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Pilz M, Cavelius P, Qoura F, Awad D, Brück T. Lipopeptides development in cosmetics and pharmaceutical applications: A comprehensive review. Biotechnol Adv 2023; 67:108210. [PMID: 37460047 DOI: 10.1016/j.biotechadv.2023.108210] [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: 01/26/2023] [Revised: 07/05/2023] [Accepted: 07/09/2023] [Indexed: 07/25/2023]
Abstract
Lipopeptides are surface active, natural products of bacteria, fungi and green-blue algae origin, having diverse structures and functionalities. In analogy, a number of chemical synthesis techniques generated new designer lipopeptides with desirable features and functions. Lipopetides are self-assembly guided, supramolecular compounds which have the capacity of high-density presentation of the functional epitopes at the surface of the nanostructures. This feature contributes to their successful application in several industry sectors, including food, feed, personal care, and pharmaceutics. In this comprehensive review, the novel class of ribosomally synthesized lipopeptides is introduced alongside the more commonly occuring non-ribosomal lipopeptides. We highlight key representatives of the most researched as well as recently described lipopeptide families, with emphasis on structural features, self-assembly and associated functions. The common biological, chemical and hybrid production routes of lipopeptides, including prominent analogues and derivatives are also discussed. Furthermore, genetic engineering strategies aimed at increasing lipopeptide yields, diversity and biological activity are summarized and exemplified. With respect to application, this work mainly details the potential of lipopeptides in personal care and cosmetics industry as cleansing agents, moisturizer, anti-aging/anti-wrinkling, skin whitening and preservative agents as well as the pharmaceutical industry as anitimicrobial agents, vaccines, immunotherapy, and cancer drugs. Given that this review addresses human applications, we conclude on the topic of safety of lipopeptide formulations and their sustainable production.
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Affiliation(s)
- Melania Pilz
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Philipp Cavelius
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Farah Qoura
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany
| | - Dania Awad
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
| | - Thomas Brück
- Werner Siemens-Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), 85748 Garching, Germany.
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Secretome of Paenibacillus sp. S-12 provides an insight about its survival and possible pathogenicity. Folia Microbiol (Praha) 2023:10.1007/s12223-023-01032-4. [PMID: 36642775 DOI: 10.1007/s12223-023-01032-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
Our aim in this study was to characterize and investigate the secretome of Paenibacillus sp. S-12 by nanoLC-MS/MS tool-based analysis of trypsin digested culture supernatant proteins. Using a bioinformatics and combined approach of mass spectrometry, we identified 657 proteins in the secretome. Bioinformatic tools such as PREDLIPO, SecretomeP 2.0, SignalP 4.1, and PSORTb were used for the subcellular localization and categorization of secretome on basis of signal peptides. Among the identified proteins, more than 25% of the secretome proteins were associated with virulence proteins including flagellar, adherence, and immune modulators. Gene ontology analysis using Blast2GO tools categorized 60 proteins of the secretome into biological processes, cellular components, and molecular functions. KEGG pathway analysis identified the enzymes or proteins involved in various biosynthesis and degradation pathways. Functional analysis of secretomes reveals a large number of proteins involved in the uptake and exchange of nutrients, colonization, and chemotaxis. A good number of proteins were involved in survival and defense mechanism against oxidative stress, the production of toxins and antimicrobial compounds. The present study is the first report of the in-depth protein profiling of Paenibacillus bacterium. In summary, the current findings of Paenibacillus sp. S-12 secretome provide basic information to understand its survival and the possible pathogenic mechanism.
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Screening and Characterization of Two Extracellular Polysaccharide-Producing Bacteria from the Biocrust of the Mu Us Desert. Molecules 2021; 26:molecules26185521. [PMID: 34576992 PMCID: PMC8466918 DOI: 10.3390/molecules26185521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 11/17/2022] Open
Abstract
The extracellular polysaccharide (EPS) matrix embedding microbial cells and soil particles plays an important role in the development of biological soil crusts (BSCs), which is widely recognized as beneficial to soil fertility in dryland worldwide. This study examined the EPS-producing bacterial strains YL24-1 and YL24-3 isolated from sandy soil in the Mu Us Desert in Yulin, Shaanxi province, China. The strains YL24-1 and YL24-3 were able to efficiently produce EPS; the levels of EPS were determined to be 257.22 μg/mL and 83.41 μg/mL in cultures grown for 72 h and were identified as Sinorhizobium meliloti and Pedobacter sp., respectively. When the strain YL24-3 was compared to Pedobacter yulinensis YL28-9T using 16S rRNA gene sequencing, the resemblance was 98.6% and the strain was classified as Pedobacter sp. using physiological and biochemical analysis. Furthermore, strain YL24-3 was also identified as a subspecies of Pedobacter yulinensis YL28-9T on the basis of DNA–DNA hybridization and polar lipid analysis compared with YL28-9T. On the basis of the EPS-related genes of relevant strains in the GenBank, several EPS-related genes were cloned and sequenced in the strain YL24-1, including those potentially involved in EPS synthesis, assembly, transport, and secretion. Given the differences of the strains in EPS production, it is possible that the differences in gene sequences result in variations in the enzyme/protein activities for EPS biosynthesis, assembly, transport, and secretion. The results provide preliminary evidence of various contributions of bacterial strains to the formation of EPS matrix in the Mu Us Desert.
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de Araújo TF, Ortega DB, da Costa RA, Andrade IEPC, Fulgêncio DLA, Mendonça ML, Costa FS, Leite ML, Ramada MHS, Barreto CC. Co-occurrence of linear and cyclic pelgipeptins in broth cultures of Paenibacillus elgii AC13. Braz J Microbiol 2021; 52:1825-1833. [PMID: 34435341 DOI: 10.1007/s42770-021-00597-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/15/2021] [Indexed: 10/20/2022] Open
Abstract
Paenibacillus elgii AC13 produces antimicrobial lipopeptides of agricultural and pharmaceutical importance. It secretes four cyclic lipopeptides named pelgipeptins, previously characterized in P. elgii B69. These lipopeptides result from the expression of a nonribosomal peptide gene cluster. P. elgii AC13 also produced two linear lipopeptides with ratios of [M + H] + 1105 and 1119 m/z. These compounds were previously observed in Paenibacillus sp. strain OSY-N, but due to purification difficulties, their characterization was executed using synthetically produced linear pelgipeptins. In the present study, purification was achieved from the supernatants of cultures from three complex media by high-performance liquid chromatography. The partial characterization of linear pelgipeptins revealed the similar antimicrobial activity and cytotoxicity of their synthetically produced counterparts, known as paenipeptins. Cyclic forms were highly stable to changes in pH, temperature, and organic extraction with n-butanol as shown by mass spectrometry (MALDI-TOF); therefore, these steps did not cause the hydrolysis of pelgipeptins. A low-activity thioesterase could also generate the linear isoforms observed; this enzyme catalyzes the cyclization process and is coded in the same gene cluster. Alternatively, the cyclic forms were hydrolyzed by an unknown protease produced during growth in the complex medium used in the present study. Although culture conditions are known to produce pelgipeptins with different yields and amino acid compositions, the occurrence of linear and cyclic forms simultaneously has not yet been reported. A mixture of cyclic and linear pelgipeptins presents a potential advantage of the higher antimicrobial activity of cyclic forms combined with the lower cytotoxicity of linear isoforms.
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Affiliation(s)
- Thiago Fellipe de Araújo
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | - Daniel Barros Ortega
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | - Rosiane Andrade da Costa
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | | | - Débora Luiza Albano Fulgêncio
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | - Marise Leite Mendonça
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | - Flávio Silva Costa
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | - Michel Lopes Leite
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | - Marcelo Henrique Soller Ramada
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil
| | - Cristine Chaves Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Universidade Católica de Brasília, SGAN 916, Brasília, DF, 70790-160, Brazil.
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Fulgêncio DLA, da Costa RA, Guilhelmelli F, Silva CMDS, Ortega DB, de Araujo TF, Silva PS, Silva-Pereira I, Albuquerque P, Barreto CC. In vitro antifungal activity of pelgipeptins against human pathogenic fungi and Candida albicans biofilms. AIMS Microbiol 2021; 7:28-39. [PMID: 33659767 PMCID: PMC7921374 DOI: 10.3934/microbiol.2021003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/11/2021] [Indexed: 12/13/2022] Open
Abstract
Systemic mycoses have become a major cause of morbidity and mortality, particularly among immunocompromised hosts and long-term hospitalized patients. Conventional antifungal agents are limited because of not only their costs and toxicity but also the rise of resistant strains. Lipopeptides from Paenibacillus species exhibit antimicrobial activity against a wide range of human and plant bacterial pathogens. However, the antifungal potential of these compounds against important human pathogens has not yet been fully evaluated, except for Candida albicans. Paenibacillus elgii produces a family of lipopeptides named pelgipeptins, which are synthesized by a non-ribosomal pathway, such as polymyxin. The present study aimed to evaluate the activity of pelgipeptins produced by P. elgii AC13 against Cryptococcus neoformans, Paracoccidioides brasiliensis, and Candida spp. Pelgipeptins were purified from P. elgii AC13 cultures and characterized by high-performance liquid chromatography (HPLC) and mass spectrometry (MALDI-TOF MS). The in vitro antifugal activity of pelgipeptins was evaluated against C. neoformans H99, P. brasiliensis PB18, C. albicans SC 5314, Candida glabrata ATCC 90030, and C. albicans biofilms. Furthermore, the minimal inhibitory concentration (MIC) was determined according to the CLSI microdilution method. Fluconazole and amphotericin B were also used as a positive control. Pelgipeptins A to D inhibited the formation and development of C. albicans biofilms and presented activity against all tested microorganisms. The minimum inhibitory concentration values ranged from 4 to 64 µg/mL, which are in the same range as fluconazole MICs. These results highlight the potential of pelgipeptins not only as antimicrobials against pathogenic fungi that cause systemic mycoses but also as coating agents to prevent biofilm formation on medical devices.
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Affiliation(s)
| | - Rosiane Andrade da Costa
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
| | - Fernanda Guilhelmelli
- Laboratory of Molecular Biology, Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Calliandra Maria de Souza Silva
- Laboratory of Molecular Biology, Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Daniel Barros Ortega
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
| | - Thiago Fellipe de Araujo
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
| | - Philippe Spezia Silva
- Laboratory of Molecular Biology, Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Ildinete Silva-Pereira
- Laboratory of Molecular Biology, Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil
| | - Patrícia Albuquerque
- Laboratory of Molecular Biology, Department of Cellular Biology, Institute of Biological Sciences, University of Brasília, Brasília, Brazil.,Faculty of Ceilandia, University of Brasília, Brasília, Brazil
| | - Cristine Chaves Barreto
- Graduate Program in Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasília, Brazil
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Sampaio de Oliveira KB, Leite ML, Rodrigues GR, Duque HM, da Costa RA, Cunha VA, de Loiola Costa LS, da Cunha NB, Franco OL, Dias SC. Strategies for recombinant production of antimicrobial peptides with pharmacological potential. Expert Rev Clin Pharmacol 2020; 13:367-390. [PMID: 32357080 DOI: 10.1080/17512433.2020.1764347] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION The need to develop new drugs for the control of pathogenic microorganisms has redoubled efforts to prospect for antimicrobial peptides (AMPs) from natural sources and to characterize its structure and function. These molecules present a broad spectrum of action against different microorganisms and frequently present promiscuous action, with anticancer and immunomodulatory activities. Furthermore, AMPs can be used as biopharmaceuticals in the treatment of hospital-acquired infections and other serious diseases with relevant social and economic impacts.Areas covered: The low yield and the therefore difficult extraction and purification process in AMPs are problems that limit their industrial application and scientific research. Thus, optimized heterologous expression systems were developed to significantly boost AMP yields, allow high efficiency in purification and structural optimization for the increase of therapeutic activity.Expert opinion: This review provides an update on recent developments in the recombinant production of ribosomal and non-ribosomal synthesis of AMPs and on strategies to increase the expression of genes encoding AMPs at the transcriptional and translational levels and regulation of the post-translational modifications. Moreover, there are detailed reports of AMPs that have already reached marketable status or are in the pipeline under advanced stages of preclinical testing.
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Affiliation(s)
- Kamila Botelho Sampaio de Oliveira
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Michel Lopes Leite
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Gisele Regina Rodrigues
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Rosiane Andrade da Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Victor Albuquerque Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Lorena Sousa de Loiola Costa
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Nicolau Brito da Cunha
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil
| | - Octavio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Patologia Molecular, Campus Darcy Ribeiro , Brasília, Brazil.,S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco , Campo Grande, Mato Grosso do Sul, Brazil
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília , Brasília, Brazil.,Universidade de Brasília, Pós-graduação em Biologia Animal, Campus Darcy Ribeiro , Brasília, Brazil
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7
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Song M, Liu Y, Huang X, Ding S, Wang Y, Shen J, Zhu K. A broad-spectrum antibiotic adjuvant reverses multidrug-resistant Gram-negative pathogens. Nat Microbiol 2020; 5:1040-1050. [PMID: 32424338 DOI: 10.1038/s41564-020-0723-z] [Citation(s) in RCA: 222] [Impact Index Per Article: 55.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 04/14/2020] [Indexed: 12/13/2022]
Abstract
The rapid emergence and dissemination of multidrug-resistant (MDR) bacterial pathogens pose a serious threat to global healthcare. One particular concern is the carbapenem-resistant Enterobacteriaceae (CRE), a group of Gram-negative bacteria that have evolved resistance to all or nearly all available antibiotics. Coupled with the fact of barren antibiotic development pipeline nowadays, a critical approach is to revitalize existing antibiotics using antibiotic adjuvants. We found a short linear antibacterial peptide (SLAP)-S25 carrying four non-natural amino acids of 2,4-diaminobutanoic acid (Dab), which solely showed weak antibacterial activity but boosted the efficacy of antibiotics covering all major classes, including cefepime, colistin, ofloxacin, rifampicin, tetracycline and vancomycin, against MDR Gram-negative pathogens. Mechanistic studies showed that SLAP-S25 triggers membrane damage by binding to both lipopolysaccharide (LPS) in the outer membrane and phosphatidylglycerol (PG) in bacterial cytoplasmic membrane, to potentiate antibiotic efficacy through collaborative strategies. Lastly, SLAP-S25 effectively enhanced the activity of colistin against MDR Escherichia coli-associated infections in three animal models. Our findings provide a potential therapeutic option using existing antibiotics in combination with broad-spectrum antibiotic adjuvants, to address the prevalent infections caused by MDR Gram-negative pathogens worldwide.
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Affiliation(s)
- Meirong Song
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yuan Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Institute of Comparative Medicine, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Xiaoyong Huang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Shuangyang Ding
- National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China
| | - Yang Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianzhong Shen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China. .,National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China. .,Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety and Beijing Laboratory for Food Quality and Safety, China Agricultural University, Beijing, China.
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing, China. .,National Center for Veterinary Drug Safety Evaluation, College of Veterinary Medicine, China Agricultural University, Beijing, China.
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Kim J, Le KD, Yu NH, Kim JI, Kim JC, Lee CW. Structure and antifungal activity of pelgipeptins from Paenibacillus elgii against phytopathogenic fungi. PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY 2020; 163:154-163. [PMID: 31973853 DOI: 10.1016/j.pestbp.2019.11.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 05/27/2023]
Abstract
Paenibacillus elgii JCK1400 shows strong antifungal activity against various plant pathogenic fungi in vitro, but little is known about its mode of action. Four antifungal lipopeptides were isolated from P. elgii JCK1400 using bioassay-directed fractionation. Their chemical structures were determined to be pelgipeptins (PGPs) using electrospray ionization tandem mass spectrometry (ESI-MS/MS) and nuclear magnetic resonance (NMR) spectroscopy. Among the four lipopeptides, PGP-C showed the strongest mycelial growth inhibitory activity against several plant pathogenic fungi-with minimum inhibitory concentration (MIC) values ranging from 4 to 32 μg mL-1-followed by PGP-D, -A, and -B. In pot experiments, PGP-C also effectively suppressed the development of important fungal diseases in crops. In particular, PGP-C was effective in controlling tomato grey mold and wheat leaf rust, with control values of 91% and 73%, respectively, at a concentration of 125 μg mL-1. The fermentation broth of the antagonistic bacterium reduced the development of creeping bentgrass dollar spot and Kentucky bluegrass brown patch in a dose-dependent manner. However, our study on the effect of PGP-C on the fungal cell membrane-using microscopic observation with propidium iodide (PI) fluorescence-indicated that PGP-C does not target the fungal cell walls, but instead targets the cell membranes. This is the first study to report the in vitro and in vivo antifungal activity of PGP-C against various plant pathogenic fungi. Our results suggest that P. elgii JCK1400, which produces PGPs, could serve as a potential biocontrol agent for plant diseases caused by various fungi.
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Affiliation(s)
- Jueun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Khanh Duy Le
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Nan Hee Yu
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jae Il Kim
- Department of Life Science, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea.
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
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Le KD, Kim J, Yu NH, Kim B, Lee CW, Kim JC. Biological Control of Tomato Bacterial Wilt, Kimchi Cabbage Soft Rot, and Red Pepper Bacterial Leaf Spot Using Paenibacillus elgii JCK-5075. FRONTIERS IN PLANT SCIENCE 2020; 11:775. [PMID: 32714339 PMCID: PMC7340725 DOI: 10.3389/fpls.2020.00775] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/15/2020] [Indexed: 05/14/2023]
Abstract
The over and repeated use of chemical bactericides to control plant bacterial diseases has resulted in unwanted effects, such as environmental pollution, residual toxicity, and resistance buildup in bacterial pathogens. Many previous studies have aimed to develop biological control agents to replace chemical bactericides. In this study, the antibacterial efficacy of the fermentation broth of Paenibacillus elgii JCK-5075 and its antibacterial compounds were evaluated against plant pathogenic bacteria, using both in vitro and in vivo bioassays. Pelgipeptins (PGPs) A, B, C, and D that were isolated from P. elgii JCK-5075 displayed broad-spectrum antibacterial activity against various plant pathogenic bacteria. The fermentation broth of P. elgii JCK-5075, at 5-fold dilution, effectively suppressed the development of tomato bacterial wilt, Kimchi cabbage soft rot, and red pepper bacterial leaf spot in pot experiments with control values of 81, 84, and 67%, respectively. PGP-A and C, at 200 μg/ml, were also found to markedly reduce the development of Kimchi cabbage bacterial soft rot by 75% and tomato bacterial wilt by 83%, respectively, and their disease control efficacy was comparable to that of oxolinic acid with control values of 81 and 85%, respectively. Additionally, the antibacterial activity of PGP-C was found to be directly correlated with membrane damage mechanisms. These results indicates that P. elgii JCK-5075 producing PGPs could be used as a biocontrol agent for the control of plant bacterial diseases. This is the first report on the in vitro and in vivo antibacterial activity of PGPs against bacterial plant pathogens.
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Affiliation(s)
- Khanh Duy Le
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Jueun Kim
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
| | - Nan Hee Yu
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Bora Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University, Gwangju, South Korea
- *Correspondence: Chul Won Lee,
| | - Jin-Cheol Kim
- Department of Agricultural Chemistry, Institute of Environmentally Friendly Agriculture, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, South Korea
- Jin-Cheol Kim,
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10
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Olishevska S, Nickzad A, Déziel E. Bacillus and Paenibacillus secreted polyketides and peptides involved in controlling human and plant pathogens. Appl Microbiol Biotechnol 2019; 103:1189-1215. [DOI: 10.1007/s00253-018-9541-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/22/2018] [Accepted: 11/23/2018] [Indexed: 12/25/2022]
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11
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Costa RA, Ortega DB, Fulgêncio DL, Costa FS, Araújo TF, Barreto CC. Checkerboard testing method indicates synergic effect of pelgipeptins against multidrug resistant Klebsiella pneumoniae. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.biori.2018.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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12
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Isolation and structural elucidation of pelgipeptin E, a novel pore-forming pelgipeptin analog from Paenibacillus elgii with low hemolytic activity. J Antibiot (Tokyo) 2018; 71:1008-1017. [PMID: 30135470 DOI: 10.1038/s41429-018-0095-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/18/2018] [Accepted: 07/31/2018] [Indexed: 01/06/2023]
Abstract
Pelgipeptins are cyclic lipopeptides composed of nine amino acids and a short fatty acid chain. In the present study, we report a novel pelgipeptin peptide that was isolated from Paenibacillus elgii BC34-6 and named pelgipeptin E (PGP-E). The molecular mass of PGP-E was 1072 Da as determined by liquid chromatography-mass spectrometry and the amino acid sequence was elucidated by tandem mass spectrometry. The complete molecular structure of PGP-E was characterized using 2D NMR spectroscopy. PGP-E consisted of a cyclic peptide backbone of Dab1-Val2-Dab3-Phe4-Leu5-Dab6-Val7-Leu8-Ser9 and a lipid chain (-CH2CH2CH3). PGP-E had broad antimicrobial activity against gram-negative and -positive bacteria, including methicillin-resistant Staphylococcus aureus strains. Furthermore, the mode of action of PGP-E was investigated using calcein dye leakage and membrane depolarization assays, which suggest that PGP-E acts via a membrane-active mechanism. The hemolytic activity of PGP-E was significantly lower than that of melittin, a well-known membrane-active peptide derived from bee venom. These results suggest that PGP-E is a potential candidate in the development of new peptide antibiotics.
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Huang E, Yang X, Zhang L, Moon SH, Yousef AE. New Paenibacillus strain produces a family of linear and cyclic antimicrobial lipopeptides: cyclization is not essential for their antimicrobial activity. FEMS Microbiol Lett 2018; 364:3052911. [PMID: 28333237 DOI: 10.1093/femsle/fnx049] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/23/2017] [Indexed: 11/14/2022] Open
Abstract
A new bacterial isolate, Paenibacillus sp. OSY-N, showed potent antimicrobial activity against Gram-negative and Gram-positive bacteria. Antimicrobials produced by this strain were purified by reverse-phase high-performance liquid chromatography. Structural analysis, using mass spectrometry, of a single active HPLC fraction revealed two known cyclic lipopeptides (BMY-28160 and permetin A), a new cyclic lipopeptide, and the linear counterparts of these cyclic compounds. The latter were designated as paenipeptins A, B and C, respectively. The paenipeptins have not been reported before as naturally occurring products. Paenipeptins B and C differ at the acyl side chain; paenipeptin C contains a C8-, instead of C7-fatty acyl side chain. To demonstrate unequivocally the antimicrobial activity of the linear forms of this family of cyclic lipopeptides, analogs of the paenipeptins were synthesized chemically and their antimicrobial activity was tested individually. The synthetic linear lipopeptide with an octanoic acid side chain (designated as paenipeptin C΄) showed potent antimicrobial activity with minimum inhibitory concentrations of 0.5-4.0 μg/mL for Gram-negative and 0.5-32 μg/mL for Gram-positive bacteria. Findings demonstrated that peptide cyclization in this lipopeptide family is not essential for their antimicrobial activity. Most importantly, linear lipopeptides are more accessible than their cyclic counterparts through chemical synthesis.
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Affiliation(s)
- En Huang
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Xu Yang
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Road, Columbus, OH 43210, USA
| | - Liwen Zhang
- Mass Spectrometry and Proteomics Facility, The Ohio State University, OH 43210, USA
| | - Sun Hee Moon
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Ahmed E Yousef
- Department of Food Science and Technology, The Ohio State University, 2015 Fyffe Road, Columbus, OH 43210, USA.,Department of Microbiology, The Ohio State University, 484 West 12th Avenue, OH 43210, USA
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Zhao P, Xue Y, Gao W, Li J, Zu X, Fu D, Bai X, Zuo Y, Hu Z, Zhang F. Bacillaceae-derived peptide antibiotics since 2000. Peptides 2018; 101:10-16. [PMID: 29269072 DOI: 10.1016/j.peptides.2017.12.018] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 12/18/2017] [Accepted: 12/18/2017] [Indexed: 10/18/2022]
Abstract
Members of the Bacillaceae family, including Bacillus spp., Brevibacillus spp., Paenibacillus spp., Aneurinibacillus sp., and Halobacillus sp., are an important source of structurally diverse classes of short peptides of ∼ 30 residues or fewer possessing peculiar and rapid killing activity against various pathogens. Additionally, many have unique structures that enhance resistance to hydrolysis by proteases, and these are ideal therapeutic tools and potential alternatives to current antibiotics. The need for novel antibiotic lead compounds is urgent, and this review summarises 119 Bacillaceae compounds published since 2000, including 12 surfactin-like lipopeptides, 16 iturinic lipopeptides, fengycin C, 33 other cyclic lipopeptides, 26 linear lipopeptides, two thiopeptides, four 2,5-diketopiperazines, 20 typical cyclic peptides, and five standard linear peptides. The current and potential therapeutic applications of these peptides, including structure, antibacterial, antifungal, and antiviral activities, are discussed.
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Affiliation(s)
- Pengchao Zhao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yun Xue
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China.
| | - Weina Gao
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Jinghua Li
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xiangyang Zu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Dongliao Fu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Xuefei Bai
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Yanjun Zuo
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Zhigang Hu
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
| | - Fengshou Zhang
- College of Medical Technology and Engineering, Henan University of Science and Technology, Luoyang, 471023, China
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First Insights into the Draft Genome Sequence of the Endophyte Paenibacillus amylolyticus Strain GM1FR, Isolated from Festuca rubra L. GENOME ANNOUNCEMENTS 2018; 6:6/4/e01516-17. [PMID: 29371353 PMCID: PMC5786679 DOI: 10.1128/genomea.01516-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Paenibacillus amylolyticus strain GM1FR is an endophyte isolated from aerial plant tissues of Festuca rubra L. Here, we report the draft genome sequence (7.3 Mb) of GM1FR containing 6,241 protein-coding genes, some of which are potentially involved in plant growth promotion and biocontrol.
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Mountford SJ, Mohanty B, Roberts KD, Yu HH, Scanlon MJ, Nation RL, Velkov T, Li J, Thompson PE. The first total synthesis and solution structure of a polypeptin, PE2, a cyclic lipopeptide with broad spectrum antibiotic activity. Org Biomol Chem 2017; 15:7173-7180. [PMID: 28812779 DOI: 10.1039/c7ob01493g] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first total synthesis of a polypeptin, PE2, as well as its solution structure is reported. Synthesis in optically pure form confirms the proposed stereochemistry of the polypeptins at the 3-position on the 3-hydroxy depsipeptide moiety. We have also determined the NMR structure of PE2 in aqueous solution, showing it to form a stable ring conformation. The synthetic peptide shows anti-bacterial activity consistent with reports for naturally derived counterparts.
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Affiliation(s)
- Simon J Mountford
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville 3052, Australia.
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17
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Ahangari A, Salouti M, Saghatchi F. Gentamicin-gold nanoparticles conjugate: a contrast agent for X-ray imaging of infectious foci due to Staphylococcus aureus. IET Nanobiotechnol 2017; 10:190-4. [PMID: 27463788 DOI: 10.1049/iet-nbt.2015.0034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
There is no optimal imaging method for the detection of unknown infectious foci in some diseases. This study introduces a novel method in X-ray imaging of infection foci due to Staphylococcus aureus by developing a contrast agent based on gold nanoparticles (GNPs). GNPs in spherical shape were synthesised by the reduction of tetrachloroauric acid with sodium citrate. Then gentamicin was bound directly to citrate functionalised GNPs and the complex was stabilised by polyethylene glycol. The interaction of gentamicin with GNPs was confirmed by ultraviolet-visible and Fourier transform infrared spectroscopies. The stability of complex was studied in human blood up to 6 h. The stability of conjugate was found to be high in human blood with no aggregation. The biodistribution study showed localisation of gentamicin-GNPs conjugate at the site of Staphylococcal infection. The infection site was properly visualised in X-ray images in mouse model using the gentamicin-GNPs conjugate as a contrast agent. The results demonstrated that one may consider the potential of new nanodrug as a contrast agent for X-ray imaging of infection foci in human beings which needs more investigations.
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Affiliation(s)
- Azam Ahangari
- Young Researchers and Elite Club, Hidaj Branch, Islamic Azad University, Hidaj, Iran
| | - Mojtaba Salouti
- Biology Research Center, Zanjan Branch, Islamic Azad University, Zanjan, Iran.
| | - Faranak Saghatchi
- Department of Radiology, Faculty of Paramedical and Health Sciences, Zanjan University of Medical Science, Zanjan, Iran
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18
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Zhao X, Kuipers OP. Identification and classification of known and putative antimicrobial compounds produced by a wide variety of Bacillales species. BMC Genomics 2016; 17:882. [PMID: 27821051 PMCID: PMC5100339 DOI: 10.1186/s12864-016-3224-y] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2016] [Accepted: 10/27/2016] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gram-positive bacteria of the Bacillales are important producers of antimicrobial compounds that might be utilized for medical, food or agricultural applications. Thanks to the wide availability of whole genome sequence data and the development of specific genome mining tools, novel antimicrobial compounds, either ribosomally- or non-ribosomally produced, of various Bacillales species can be predicted and classified. Here, we provide a classification scheme of known and putative antimicrobial compounds in the specific context of Bacillales species. RESULTS We identify and describe known and putative bacteriocins, non-ribosomally synthesized peptides (NRPs), polyketides (PKs) and other antimicrobials from 328 whole-genome sequenced strains of 57 species of Bacillales by using web based genome-mining prediction tools. We provide a classification scheme for these bacteriocins, update the findings of NRPs and PKs and investigate their characteristics and suitability for biocontrol by describing per class their genetic organization and structure. Moreover, we highlight the potential of several known and novel antimicrobials from various species of Bacillales. CONCLUSIONS Our extended classification of antimicrobial compounds demonstrates that Bacillales provide a rich source of novel antimicrobials that can now readily be tapped experimentally, since many new gene clusters are identified.
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Affiliation(s)
- Xin Zhao
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, People's Republic of China
| | - Oscar P Kuipers
- Department of Molecular Genetics, University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands.
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Aw YK, Ong KS, Lee LH, Cheow YL, Yule CM, Lee SM. Newly Isolated Paenibacillus tyrfis sp. nov., from Malaysian Tropical Peat Swamp Soil with Broad Spectrum Antimicrobial Activity. Front Microbiol 2016; 7:219. [PMID: 26973605 PMCID: PMC4771734 DOI: 10.3389/fmicb.2016.00219] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/10/2016] [Indexed: 12/21/2022] Open
Abstract
Emergence of antimicrobial resistance coupled with the slowdown in discovery of new antimicrobial compounds points to serious consequences for human health. Therefore, scientists are looking for new antimicrobial compounds from unique and understudied ecosystems such as tropical peat swamp forests. Over the course of isolating antimicrobial producing bacteria from North Selangor tropical peat swamp forest, Malaysia, a Gram variable, rod shaped, endospore forming, facultative anaerobic novel strain MSt1T that exerts potent and broad spectrum antimicrobial activity was isolated. Phylogenetic analysis using 16S rRNA gene sequences showed that strain MSt1T belonged to the genus Paenibacillus with the highest similarity to Paenibacillus elgii SD17T (99.5%). Whole genome comparison between strain MSt1T with its closely related species using average nucleotide identity (ANI) revealed that similarity between strain MSt1T with P. elgii B69 (93.45%) and Paenibacillus ehimensis A2 (90.42%) was below the recommended threshold of 95%. Further analysis using in silico pairwise DDH also showed that similarity between strain MSt1T with P. elgii B69 (55.4%) and P. ehimensis A2 (43.7%) was below the recommended threshold of 70%. Strain MSt1T contained meso-diaminopilemic acid in the cell wall and MK-7 as the major menaquinone. The major fatty acids of strain MSt1T were anteiso-C15:0 (48.2%) and C16:0 (29.0%) whereas the polar lipid profile consisted of phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, one unknown lipid, two unknown glycolipids, and one unknown phospholipid. Total DNA G+C content of strain MSt1T was 51.5 mol%. The extract from strain MSt1T exerted strong antimicrobial activity against Escherichia coli ATCC 25922 (MIC = 1.5 μg/mL), MRSA ATCC 700699 (MIC = 25 μg/mL) and Candida albicans IMR (MIC = 12.5 μg/mL). Partially purified active fraction exerted a strong effect against E. coli ATCC 25922 resulting in cell rupture when viewed with SEM. Based on distinctive taxonomic differences between strain MSt1T when compared to its closely related type species, we propose that strain MSt1T represents a novel species within the genus of Paenibacillus, for which the name Paenibacillus tyrfis sp. nov. (= DSM 100708T = MCCC 1K01247T) is proposed.
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Affiliation(s)
- Yoong-Kit Aw
- Tropical Biology Multidisciplinary Platform, School of Science, Monash University MalaysiaBandar Sunway, Malaysia; School of Science, Monash University MalaysiaBandar Sunway, Malaysia
| | - Kuan-Shion Ong
- Tropical Biology Multidisciplinary Platform, School of Science, Monash University MalaysiaBandar Sunway, Malaysia; School of Science, Monash University MalaysiaBandar Sunway, Malaysia
| | - Learn-Han Lee
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia Bandar Sunway, Malaysia
| | - Yuen-Lin Cheow
- School of Science, Monash University Malaysia Bandar Sunway, Malaysia
| | - Catherine M Yule
- Tropical Biology Multidisciplinary Platform, School of Science, Monash University MalaysiaBandar Sunway, Malaysia; School of Science, Monash University MalaysiaBandar Sunway, Malaysia
| | - Sui-Mae Lee
- Tropical Biology Multidisciplinary Platform, School of Science, Monash University MalaysiaBandar Sunway, Malaysia; School of Science, Monash University MalaysiaBandar Sunway, Malaysia
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20
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Inès M, Dhouha G. Lipopeptide surfactants: Production, recovery and pore forming capacity. Peptides 2015; 71:100-12. [PMID: 26189973 DOI: 10.1016/j.peptides.2015.07.006] [Citation(s) in RCA: 113] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 06/30/2015] [Accepted: 07/03/2015] [Indexed: 12/26/2022]
Abstract
Lipopeptides are microbial surface active compounds produced by a wide variety of bacteria, fungi and yeast. They are characterized by highly structural diversity and have the ability to decrease the surface and interfacial tension at the surface and interface, respectively. Surfactin, iturin and fengycin of Bacillus subtilis are among the most studied lipopeptides. This review will present the main factors encountering lipopeptides production along with the techniques developed for their extraction and purification. Moreover, we will discuss their ability to form pores and destabilize biological membrane permitting their use as antimicrobial, hemolytic and antitumor agents. These open great potential applications in biomediacal, pharmaceutic and agriculture fields.
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Affiliation(s)
- Mnif Inès
- Higher Institute of Biotechnology, Tunisia; Unit Enzymes and Bioconversion, National School of Engineers, Tunisia.
| | - Ghribi Dhouha
- Higher Institute of Biotechnology, Tunisia; Unit Enzymes and Bioconversion, National School of Engineers, Tunisia
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21
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Vater J, Niu B, Dietel K, Borriss R. Characterization of Novel Fusaricidins Produced by Paenibacillus polymyxa-M1 Using MALDI-TOF Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1548-1558. [PMID: 26100395 DOI: 10.1007/s13361-015-1130-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Revised: 02/18/2015] [Accepted: 03/03/2015] [Indexed: 06/04/2023]
Abstract
Paenibacillus polymyxa-M1 is a potent producer of bioactive compounds, such as lipopeptides, polyketides, and lantibiotics of biotechnological and medical interest. Genome sequencing revealed nine gene clusters for nonribosomal biosynthesis of such agents. Here we report on the investigation of the fusaricidins, a complex of cyclic lipopeptides containing 15-guanidino-3-hydroxypentadecanoic acid (GHPD) as fatty acid component by matrix-assisted laser-desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). More than 20 variants of these compounds were detected and characterized in detail. Mass spectrometric sequence analysis was performed by MALDI-LIFT-TOF/TOF fragment analysis. The obtained product ion spectra show a specific processing in the fatty acid part. GHPD is cleaved between the α- and ß-position yielding two fragments a and b, one bearing the end-standing guanidine group and another one comprising the residual two C-atoms of GHPD with the attached peptide moiety. The complete sequence of all fusaricidins was derived from sets of bn- and yn-ions. The fusaricidin complex can be divided into four lipopeptide families, three of them showing variations of the amino acid in position 3, Val or Ile for the first and Tyr or Phe for families 2 and 3, respectively. A collection of novel fusaricidins was detected differing from those of families 1-3 by an additional residue of 71 Da (family 4). LIFT-TOF/TOF fragment spectra of these species imply that in their peptide moiety, an Ala-residue is attached by an ester bond to the free hydroxyl group of Thr4. More than 10 novel fusaricidins were characterized mass spectrometrically.
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Affiliation(s)
- Joachim Vater
- Institut für Chemie, Technische Universität Berlin, Mueller-Breslau-Straße 10, 10623, Berlin, Germany,
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22
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Genome mining: Prediction of lipopeptides and polyketides from Bacillus and related Firmicutes. Comput Struct Biotechnol J 2015; 13:192-203. [PMID: 25893081 PMCID: PMC4397504 DOI: 10.1016/j.csbj.2015.03.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 03/15/2015] [Accepted: 03/16/2015] [Indexed: 11/20/2022] Open
Abstract
Bacillus and related genera in the Bacillales within the Firmicutes harbor a variety of secondary metabolite gene clusters encoding polyketide synthases and non-ribosomal peptide synthetases responsible for remarkable diverse number of polyketides (PKs) and lipopeptides (LPs). These compounds may be utilized for medical and agricultural applications. Here, we summarize the knowledge on structural diversity and underlying gene clusters of LPs and PKs in the Bacillales. Moreover, we evaluate by using published prediction tools the potential metabolic capacity of these bacteria to produce type I PKs or LPs. The huge sequence repository of bacterial genomes and metagenomes provides the basis for such genome-mining to reveal the potential for novel structurally diverse secondary metabolites. The otherwise cumbersome task to isolate often unstable PKs and deduce their structure can be streamlined. Using web based prediction tools, we identified here several novel clusters of PKs and LPs from genomes deposited in the database. Our analysis suggests that a substantial fraction of predicted LPs and type I PKs are uncharacterized, and their functions remain to be studied. Known and predicted LPs and PKs occurred in the majority of the plant associated genera, predominantly in Bacillus and Paenibacillus. Surprisingly, many genera from other environments contain no or few of such compounds indicating the role of these secondary metabolites in plant-associated niches.
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Fracchia L, J. Banat J, Cavallo M, Ceresa C, M. Banat I. Potential therapeutic applications of microbial surface-active compounds. AIMS BIOENGINEERING 2015. [DOI: 10.3934/bioeng.2015.3.144] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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24
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Cochrane SA, Vederas JC. Lipopeptides from Bacillus and Paenibacillus spp.: A Gold Mine of Antibiotic Candidates. Med Res Rev 2014; 36:4-31. [DOI: 10.1002/med.21321] [Citation(s) in RCA: 261] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - John C. Vederas
- Department of Chemistry; University of Alberta; Alberta Canada
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25
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Schild HA, Fuchs SW, Bode HB, Grünewald B. Low-molecular-weight metabolites secreted by Paenibacillus larvae as potential virulence factors of American foulbrood. Appl Environ Microbiol 2014; 80:2484-92. [PMID: 24509920 PMCID: PMC3993163 DOI: 10.1128/aem.04049-13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 02/04/2014] [Indexed: 11/20/2022] Open
Abstract
The spore-forming bacterium Paenibacillus larvae causes a severe and highly infective bee disease, American foulbrood (AFB). Despite the large economic losses induced by AFB, the virulence factors produced by P. larvae are as yet unknown. To identify such virulence factors, we experimentally infected young, susceptible larvae of the honeybee, Apis mellifera carnica, with different P. larvae isolates. Honeybee larvae were reared in vitro in 24-well plates in the laboratory after isolation from the brood comb. We identified genotype-specific differences in the etiopathology of AFB between the tested isolates of P. larvae, which were revealed by differences in the median lethal times. Furthermore, we confirmed that extracts of P. larvae cultures contain low-molecular-weight compounds, which are toxic to honeybee larvae. Our data indicate that P. larvae secretes metabolites into the medium with a potent honeybee toxic activity pointing to a novel pathogenic factor(s) of P. larvae. Genome mining of P. larvae subsp. larvae BRL-230010 led to the identification of several biosynthesis gene clusters putatively involved in natural product biosynthesis, highlighting the potential of P. larvae to produce such compounds.
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Affiliation(s)
- Hedwig-Annabell Schild
- Institut für Bienenkunde, Polytechnische Gesellschaft, Oberursel, Germany
- Institut für Zellbiologie und Neurowissenschaft, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Sebastian W. Fuchs
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Helge B. Bode
- Merck-Stiftungsprofessur für Molekulare Biotechnologie, Fachbereich Biowissenschaften, Goethe-Universität Frankfurt, Frankfurt am Main, Germany
| | - Bernd Grünewald
- Institut für Bienenkunde, Polytechnische Gesellschaft, Oberursel, Germany
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26
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Moreno Switt AI, Andrus AD, Ranieri ML, Orsi RH, Ivy R, den Bakker HC, Martin NH, Wiedmann M, Boor KJ. Genomic comparison of sporeforming bacilli isolated from milk. BMC Genomics 2014; 15:26. [PMID: 24422886 PMCID: PMC3902026 DOI: 10.1186/1471-2164-15-26] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/08/2014] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Sporeformers in the order Bacillales are important contributors to spoilage of pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6°C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under these conditions. To gain a better understanding of genomic features of these important spoilage organisms and to identify candidate genomic features that may facilitate cold growth in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers representing isolates that can and cannot grow in milk at 6°C. RESULTS The genomes for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and Viridibacillus into three distinct well supported clades and further classified the Paenibacillus strains characterized here into three distinct clades, including (i) clade I, which contains one strain able to grow at 6°C in skim milk broth and one strain not able to grow under these conditions, (ii) clade II, which contains three strains able to grow at 6°C in skim milk broth, and (iii) clade III, which contains two strains unable to grow under these conditions. While all Paenibacillus genomes were found to include multiple copies of genes encoding β-galactosidases, clade II strains showed significantly higher numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of strains able to grow at 6°C and strains unable to grow at this temperature identified numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at 6°C, including peptidases with cold-adapted features (flexibility and disorder regions in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone DnaJ). CONCLUSIONS Through a comparative genomics approach we identified a number of genomic features that may relate to the ability of selected Paenibacillus strains to cause spoilage of refrigerated fluid milk. With additional experimental evidence, these data will facilitate identification of targets to detect and control Gram positive spore formers in fluid milk.
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Affiliation(s)
- Andrea I Moreno Switt
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Alexis D Andrus
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Matthew L Ranieri
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Renato H Orsi
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Reid Ivy
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Henk C den Bakker
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Nicole H Martin
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Martin Wiedmann
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Kathryn J Boor
- 345 Stocking Hall, Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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Cardozo VF, Oliveira AG, Nishio EK, Perugini MRE, Andrade CGTJ, Silveira WD, Durán N, Andrade G, Kobayashi RKT, Nakazato G. Antibacterial activity of extracellular compounds produced by a Pseudomonas strain against methicillin-resistant Staphylococcus aureus (MRSA) strains. Ann Clin Microbiol Antimicrob 2013; 12:12. [PMID: 23773484 PMCID: PMC3695862 DOI: 10.1186/1476-0711-12-12] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Accepted: 06/08/2013] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The emergence of multidrug-resistant bacteria is a world health problem. Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA) strains, is one of the most important human pathogens associated with hospital and community-acquired infections. The aim of this work was to evaluate the antibacterial activity of a Pseudomonas aeruginosa-derived compound against MRSA strains. METHODS Thirty clinical MRSA strains were isolated, and three standard MRSA strains were evaluated. The extracellular compounds were purified by vacuum liquid chromatography. Evaluation of antibacterial activity was performed by agar diffusion technique, determination of the minimal inhibitory concentration, curve of growth and viability and scanning electron microscopy. Interaction of an extracellular compound with silver nanoparticle was studied to evaluate antibacterial effect. RESULTS The F3 (ethyl acetate) and F3d (dichloromethane- ethyl acetate) fractions demonstrated antibacterial activity against the MRSA strains. Phenazine-1-carboxamide was identified and purified from the F3d fraction and demonstrated slight antibacterial activity against MRSA, and synergic effect when combined with silver nanoparticles produced by Fusarium oxysporum. Organohalogen compound was purified from this fraction showing high antibacterial effect. Using scanning electron microscopy, we show that the F3d fraction caused morphological changes to the cell wall of the MRSA strains. CONCLUSIONS These results suggest that P. aeruginosa-produced compounds such as phenazines have inhibitory effects against MRSA and may be a good alternative treatment to control infections caused by MRSA.
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Affiliation(s)
- Viviane F Cardozo
- Department of Microbiology, Biology Sciences Center, University of Londrina State, Londrina, PR CP 86005-990, Brazil
| | - Admilton G Oliveira
- Department of Microbiology, Biology Sciences Center, University of Londrina State, Londrina, PR CP 86005-990, Brazil
| | - Erick K Nishio
- Department of Microbiology, Biology Sciences Center, University of Londrina State, Londrina, PR CP 86005-990, Brazil
| | - Marcia RE Perugini
- Department of Pathology, Clinical Analysis and Toxicological, University of Londrina State, Londrina, PR CP 86038-440, Brazil
| | - Célia GTJ Andrade
- Department of General Biology, University of Londrina State, Londrina, PR CP 86051-990, Brazil
| | - Wanderley D Silveira
- Department of Genetics, Evolution and Bioagent, Biology Institute, Campinas State University (UNICAMP), Campinas, SP CP 13083-970, Brazil
| | - Nelson Durán
- Department of Physical Chemistry, Chemistry Institute Campinas State University (UNICAMP), Campinas, SP CP 13083-970, Brazil
| | - Galdino Andrade
- Department of Microbiology, Biology Sciences Center, University of Londrina State, Londrina, PR CP 86005-990, Brazil
| | - Renata KT Kobayashi
- Department of Microbiology, Biology Sciences Center, University of Londrina State, Londrina, PR CP 86005-990, Brazil
| | - Gerson Nakazato
- Department of Microbiology, Biology Sciences Center, University of Londrina State, Londrina, PR CP 86005-990, Brazil
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Huang Z, Hu Y, Shou L, Song M. Isolation and partial characterization of cyclic lipopeptide antibiotics produced by Paenibacillus ehimensis B7. BMC Microbiol 2013; 13:87. [PMID: 23594351 PMCID: PMC3637185 DOI: 10.1186/1471-2180-13-87] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 04/11/2013] [Indexed: 10/07/2023] Open
Abstract
BACKGROUND The prevalence of drug-resistant bacteria has encouraged the search for novel antimicrobial compounds. Food-associated microorganisms, as a source of new antibiotics, have recently received considerable attention. The objective of this study was to find novel antimicrobial agents produced by food microorganisms. RESULTS A bacterial strain B7, which has potent antimicrobial activity, was isolated from a sample of dairy waste. This strain was identified as Paenibacillus ehimensis based on the 16S rRNA gene sequence analysis, physiological and biochemical characterization. Two active compounds (PE1 and PE2) were obtained from P. ehimensis B7. Mass spectrometry (MS) analysis showed that the molecular masses of PE1 and PE2 were 1,114 and 1,100 Da, respectively. The tandem MS and amino acid analysis indicated that PE1 and PE2 were analogs of polypeptin, and PE2 was characterized as a new member of this family. Both compounds were active against all tested bacterial pathogens, including methicillin resistant Staphylococcus aureus, Escherichia coli, and pan-drug resistant Pseudomonas aeruginosa clinical isolate. Time-kill assays demonstrated that at 4 × MIC (minimum inhibitory concentration), PE1 and PE2 rapidly reduced the number of viable cells by at least 3-orders of magnitude, indicating that they were bactericidal antibiotics. CONCLUSIONS In the present work, two cationic lipopeptide antibiotics (PE1 and PE2) were isolated from P. ehimensis B7 and characterized. These two peptides showed broad antimicrobial activity against all tested human pathogens and are worthy of further study.
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Naing KW, Anees M, Kim SJ, Nam Y, Kim YC, Kim KY. Characterization of antifungal activity of Paenibacillus ehimensis KWN38 against soilborne phytopathogenic fungi belonging to various taxonomic groups. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-013-0632-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Abstract
INTRODUCTION Natural products have long been instrumental for discovering antibiotics, but many pharmaceutical companies abandoned this field and new antibiotics declined. In contrast, microbial resistance to current antibiotics has approached critical levels. AREAS COVERED This article gives historical perspectives by providing background about present-day economic realities and medical needs for antibiotic research, whose pipeline is mostly focused toward older known agents and newer semi-synthetic derivatives. Future research trends and projected technological developments open many innovative opportunities to discover novel antibacterials and find ways to control pathogenic bacteria without conventional antibiotics that provoke resistance. EXPERT OPINION The successful registration of daptomycin, retapamulin and fidaxomicin indicate the re-emergence of natural products has already begun. Semi-synthetic derivatives from other under-explored classes are progressing. More effort is being put into approaches such as total synthesis, discovery of new structural scaffolds for synthesis, alterations of biosynthetic pathways, combinatorial biosynthesis, new screening targets and new resources from which to isolate natural products. A return to successful screening of actinomycetes depends on solving the rate-limiting dereplication obstacle. Long-term solutions need to come from greater exploration of the massive numbers of uncultured microbes. An ultimate solution to the antibiotic-promoted microbial resistance cycle may lie in finding ways to control bacteria by non-lethal means.
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Chevrot R, Didelot S, Van den Bossche L, Tambadou F, Caradec T, Marchand P, Izquierdo E, Sopéna V, Caillon J, Barthélémy C, Van Schepdael A, Hoogmartens J, Rosenfeld E. A Novel Depsipeptide Produced by Paenibacillus alvei 32 Isolated from a Cystic fibrosis Patient. Probiotics Antimicrob Proteins 2012; 5:18-25. [DOI: 10.1007/s12602-012-9121-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Qian CD, Liu TZ, Zhou SL, Ding R, Zhao WP, Li O, Wu XC. Identification and functional analysis of gene cluster involvement in biosynthesis of the cyclic lipopeptide antibiotic pelgipeptin produced by Paenibacillus elgii. BMC Microbiol 2012; 12:197. [PMID: 22958453 PMCID: PMC3479019 DOI: 10.1186/1471-2180-12-197] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Accepted: 08/29/2012] [Indexed: 02/02/2023] Open
Abstract
Background Pelgipeptin, a potent antibacterial and antifungal agent, is a non-ribosomally synthesised lipopeptide antibiotic. This compound consists of a β-hydroxy fatty acid and nine amino acids. To date, there is no information about its biosynthetic pathway. Results A potential pelgipeptin synthetase gene cluster (plp) was identified from Paenibacillus elgii B69 through genome analysis. The gene cluster spans 40.8 kb with eight open reading frames. Among the genes in this cluster, three large genes, plpD, plpE, and plpF, were shown to encode non-ribosomal peptide synthetases (NRPSs), with one, seven, and one module(s), respectively. Bioinformatic analysis of the substrate specificity of all nine adenylation domains indicated that the sequence of the NRPS modules is well collinear with the order of amino acids in pelgipeptin. Additional biochemical analysis of four recombinant adenylation domains (PlpD A1, PlpE A1, PlpE A3, and PlpF A1) provided further evidence that the plp gene cluster involved in pelgipeptin biosynthesis. Conclusions In this study, a gene cluster (plp) responsible for the biosynthesis of pelgipeptin was identified from the genome sequence of Paenibacillus elgii B69. The identification of the plp gene cluster provides an opportunity to develop novel lipopeptide antibiotics by genetic engineering.
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Affiliation(s)
- Chao-Dong Qian
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang Province, P.R., China
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Mead DA, Lucas S, Copeland A, Lapidus A, Cheng JF, Bruce DC, Goodwin LA, Pitluck S, Chertkov O, Zhang X, Detter JC, Han CS, Tapia R, Land M, Hauser LJ, Chang YJ, Kyrpides NC, Ivanova NN, Ovchinnikova G, Woyke T, Brumm C, Hochstein R, Schoenfeld T, Brumm P. Complete Genome Sequence of Paenibacillus strain Y4.12MC10, a Novel Paenibacillus lautus strain Isolated from Obsidian Hot Spring in Yellowstone National Park. Stand Genomic Sci 2012; 6:381-400. [PMID: 23408395 PMCID: PMC3558958 DOI: 10.4056/sigs.2605792] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Paenibacillus sp.Y412MC10 was one of a number of organisms isolated from Obsidian Hot Spring, Yellowstone National Park, Montana, USA under permit from the National Park Service. The isolate was initially classified as a Geobacillus sp. Y412MC10 based on its isolation conditions and similarity to other organisms isolated from hot springs at Yellowstone National Park. Comparison of 16 S rRNA sequences within the Bacillales indicated that Geobacillus sp.Y412MC10 clustered with Paenibacillus species, and the organism was most closely related to Paenibacillus lautus. Lucigen Corp. prepared genomic DNA and the genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute. The genome sequence was deposited at the NCBI in October 2009 (NC_013406). The genome of Paenibacillus sp. Y412MC10 consists of one circular chromosome of 7,121,665 bp with an average G+C content of 51.2%. Comparison to other Paenibacillus species shows the organism lacks nitrogen fixation, antibiotic production and social interaction genes reported in other paenibacilli. The Y412MC10 genome shows a high level of synteny and homology to the draft sequence of Paenibacillus sp. HGF5, an organism from the Human Microbiome Project (HMP) Reference Genomes. This, combined with genomic CAZyme analysis, suggests an intestinal, rather than environmental origin for Y412MC10.
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Affiliation(s)
- David A. Mead
- Lucigen Corporation, Middleton, Wisconsin
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Susan Lucas
- DOE Joint Genome Institute, Walnut Creek, California
| | - Alex Copeland
- DOE Joint Genome Institute, Walnut Creek, California
| | - Alla Lapidus
- DOE Joint Genome Institute, Walnut Creek, California
| | | | - David C. Bruce
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Lynne A. Goodwin
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Sam Pitluck
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
| | - Olga Chertkov
- DOE Joint Genome Institute, Walnut Creek, California
| | - Xiaojing Zhang
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - John C. Detter
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Cliff S. Han
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Roxanne Tapia
- DOE Joint Genome Institute, Walnut Creek, California
- Los Alamos National Laboratory, Bioscience Division, Los Alamos, New Mexico
| | - Miriam Land
- DOE Joint Genome Institute, Walnut Creek, California
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Loren J. Hauser
- DOE Joint Genome Institute, Walnut Creek, California
- Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | | | | | | | | | - Tanja Woyke
- DOE Joint Genome Institute, Walnut Creek, California
| | | | | | | | - Phillip Brumm
- DOE Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, Wisconsin
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