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Zhu Z, Ding X, Rang J, Xia L. Application and research progress of ARTP mutagenesis in actinomycetes breeding. Gene 2024; 929:148837. [PMID: 39127415 DOI: 10.1016/j.gene.2024.148837] [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: 04/17/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Atmospheric and room temperature plasma (ARTP) is an emerging artificial mutagenesis breeding technology. In comparison to traditional physical and chemical methods, ARTP technology can induce DNA damage more effectively and obtain mutation strains with stable heredity more easily after screening. It possesses advantages such as simplicity, safety, non-toxicity, and cost-effectiveness, showing high application value in microbial breeding. This article focuses on ARTP mutagenesis breeding of actinomycetes, specifically highlighting the application of ARTP mutagenesis technology in improving the performance of strains and enhancing the biosynthetic capabilities of actinomycetes. We analyzed the advantages and challenges of ARTP technology in actinomycetes breeding and summarized the common features, specific mutation sites and metabolic pathways of ARTP mutagenic strains, which could give guidance for genetic modification. It suggested that the future research work should focus on the establishment of high throughput rapid screening methods and integrate transcriptomics, proteomics, metabonomics and other omics to delve into the genetic regulations and synthetic mechanisms of the bioactive substances in ARTP mutated actinomycetes. This article aims to provide new perspectives for actinomycetes breeding through the establishment and application of ARTP mutagenesis technology, thereby promoting source innovation and the sustainable industrial development of actinomycetes.
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Affiliation(s)
- Zirong Zhu
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Jie Rang
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China
| | - Liqiu Xia
- Hunan Provincial Key Laboratory of Microbial Molecular Biology, State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, China.
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2
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Karimian S, Farahmandzad N, Mohammadipanah F. Manipulation and epigenetic control of silent biosynthetic pathways in actinobacteria. World J Microbiol Biotechnol 2024; 40:65. [PMID: 38191749 DOI: 10.1007/s11274-023-03861-4] [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: 06/22/2023] [Accepted: 11/29/2023] [Indexed: 01/10/2024]
Abstract
Most biosynthetic gene clusters (BGCs) of Actinobacteria are either silent or expressed less than the detectable level. The non-genetic approaches including biological interactions, chemical agents, and physical stresses that can be used to awaken silenced pathways are compared in this paper. These non-genetic induction strategies often need screening approaches, including one strain many compounds (OSMAC), reporter-guided mutant selection, and high throughput elicitor screening (HiTES) have been developed. Different types of genetic manipulations applied in the induction of cryptic BGCs of Actinobacteria can be categorized as genome-wide pleiotropic and targeted approaches like manipulation of global regulatory systems, modulation of regulatory genes, ribosome and engineering of RNA polymerase or phosphopantheteine transferases. Targeted approaches including genome editing by CRISPR, mutation in transcription factors and modification of BGCs promoters, inactivation of the highly expressed biosynthetic pathways, deleting the suppressors or awakening the activators, heterologous expression, or refactoring of gene clusters can be applied for activation of pathways which are predicted to synthesize new bioactive structures in genome mining studies of Acinobacteria. In this review, the challenges and advantages of employing these approaches in induction of Actinobacteria BGCs are discussed. Further, novel natural products needed as drug for pharmaceutical industry or as biofertilizers in agricultural industry can be discovered even from known species of Actinobactera by the innovative approaches of metabolite biosynthesis elicitation.
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Affiliation(s)
- Sanaz Karimian
- Department of Biotechnology, Faculty of Biological Science, Alzahra University, Tehran, Iran
| | - Navid Farahmandzad
- Department of Biosystems Engineering, Auburn university, Auburn, AL 36849, USA
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, 14155-6455, Iran.
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3
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Zong G, Cao G, Fu J, Zhang P, Chen X, Yan W, Xin L, Wang Z, Xu Y, Zhang R. Novel mechanism of hydrogen peroxide for promoting efficient natamycin synthesis in Streptomyces. Microbiol Spectr 2023; 11:e0087923. [PMID: 37695060 PMCID: PMC10580950 DOI: 10.1128/spectrum.00879-23] [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: 02/28/2023] [Accepted: 05/21/2023] [Indexed: 09/12/2023] Open
Abstract
The mechanism of regulation of natamycin biosynthesis by Streptomyces in response to oxidative stress is unclear. Here, we first show cholesterol oxidase SgnE, which catalyzes the formation of H2O2 from sterols, triggered a series of redox-dependent interactions to stimulate natamycin production in S. gilvosporeus. In response to reactive oxygen species, residues Cys212 and Cys221 of the H2O2-sensing consensus sequence of OxyR were oxidized, resulting in conformational changes in the protein: OxyR extended its DNA-binding domain to interact with four motifs of promoter p sgnM . This acted as a redox-dependent switch to turn on/off gene transcription of sgnM, which encodes a cluster-situated regulator, by controlling the affinity between OxyR and p sgnM , thus regulating the expression of 12 genes in the natamycin biosynthesis gene cluster. OxyR cooperates with SgnR, another cluster-situated regulator and an upstream regulatory factor of SgnM, synergistically modulated natamycin biosynthesis by masking/unmasking the -35 region of p sgnM depending on the redox state of OxyR in response to the intracellular H2O2 concentration. IMPORTANCE Cholesterol oxidase SgnE is an indispensable factor, with an unclear mechanism, for natamycin biosynthesis in Streptomyces. Oxidative stress has been attributed to the natamycin biosynthesis. Here, we show that SgnE catalyzes the formation of H2O2 from sterols and triggers a series of redox-dependent interactions to stimulate natamycin production in S. gilvosporeus. OxyR, which cooperates with SgnR, acted as a redox-dependent switch to turn on/off gene transcription of sgnM, which encodes a cluster-situated regulator, by masking/unmasking its -35 region, to control the natamycin biosynthesis gene cluster. This work provides a novel perspective on the crosstalk between intracellular ROS homeostasis and natamycin biosynthesis. Application of these findings will improve antibiotic yields via control of the intracellular redox pressure in Streptomyces.
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Affiliation(s)
- Gongli Zong
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, China
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Jiafang Fu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Peipei Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Xi Chen
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Wenxiu Yan
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Lulu Xin
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Zhongxue Wang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, China
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Sun J, Li J, Yao L, Zheng Y, Yuan J, Wang D. UV-ARTP-DES compound mutagenesis breeding improves natamycin production of Streptomyces natalensis HW-2 and reveals transcriptional changes by RNA-seq. Food Sci Biotechnol 2023; 32:341-352. [PMID: 36778090 PMCID: PMC9905406 DOI: 10.1007/s10068-022-01191-z] [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: 08/10/2022] [Revised: 09/27/2022] [Accepted: 10/12/2022] [Indexed: 11/04/2022] Open
Abstract
Natamycin is widely used in food, medical and health, agriculture, and animal husbandry. In this study, Streptomyces natalensis HW-2 was used as the research object, and a mutant DES-26 with stable genetic characters was selected by UV-ARTP-DES compound mutation. The natamycin yield was 1.64 g/L, 86.36% higher than original strain. Differential expression genes were analyzed by transcriptomics, and results showed that 295 and 860 genes were significantly differentially expressed at fermentation for 48 h and 72 h. GO and KEGG analysis showed that compound mutagenesis had a significant impact on glycolysis, pentose phosphate, TCA cycle, fatty acid metabolism pathways, and several key enzyme genes in the pathways were up-regulated, and genes related to natamycin biosynthesis (pimB-pimI) and transcriptional regulator (pimR) were also up-regulated. qRT-PCR results confirmed that expression levels of these genes were consistent with transcriptional changes of RNA-Seq. Supplementary Information The online version contains supplementary material available at 10.1007/s10068-022-01191-z.
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Affiliation(s)
- Jianrui Sun
- College of Food and Bioengineering, Henan Engineering Research Center of Food Microbiology, Henan University of Science and Technology, No. 263, Kaiyuan Ave., Luoyang, 471023 Henan China
| | - Jinglan Li
- College of Food and Bioengineering, Henan Engineering Research Center of Food Microbiology, Henan University of Science and Technology, No. 263, Kaiyuan Ave., Luoyang, 471023 Henan China
| | - Linlin Yao
- College of Food and Bioengineering, Henan Engineering Research Center of Food Microbiology, Henan University of Science and Technology, No. 263, Kaiyuan Ave., Luoyang, 471023 Henan China
| | - Yingying Zheng
- College of Food and Bioengineering, Henan Engineering Research Center of Food Microbiology, Henan University of Science and Technology, No. 263, Kaiyuan Ave., Luoyang, 471023 Henan China
| | - Jiangfeng Yuan
- College of Food and Bioengineering, Henan Engineering Research Center of Food Microbiology, Henan University of Science and Technology, No. 263, Kaiyuan Ave., Luoyang, 471023 Henan China
| | - Dahong Wang
- College of Food and Bioengineering, Henan Engineering Research Center of Food Microbiology, Henan University of Science and Technology, No. 263, Kaiyuan Ave., Luoyang, 471023 Henan China
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5
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Karthick Raja Namasivayam S, Manohar M, Aravind Kumar J, Samrat K, Kande A, Arvind Bharani RS, Jayaprakash C, Lokesh S. Green chemistry principles for the synthesis of anti fungal active gum acacia-gold nanocomposite - natamycin (GA-AuNC-NT) against food spoilage fungal strain Aspergillus ochraceopealiformis and its marked Congo red dye adsorption efficacy. ENVIRONMENTAL RESEARCH 2022; 212:113386. [PMID: 35569536 DOI: 10.1016/j.envres.2022.113386] [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: 02/10/2022] [Revised: 04/19/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
In this present study, a highly stable gum acacia -gold nanocomposite fabricated with food preservative agent natamycin (GA-AuNC-NT) was prepared via green science principles under in vitro conditions. Various characterisation techniques reveal highly stable structural, functional properties of the synthesised nanocomposite with marked antifungal activity and adsorption efficacy against congo red dye. The antifungal activity was investigated against the fungal strain Aspergillus ochraceopealiformis isolated from spoiled, expired bread. The well diffusion assay, fungal hyphae fragmentation assay and spore germination inhibition assay were used to determine the antifungal activity of the synthesised nanocomposite. Potential antifungal activity of the synthesised nanocomposite was confirmed by recording zone of inhibition, high rate of hyphae fragmentation and marked spore germination inhibition against the tested fungal strain. The molecular mechanism of antifungal activity was studied by measuring oxidative stress marker genes like catalase (CAT), superoxide dismutase (SOD), peroxidase (POD) induction adopting quantitative real-time polymerase chain reaction (q RT-PCR). Among the various treatment, a notable reduction in all the tested marker genes expression was recorded in the nanocomposite treated fungal strain. Release profile studies using different solvents reveals sustained or controlled release of natamycin at the increasing periods. The synthesised nanocomposite's high safety or biocompatibility was evaluated with the Wistar animal model by determining notable changes in behavioural, biochemical, haematological and histopathological parameters. The synthesised nanocomposite did not exhibit any undesirable changes in all the tested parameters confirming the marked biosafety or biocompatibility. The nanocomposite was coated on the bread packaging material. The effect of packaging on the proximate composition, antioxidative enzymes status, and fungal growth of bread samples incubated under the incubation period were studied. Fourier transform infrared spectroscopy (FTIR) and scanning electron microscopy (SEM) studies reveal that the nanocomposite was effectively coated on the packaging material without changing size, shape, and functional groups. No changes in the proximate composition and antioxidative enzymes of the packaged bread samples incubated under different incubation periods reveal the nanocomposite's marked safety. The complete absence of the fungal growth also indicates the uniqueness of the nanocomposite. Further, the sorption studies revealed the utilisation of Langmuir mechanism and pseudo II order model successfully The present finding implies that the synthesised nanocomposite can be used as an effective, safe food preservative agent and adsorbent of toxic chemicals.
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Affiliation(s)
- S Karthick Raja Namasivayam
- Department of Research and Innovation, Saveetha School of Engineering, SIMATS, Chennai, 602105, Tamil Nadu, India.
| | - Mohith Manohar
- Centre for Bioresource Research.& Development (C-BIRD), Department of Biotechnology, Sathyabama Institute of Science and Technology, Chennai 119, Tamil Nadu, India
| | - J Aravind Kumar
- Department of Biomass & Energy Conversion, Saveetha School of Engineering, SIMATS, Chennai, 602105, Tamil Nadu, India.
| | - K Samrat
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bangalore, 560054, Karnataka, India
| | - Akhil Kande
- Centre for Bioresource Research.& Development (C-BIRD), Department of Biotechnology, Sathyabama Institute of Science and Technology, Chennai 119, Tamil Nadu, India
| | | | - C Jayaprakash
- Food Microbiology Division, Defence Food Research Laboratory (DFRL), Mysuru (Mysore), 570011, Karnataka, India
| | - S Lokesh
- Department of Energy & Environmental Engineering, Saveetha School of Engineering, SIMATS, Chennai, 602105, Tamil Nadu, India
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6
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Zong G, Fu J, Zhang P, Zhang W, Xu Y, Cao G, Zhang R. Use of elicitors to enhance or activate the antibiotic production in streptomyces. Crit Rev Biotechnol 2021; 42:1260-1283. [PMID: 34706600 DOI: 10.1080/07388551.2021.1987856] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Streptomyces is the largest and most significant genus of Actinobacteria, comprising 961 species. These Gram-positive bacteria produce many versatile and important bioactive compounds; of these, antibiotics, specifically the enhancement or activation of their production, have received extensive research attention. Recently, various biotic and abiotic elicitors have been reported to modify the antibiotic metabolism of Streptomyces, which promotes the production of new antibiotics and bioactive metabolites for improvement in the yields of endogenous products. However, some elicitors that obviously contribute to secondary metabolite production have not yet received sufficient attention. In this study, we have reviewed the functions and mechanisms of chemicals, novel microbial metabolic elicitors, microbial interactions, enzymes, enzyme inhibitors, environmental factors, and novel combination methods regarding antibiotic production in Streptomyces. This review has aimed to identify potentially valuable elicitors for stimulating the production of latent antibiotics or enhancing the synthesis of subsistent antibiotics in Streptomyces. Future applications and challenges in the discovery of new antibiotics and enhancement of existing antibiotic production using elicitors are discussed.
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Affiliation(s)
- Gongli Zong
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China.,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Jiafang Fu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Peipei Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Wenchi Zhang
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Yan Xu
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, China
| | - Rongzhen Zhang
- Key Laboratory of Industrial Biotechnology of Ministry of Education & School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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7
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Caicedo-Montoya C, Manzo-Ruiz M, Ríos-Estepa R. Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. Front Microbiol 2021; 12:677558. [PMID: 34659136 PMCID: PMC8510958 DOI: 10.3389/fmicb.2021.677558] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 08/30/2021] [Indexed: 01/07/2023] Open
Abstract
Species of the genus Streptomyces are known for their ability to produce multiple secondary metabolites; their genomes have been extensively explored to discover new bioactive compounds. The richness of genomic data currently available allows filtering for high quality genomes, which in turn permits reliable comparative genomics studies and an improved prediction of biosynthetic gene clusters (BGCs) through genome mining approaches. In this work, we used 121 genome sequences of the genus Streptomyces in a comparative genomics study with the aim of estimating the genomic diversity by protein domains content, sequence similarity of proteins and conservation of Intergenic Regions (IGRs). We also searched for BGCs but prioritizing those with potential antibiotic activity. Our analysis revealed that the pan-genome of the genus Streptomyces is clearly open, with a high quantity of unique gene families across the different species and that the IGRs are rarely conserved. We also described the phylogenetic relationships of the analyzed genomes using multiple markers, obtaining a trustworthy tree whose relationships were further validated by Average Nucleotide Identity (ANI) calculations. Finally, 33 biosynthetic gene clusters were detected to have potential antibiotic activity and a predicted mode of action, which might serve up as a guide to formulation of related experimental studies.
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Affiliation(s)
- Carlos Caicedo-Montoya
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
| | - Monserrat Manzo-Ruiz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Rigoberto Ríos-Estepa
- Grupo de Bioprocesos, Departamento de Ingeniería Química, Universidad de Antioquia (UdeA), Medellín, Colombia
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8
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Singh TA, Passari AK, Jajoo A, Bhasin S, Gupta VK, Hashem A, Alqarawi AA, Abd Allah EF. Tapping Into Actinobacterial Genomes for Natural Product Discovery. Front Microbiol 2021; 12:655620. [PMID: 34239507 PMCID: PMC8258257 DOI: 10.3389/fmicb.2021.655620] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 05/31/2021] [Indexed: 11/27/2022] Open
Abstract
The presence of secondary metabolite biosynthetic gene clusters (BGCs) makes actinobacteria well-known producers of diverse metabolites. These ubiquitous microbes are extensively exploited for their ability to synthesize diverse secondary metabolites. The extent of their ability to synthesize various molecules is yet to be evaluated. Current advancements in genome sequencing, metabolomics, and bioinformatics have provided a plethora of information about the mechanism of synthesis of these bioactive molecules. Accessing the biosynthetic gene cluster responsible for the production of metabolites has always been a challenging assignment. The genomic approach developments have opened a new gateway for examining and manipulating novel antibiotic gene clusters. These advancements have now developed a better understanding of actinobacterial physiology and their genetic regulation for the prolific production of natural products. These new approaches provide a unique opportunity to discover novel bioactive compounds that might replenish antibiotics’ exhausted stock and counter the microbes’ resistance crisis.
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Affiliation(s)
- Tanim Arpit Singh
- Department of Biosciences, Maharaja Ranjit Singh College of Professional Sciences, Indore, India.,School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Ajit Kumar Passari
- Departmento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, México City, Mexico
| | - Anjana Jajoo
- School of Life Sciences, Devi Ahilya Vishwavidyalaya, Indore, India
| | - Sheetal Bhasin
- Department of Biosciences, Maharaja Ranjit Singh College of Professional Sciences, Indore, India
| | - Vijai Kumar Gupta
- Biorefining and Advanced Materials Research Center and Center for Safe and Improved Food, Scotland's Rural College (SRUC), SRUC Barony Campus, Dumfries, United Kingdom
| | - Abeer Hashem
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.,Department of Mycology and Plant Disease Survey, Plant Pathology Research Institute, Agricultural Research Center (ARC), Giza, Egypt
| | - Abdulaziz A Alqarawi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Elsayed Fathi Abd Allah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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9
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Maksimov AY, Balandina SY, Topanov PA, Mashevskaya IV, Chaudhary S. Organic Antifungal Drugs and Targets of Their Action. Curr Top Med Chem 2021; 21:705-736. [PMID: 33423647 DOI: 10.2174/1568026621666210108122622] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 08/20/2020] [Accepted: 09/03/2020] [Indexed: 11/22/2022]
Abstract
In recent decades, there has been a significant increase in the number of fungal diseases. This is due to a wide spectrum of action, immunosuppressants and other group drugs. In terms of frequency, rapid spread and globality, fungal infections are approaching acute respiratory infections. Antimycotics are medicinal substances endorsed with fungicidal or fungistatic properties. For the treatment of fungal diseases, several groups of compounds are used that differ in their origin (natural or synthetic), molecular targets and mechanism of action, antifungal effect (fungicidal or fungistatic), indications for use (local or systemic infections), and methods of administration (parenteral, oral, outdoor). Several efforts have been made by various medicinal chemists around the world for the development of antifungal drugs with high efficacy with the least toxicity and maximum selectivity in the area of antifungal chemotherapy. The pharmacokinetic properties of the new antimycotics are also important: the ability to penetrate biological barriers, be absorbed and distributed in tissues and organs, get accumulated in tissues affected by micromycetes, undergo drug metabolism in the intestinal microflora and human organs, and in the kinetics of excretion from the body. There are several ways to search for new effective antimycotics: - Obtaining new derivatives of the already used classes of antimycotics with improved activity properties. - Screening of new chemical classes of synthetic antimycotic compounds. - Screening of natural compounds. - Identification of new unique molecular targets in the fungal cell. - Development of new compositions and dosage forms with effective delivery vehicles. The methods of informatics, bioinformatics, genomics and proteomics were extensively investigated for the development of new antimycotics. These techniques were employed in finding and identification of new molecular proteins in a fungal cell; in the determination of the selectivity of drugprotein interactions, evaluation of drug-drug interactions and synergism of drugs; determination of the structure-activity relationship (SAR) studies; determination of the molecular design of the most active, selective and safer drugs for the humans, animals and plants. In medical applications, the methods of information analysis and pharmacogenomics allow taking into account the individual phenotype of the patient, the level of expression of the targets of antifungal drugs when choosing antifungal agents and their dosage. This review article incorporates some of the most significant studies covering the basic structures and approaches for the synthesis of antifungal drugs and the directions for their further development.
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Affiliation(s)
- Alexander Yu Maksimov
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Svetlana Yu Balandina
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Pavel A Topanov
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Irina V Mashevskaya
- Department of Pharmacy and Pharmacology, Faculty of Chemistry, Perm State University, Perm 614990, Russian Federation
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry (OMC lab), Department of Chemistry, Malaviya National Institute of Technology Jaipur, Jawaharlal Nehru Marg, Jaipur 302017, India
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10
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Ramírez-Durán N, de la Haba RR, Vera-Gargallo B, Sánchez-Porro C, Alonso-Carmona S, Sandoval-Trujillo H, Ventosa A. Taxogenomic and Comparative Genomic Analysis of the Genus Saccharomonospora Focused on the Identification of Biosynthetic Clusters PKS and NRPS. Front Microbiol 2021; 12:603791. [PMID: 33776952 PMCID: PMC7990883 DOI: 10.3389/fmicb.2021.603791] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/17/2021] [Indexed: 11/13/2022] Open
Abstract
Actinobacteria are prokaryotes with a large biotechnological interest due to their ability to produce secondary metabolites, produced by two main biosynthetic gene clusters (BGCs): polyketide synthase (PKS) and non-ribosomal peptide synthetase (NRPS). Most studies on bioactive products have been carried out on actinobacteria isolated from soil, freshwater or marine habitats, while very few have been focused on halophilic actinobacteria isolated from extreme environments. In this study we have carried out a comparative genomic analysis of the actinobacterial genus Saccharomonospora, which includes species isolated from soils, lake sediments, marine or hypersaline habitats. A total of 19 genome sequences of members of Saccharomonospora were retrieved and analyzed. We compared the 16S rRNA gene-based phylogeny of this genus with evolutionary relationships inferred using a phylogenomic approach obtaining almost identical topologies between both strategies. This method allowed us to unequivocally assign strains into species and to identify some taxonomic relationships that need to be revised. Our study supports a recent speciation event occurring between Saccharomonospora halophila and Saccharomonospora iraqiensis. Concerning the identification of BGCs, a total of 18 different types of BGCs were detected in the analyzed genomes of Saccharomonospora, including PKS, NRPS and hybrid clusters which might be able to synthetize 40 different putative products. In comparison to other genera of the Actinobacteria, members of the genus Saccharomonospora showed a high degree of novelty and diversity of BGCs.
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Affiliation(s)
- Ninfa Ramírez-Durán
- Faculty of Medicine, Autonomous University of the State of Mexico, Toluca, Mexico.,Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | - Rafael R de la Haba
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | - Blanca Vera-Gargallo
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | - Cristina Sánchez-Porro
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
| | | | - Horacio Sandoval-Trujillo
- Department of Biological Systems, Metropolitan Autonomous University-Xochimilco, Mexico City, Mexico
| | - Antonio Ventosa
- Department of Microbiology and Parasitology, Faculty of Pharmacy, University of Sevilla, Seville, Spain
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11
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Liao Z, Song Z, Xu J, Ma Z, Bechthold A, Yu X. Identification of a gene from Streptomyces rimosus M527 negatively affecting rimocidin biosynthesis and morphological differentiation. Appl Microbiol Biotechnol 2020; 104:10191-10202. [PMID: 33057790 DOI: 10.1007/s00253-020-10955-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/01/2020] [Accepted: 10/07/2020] [Indexed: 12/17/2022]
Abstract
The polyene macrolide rimocidin, produced by Streptomyces rimosus M527, was found to be highly effective against a broad range of fungal plant pathogens. Current understanding of the regulatory mechanism of rimocidin biosynthesis and morphological differentiation in S. rimosus M527 is limited. NsdA is considered a negative regulator involved in morphological differentiation and biosynthesis of secondary metabolites in some Streptomyces species. In this study, nsdAsr was cloned from S. rimosus M527. The role of nsdAsr in rimocidin biosynthesis and morphological differentiation was investigated by gene deletion, complementation, and over-expression. A ΔnsdAsr mutant was obtained using CRISPR/Cas9. The mutant produced more rimocidin (46%) and accelerated morphological differentiation than the wild-type strain. Over-expression of nsdAsr led to a decrease in rimocidin production and impairment of morphological differentiation. Quantitative RT-PCR analysis revealed that transcription of rim genes responsible for rimocidin biosynthesis was upregulated in the ΔnsdAsr mutant but downregulated in the nsdAsr over-expression strain. Similar effects have been described for Streptomyces coelicolor M145 and the industrial toyocamycin-producing strain Streptomyces diastatochromogenes 1628. KEY POINTS: • A negative regulator for sporulation and rimocidin production was identified. • The CRISPR/Cas9 system was used for gene deletion in S. rimosus M527.
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Affiliation(s)
- Zhijun Liao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China
| | - Zhangqing Song
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China
| | - Jie Xu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China
| | - Zheng Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China.
| | - Andreas Bechthold
- Institute for Pharmaceutical Sciences, Pharmaceutical Biology and Biotechnology, University of Freiburg, 79104, Freiburg, Germany
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Xueyuan Street, Xiasha Higher Education District, Hangzhou, 310018, Zhejiang Province, China.
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12
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Lee N, Hwang S, Kim J, Cho S, Palsson B, Cho BK. Mini review: Genome mining approaches for the identification of secondary metabolite biosynthetic gene clusters in Streptomyces. Comput Struct Biotechnol J 2020; 18:1548-1556. [PMID: 32637051 PMCID: PMC7327026 DOI: 10.1016/j.csbj.2020.06.024] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 01/04/2023] Open
Abstract
Streptomyces are a large and valuable resource of bioactive and complex secondary metabolites, many of which have important clinical applications. With the advances in high throughput genome sequencing methods, various in silico genome mining strategies have been developed and applied to the mapping of the Streptomyces genome. These studies have revealed that Streptomyces possess an even more significant number of uncharacterized silent secondary metabolite biosynthetic gene clusters (smBGCs) than previously estimated. Linking smBGCs to their encoded products has played a critical role in the discovery of novel secondary metabolites, as well as, knowledge-based engineering of smBGCs to produce altered products. In this mini review, we discuss recent progress in Streptomyces genome sequencing and the application of genome mining approaches to identify and characterize smBGCs. Furthermore, we discuss several challenges that need to be overcome to accelerate the genome mining process and ultimately support the discovery of novel bioactive compounds.
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Affiliation(s)
- Namil Lee
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Soonkyu Hwang
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jihun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Bernhard Palsson
- Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby 2800, Denmark
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Intelligent Synthetic Biology Center, Daejeon 34141, Republic of Korea
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13
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Zhao X, Wang Y, Xu X, Tian K, Zhou D, Meng F, Zhang H, Huo H. Genomics analysis of the steroid estrogen-degrading bacterium Serratia nematodiphila DH-S01. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1764388] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Affiliation(s)
- Xueying Zhao
- Department of Environmental Engineering, School of Environment, Northeast Normal University, Jilin Province, PR China
| | - Yaojia Wang
- Department of Environmental Engineering, School of Environment, Northeast Normal University, Jilin Province, PR China
| | - Xin Xu
- Department of Environmental Engineering, School of Environment, Northeast Normal University, Jilin Province, PR China
| | - Kejian Tian
- Department of Environmental Engineering, School of Environment, Northeast Normal University, Jilin Province, PR China
| | - Dongwen Zhou
- Department of Environmental Engineering, School of Environment, Northeast Normal University, Jilin Province, PR China
| | - Fanxing Meng
- Department of Environmental Engineering, School of Environment, Northeast Normal University, Jilin Province, PR China
| | - Hongyan Zhang
- Department of Biological Science, School of Life Sciences, Northeast Normal University, Jilin Province, PR China
| | - Hongliang Huo
- Department of Environmental Engineering, School of Environment, Northeast Normal University, Jilin Province, PR China
- Jilin Province Water Pollution Control and Resource Engineering Laboratory, Jilin Province, PR China
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14
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Xia H, Li X, Li Z, Zhan X, Mao X, Li Y. The Application of Regulatory Cascades in Streptomyces: Yield Enhancement and Metabolite Mining. Front Microbiol 2020; 11:406. [PMID: 32265866 PMCID: PMC7105598 DOI: 10.3389/fmicb.2020.00406] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Streptomyces is taken as an important resource for producing the most abundant antibiotics and other bio-active natural products, which have been widely used in pharmaceutical and agricultural areas. Usually they are biosynthesized through secondary metabolic pathways encoded by cluster situated genes. And these gene clusters are stringently regulated by interweaved transcriptional regulatory cascades. In the past decades, great advances have been made to elucidate the regulatory mechanisms involved in antibiotic production in Streptomyces. In this review, we summarized the recent advances on the regulatory cascades of antibiotic production in Streptomyces from the following four levels: the signals triggering the biosynthesis, the global regulators, the pathway-specific regulators and the feedback regulation. The production of antibiotic can be largely enhanced by rewiring the regulatory networks, such as overexpression of positive regulators, inactivation of repressors, fine-tuning of the feedback and ribosomal engineering in Streptomyces. The enormous amount of genomic sequencing data implies that the Streptomyces has potential to produce much more antibiotics for the great diversities and wide distributions of biosynthetic gene clusters in Streptomyces genomes. Most of these gene clusters are defined cryptic for unknown or undetectable natural products. In the synthetic biology era, activation of the cryptic gene clusters has been successfully achieved by manipulation of the regulatory genes. Chemical elicitors, rewiring regulatory gene and ribosomal engineering have been employed to crack the potential of cryptic gene clusters. These have been proposed as the most promising strategy to discover new antibiotics. For the complex of regulatory network in Streptomyces, we proposed that the discovery of new antibiotics and the optimization of industrial strains would be greatly promoted by further understanding the regulatory mechanism of antibiotic production.
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Affiliation(s)
- Haiyang Xia
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xiaofang Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Zhangqun Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xinqiao Zhan
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China
| | - Xuming Mao
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yongquan Li
- Institute of Biopharmaceuticals, Taizhou University, Taizhou, China.,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, Hangzhou, China
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15
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Genome mining and homologous comparison strategy for digging exporters contributing self-resistance in natamycin-producing Streptomyces strains. Appl Microbiol Biotechnol 2019; 104:817-831. [DOI: 10.1007/s00253-019-10131-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/30/2019] [Accepted: 09/08/2019] [Indexed: 02/04/2023]
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16
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Barreiro C, Martínez-Castro M. Regulation of the phosphate metabolism in Streptomyces genus: impact on the secondary metabolites. Appl Microbiol Biotechnol 2019; 103:1643-1658. [DOI: 10.1007/s00253-018-09600-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 12/20/2018] [Accepted: 12/21/2018] [Indexed: 12/30/2022]
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17
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Barreales EG, Payero TD, de Pedro A, Aparicio JF. Phosphate effect on filipin production and morphological differentiation in Streptomyces filipinensis and the role of the PhoP transcription factor. PLoS One 2018; 13:e0208278. [PMID: 30521601 PMCID: PMC6283541 DOI: 10.1371/journal.pone.0208278] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 11/14/2018] [Indexed: 12/13/2022] Open
Abstract
The biosynthesis of the antifungal filipin in Streptomyces filipinensis is very sensitive to phosphate regulation. Concentrations as low as 2.5 mM block filipin production. This effect is, at least in part, produced by repression of the transcription of most filipin biosynthetic genes. The role of the two-component PhoRP system in this process was investigated. The phoRP system of S. filipinensis was cloned and transcriptionally characterised. PhoP binds to two PHO boxes present in one of its two promoters. Filipin production was greatly increased in ΔphoP and ΔphoRP mutants, in agreement with a higher transcription of the fil genes, and the effect of phosphate repression on the antibiotic production of these strains was significantly reduced. No PhoP binding was observed by electrophoretic mobility gel shift assays (EMSAs) with the promoter regions of the fil gene cluster thus suggesting an indirect effect of mutations. Binding assays with cell-free extracts from the wild-type and mutant strains on fil genes promoters revealed retardation bands in the parental strain that were absent in the mutants, thus suggesting that binding of the putative transcriptional regulator or regulators controlled by PhoP was PhoP dependent. Noteworthy, PhoP or PhoRP deletion also produced a dramatic decrease in sporulation ability, thus indicating a clear relationship between the phosphate starvation response mediated by PhoP and the sporulation process in S. filipinensis. This effect was overcome upon gene complementation, but also by phosphate addition, thus suggesting that alternative pathways take control in the absence of PhoRP.
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Affiliation(s)
- Eva G. Barreales
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Tamara D. Payero
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Antonio de Pedro
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Jesús F. Aparicio
- Area de Microbiología, Departamento de Biología Molecular, Universidad de León, León, Spain
- * E-mail:
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18
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Son S, Jang M, Lee B, Hong YS, Ko SK, Jang JH, Ahn JS. Ulleungdin, a Lasso Peptide with Cancer Cell Migration Inhibitory Activity Discovered by the Genome Mining Approach. JOURNAL OF NATURAL PRODUCTS 2018; 81:2205-2211. [PMID: 30251851 DOI: 10.1021/acs.jnatprod.8b00449] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The advances of genomic sequence analyses and genome mining tools have enabled the exploration of untapped microbial natural products. Through genome mining studies to discover cryptic natural products, we found biosynthetic genes encoding a new lasso peptide in the genome sequence of a soil bacterium, Streptomyces sp. KCB13F003 isolated from Ulleung Island (a small volcanic island), Korea. The production and purification of the encoded peptide, named ulleungdin, were achieved by optimizing the culture conditions followed by LC-MS-targeted isolation. Structure elucidation was performed by NMR spectroscopic and MS spectrometric analyses and chemical means (Marfey's and GITC derivatizations), proving ulleungdin to be a new 15-mer class II lasso peptide with a threaded structure. Biological evaluation with the cell invasion assay and time-lapse cell tracking analysis revealed that ulleungdin has significant inhibitory activities against cancer cell invasion and migration.
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Affiliation(s)
- Sangkeun Son
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
| | - Mina Jang
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Byeongsan Lee
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
| | - Young-Soo Hong
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Sung-Kyun Ko
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Jae-Hyuk Jang
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
| | - Jong Seog Ahn
- Anticancer Agent Research Center , Korea Research Institute of Bioscience and Biotechnology (KRIBB) , Cheongju 28116 , Korea
- Department of Biomolecular Science, KRIBB School of Bioscience , Korea University of Science and Technology (UST) , Daejeon 34141 , Korea
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19
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Li L, Yuan L, Shi Y, Xie X, Chai A, Wang Q, Li B. Comparative genomic analysis of Pseudomonas amygdali pv. lachrymans NM002: Insights into its potential virulence genes and putative invasion determinants. Genomics 2018; 111:1493-1503. [PMID: 30336277 DOI: 10.1016/j.ygeno.2018.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 09/30/2018] [Accepted: 10/04/2018] [Indexed: 12/01/2022]
Abstract
Pseudomonas amygdali pv. lachrymans is currently of important plant pathogenic bacteria that causes cucumber angular leaf spot worldwide. The pathogen has been studied for its roles in pathogenicity and plant inheritance resistance. To further delineate traits critical to virulence, invasion and survival in the phyllosphere, we reported the first complete genome of P. amygdali pv. lachrymans NM002. Analysis of the whole genome in comparison with three closely-related representative pathovars of P. syringae identified the conservation of virulence genes, including flagella and chemotaxis, quorum-sensing systems, two-component systems, and lipopolysaccharide and antiphagocytosis. It also revealed differences of invasion determinants, such as type III effectors, phytotoxin (coronatine, syringomycin and phaseolotoxin) and cell wall-degrading enzyme, which may contribute to infectivity. The aim of this study was to derive genomic information that would reveal the probable molecular mechanisms underlying the virulence, infectivity and provide a better understanding of the pathogenesis of the P. syringae pathovars.
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Affiliation(s)
- Lei Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lifang Yuan
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China; Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Yanxia Shi
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xuewen Xie
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ali Chai
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Wang
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Baoju Li
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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20
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Wang H, He X, Sun C, Gao J, Liu X, Liu H. Enhanced natamycin production by co-expression of Vitreoscilla hemoglobin and antibiotic positive regulators in Streptomyces gilvosporeus. BIOTECHNOL BIOTEC EQ 2018. [DOI: 10.1080/13102818.2017.1419073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Haixia Wang
- MOE Key Laboratory of Industrial Fermentation Microbiology, Department of Biotechnology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
| | - Xihong He
- MOE Key Laboratory of Industrial Fermentation Microbiology, Department of Biotechnology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
| | - Chunjie Sun
- MOE Key Laboratory of Industrial Fermentation Microbiology, Department of Biotechnology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
| | - Junqian Gao
- MOE Key Laboratory of Industrial Fermentation Microbiology, Department of Biotechnology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
| | - Xiaoguang Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, Department of Biotechnology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
| | - Hao Liu
- MOE Key Laboratory of Industrial Fermentation Microbiology, Department of Biotechnology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin, P.R. China
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