobacterium and enables the description of Agrobacterium divergens sp. nov. Syst Appl Microbiol 2023; 46:126420. [PMID: 37031612 DOI: 10.1016/j.syapm.2023.126420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
The genus Agrobacterium was initially described as mainly phytopathogenic strains. Nowadays, the genus includes phytopathogenic and non-phytopathogenic bacteria that are distinctive among the Rhizobiaceae family. Recently we have isolated two closely related strains, LMG 31531T and LMG 31532, from soil and plant roots, respectively. Both strains differ from previously reported species based on the genomic and phenotypic data. A. arsenijevicii KFB 330T and A. fabacearum LMG 31642T showed the highest 16S rRNA similarity (98.9 %), followed by A. nepotum LMG 26435T (98.7 %). A clear genomic feature that distinguishes LMG 31531T and LMG 31532 from other Agrobacterium species is the absence of a linear chromid. Nevertheless, typical values of the core-proteome Average Amino Acid Identity (cpAAI > 85 %) and 16S rRNA gene sequence similarity (>96 %) when compared to other members of the genus confirm the position of these two strains as part of the Agrobacterium genus. They are therefore described as Agrobacterium divergens sp. nov. Besides, our comparative genomic study and survey for clade-specific markers resulted in the discovery of conserved proteins that provide insights into the functional evolution of this genus.
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Yue Z, Liu Y, Chen Y, Chen C, Zhang J, He L, Ma K. Comprehensive Genomics and Proteomics Analysis Reveals the Multiple Response Strategies of Endophytic Bacillus sp. WR13 to Iron Limitation. Microorganisms 2023; 11:microorganisms11020367. [PMID: 36838332 PMCID: PMC9961900 DOI: 10.3390/microorganisms11020367] [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: 01/15/2023] [Revised: 01/25/2023] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
Iron (Fe) is an important metal element for the growth of bacteria. Many bacteria respond to Fe limitation through a variety of strategies. We previously isolated an endophyte Bacillus sp. WR13 from wheat root. However, whether and how this strain can cope with Fe-deficient environments remains unclear. In this study, the growth of WR13 under Fe starvation was investigated, and the underlying mechanisms of WR13 in response to Fe starvation were elucidated via genomics and iTRAQ-based proteomics. Under Fe limitation, WR13 showed a growth pattern similar to that of Fe sufficiency. Genomics analysis demonstrated that WR13 had gene clusters related to siderophore synthesis (dhbACEBF), transportation (bcbE), uptake (feuABC-yusV) and hydrolysis (besA). These genes were significantly up-regulated in Fe-starved WR13, which resulted in more siderophore production. Proteomics data revealed that many Fe-containing proteins such as ACO, HemQ, ferredoxin, CNP, and SufD were significantly reduced under Fe limitation. Meanwhile, significant decreases in many proteins involved in glycolysis, TCA cycle, pentose phosphate pathway; asparagine, glutamine, methionine, and serine metabolism; and phospholipid hydrolysis were also observed. Overall, this study shows that Bacillus sp. WR13 was able to respond to Fe limitation via multiple strategies and provides a theoretical basis for the application of WR13 in Fe-deficient soil.
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Affiliation(s)
- Zonghao Yue
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
| | - Yongchuang Liu
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
| | - Yanjuan Chen
- School of Mechanical and Electrical Engineering, Zhoukou Normal University, Zhoukou 466001, China
| | - Can Chen
- Henan Key Laboratory of Plant Molecular Breeding and Bioreactor, Zhoukou 466001, China
| | - Ju Zhang
- Henan Key Laboratory of Plant Molecular Breeding and Bioreactor, Zhoukou 466001, China
| | - Le He
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
| | - Keshi Ma
- College of Life Sciences and Agronomy, Zhoukou Normal University, Zhoukou 466001, China
- Correspondence: ; Tel.: +86-158-9672-0176
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Kim J, Chhetri G, Kim I, So Y, Seo T. Paenibacillus agilis sp. nov., Paenibacillus cremeus sp. nov. and Paenibacillus terricola sp. nov., isolated from rhizosphere soils. Int J Syst Evol Microbiol 2022; 72. [PMID: 36748605 DOI: 10.1099/ijsem.0.005640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Members of the genus Paenibacillus are well known for their metabolic versatility and great application potential in plant growth promotion. Three novel bacterial strains, designated N4T, JC52T and PR3T, were isolated from rhizosphere soils and characterized by using a polyphasic taxonomic approach. The 16S rRNA gene sequence phylogenetic and phylogenomic analysis revealed that the three strains belonged to the genus Paenibacillus and formed three independent branches distinct from all reference strains. The results of DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) analyses between the three strains and their relatives further demonstrated that the three strains represented different novel genospecies. Strain N4T exhibited the highest similarity, ANI and digital DDH values with Paenibacillus assamensis DSM 18201T (99.0/87.5/33.9 %) and Paenibacillus insulae DS80T (97.2/-/18.2±1.2 %). Values for JC52T with Paenibacillus validus NBRC 15382T were 96.9, 73.3 and 19.6 %, and with Paenibacillus rigui JCM 16352T were 96.1, 72.1 and 19.3 %. Values for PR3T with Paenibacillus ginsengiterrae DCY89T were 98.2, - and 31.8±1.5 %, with Paenibacillus cellulosilyticus ASM318225v1T were 97.8, 83.3 and 26.7 %, and with Paenibacillus kobensis NBRC 15729T were 97.6, 75.7 and 20.4 %. Cells of the three novel bacterial strains were Gram-positive, spore-forming, motile and rod-shaped. The novel species contained anteiso-C15 : 0 and MK-7 as the predominant fatty acid and menaquinone, respectively. The novel strains have numerous similar known clusters of non-ribosomal peptide synthetases, siderophores, lanthipeptide, lassopeptide-like bacillibactin, paeninodin and polyketide-like chejuenolide A/B lankacidin C. Based on the distinct morphological, physiological, chemotaxonomic and phylogenetic differences from their closest phylogenetic neighbours, we propose that strains N4T, JC52T and PR3T represent novel species of the genus Paenibacillus, with the names Paenibacillus agilis sp. nov. (=KACC 19717T=JCM 32775T), Paenibacillus cremeus sp. nov. (=KACC 21221T=NBRC 113867T) and Paenibacillus terricola sp. nov. (=KACC 21455T=NBRC 114385T), respectively.
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Affiliation(s)
- Jiyoun Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Geeta Chhetri
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Inhyup Kim
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Yoonseop So
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
| | - Taegun Seo
- Department of Life Science, Dongguk University-Seoul, Goyang 10326, South Korea
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Ribeiro HG, Nilsson A, Melo LDR, Oliveira A. Analysis of intact prophages in genomes of Paenibacillus larvae: An important pathogen for bees. Front Microbiol 2022; 13:903861. [PMID: 35923395 PMCID: PMC9341999 DOI: 10.3389/fmicb.2022.903861] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 06/24/2022] [Indexed: 11/13/2022] Open
Abstract
Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious and worldwide spread bacterial disease that affects honeybee brood. In this study, all complete P. larvae genomes available on the NCBI database were analyzed in order to detect presence of prophages using the PHASTER software. A total of 55 intact prophages were identified in 11 P. larvae genomes (5.0 ± 2.3 per genome) and were further investigated for the presence of genes encoding relevant traits related to P. larvae. A closer look at the prophage genomes revealed the presence of several putative genes such as metabolic and antimicrobial resistance genes, toxins or bacteriocins, potentially influencing host performance. Some of the coding DNA sequences (CDS) were present in all ERIC-genotypes, while others were only found in a specific genotype. While CDS encoding toxins and antitoxins such as HicB and MazE were found in prophages of all bacterial genotypes, others, from the same category, were provided by prophages particularly to ERIC I (enhancin-like toxin), ERIC II (antitoxin SocA) and ERIC V strains (subunit of Panton-Valentine leukocidin system (PVL) LukF-PV). This is the first in-depth analysis of P. larvae prophages. It provides better knowledge on their impact in the evolution of virulence and fitness of P. larvae, by discovering new features assigned by the viruses.
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Affiliation(s)
- Henrique G. Ribeiro
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Anna Nilsson
- Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Luís D. R. Melo
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- *Correspondence: Luís D. R. Melo,
| | - Ana Oliveira
- LIBRO – Laboratório de Investigação em Biofilmes Rosário Oliveira, Centre of Biological Engineering, University of Minho, Braga, Portugal
- LABBELS – Associate Laboratory on Biotechnology and Bioengineering, and Electromechanical Systems, Centre of Biological Engineering, University of Minho, Braga, Portugal
- Ana Oliveira,
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Hoke AK, Reynoso G, Smith MR, Gardner MI, Lockwood DJ, Gilbert NE, Wilhelm SW, Becker IR, Brennan GJ, Crider KE, Farnan SR, Mendoza V, Poole AC, Zimmerman ZP, Utz LK, Wurch LL, Steffen MM. Genomic signatures of Lake Erie bacteria suggest interaction in the Microcystis phycosphere. PLoS One 2021; 16:e0257017. [PMID: 34550975 PMCID: PMC8457463 DOI: 10.1371/journal.pone.0257017] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/20/2021] [Indexed: 11/18/2022] Open
Abstract
Microbial interactions in harmful algal bloom (HAB) communities have been examined in marine systems, but are poorly studied in fresh waters. To investigate HAB-microbe interactions, we isolated bacteria with close associations to bloom-forming cyanobacteria, Microcystis spp., during a 2017 bloom in the western basin of Lake Erie. The genomes of five isolates (Exiguobacterium sp. JMULE1, Enterobacter sp. JMULE2, Deinococcus sp. JMULE3, Paenibacillus sp. JMULE4, and Acidovorax sp. JMULE5.) were sequenced on a PacBio Sequel system. These genomes ranged in size from 3.1 Mbp (Exiguobacterium sp. JMULE1) to 5.7 Mbp (Enterobacter sp. JMULE2). The genomes were analyzed for genes relating to critical metabolic functions, including nitrogen reduction and carbon utilization. All five of the sequenced genomes contained genes that could be used in potential signaling and nutrient exchange between the bacteria and cyanobacteria such as Microcystis. Gene expression signatures of algal-derived carbon utilization for two isolates were identified in Microcystis blooms in Lake Erie and Lake Tai (Taihu) at low levels, suggesting these organisms are active and may have a functional role during Microcystis blooms in aggregates, but were largely missing from whole water samples. These findings build on the growing evidence that the bacterial microbiome associated with bloom-forming algae have the functional potential to contribute to nutrient exchange within bloom communities and interact with important bloom formers like Microcystis.
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Affiliation(s)
- Alexa K. Hoke
- James Madison University, Harrisonburg, VA, United States of America
| | - Guadalupe Reynoso
- James Madison University, Harrisonburg, VA, United States of America
- Virginia Tech, Blacksburg, VA, United States of America
| | - Morgan R. Smith
- James Madison University, Harrisonburg, VA, United States of America
- Texas A&M University, College Station, TX, United States of America
| | - Malia I. Gardner
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Naomi E. Gilbert
- James Madison University, Harrisonburg, VA, United States of America
- University of Tennessee, Knoxville, TN, United States of America
| | | | | | - Grant J. Brennan
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Shannon R. Farnan
- James Madison University, Harrisonburg, VA, United States of America
| | - Victoria Mendoza
- James Madison University, Harrisonburg, VA, United States of America
| | - Alison C. Poole
- James Madison University, Harrisonburg, VA, United States of America
| | | | - Lucy K. Utz
- James Madison University, Harrisonburg, VA, United States of America
| | - Louie L. Wurch
- James Madison University, Harrisonburg, VA, United States of America
| | - Morgan M. Steffen
- James Madison University, Harrisonburg, VA, United States of America
- * E-mail:
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10
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Villa-Rodriguez E, Moreno-Ulloa A, Castro-Longoria E, Parra-Cota FI, de Los Santos-Villalobos S. Integrated omics approaches for deciphering antifungal metabolites produced by a novel Bacillus species, B. cabrialesii TE3 T, against the spot blotch disease of wheat (Triticum turgidum L. subsp. durum). Microbiol Res 2021; 251:126826. [PMID: 34298216 DOI: 10.1016/j.micres.2021.126826] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 07/01/2021] [Accepted: 07/12/2021] [Indexed: 10/20/2022]
Abstract
Bipolaris sorokiniana is an important biotic constraint for global wheat production, causing spot blotch disease. In this work, we present a comprehensive characterization of the cell-free culture filtrate (CF) and precipitated fraction (PF) of Bacillus cabrialesii TE3T showing an effective inhibition of spot blotch. Our results indicated that CF produced by B. cabrialesii TE3T inhibits the growth of B. sorokiniana through stable metabolites (after autoclaving and proteinase K treatment). Antifungal metabolites in CF and PF were explored by an integrated genomic-metabolomic approach. Genome-mining revealed that strain TE3T contains the biosynthetic potential to produce wide spectrum antifungal (surfactin, fengycin, and rhizocticin A) and antibacterial metabolites (bacillaene, bacilysin, bacillibactin, and subtilosin A), and through bioactivity-guided LC-ESI-MS/MS approach we determined that a lipopeptide complex of surfactin and fengycin homologs was responsible for antifungal activity exhibited by B. cabrialesii TE3T against the studied phytopathogen. In addition, our results demonstrate that i) a lipopeptide complex inhibits B. sorokiniana by disrupting its cytoplasmatic membrane and ii) reduced spot blotch disease by 93 %. These findings show the potential application of metabolites produced by strain TE3T against B. sorokiniana and provide the first insight into antifungal metabolites produced by the novel Bacillus species, Bacillus cabrialesii.
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Affiliation(s)
- Eber Villa-Rodriguez
- Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, Mexico
| | - Aldo Moreno-Ulloa
- Laboratorio MS2, Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Ensenada, Mexico
| | - Ernestina Castro-Longoria
- Departamento de Microbiología, Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California (CICESE), Ensenada, Mexico
| | - Fannie I Parra-Cota
- Campo Experimental Norman E. Borlaug- INIFAP, Norman E. Borlaug Km. 12, C.P. 85000, Ciudad Obregón, Sonora, Mexico
| | - Sergio de Los Santos-Villalobos
- Departamento de Ciencias Agronómicas y Veterinarias, Laboratorio de Biotecnología del Recurso Microbiano, Instituto Tecnológico de Sonora, 5 de febrero 818 Sur, C.P. 85000, Col. Centro, Ciudad Obregón, Sonora, Mexico.
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11
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Brudzynski K. Honey as an Ecological Reservoir of Antibacterial Compounds Produced by Antagonistic Microbial Interactions in Plant Nectars, Honey and Honey Bee. Antibiotics (Basel) 2021; 10:551. [PMID: 34065141 PMCID: PMC8151657 DOI: 10.3390/antibiotics10050551] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 04/08/2023] Open
Abstract
The fundamental feature of "active honeys" is the presence and concentration of antibacterial compounds. Currently identified compounds and factors have been described in several review papers without broader interpretation or links to the processes for their formation. In this review, we indicate that the dynamic, antagonistic/competitive microbe-microbe and microbe-host interactions are the main source of antibacterial compounds in honey. The microbial colonization of nectar, bees and honey is at the center of these interactions that in consequence produce a range of defence molecules in each of these niches. The products of the microbial interference and exploitive competitions include antimicrobial peptides, antibiotics, surfactants, inhibitors of biofilm formation and quorum sensing. Their accumulation in honey by horizontal transfer might explain honey broad-spectrum, pleiotropic, antibacterial activity. We conclude that honey is an ecological reservoir of antibacterial compounds produced by antagonistic microbial interactions in plant nectars, honey and honey bee. Thus, refocusing research on secondary metabolites resulting from these microbial interactions might lead to discovery of new antibacterial compounds in honey that are target-specific, i.e., acting on specific cellular components or inhibiting the essential cellular function.
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Affiliation(s)
- Katrina Brudzynski
- Department of Drug Discovery, Bee-Biomedicals Inc., St. Catharines, ON L2T 3T4, Canada;
- Formerly Department of Biological Sciences, Brock University, St. Catharines, ON L2T 3T4, Canada
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12
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Mishra AK, Baek KH. Salicylic Acid Biosynthesis and Metabolism: A Divergent Pathway for Plants and Bacteria. Biomolecules 2021; 11:705. [PMID: 34065121 PMCID: PMC8150894 DOI: 10.3390/biom11050705] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 01/24/2023] Open
Abstract
Salicylic acid (SA) is an active secondary metabolite that occurs in bacteria, fungi, and plants. SA and its derivatives (collectively called salicylates) are synthesized from chorismate (derived from shikimate pathway). SA is considered an important phytohormone that regulates various aspects of plant growth, environmental stress, and defense responses against pathogens. Besides plants, a large number of bacterial species, such as Pseudomonas, Bacillus, Azospirillum, Salmonella, Achromobacter, Vibrio, Yersinia, and Mycobacteria, have been reported to synthesize salicylates through the NRPS/PKS biosynthetic gene clusters. This bacterial salicylate production is often linked to the biosynthesis of small ferric-ion-chelating molecules, salicyl-derived siderophores (known as catecholate) under iron-limited conditions. Although bacteria possess entirely different biosynthetic pathways from plants, they share one common biosynthetic enzyme, isochorismate synthase, which converts chorismate to isochorismate, a common precursor for synthesizing SA. Additionally, SA in plants and bacteria can undergo several modifications to carry out their specific functions. In this review, we will systematically focus on the plant and bacterial salicylate biosynthesis and its metabolism.
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Affiliation(s)
| | - Kwang-Hyun Baek
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Korea;
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13
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The Buzz about ADP-Ribosylation Toxins from Paenibacillus larvae, the Causative Agent of American Foulbrood in Honey Bees. Toxins (Basel) 2021; 13:toxins13020151. [PMID: 33669183 PMCID: PMC7919650 DOI: 10.3390/toxins13020151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/02/2021] [Accepted: 02/11/2021] [Indexed: 11/26/2022] Open
Abstract
The Gram-positive, spore-forming bacterium Paenibacillus larvae is the etiological agent of American Foulbrood, a highly contagious and often fatal honey bee brood disease. The species P. larvae comprises five so-called ERIC-genotypes which differ in virulence and pathogenesis strategies. In the past two decades, the identification and characterization of several P. larvae virulence factors have led to considerable progress in understanding the molecular basis of pathogen-host-interactions during P. larvae infections. Among these virulence factors are three ADP-ribosylating AB-toxins, Plx1, Plx2, and C3larvin. Plx1 is a phage-born toxin highly homologous to the pierisin-like AB-toxins expressed by the whites-and-yellows family Pieridae (Lepidoptera, Insecta) and to scabin expressed by the plant pathogen Streptomyces scabiei. These toxins ADP-ribosylate DNA and thus induce apoptosis. While the presumed cellular target of Plx1 still awaits final experimental proof, the classification of the A subunits of the binary AB-toxins Plx2 and C3larvin as typical C3-like toxins, which ADP-ribosylate Rho-proteins, has been confirmed experimentally. Normally, C3-exoenzymes do not occur together with a B subunit partner, but as single domain toxins. Interestingly, the B subunits of the two P. larvae C3-like toxins are homologous to the B-subunits of C2-like toxins with striking structural similarity to the PA-63 protomer of Bacillus anthracis.
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14
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Lee SA, Kim TW, Heo J, Sang MK, Song J, Kwon SW, Weon HY. Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov., isolated from the rhizosphere of tomato (Solanum lycopersicum). J Microbiol 2020; 58:832-840. [PMID: 32989640 DOI: 10.1007/s12275-020-0258-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 08/26/2020] [Accepted: 08/31/2020] [Indexed: 11/25/2022]
Abstract
Two Gram-stain-positive, rod-shaped, endospore-forming bacteria, designated 12200R-189T and 14171R-81T were isolated from the rhizosphere of tomato plants. The 16S rRNA gene sequence similarity between strains 12200R-189T and 14171R-81T were 97.2%. Both strains showed the highest 16S rRNA gene sequence similarities to Paenibacillus sacheonensis SY01T (96.3% and 98.0%, respectively). The genome of strain 12200R-189T was approximately 6.7 Mb in size with 5,750 protein-coding genes (CDSs) and the G + C content was 58.1 mol%, whereas that of strain 14171R-81T comprised one chromosome of 7.0 Mb and two plasmids (0.2 Mb each) with 6,595 CDSs and the G + C content was 54.5 mol%. Comparative genome analysis revealed that average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among 12200R-189T, 14171R-81T, and other closely related species were below the cut-off levels 95% and 70%, respectively. Strain 12200R-189T grew at a temperature range of 15-40°C, pH 6.0-9.0, and 0-3% NaCl (w/v), whereas strain 14171R-81T grew at a temperature range of 10-37°C, pH 6.0-8.0, and 0-1% NaCl (w/v). Menaquinone-7 (MK-7) was the only isoprenoid quinone detected in both strains. The predominant cellular fatty acids (> 10%) were iso-C15:0, anteiso-C15:0, and iso-C16:0. The polar lipids of strain 12200R-189T were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), aminophospholipid (APL), phospholipid (PL), phosphatidylglycolipid (PGL), and four aminophosphoglycolipids (APGLs) and those of strain 14171R-81T were DPG, PG, PE, APL, three PLs, two PGLs, and three APGLs. Based on phylogenetic, genomic, phenotypic, and chemotaxonomic analyses, strains 12200R-189T and 14171R-81T represent two novel species of the genus Paenibacillus, for which the names Paenibacillus lycopersici sp. nov. and Paenibacillus rhizovicinus sp. nov. are proposed. The type strains are 12200R-189T (= KACC 19916T = CCTCC AB 2020027T) and 14171R-81T (= KACC 19915T = CCTCC AB 2020026T).
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Affiliation(s)
- Shin Ae Lee
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Tae-Wan Kim
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jun Heo
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Mee-Kyung Sang
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Jaekyeong Song
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Soon-Wo Kwon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Hang-Yeon Weon
- Agricultural Microbiology Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
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15
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Padayachee T, Nzuza N, Chen W, Nelson DR, Syed K. Impact of lifestyle on cytochrome P450 monooxygenase repertoire is clearly evident in the bacterial phylum Firmicutes. Sci Rep 2020; 10:13982. [PMID: 32814804 PMCID: PMC7438502 DOI: 10.1038/s41598-020-70686-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 07/30/2020] [Indexed: 12/18/2022] Open
Abstract
Cytochrome P450 monooxygenases (CYPs/P450s), heme thiolate proteins, are well known for their role in organisms' primary and secondary metabolism. Research on eukaryotes such as animals, plants, oomycetes and fungi has shown that P450s profiles in these organisms are affected by their lifestyle. However, the impact of lifestyle on P450 profiling in bacteria is scarcely reported. This study is such an example where the impact of lifestyle seems to profoundly affect the P450 profiles in the bacterial species belonging to the phylum Firmicutes. Genome-wide analysis of P450s in 972 Firmicutes species belonging to 158 genera revealed that only 229 species belonging to 37 genera have P450s; 38% of Bacilli species, followed by 14% of Clostridia and 2.7% of other Firmicutes species, have P450s. The pathogenic or commensal lifestyle influences P450 content to such an extent that species belonging to the genera Streptococcus, Listeria, Staphylococcus, Lactobacillus, Lactococcus and Leuconostoc do not have P450s, with the exception of a handful of Staphylococcus species that have a single P450. Only 18% of P450s are found to be involved in secondary metabolism and 89 P450s that function in the synthesis of specific secondary metabolites are predicted. This study is the first report on comprehensive analysis of P450s in Firmicutes.
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Affiliation(s)
- Tiara Padayachee
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa
| | - Nomfundo Nzuza
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa
| | - Wanping Chen
- Department of Molecular Microbiology and Genetics, University of Göttingen, 37077, Göttingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Khajamohiddin Syed
- Department of Biochemistry and Microbiology, Faculty of Science and Agriculture, University of Zululand, 1 Main Road Vulindlela, KwaDlangezwa, 3886, South Africa.
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16
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Miljaković D, Marinković J, Balešević-Tubić S. The Significance of Bacillus spp. in Disease Suppression and Growth Promotion of Field and Vegetable Crops. Microorganisms 2020; 8:microorganisms8071037. [PMID: 32668676 PMCID: PMC7409232 DOI: 10.3390/microorganisms8071037] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022] Open
Abstract
Bacillus spp. produce a variety of compounds involved in the biocontrol of plant pathogens and promotion of plant growth, which makes them potential candidates for most agricultural and biotechnological applications. Bacilli exhibit antagonistic activity by excreting extracellular metabolites such as antibiotics, cell wall hydrolases, and siderophores. Additionally, Bacillus spp. improve plant response to pathogen attack by triggering induced systemic resistance (ISR). Besides being the most promising biocontrol agents, Bacillus spp. promote plant growth via nitrogen fixation, phosphate solubilization, and phytohormone production. Antagonistic and plant growth-promoting strains of Bacillus spp. might be useful in formulating new preparations. Numerous studies of a wide range of plant species revealed a steady increase in the number of Bacillus spp. identified as potential biocontrol agents and plant growth promoters. Among different mechanisms of action, it remains unclear which individual or combined traits could be used as predictors in the selection of the best strains for crop productivity improvement. Due to numerous factors that influence the successful application of Bacillus spp., it is necessary to understand how different strains function in biological control and plant growth promotion, and distinctly define the factors that contribute to their more efficient use in the field.
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Affiliation(s)
- Dragana Miljaković
- Department of Microbiological Preparations, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
- Correspondence:
| | - Jelena Marinković
- Department of Microbiological Preparations, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Svetlana Balešević-Tubić
- Soybean Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
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17
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Khurana H, Sharma M, Verma H, Lopes BS, Lal R, Negi RK. Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential. Genomics 2020; 112:3191-3200. [PMID: 32512145 DOI: 10.1016/j.ygeno.2020.06.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 05/17/2020] [Accepted: 06/02/2020] [Indexed: 12/16/2022]
Abstract
The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.
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Affiliation(s)
- Himani Khurana
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Monika Sharma
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India
| | - Helianthous Verma
- Molecular Biology and Genomics Research Laboratory, Ramjas College, University of Delhi, Delhi 110007, India
| | - Bruno Silvester Lopes
- School of Medicine, Medical Sciences and Nutrition, Medical Microbiology, 0:025 Polwarth Building, Aberdeen AB25 2ZD, UK
| | - Rup Lal
- The Energy and Resources Institute, Darbari Seth Block, IHC Complex, Lodhi Road, New Delhi 110003, India.
| | - Ram Krishan Negi
- Fish Molecular Biology Laboratory, Department of Zoology, University of Delhi, Delhi 110007, India.
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18
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Turner M, Tremblay O, Heney K, Lugo M, Ebeling J, Genersch E, Merrill A. Characterization of C3larvinA, a novel RhoA-targeting ADP-ribosyltransferase toxin produced by the honey bee pathogen, Paenibacillus larvae. Biosci Rep 2020; 40:BSR20193405. [PMID: 31844879 PMCID: PMC6954368 DOI: 10.1042/bsr20193405] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 11/15/2019] [Accepted: 12/13/2019] [Indexed: 01/13/2023] Open
Abstract
C3larvinA is a putative virulence factor produced by Paenibacillus larvae enterobacterial-repetitive-intergenic-consensus (ERIC) III/IV (strain 11-8051). Biochemical, functional and structural analyses of C3larvinA revealed that it belongs to the C3-like mono-ADP-ribosylating toxin subgroup. Mammalian RhoA was the target substrate for its transferase activity suggesting that it may be the biological target of C3larvinA. The kinetic parameters of the NAD+ substrate for the transferase (KM = 75 ± 10 µM) and glycohydrolase (GH) (KM = 107 ± 20 µM) reactions were typical for a C3-like bacterial toxin, including the Plx2A virulence factor from Paenibacillus larvae ERIC I. Upon cytoplasmic expression in yeast, C3larvinA caused a growth-defective phenotype indicating that it is an active C3-like toxin and is cytotoxic to eukaryotic cells. The catalytic variant of the Q187-X-E189 motif in C3larvinA showed no cytotoxicity toward yeast confirming that the cytotoxicity of this factor depends on its enzymatic activity. A homology consensus model of C3larvinA with NAD+ substrate was built on the structure of Plx2A, provided additional confirmation that C3larvinA is a member of the C3-like mono-ADP-ribosylating toxin subgroup. A homology model of C3larvinA with NADH and RhoA was built on the structure of the C3cer-NADH-RhoA complex which provided further evidence that C3larvinA is a C3-like toxin that shares an identical catalytic mechanism with C3cer from Bacillus cereus. C3larvinA induced actin cytoskeleton reorganization in murine macrophages, whereas in insect cells, vacuolization and bi-nucleated cells were observed. These cellular effects are consistent with C3larvinA disrupting RhoA function by covalent modification that is shared among C3-like bacterial toxins.
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Affiliation(s)
- Madison Turner
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Olivier Tremblay
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Kayla A. Heney
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Miguel R. Lugo
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
| | - Julia Ebeling
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf 16540, Germany
| | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf 16540, Germany
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen, Berlin 14163, Germany
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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19
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Xie S, Vallet M, Sun C, Kunert M, David A, Zhang X, Chen B, Lu X, Boland W, Shao Y. Biocontrol Potential of a Novel Endophytic Bacterium From Mulberry ( Morus) Tree. Front Bioeng Biotechnol 2020; 7:488. [PMID: 32039187 PMCID: PMC6990687 DOI: 10.3389/fbioe.2019.00488] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/30/2019] [Indexed: 01/18/2023] Open
Abstract
Mulberry (Morus) is an economically important woody tree that is suitable for use in sericulture as forage and in medicine. However, this broad-leaved tree is facing multiple threats ranging from phytopathogens to insect pests. Here, a Gram-positive, endospore-forming bacterium (ZJU1) was frequently isolated from healthy mulberry plants by screening for foliar endophytes showing antagonism against pathogens and pests. Whole-genome sequencing and annotation resulted in a genome size of 4.06 Mb and classified the bacterium as a novel strain of Bacillus amyloliquefaciens that has rarely been identified from tree leaves. An integrative approach combining traditional natural product chemistry, activity bioassays, and high-resolution mass spectrometry confirmed that strain ZJU1 uses a blend of antimicrobials including peptides and volatile organic compounds to oppose Botrytis cinerea, a major phytopathogenic fungus causing mulberry gray mold disease. We showed that the inoculation of endophyte-free plants with ZJU1 significantly decreased both leaf necrosis and mortality under field conditions. In addition to the direct interactions of endophytes with foliar pathogens, in planta studies suggested that the inoculation of endophytes also induced plant systemic defense, including high expression levels of mulberry disease resistance genes. Moreover, when applied to the generalist herbivore Spodoptera litura, ZJU1 was sufficient to reduce the pest survival rate below 50%. A previously undiscovered crystal toxin (Cry10Aa) could contribute to this insecticidal effect against notorious lepidopteran pests. These unique traits clearly demonstrate that B. amyloliquefaciens ZJU1 is promising for the development of successful strategies for biocontrol applications. The search for new plant-beneficial microbes and engineering microbiomes is therefore of great significance for sustainably improving plant performance.
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Affiliation(s)
- Sen Xie
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Marine Vallet
- Max Planck Fellow Group on Plankton Community Interaction, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Maritta Kunert
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Anja David
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Xiancui Zhang
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Bosheng Chen
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xingmeng Lu
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Wilhelm Boland
- Department of Bioorganic Chemistry, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Yongqi Shao
- Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China.,Key Laboratory for Molecular Animal Nutrition, Ministry of Education, Hangzhou, China
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20
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Beims H, Bunk B, Erler S, Mohr KI, Spröer C, Pradella S, Günther G, Rohde M, von der Ohe W, Steinert M. Discovery of Paenibacillus larvae ERIC V: Phenotypic and genomic comparison to genotypes ERIC I-IV reveal different inventories of virulence factors which correlate with epidemiological prevalences of American Foulbrood. Int J Med Microbiol 2020; 310:151394. [PMID: 31959580 DOI: 10.1016/j.ijmm.2020.151394] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/16/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022] Open
Abstract
Paenibacillus larvae is the etiological agent of American Foulbrood (AFB), a highly contagious brood disease of honey bees (Apis mellifera). AFB requires mandatory reporting to the veterinary authority in many countries and until now four genotypes, P. larvae ERIC I-IV, have been identified. We isolated a new genotype, ERIC V, from a Spanish honey sample. After a detailed phenotypic comparison with the reference strains of the ERIC I-IV genotypes, including spore morphology, non-ribosomal peptide (NRP) profiling, and in vivo infections of A. mellifera larvae, we established a genomic DNA Macrorestriction Fragment Pattern Analysis (MRFPA) scheme for future epidemiologic discrimination. Whole genome comparison of the reference strains and the new ERIC V genotype (DSM 106052) revealed that the respective virulence gene inventories of the five genotypes corresponded with the time needed to kill 100 % of the infected bee larvae (LT100) in in vivo infection assays. The rarely isolated P. larvae genotypes ERIC II I-V with a fast-killing phenotype (LT100 3 days) harbor genes with high homology to virulence factors of other insect pathogens. These virulence genes are absent in the epidemiologically prevalent genotypes ERIC I (LT100 12 days) and ERIC II (LT100 7 days), which exhibit slower killing phenotypes. Since killing-retardation is known to reduce the success of hygienic cleaning by nurse bees, the identified absence of virulence factors might explain the epidemiological prevalences of ERIC genotypes. The discovery of the P. larvae ERIC V isolate suggests that more unknown ERIC genotypes exist in bee colonies. Since inactivation or loss of a few genes can transform a fast-killing phenotype into a more dangerous slow-killing phenotype, these rarely isolated genotypes may represent a hidden reservoir for future AFB outbreaks.
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Affiliation(s)
- Hannes Beims
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany; Lower Saxony State Office for Consumer Protection and Food Safety, Institute of Apiculture, Celle, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silvio Erler
- Martin-Luther-Universität Halle-Wittenberg, Institut für Biologie-Zoologie, Halle, Germany
| | - Kathrin I Mohr
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Department Microbial Drugs, Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Silke Pradella
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Gabi Günther
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany
| | - Manfred Rohde
- Central Facility for Microscopy, Helmholtz Centre for Infection Research, Department Microbial Drugs, Braunschweig, Germany
| | - Werner von der Ohe
- Lower Saxony State Office for Consumer Protection and Food Safety, Institute of Apiculture, Celle, Germany
| | - Michael Steinert
- Institut für Mikrobiologie, Technische Universität Braunschweig, Germany.
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21
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Erban T, Zitek J, Bodrinova M, Talacko P, Bartos M, Hrabak J. Comprehensive proteomic analysis of exoproteins expressed by ERIC I, II, III and IV Paenibacillus larvae genotypes reveals a wide range of virulence factors. Virulence 2019; 10:363-375. [PMID: 30957692 PMCID: PMC6527061 DOI: 10.1080/21505594.2019.1603133] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 03/28/2019] [Accepted: 03/28/2019] [Indexed: 11/12/2022] Open
Abstract
American foulbrood is a quarantine disease of the honeybee Apis mellifera L. in many countries and contributes greatly to colony losses. We performed a label-free proteomics study of exoprotein fractions produced in vitro by Paenibacillus larvae reference strains of the ERIC I-IV genotypes. A quantitative comparison was performed of previous studied protein-based virulence factors and many newly identified putative virulence factors. Among the multiple proteases identified, key virulence factors included the microbial collagenase ColA and immune inhibitor A (InhA, an analog of the Bacillus thuringiensis protein InhA). Both of these virulence factors were detected in ERICs II-IV but were absent from ERIC I. Furthermore, the different S-layer proteins and polysaccharide deacetylases prevailed in ERICs II-IV. Thus, the expression patterns of these virulence factors corresponded with the different speeds at which honeybee larvae are known to be killed by ERICs II-IV compared to ERIC I. In addition, putative novel toxin-like proteins were identified, including vegetative insecticidal protein Vip1, a mosquitocidal toxin, and epsilon-toxin type B, which exhibit similarity to homologs present in Bacillus thuringiensis or Lysinibacillus sphaericus. Furthermore, a putative bacteriocin similar to Lactococcin 972 was identified in all assayed genotypes. It appears that P. larvae shares virulence factors similar to those of the Bacillus cereus group. Overall, the results provide novel information regarding P. larvae virulence potential, and a comprehensive exoprotein comparison of all four ERICs was performed for the first time. The identification of novel virulence factors can explain differences in the virulence of isolates.
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Affiliation(s)
- Tomas Erban
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
| | - Justyna Zitek
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
- Department of Parasitology, Faculty of Science, Charles University, Prague 2, Czechia
| | - Miroslava Bodrinova
- Proteomics and Metabolomics Laboratory, Crop Research Institute, Prague, Czechia
| | - Pavel Talacko
- Proteomics Core Facility, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Milan Bartos
- BioVendor – Laboratorni medicina a.s., Brno, Czechia
| | - Jaroslav Hrabak
- Laboratory of Antibiotic Resistance and Applications of Mass Spectrometry in Microbiology, Biomedical Center and Institute of Microbiology, Faculty of Medicine in Plzen, Charles University, Plzen, Czechia
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Fe(III)-based immobilized metal-affinity chromatography (IMAC) method for the separation of the catechol siderophore from Bacillus tequilensis CD36. 3 Biotech 2018; 8:392. [PMID: 30175029 DOI: 10.1007/s13205-018-1396-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 08/07/2018] [Indexed: 12/15/2022] Open
Abstract
Catechol siderophore plays an important role in microbial ecology, agriculture, and medicine, but its research is often limited by the difficulty in acquisition of it in large quantities. Based on evidence from the coordination chemistry and chemical biology, catechol siderophore could chelate Fe3+ with high affinity. Therefore, Fe(III)-based immobilized metal-affinity chromatography (IMAC) was applied to capture siderophore from the culture filtrate of Bacillus tequilensis CD36. The ethanol-precipitated sample and the separated sample from Fe(III)-based IMAC were analyzed by liquid chromatography-mass spectrometry. According to the result, the pure siderophore DHB-Gly-Thr could be extracted from the ethanol-precipitated sample. Compared with other purifications, Fe(III)-based IMAC was convenient and had fewer steps. In addition, it also reduced the use of toxic chemical solvents in some traditional extraction process, such as extraction and ion exchange chromatography. Fe(III)-based IMAC was successfully used in separation of the catechol siderophore from B. tequilensis CD36. The results revealed that Fe(III)-based IMAC was an efficient and environmentally friendly method for the separation and purification of catechol siderophore.
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Fünfhaus A, Göbel J, Ebeling J, Knispel H, Garcia-Gonzalez E, Genersch E. Swarming motility and biofilm formation of Paenibacillus larvae, the etiological agent of American Foulbrood of honey bees (Apis mellifera). Sci Rep 2018; 8:8840. [PMID: 29892084 PMCID: PMC5995878 DOI: 10.1038/s41598-018-27193-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 05/29/2018] [Indexed: 12/19/2022] Open
Abstract
American Foulbrood is a worldwide distributed, fatal disease of the brood of the Western honey bee (Apis mellifera). The causative agent of this fatal brood disease is the Gram-positive, spore-forming bacterium Paenibacillus larvae, which can be classified into four different genotypes (ERIC I-IV), with ERIC I and II being the ones isolated from contemporary AFB outbreaks. P. larvae is a peritrichously flagellated bacterium and, hence, we hypothesized that P. larvae is capable of coordinated and cooperative multicellular behaviors like swarming motility and biofilm formation. In order to analyze these behaviors of P. larvae, we firstly established appropriate functional assays. Using these assays we demonstrated that P. larvae ERIC II, but not P. larvae ERIC I, was capable of swarming. Swarming motility was hampered in a P. larvae ERIC II-mutant lacking production of paenilarvin, an iturin-like lipopeptide exclusively expressed by this genotype. Both genotypes were able to form free floating biofilm aggregates loosely attached to the walls of the culture wells. Visualizing the biofilms by Congo red and thioflavin S staining suggested structural differences between the biofilms formed. Biofilm formation was shown to be independent from paenilarvin production because the paenilarvin deficient mutant was comparably able to form a biofilm.
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Affiliation(s)
- Anne Fünfhaus
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Josefine Göbel
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Julia Ebeling
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Henriette Knispel
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Eva Garcia-Gonzalez
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany.
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen, Berlin, Germany.
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Felicioli A, Turchi B, Fratini F, Giusti M, Nuvoloni R, Dani FR, Sagona S. Proteinase pattern of honeybee prepupae from healthy and American Foulbrood infected bees investigated by zymography. Electrophoresis 2018; 39:2160-2167. [PMID: 29761912 DOI: 10.1002/elps.201800112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/02/2018] [Accepted: 05/02/2018] [Indexed: 11/05/2022]
Abstract
American foulbrood disease (AFB) is the main devastating disease that affects honeybees' brood, caused by Paenibacillus larvae. The trend of the research on AFB has addressed the mechanisms by which P. larvae bacteria kill honeybee larvae. Since prepupae could react to the infection of AFB by increasing protease synthesis, the aim of this work was to compare protease activity in worker prepupae belonging to healthy colonies and to colonies affected by AFB. This investigation was performed by zymography. In gel, proteolytic activity was observed in prepupae extracts belonging only to the healthy colonies. In the prepupae extracts, 2D zimography followed by protein identification by MS allowed to detect Trypsin-1 and Chymotrypsin-1, which were not observed in diseased specimens. Further investigations are needed to clarify the involvement of these proteinases in the immune response of honeybee larvae and the mechanisms by which P. larvae inhibits protease production in its host.
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Affiliation(s)
| | - Barbara Turchi
- Department of Veterinary Science, Pisa University, Pisa, Italy
| | - Filippo Fratini
- Department of Veterinary Science, Pisa University, Pisa, Italy
| | - Matteo Giusti
- Department of Veterinary Science, Pisa University, Pisa, Italy
| | | | - Francesca Romana Dani
- Department of Biology, University of Firenze, Sesto Fiorentino, Italy.,Mass Spectrometry Centre (CISM) of Florence University, Sesto Fiorentino, Italy
| | - Simona Sagona
- Department of Veterinary Science, Pisa University, Pisa, Italy
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25
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Fünfhaus A, Ebeling J, Genersch E. Bacterial pathogens of bees. CURRENT OPINION IN INSECT SCIENCE 2018; 26:89-96. [PMID: 29764667 DOI: 10.1016/j.cois.2018.02.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 01/09/2018] [Accepted: 02/02/2018] [Indexed: 05/09/2023]
Abstract
Pollination is an indispensable ecosystem service provided by many insects, especially by wild and managed bee species. Hence, reports on large scale honey bee colony losses and on population declines of many wild bees were alarming and resulted in increased awareness of the importance of bee health and increased interest in bee pathogens. To serve this interest, this review will give a comprehensive overview on bacterial bee pathogens by covering not only the famous pathogens (Paenibacillus larvae, Melissococcus plutonius), but also the orphan pathogens which have largely been neglected by the scientific community so far (spiroplasmas) and the pathogens which were only recently discovered as being pathogenic to bees (Serratia marcescens, Lysinibacillus sphaericus).
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Affiliation(s)
- Anne Fünfhaus
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany
| | - Julia Ebeling
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany
| | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany; Freie Universität Berlin, Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen, Robert-von-Ostertag-Str. 7-13, 14163 Berlin, Germany.
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26
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Draft Genome Sequence of the Endophyte Paenibacillus sp. Strain GM2FR Isolated from Festuca rubra. GENOME ANNOUNCEMENTS 2018; 6:6/6/e00017-18. [PMID: 29439031 PMCID: PMC5805869 DOI: 10.1128/genomea.00017-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we report the 7.4-Mb draft genome sequence of Paenibacillus sp. strain GM2FR, an endophytic bacterium isolated from aerial plant tissues of Festuca rubra L. Genome analysis revealed 6,652 coding gene sequences and several gene clusters involved in plant growth promotion, such as that for the siderophore bacillibactin.
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27
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Forsgren E, Locke B, Sircoulomb F, Schäfer MO. Bacterial Diseases in Honeybees. CURRENT CLINICAL MICROBIOLOGY REPORTS 2018. [DOI: 10.1007/s40588-018-0083-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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28
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Descamps T, De Smet L, De Vos P, de Graaf D. Unbiased random mutagenesis contributes to a better understanding of the virulent behaviour ofPaenibacillus larvae. J Appl Microbiol 2017; 124:28-41. [DOI: 10.1111/jam.13611] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/09/2017] [Accepted: 09/28/2017] [Indexed: 01/12/2023]
Affiliation(s)
- T. Descamps
- Laboratory of Molecular Entomology and Bee Pathology; Faculty of Sciences; Ghent University; Ghent Belgium
| | - L. De Smet
- Laboratory of Molecular Entomology and Bee Pathology; Faculty of Sciences; Ghent University; Ghent Belgium
| | - P. De Vos
- Laboratory of Microbiology; Faculty of Sciences; Ghent University; Ghent Belgium
| | - D.C. de Graaf
- Laboratory of Molecular Entomology and Bee Pathology; Faculty of Sciences; Ghent University; Ghent Belgium
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29
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Ebeling J, Fünfhaus A, Knispel H, Krska D, Ravulapalli R, Heney KA, Lugo MR, Merrill AR, Genersch E. Characterization of the toxin Plx2A, a RhoA-targeting ADP-ribosyltransferase produced by the honey bee pathogenPaenibacillus larvae. Environ Microbiol 2017; 19:5100-5116. [DOI: 10.1111/1462-2920.13989] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 10/24/2017] [Accepted: 11/04/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Julia Ebeling
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
| | - Anne Fünfhaus
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
| | - Henriette Knispel
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
| | - Daniel Krska
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | | | - Kayla A. Heney
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | - Miguel R. Lugo
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | - A. Rod Merrill
- Department of Molecular and Cellular Biology; Guelph ON Canada N1G 2W1
| | - Elke Genersch
- Department of Molecular Microbiology and Bee Diseases; Institute for Bee Research; 16540 Hohen Neuendorf Germany
- Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen; Freie Universität Berlin; 14163 Berlin Germany
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30
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Li J, Liu S, Jiang Z, Sun C. Catechol amide iron chelators produced by a mangrove-derived Bacillus subtilis. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.07.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Erban T, Ledvinka O, Kamler M, Nesvorna M, Hortova B, Tyl J, Titera D, Markovic M, Hubert J. Honeybee (Apis mellifera)-associated bacterial community affected by American foulbrood: detection of Paenibacillus larvae via microbiome analysis. Sci Rep 2017; 7:5084. [PMID: 28698604 PMCID: PMC5506040 DOI: 10.1038/s41598-017-05076-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/24/2017] [Indexed: 12/15/2022] Open
Abstract
Honeybee (Apis mellifera L.) workers act as passive vectors of Paenibacillus larvae spores, which cause the quarantine disease American foulbrood (AFB). We assessed the relative proportions of P. larvae within the honeybee microbiome using metabarcoding analysis of the 16 S rRNA gene. The microbiome was analyzed in workers outside of the AFB zone (control - AFB0), in workers from asymptomatic colonies in an AFB apiary (AFB1), and in workers from colonies exhibiting clinical AFB symptoms (AFB2). The microbiome was processed for the entire community and for a cut-off microbiome comprising pathogenic/environmental bacteria following the removal of core bacterial sequences; varroosis levels were considered in the statistical analysis. No correlation was observed between AFB status and varroosis level, but AFB influenced the worker bee bacterial community, primarily the pathogenic/environmental bacteria. There was no significant difference in the relative abundance of P. larvae between the AFB1 and AFB0 colonies, but we did observe a 9-fold increase in P. larvae abundance in AFB2 relative to the abundance in AFB1. The relative sequence numbers of Citrobacter freundii and Hafnia alvei were higher in AFB2 and AFB1 than in AFB0, whereas Enterococcus faecalis, Klebsiella oxytoca, Spiroplasma melliferum and Morganella morganii were more abundant in AFB0 and AFB1 than in AFB2.
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Affiliation(s)
- Tomas Erban
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia.
| | - Ondrej Ledvinka
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
- Czech Hydrometeorological Institute, Na Sabatce 2050/17, Prague 412, CZ-143 06, Czechia
| | - Martin Kamler
- Bee Research Institute at Dol, Maslovice-Dol 94, Libcice nad Vltavou, CZ-252 66, Czechia
| | - Marta Nesvorna
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
| | - Bronislava Hortova
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
| | - Jan Tyl
- Bee Research Institute at Dol, Maslovice-Dol 94, Libcice nad Vltavou, CZ-252 66, Czechia
| | - Dalibor Titera
- Bee Research Institute at Dol, Maslovice-Dol 94, Libcice nad Vltavou, CZ-252 66, Czechia
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, Prague 6-Suchdol, Czechia
| | - Martin Markovic
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
| | - Jan Hubert
- Crop Research Institute, Drnovska 507/73, Prague 6-Ruzyne, CZ-161 06, Czechia
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32
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Grady EN, MacDonald J, Liu L, Richman A, Yuan ZC. Current knowledge and perspectives of Paenibacillus: a review. Microb Cell Fact 2016; 15:203. [PMID: 27905924 PMCID: PMC5134293 DOI: 10.1186/s12934-016-0603-7] [Citation(s) in RCA: 433] [Impact Index Per Article: 54.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 11/24/2016] [Indexed: 12/11/2022] Open
Abstract
Isolated from a wide range of sources, the genus Paenibacillus comprises bacterial species relevant to humans, animals, plants, and the environment. Many Paenibacillus species can promote crop growth directly via biological nitrogen fixation, phosphate solubilization, production of the phytohormone indole-3-acetic acid (IAA), and release of siderophores that enable iron acquisition. They can also offer protection against insect herbivores and phytopathogens, including bacteria, fungi, nematodes, and viruses. This is accomplished by the production of a variety of antimicrobials and insecticides, and by triggering a hypersensitive defensive response of the plant, known as induced systemic resistance (ISR). Paenibacillus-derived antimicrobials also have applications in medicine, including polymyxins and fusaricidins, which are nonribosomal lipopeptides first isolated from strains of Paenibacillus polymyxa. Other useful molecules include exo-polysaccharides (EPS) and enzymes such as amylases, cellulases, hemicellulases, lipases, pectinases, oxygenases, dehydrogenases, lignin-modifying enzymes, and mutanases, which may have applications for detergents, food and feed, textiles, paper, biofuel, and healthcare. On the negative side, Paenibacillus larvae is the causative agent of American Foulbrood, a lethal disease of honeybees, while a variety of species are opportunistic infectors of humans, and others cause spoilage of pasteurized dairy products. This broad review summarizes the major positive and negative impacts of Paenibacillus: its realised and prospective contributions to agriculture, medicine, process manufacturing, and bioremediation, as well as its impacts due to pathogenicity and food spoilage. This review also includes detailed information in Additional files 1, 2, 3 for major known Paenibacillus species with their locations of isolation, genome sequencing projects, patents, and industrially significant compounds and enzymes. Paenibacillus will, over time, play increasingly important roles in sustainable agriculture and industrial biotechnology.
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Affiliation(s)
- Elliot Nicholas Grady
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Jacqueline MacDonald
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
| | - Linda Liu
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Alex Richman
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada, 1391 Sandford Street, London, ON N5V 4T3 Canada
- Department of Microbiology & Immunology, Schulich School of Medicine & Dentistry, University of Western Ontario, Dental Science Building Rm. 3014, London, ON N6A 5C1 Canada
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Dingman DW. Functionality of Tn916 in Paenibacillus larvae. Arch Microbiol 2016; 199:487-493. [PMID: 27864589 DOI: 10.1007/s00203-016-1321-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/07/2016] [Accepted: 11/12/2016] [Indexed: 11/26/2022]
Abstract
The conjugative transposon Tn916 was determined to be functional in Paenibacillus larvae in regard to expression of tetracycline resistance and conjugative transfer. Expression of erythromycin resistance, using Tn916ΔE, was also observed. Conjugative transfer experiments employing Paenibacillus popilliae strains Tc1001 and Em1001 as transposon donors and experiments using different P. larvae subspecies or different transposon-containing strains demonstrated interspecies and intraspecies transfer occurred for Tn916 and Tn916ΔE. Southern hybridization analysis of several Tn916-containing P. larvae isolates showed that the transposon randomly inserted into the bacterial chromosome with an indication that hot spot insertion had occurred. Hybridization analysis indicated single-copy insertion of Tn916 into the genome predominated. However, selection of multiple-resistant isolates (i.e., isolates containing Tn916 and Tn916ΔE) demonstrated that multiple copies of the transposon could coexist in the bacterial genome. Growth of transposon-containing isolates in broth medium in the absence of selective antibiotic pressure showed that Tn916 and Tn916ΔE were stably maintained in the bacterium.
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Affiliation(s)
- Douglas W Dingman
- Department of Entomology, Connecticut Agricultural Experiment Station, 123 Huntington Street, P.O. Box 1106, New Haven, CT, 06504, USA.
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34
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Hertlein G, Seiffert M, Gensel S, Garcia-Gonzalez E, Ebeling J, Skobalj R, Kuthning A, Süssmuth RD, Genersch E. Biological Role of Paenilarvins, Iturin-Like Lipopeptide Secondary Metabolites Produced by the Honey Bee Pathogen Paenibacillus larvae. PLoS One 2016; 11:e0164656. [PMID: 27760211 PMCID: PMC5070912 DOI: 10.1371/journal.pone.0164656] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/28/2016] [Indexed: 12/16/2022] Open
Abstract
The Gram-positive bacterium Paenibacillus larvae (P. larvae) is the causative agent of a deadly honey bee brood disease called American Foulbrood (AFB). AFB is a notifiable epizootic in most countries and, hence, P. larvae is of considerable relevance for veterinarians and apiculturists alike. Over the last decade, much progress has been made in the understanding of the (patho)biology of P. larvae. Recently, several non-ribosomally produced peptides (NRP) and peptide/polyketide (NRP/PK) hybrids produced by P. larvae were identified. Among these NRPs were iturin-like lipopeptides, the paenilarvins A-C. Iturins are known to exhibit strong anti-fungal activity; for some iturins, cytotoxic activity towards mammalian erythrocytes and human cancer cell lines are described. We here present our results on the analysis of the natural function of the paenilarvins during pathogenesis of P. larvae infections. We demonstrated production of paenilarvins in infected larvae. However, we could neither demonstrate cytotoxicity of paenilarvins towards cultured insect cells nor towards larvae in feeding assays. Accordingly, exposure bioassays performed with larvae infected by wild-type P. larvae and a knockout mutant of P. larvae lacking production of paenilarvins did not substantiate a role for the paenilarvins as virulence factor. Further experiments are necessary to analyze the relevance of the paenilarvins' anti-fungal activity for P. larvae infections in the presence of fungal competitors in the larval midgut or cadaver.
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Affiliation(s)
- Gillian Hertlein
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Marlene Seiffert
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Sebastian Gensel
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Eva Garcia-Gonzalez
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Julia Ebeling
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
| | - Ranko Skobalj
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | - Anja Kuthning
- Technische Universität Berlin, Institut für Chemie, Berlin, Germany
| | | | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Hohen Neuendorf, Germany
- Freie Universität Berlin, Fachbereich Veterinärmedizin, Institut für Mikrobiologie und Tierseuchen, Berlin, Germany
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35
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Biology of Paenibacillus larvae, a deadly pathogen of honey bee larvae. Appl Microbiol Biotechnol 2016; 100:7387-95. [PMID: 27394713 DOI: 10.1007/s00253-016-7716-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 06/28/2016] [Accepted: 06/30/2016] [Indexed: 01/23/2023]
Abstract
The gram-positive bacterium Paenibacillus larvae is the etiological agent of American Foulbrood of honey bees, a notifiable disease in many countries. Hence, P. larvae can be considered as an entomopathogen of considerable relevance in veterinary medicine. P. larvae is a highly specialized pathogen with only one established host, the honey bee larva. No other natural environment supporting germination and proliferation of P. larvae is known. Over the last decade, tremendous progress in the understanding of P. larvae and its interactions with honey bee larvae at a molecular level has been made. In this review, we will present the recent highlights and developments in P. larvae research and discuss the impact of some of the findings in a broader context to demonstrate what we can learn from studying "exotic" pathogens.
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Lee DE, Lee S, Jang ES, Shin HW, Moon BS, Lee CH. Metabolomic Profiles of Aspergillus oryzae and Bacillus amyloliquefaciens During Rice Koji Fermentation. Molecules 2016; 21:molecules21060773. [PMID: 27314317 PMCID: PMC6273993 DOI: 10.3390/molecules21060773] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 12/18/2022] Open
Abstract
Rice koji, used early in the manufacturing process for many fermented foods, produces diverse metabolites and enzymes during fermentation. Using gas chromatography time-of-flight mass spectrometry (GC-TOF-MS), ultrahigh-performance liquid chromatography linear trap quadrupole ion trap tandem mass spectrometry (UHPLC-LTQ-IT-MS/MS), and multivariate analysis we generated the metabolite profiles of rice koji produced by fermentation with Aspergillus oryzae (RK_AO) or Bacillus amyloliquefaciens (RK_BA) for different durations. Two principal components of the metabolomic data distinguished the rice koji samples according to their fermenter species and fermentation time. Several enzymes secreted by the fermenter species, including α-amylase, protease, and β-glucosidase, were assayed to identify differences in expression levels. This approach revealed that carbohydrate metabolism, serine-derived amino acids, and fatty acids were associated with rice koji fermentation by A. oryzae, whereas aromatic and branched chain amino acids, flavonoids, and lysophospholipids were more typical in rice koji fermentation by B. amyloliquefaciens. Antioxidant activity was significantly higher for RK_BA than for RK_AO, as were the abundances of flavonoids, including tricin, tricin glycosides, apigenin glycosides, and chrysoeriol glycosides. In summary, we have used MS-based metabolomics and enzyme activity assays to evaluate the effects of using different microbial species and fermentation times on the nutritional profile of rice koji.
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Affiliation(s)
- Da Eun Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea.
| | - Sunmin Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea.
| | - Eun Seok Jang
- Foods Research Institute, CJ CheilJedang Corp., Suwon 16495, Korea.
| | - Hye Won Shin
- Foods Research Institute, CJ CheilJedang Corp., Suwon 16495, Korea.
| | - Byoung Seok Moon
- Foods Research Institute, CJ CheilJedang Corp., Suwon 16495, Korea.
| | - Choong Hwan Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Korea.
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Poppinga L, Genersch E. Molecular pathogenesis of American Foulbrood: how Paenibacillus larvae kills honey bee larvae. CURRENT OPINION IN INSECT SCIENCE 2015; 10:29-36. [PMID: 29588011 DOI: 10.1016/j.cois.2015.04.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/17/2015] [Accepted: 04/21/2015] [Indexed: 06/08/2023]
Abstract
American Foulbrood caused by Paenibacillus larvae is one of the unsolved health problems honey bee colonies are suffering from. In the recent past, considerable progress has been achieved in understanding molecular details of P. larvae infections of honey bee larvae. This was facilitated by the development of molecular tools for manipulating P. larvae and by the availability of complete genome sequences of different P. larvae genotypes. We here report on several peptides and proteins that have recently been identified, biochemically analyzed, and proposed to act as virulence factors of P. larvae. For some of them, experimental proof for their role as virulence factor has been provided allowing presenting a preliminary model for the molecular pathogenesis of American Foulbrood.
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Affiliation(s)
- Lena Poppinga
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany
| | - Elke Genersch
- Institute for Bee Research, Department of Molecular Microbiology and Bee Diseases, Friedrich-Engels-Str. 32, 16540 Hohen Neuendorf, Germany.
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Müller S, Garcia-Gonzalez E, Genersch E, Süssmuth RD. Involvement of secondary metabolites in the pathogenesis of the American foulbrood of honey bees caused by Paenibacillus larvae. Nat Prod Rep 2015; 32:765-78. [DOI: 10.1039/c4np00158c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Gram-positive spore-forming bacterium Paenibacillus larvae is the causative agent of the fatal disease American Foulbrood of the western honey bee. This article highlights recent findings on secondary metabolites synthesized by P. larvae.
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Affiliation(s)
| | - Eva Garcia-Gonzalez
- Institute for Bee Research
- Department of Molecular Microbiology and Bee Diseases
- Hohen Neuendorf
- Germany
| | - Elke Genersch
- Institute for Bee Research
- Department of Molecular Microbiology and Bee Diseases
- Hohen Neuendorf
- Germany
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Tang Y, Frewert S, Harmrolfs K, Herrmann J, Karmann L, Kazmaier U, Xia L, Zhang Y, Müller R. Heterologous expression of an orphan NRPS gene cluster from Paenibacillus larvae in Escherichia coli revealed production of sevadicin. J Biotechnol 2014; 194:112-4. [PMID: 25529345 DOI: 10.1016/j.jbiotec.2014.12.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Revised: 12/08/2014] [Accepted: 12/11/2014] [Indexed: 12/11/2022]
Abstract
The Gram-positive bacterium Paenibacillus larvae is the causative agent of the fateful honey bee disease American Foulbrood (AFB). Sequence analysis of P. larvae genomic DNA showed the presence of numerous nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS) encoding gene clusters, not correlating with secondary metabolite production. As NRPS and PKS derived metabolites are known to exhibit diverse biological activities, their identification is of particular interest for infection and drug research. Here an 11.6kb orphan NRPS gene cluster was directly cloned from the genomic DNA of P. larvae and expressed in Escherichia coli resulting in the production of sevadicin. Isolation of the metabolite was followed by structural characterization, synthesis and bioactivity studies.
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Affiliation(s)
- Ying Tang
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, PR China; Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Simon Frewert
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Kirsten Harmrolfs
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Jennifer Herrmann
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany
| | - Lisa Karmann
- Institute for Organic Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Uli Kazmaier
- Institute for Organic Chemistry, Saarland University, 66123 Saarbrücken, Germany
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, PR China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Life Science College, Shandong University, 250100 Jinan, PR China.
| | - Rolf Müller
- Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland, Helmholtz Centre for Infection Research & Pharmaceutical Biotechnology, Saarland University, 66123 Saarbrücken, Germany.
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