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Abstract
This review serves as an update to the previous Nocardia review by Brown-Elliott et al. published in 2006 (B. A. Brown-Elliott, J. M. Brown, P. S. Conville, and R. J. Wallace. Jr., Clin Microbiol Rev 19:259-282, 2006, https://doi.org/10.1128/CMR.19.2.259-282.2006). Included is a discussion on the taxonomic expansion of the genus, current identification methods, and the impact of new technology (including matrix-assisted laser desorption ionization-time of flight [MALDI-TOF] and whole genome sequencing) on diagnosis and treatment. Clinical manifestations, the epidemiology, and geographic distribution are briefly discussed. An additional section on actinomycotic mycetoma is added to address this often-neglected disease.
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Affiliation(s)
- Rita M. Traxler
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Melissa E. Bell
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Brent Lasker
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Brendan Headd
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Wun-Ju Shieh
- Infectious Diseases Pathology Branch (IDPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R. McQuiston
- Bacterial Special Pathogens Branch (BSPB), Division of High-Consequence Pathogens and Pathology (DHCPP), National Center for Emerging and Zoonotic Infectious Diseases (NCEZID), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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Xu S, Wei M, Li G, Li Z, Che Y, Han L, Jia W, Li F, Li D, Li Z, Lal R. Comprehensive Analysis of the Nocardia cyriacigeorgica Complex Reveals Five Species-Level Clades with Different Evolutionary and Pathogenicity Characteristics. mSystems. [PMID: 35430877 PMCID: PMC9239197 DOI: 10.1128/msystems.01406-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nocardia cyriacigeorgica is a common etiological agent of nocardiosis that has increasingly been implicated in serious pulmonary infections, especially in immunocompromised individuals. However, the evolution, diversity, and pathogenesis of N. cyriacigeorgica have remained unclear. Here, we performed a comparative genomic analysis using 91 N. cyriacigeorgica strains, 45 of which were newly sequenced in this study. Phylogenetic and average nucleotide identity (ANI) analyses revealed that N. cyriacigeorgica contained five species-level clades (8.6 to 14.6% interclade genetic divergence), namely, the N. cyriacigeorgica complex (NCC). Further pan-genome analysis revealed extensive differences among the five clades in nine functional categories, such as energy production, lipid metabolism, secondary metabolites, and signal transduction mechanisms. All 2,935 single-copy core genes undergoing purifying selection were highly conserved across NCC. However, clades D and E exhibited reduced selective constraints, compared to clades A to C. Horizontal gene transfer (HGT) and mobile genetic elements contributed to genomic plasticity, and clades A and B had experienced a higher level of HGT events than other clades. A total of 129 virulence factors were ubiquitous across NCC, such as the mce operon, hemolysin, and type VII secretion system (T7SS). However, different distributions of three toxin-coding genes and two new types of mce operons were detected, which might contribute to pathogenicity differences among the members of the NCC. Overall, our study provides comprehensive insights into the evolution, genetic diversity, and pathogenicity of NCC, facilitating the prevention of infections. IMPORTANCENocardia species are opportunistic bacterial pathogens that can affect all organ systems, primarily the skin, lungs, and brain. N. cyriacigeorgica is the most prevalent species within the genus, exhibits clinical significance, and can cause severe infections when disseminated throughout the body. However, the evolution, diversity, and pathogenicity of N. cyriacigeorgica remain unclear. Here, we have conducted a comparative genomic analysis of 91 N. cyriacigeorgica strains and revealed that N. cyriacigeorgica is not a single species but is composed of five closely related species. In addition, we discovered that these five species differ in many ways, involving selection pressure, horizontal gene transfer, functional capacity, pathogenicity, and antibiotic resistance. Overall, our work provides important clues in dissecting the evolution, genetic diversity, and pathogenicity of NCC, thereby advancing prevention measures against these infections.
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Buresova‐Faitova A, Kopecky J, Sagova‐Mareckova M, Alonso L, Vautrin F, Moënne‐Loccoz Y, Rodriguez‐Nava V. Comparison of
Actinobacteria
communities from human‐impacted and pristine karst caves. Microbiologyopen 2022; 11:e1276. [PMID: 35478281 PMCID: PMC8988830 DOI: 10.1002/mbo3.1276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 03/10/2022] [Accepted: 03/10/2022] [Indexed: 11/07/2022] Open
Abstract
Actinobacteria are important cave inhabitants, but knowledge of how anthropization and anthropization‐related visual marks affect this community on cave walls is lacking. We compared Actinobacteria communities among four French limestone caves (Mouflon, Reille, Rouffignac, and Lascaux) ranging from pristine to anthropized, and within Lascaux Cave between marked (wall visual marks) and unmarked areas in different rooms (Sas‐1, Passage, Apse, and Diaclase). In addition to the 16S rRNA gene marker, 441 bp fragments of the hsp65 gene were used and an hsp65‐related taxonomic database was constructed for the identification of Actinobacteria to the species level by Illumina‐MiSeq analysis. The hsp65 marker revealed higher resolution for species and higher richness (99% operational taxonomic units cutoff) versus the 16S rRNA gene; however, more taxa were identified at higher taxonomic ranks. Actinobacteria communities varied between Mouflon and Reille caves (both pristine), and Rouffignac and Lascaux (both anthropized). Rouffignac displayed high diversity of Nocardia, suggesting human inputs, and Lascaux exhibited high Mycobacterium relative abundance, whereas Gaiellales were typical in pristine caves and the Diaclase (least affected area of Lascaux Cave). Within Lascaux, Pseudonocardiaceae dominated on unmarked walls and Streptomycetaceae (especially Streptomyces mirabilis) on marked walls, indicating a possible role in mark formation. A new taxonomic database was developed. Although not all Actinobacteria species were represented, the use of the hsp65 marker enabled species‐level variations of the Actinobacteria community to be documented based on the extent of anthropogenic pressure. This approach proved effective when comparing different limestone caves or specific conditions within one cave.
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Affiliation(s)
- Andrea Buresova‐Faitova
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
- Department of Ecology, Faculty of ScienceCharles University in PraguePrague 2PragueCzech Republic
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Jan Kopecky
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Marketa Sagova‐Mareckova
- Laboratory for Epidemiology and Ecology of MicroorganismsCrop Research InstitutePrahaCzech Republic
| | - Lise Alonso
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Florian Vautrin
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Yvan Moënne‐Loccoz
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
| | - Veronica Rodriguez‐Nava
- CNRS, INRAe, VetAgro Sup, UMR 5557 Ecologie MicrobienneUniversité de Lyon, Université Claude Bernard Lyon 1VilleurbanneFrance
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Nouioui I, Ha SM, Baek I, Chun J, Goodfellow M. Genome insights into the pharmaceutical and plant growth promoting features of the novel species Nocardia alni sp. nov. BMC Genomics 2022; 23:70. [PMID: 35062865 PMCID: PMC8783487 DOI: 10.1186/s12864-021-08257-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Recent studies highlighted the biosynthetic potential of nocardiae to produce diverse novel natural products comparable to that of Streptomyces, thereby making them an attractive source of new drug leads. Many of the 119 Nocardia validly named species were isolated from natural habitats but little is known about the diversity and the potential of the endophytic nocardiae of root nodule of actinorhizal plants. RESULTS The taxonomic status of an actinobacterium strain, designated ncl2T, was established in a genome-based polyphasic study. The strain was Gram-stain-positive, produced substrate and aerial hyphae that fragmented into coccoid and rod-like elements and showed chemotaxonomic properties that were also typical of the genus Nocardia. It formed a distinct branch in the Nocardia 16S rRNA gene tree and was most closely related to the type strains of Nocardia nova (98.6%), Nocardia jiangxiensis (98.4%), Nocardia miyuensis (97.8%) and Nocardia vaccinii (97.7%). A comparison of the draft genome sequence generated for the isolate with the whole genome sequences of its closest phylogenetic neighbours showed that it was most closely related to the N. jiangxiensis, N. miyuensis and N. vaccinii strains, a result underpinned by average nucleotide identity and digital DNA-DNA hybridization data. Corresponding taxogenomic data, including those from a pan-genome sequence analysis showed that strain ncl2T was most closely related to N. vaccinii DSM 43285T. A combination of genomic, genotypic and phenotypic data distinguished these strains from one another. Consequently, it is proposed that strain ncl2T (= DSM 110931T = CECT 30122T) represents a new species within the genus Nocardia, namely Nocardia alni sp. nov. The genomes of the N. alni and N. vaccinii strains contained 36 and 29 natural product-biosynthetic gene clusters, respectively, many of which were predicted to encode for a broad range of novel specialised products, notably antibiotics. Genome mining of the N. alni strain and the type strains of its closest phylogenetic neighbours revealed the presence of genes associated with direct and indirect mechanisms that promote plant growth. The core genomes of these strains mainly consisted of genes involved in amino acid transport and metabolism, energy production and conversion and transcription. CONCLUSIONS Our genome-based taxonomic study showed that isolate ncl2T formed a new centre of evolutionary variation within the genus Nocardia. This novel endophytic strain contained natural product biosynthetic gene clusters predicted to synthesize novel specialised products, notably antibiotics and genes associated with the expression of plant growth promoting compounds.
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Affiliation(s)
- Imen Nouioui
- Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, 38124, Braunschweig, Germany.
| | - Sung-Min Ha
- Department of Integrative Biology and Physiology, University of California Los Angeles, 610 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Inwoo Baek
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Jongsik Chun
- School of Biological Sciences & Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- ChunLab, Inc, Seoul, Korea
| | - Michael Goodfellow
- School of Natural and Environmental Sciences, Newcastle University, Ridley Building 2, NE1 7RU, Newcastle upon Tyne, UK
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Wu J, Li X, Zhang T, Lin X, Chen YC. Disseminated Nocardia farcinica involves the spinal cord: a case report and review of the literature. BMC Infect Dis 2021; 21:1224. [PMID: 34876035 PMCID: PMC8650257 DOI: 10.1186/s12879-021-06905-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/25/2021] [Indexed: 11/10/2022] Open
Abstract
Background Nocardia is a relatively rare opportunistic pathogenic bacteria group, commonly seen in patients with immunocompromised or defective immune system. It can affect multiple organs of the body and cause disseminated infection, among which most occurs in the lung, secondly in the nervous system, soft tissues, rare in the spinal cord and pituitary. No case has been reported involving lung, spinal cord, skin and pituitary gland at the same time. Case presentation We report a 55-year-old female with Nocardia infection involving the lung, skin, spinal cord, and pituitary gland. The patient underwent a full set of imaging examinations and showed typical imaging findings. Chest computed tomography (CT) showed multiple nodules with cavities in the lungs. The magnetic resonance imaging (MRI) of the vertebral body showed abnormal signal of the entire spinal cord with cavity formation and ring enhancement. The subcutaneous nodules of the abdomen were punctured under ultrasound. Through the etiological tissue culture of subcutaneous nodules and the second generation sequencing of cerebrospinal fluid, the diagnosis was finally confirmed. Conclusion Disseminated Nocardiosis is an uncommon disease. This article will report a rare case of disseminated Nocardiosis simultaneously involving the lung, spinal cord, subcutaneous soft tissue and pituitary gland, especially with neuropathy as the initial symptom. Imaging is helpful for the early diagnosis of the disease and pathological and microbiological examinations are helpful for its confirming.
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Affiliation(s)
- Jing Wu
- Department of Radiology, Nanjing First Hospital, Nanjing Medical University, No.68, Changle Road, Nanjing, 21006, People's Republic of China
| | - Xiaoran Li
- Department of Radiology, Nanjing Gaochun People's Hospital, Nanjing, Jiangsu, People's Republic of China
| | - Tao Zhang
- Department of Radiology, Nanjing First Hospital, Nanjing Medical University, No.68, Changle Road, Nanjing, 21006, People's Republic of China
| | - Xin Lin
- Department of Laboratory, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People's Republic of China
| | - Yu-Chen Chen
- Department of Radiology, Nanjing First Hospital, Nanjing Medical University, No.68, Changle Road, Nanjing, 21006, People's Republic of China.
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Sarkar B, Gupta AM, Mandal S. Insights from the comparative genome analysis of natural rubber degrading Nocardia species. Bioinformation 2021; 17:880-890. [PMID: 35574501 PMCID: PMC9070631 DOI: 10.6026/97320630017880] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/16/2021] [Accepted: 10/16/2021] [Indexed: 11/23/2022] Open
Abstract
Nocardia are known to be a facultative human pathogen and can cause infection in immune compromised patients. Though the details research on the virulence factors of Nocardia are scanty but numerous genes that code such factors were reported from different species of Nocardia. Despite of the presence of several virulence factors, species of this genus have been shown to have role in remediation of many toxic and hazardous materials from the environment. In this study, genome sequences of rubber degrading Nocardia sp. BSTN01 and N.nova SH22a have been analyzed to locate the potential virulence genes. Also, the genomes of facultative pathogenic Nocardia like, N.africana, N. brasiliensis, N. kruczakiae, N. transvalensis and N. veterana have been analyzed to find the gene encoding latex clearing protein (Lcp), a rubber oxygenase enzyme of Gram-positive action bacteria. The study provides an insight about the potentiality of rubberdegrading Nocardia species to emerge as future human pathogens and also the probability of a serious concern if the studied facultative pathogens of Nocardia like N. africana, N. brasiliensis, N. kruczakiae, N. transvalensis and N. veterana are capable of degrading rubber, a regularly used material in clinics. Moreover, use of such possible pathogenic strains for their known role in bioremediation of rubber waste from the environment might be deleterious.
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Affiliation(s)
- Biraj Sarkar
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
| | - Aayatti Mallick Gupta
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata-700 106, India
| | - Sukhendu Mandal
- Laboratory of Molecular Bacteriology, Department of Microbiology, University of Calcutta, 35, Ballygunge Circular Road, Kolkata, 700019, India
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Engelbrecht A, Saad H, Gross H, Kaysser L. Natural Products from Nocardia and Their Role in Pathogenicity. Microb Physiol 2021; 31:217-232. [PMID: 34139700 DOI: 10.1159/000516864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/26/2021] [Indexed: 11/19/2022]
Abstract
Nocardia spp. are filamentous Actinobacteria of the order Corynebacteriales and mostly known for their ability to cause localized and systemic infections in humans. However, the onset and progression of nocardiosis is only poorly understood, in particular the mechanisms of strain-specific presentations. Recent genome sequencing has revealed an extraordinary capacity for the production of specialized small molecules. Such secondary metabolites are often crucial for the producing microbe to survive the challenges of different environmental conditions. An interesting question thus concerns the role of these natural products in Nocardia-associated pathogenicity and immune evasion in a human host. In this review, a summary and discussion of Nocardia metabolites is presented, which may play a part in nocardiosis because of their cytotoxic, immunosuppressive and metal-chelating properties or otherwise vitally important functions. This review also contains so far unpublished data concerning the biosynthesis of these molecules that were obtained by detailed bioinformatic analyses.
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Affiliation(s)
- Alicia Engelbrecht
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Hamada Saad
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Department of Phytochemistry and Plant Systematics, Division of Pharmaceutical Industries, National Research Centre, Cairo, Egypt
| | - Harald Gross
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany
| | - Leonard Kaysser
- Department of Pharmaceutical Biology, University of Tübingen, Tübingen, Germany.,Institute for Drug Discovery, University of Leipzig, Leipzig, Germany
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Vautrin F, Pujic P, Paquet C, Bergeron E, Mouniée D, Marchal T, Salord H, Bonnet JM, Cournoyer B, Winiarski T, Louzier V, Rodriguez-Nava V. Microbial risk assessment of Nocardia cyriacigeorgica in polluted environments, case of urban rainfall water. Comput Struct Biotechnol J 2021; 19:384-400. [PMID: 33489008 DOI: 10.1016/j.csbj.2020.12.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 12/29/2022] Open
Abstract
Urban infiltration basins are a reservoir of a high diversity of Nocardia encompassing both pathogenic and not-pathogenic species. Relative abundance of pathogenic Nocardia species presents a positive correlation with metal trace elements. High infraspecific variability within N. cyriacigeorgica, forming three phylogroups. Environmental N. cyriacigeorgica strains may be as virulent as clinical GUH-2 strain. hsp65 marker can be used by metabarcoding approach for assessment of environmental Nocardia biodiversity.
Urban Infiltration Basins (UIBs) are used to manage urban runoff transfers and feed aquifers. These UIBs can accumulate urban pollutants and favor the growth of potentially pathogenic biological agents as Nocardia. Objectives To assess the spatio-temporal dynamics of pathogenic Nocardia in UIBs and to stablish phylogenetic relationships between clinical and UIB N. cyriacigeorgica strains. To assess pathogenicity associated with environmental N. cyriacigeorgica using an animal model, and to identify genetic elements that may be associated to its virulence. Methods A well-characterized UIB in terms of chemical pollutants from Lyon area was used in this study during a whole year. Cultural and Next-Generation-Sequencing methods were used for Nocardia detection and typing. Clinical and environmental isolates phylogenetic relationships and virulences were compared with Multilocus-Sequence-Analysis study together with a murine model. Results In autumn, N. cyriacigeorgica and N. nova were the pathogenic most prevalent species in the UIB. The complex N. abscessus/asiatica was also detected together with some other non-pathogenic species. The presence of pathogenic Nocardia was positively correlated to metallic trace elements. Up to 1.0 × 103 CFU/g sediment of N. cyriacigeorgica and 6 OTUs splited in two different phylogroups were retrieved and were close to clinical strains. The EML446 tested UIB isolate showed significant infectivity in mice with pulmonary damages similar to clinical clone (GUH-2). Conclusion Hsp65 marker-based metabarcoding approach allowed detecting N. cyriacigeogica as the most abundant Nocardia pathogenic species in a UIB. Metal trace elements-polluted environments can be reservoirs of pathogenic Nocardia which may have a similar virulence to clinical strains.
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Ji X, Zhang X, Sun L, Hou X, Song J, Tan X, Song H, Qiu X, Li M, Tang L, Han L, Li Z. Mce1C and Mce1D facilitate N. farcinica invasion of host cells and suppress immune responses by inhibiting innate signaling pathways. Sci Rep 2020; 10:14908. [PMID: 32913259 PMCID: PMC7484815 DOI: 10.1038/s41598-020-71860-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/06/2020] [Indexed: 11/22/2022] Open
Abstract
The mammalian cell entry (Mce) family of proteins consists of invasin-like membrane-associated proteins. The roles of Mce1C and Mce1D proteins in host–pathogen interactions have not been investigated. In this study, we demonstrate that Mce1C and Mce1D protein is localized in the cell wall fraction of N. farcinica. Both N. farcinica Mce1C and Mce1D proteins are expressed at the level of protein and mRNA and elicit antibody responses during infection. Mce1C and Mce1D facilitate the internalization of Escherichia coli expressing Mce1C protein or latex beads coated with Mce1D protein by HeLa cells, respectively. We further demonstrate that Mce1C and Mce1D can suppress the secretion of the proinflammatory factors TNF-α and IL-6 in macrophages infected with Mycobacterium smegmatis expressing Mce1C or Mce1D and promote the survival of M. smegmatis expressing Mce1C or Mce1D in macrophages. In addition, Mce1C and Mce1D supress the activation of the NF-κB and MAPK signaling pathways by blocking the phosphorylation of AKT, P65, ERK1/2, JNK, or P38 in macrophages. These findings suggest that Mce1C and Mce1D proteins facilitate N. farcinica invasion of HeLa cells and suppress host innate immune responses by manipulating NF-κB and MAPK signaling pathways, which may provide a target for N. farcinica treatment.
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Affiliation(s)
- Xingzhao Ji
- Shandong Academy of Clinical Medicine, Provincial Hospital Affiliated to Shandong First Medical University, Jinan, 250000, China.,State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China
| | - Xiujuan Zhang
- Department of Endocrinology, Beijing Chaoyang Hospital, Capital Medical University, Beijing, China
| | - Lina Sun
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China
| | - Xuexin Hou
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China
| | - Jingdong Song
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaoluo Tan
- Chenzhou Center for Disease Control and Prevention, Chenzhou, China
| | - Han Song
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China
| | - Xiaotong Qiu
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China
| | - Minghui Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China
| | - Lu Tang
- First Affiliated Hospital of Chengdu Medical College, Chengdu, China
| | - Lichao Han
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road Changping District, Beijing, 102206, China.
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Affiliation(s)
- Heer H. Mehta
- Department of BioSciences, Rice University, Houston, Texas, United States of America
- * E-mail:
| | - Yousif Shamoo
- Department of BioSciences, Rice University, Houston, Texas, United States of America
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Dhakal D, Rayamajhi V, Mishra R, Sohng JK. Bioactive molecules from Nocardia: diversity, bioactivities and biosynthesis. ACTA ACUST UNITED AC 2019; 46:385-407. [DOI: 10.1007/s10295-018-02120-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/19/2018] [Indexed: 02/06/2023]
Abstract
Abstract
Nocardia spp. are catalase positive, aerobic, and non-motile Gram-positive filamentous bacteria. Many Nocarida spp. have been reported as unusual causes of diverse clinical diseases in both humans and animals. Therefore, they have been studied for a long time, primarily focusing on strain characterization, taxonomic classification of new isolates, and host pathophysiology. Currently, there are emerging interests in isolating bioactive molecules from diverse actinobacteria including Nocardia spp. and studying their biosynthetic mechanisms. In addition, these species possess significant metabolic capacity, which has been utilized for generating diverse functionalized bioactive molecules by whole cell biotransformation. This review summarizes the structural diversity and biological activities of compounds biosynthesized or biotransformed by Nocardia spp. Furthermore, the recent advances on biosynthetic mechanisms and genetic engineering approaches for enhanced production or structural/functional modification are presented.
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Affiliation(s)
- Dipesh Dhakal
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
| | - Vijay Rayamajhi
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
| | - Ravindra Mishra
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
| | - Jae Kyung Sohng
- 0000 0004 0533 4202 grid.412859.3 Department of Life Science and Biochemical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
- 0000 0004 0533 4202 grid.412859.3 Department of BT-Convergent Pharmaceutical Engineering SunMoon University 70 Sunmoon-ro 221, Tangjeong-myeon 31460 Asan-si Chungnam Republic of Korea
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Bernardin Souibgui C, Zoropogui A, Voisin J, Ribun S, Vasselon V, Pujic P, Rodriguez-Nava V, Belly P, Cournoyer B, Blaha D. Virulence test using nematodes to prescreen Nocardia species capable of inducing neurodegeneration and behavioral disorders. PeerJ 2017; 5:e3823. [PMID: 29038748 PMCID: PMC5639870 DOI: 10.7717/peerj.3823] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 08/28/2017] [Indexed: 01/03/2023] Open
Abstract
Background Parkinson’s disease (PD) is a disorder characterized by dopaminergic neuron programmed cell death. The etiology of PD remains uncertain—some cases are due to selected genes associated with familial heredity, others are due to environmental exposure to toxic components, but over 90% of cases have a sporadic origin. Nocardia are Actinobacteria that can cause human diseases like nocardiosis. This illness can lead to lung infection or central nervous system (CNS) invasion in both immunocompromised and immunocompetent individuals. The main species involved in CNS are N. farcinica, N. nova, N. brasiliensis and N. cyriacigeorgica. Some studies have highlighted the ability of N. cyriacigeorgica to induce Parkinson’s disease-like symptoms in animals. Actinobacteria are known to produce a large variety of secondary metabolites, some of which can be neurotoxic. We hypothesized that neurotoxic secondary metabolite production and the onset of PD-like symptoms in animals could be linked. Methods Here we used a method to screen bacteria that could induce dopaminergic neurodegeneration before performing mouse experiments. Results The nematode Caenorhabditis elegans allowed us to demonstrate that Nocardia strains belonging to N. cyriacigeorgica and N. farcinica species can induce dopaminergic neurodegeneration. Strains of interest involved with the nematodes in neurodegenerative disorders were then injected in mice. Infected mice had behavioral disorders that may be related to neuronal damage, thus confirming the ability of Nocardia strains to induce neurodegeneration. These behavioral disorders were induced by N. cyriacigeorgica species (N. cyriacigeorgica GUH-2 and N. cyriacigeorgica 44484) and N. farcinica 10152. Discussion We conclude that C. elegans is a good model for detecting Nocardia strains involved in neurodegeneration. This model allowed us to detect bacteria with high neurodegenerative effects and which should be studied in mice to characterize the induced behavioral disorders and bacterial dissemination.
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Affiliation(s)
- Claire Bernardin Souibgui
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Anthony Zoropogui
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Jeremy Voisin
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Sebastien Ribun
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Valentin Vasselon
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Petar Pujic
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Veronica Rodriguez-Nava
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Patrick Belly
- Department of Clinical and Morphological Pathology, Université de Lyon, VetAgro Sup Campus Vétérinaire de Lyon, Marcy L'Etoile, France, Université Claude Bernard (Lyon I), France.,Université Claude Bernard (Lyon I), France
| | - Benoit Cournoyer
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
| | - Didier Blaha
- UMR CNRS5557, INRA1418 Ecologie Microbienne, Université Lyon 1, VetAgro Sup, Université Claude Bernard (Lyon I), Lyon, France
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Chen W, Liu Y, Zhang L, Gu X, Liu G, Shahid M, Gao J, Ali T, Han B. Nocardia cyriacigeogica from Bovine Mastitis Induced In vitro Apoptosis of Bovine Mammary Epithelial Cells via Activation of Mitochondrial-Caspase Pathway. Front Cell Infect Microbiol 2017; 7:194. [PMID: 28573110 PMCID: PMC5435817 DOI: 10.3389/fcimb.2017.00194] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 05/03/2017] [Indexed: 11/13/2022] Open
Abstract
Nocardia is one of the causing agents of bovine mastitis and increasing prevalence of nocardial mastitis in shape of serious outbreaks has been reported from many countries. However, the mechanisms by which this pathogen damages the bovine mammary epithelial cells (bMECs) is not yet studied. Therefore, this study was designed with the aim to evaluate the apoptotic effects elicited by Nocardia and to investigate the pathway by which the Nocardia induce apoptosis in bMECs. Clinical Nocardia cyriacigeorgica strain from bovine mastitis was used to infect the bMECs for different time intervals, viz. 1, 3, 6, 12, and 18 h, and then the induced effects on bMECs were studied using adhesion and invasion assays, release of lactate dehydrogenase (LDH), apoptosis analysis by annexin V and propidium iodide (PI) double staining, morphological, and ultrastructural observations under scanning electron microscope (SEM) and transmission electron microscope (TEM), mitochondrial transmembrane potential (ΔΨm) assay using flow cytometry, and the protein quantification of mitochondrial cytochrome c and caspase-9 and caspase-3 by western blotting. The results of this study showed that N. cyriacigeorgica possessed the abilities of adhesion and invasion to bMECs. N. cyriacigeorgica was found to collapse mitochondrial transmembrane potential, significantly (p < 0.05) release mitochondrial cytochrome c and ultimately induce cell apoptosis. Additionally, it promoted casepase-9 (p < 0.01) and casepase-3 (p < 0.05) levels, significantly (p < 0.01) increased the release of LDH and promoted DNA fragmentation which further confirmed the apoptosis. Furthermore, N. cyriacigeorgica induced apoptosis/necrosis manifested specific ultrastructure features under TEM, such as swollen endoplasmic reticulum, cristae degeneration, and swelling of mitochondria, vesicle formation on the cell surface, rupturing of cell membrane and nuclear membrane, clumping, fragmentation, and margination of chromatin. The present study is the first comprehensive insight into patho-morphological ultrastructural features of apoptosis/necrosis induced by N. cyriacigeorgica, which concluded that the clinical N. cyriacigeorgica induced apoptotic changes in the bMECs through mitochondrial-caspase dependent apoptotic pathway.
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Affiliation(s)
- Wei Chen
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Yongxia Liu
- Department of Veterinary Clinics, College of Veterinary Medicine, Shandong Agricultural UniversityTai'an, China
| | - Limei Zhang
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Xiaolong Gu
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Gang Liu
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Muhammad Shahid
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Jian Gao
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Tariq Ali
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
| | - Bo Han
- Department of Veterinary Clinics, College of Veterinary Medicine, China Agricultural UniversityBeijing, China
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Yasuike M, Nishiki I, Iwasaki Y, Nakamura Y, Fujiwara A, Shimahara Y, Kamaishi T, Yoshida T, Nagai S, Kobayashi T, Katoh M. Analysis of the complete genome sequence of Nocardia seriolae UTF1, the causative agent of fish nocardiosis: The first reference genome sequence of the fish pathogenic Nocardia species. PLoS One 2017; 12:e0173198. [PMID: 28257489 PMCID: PMC5336288 DOI: 10.1371/journal.pone.0173198] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 02/16/2017] [Indexed: 01/15/2023] Open
Abstract
Nocardiosis caused by Nocardia seriolae is one of the major threats in the aquaculture of Seriola species (yellowtail; S. quinqueradiata, amberjack; S. dumerili and kingfish; S. lalandi) in Japan. Here, we report the complete nucleotide genome sequence of N. seriolae UTF1, isolated from a cultured yellowtail. The genome is a circular chromosome of 8,121,733 bp with a G+C content of 68.1% that encodes 7,697 predicted proteins. In the N. seriolae UTF1 predicted genes, we found orthologs of virulence factors of pathogenic mycobacteria and human clinical Nocardia isolates involved in host cell invasion, modulation of phagocyte function and survival inside the macrophages. The virulence factor candidates provide an essential basis for understanding their pathogenic mechanisms at the molecular level by the fish nocardiosis research community in future studies. We also found many potential antibiotic resistance genes on the N. seriolae UTF1 chromosome. Comparative analysis with the four existing complete genomes, N. farcinica IFM 10152, N. brasiliensis HUJEG-1 and N. cyriacigeorgica GUH-2 and N. nova SH22a, revealed that 2,745 orthologous genes were present in all five Nocardia genomes (core genes) and 1,982 genes were unique to N. seriolae UTF1. In particular, the N. seriolae UTF1 genome contains a greater number of mobile elements and genes of unknown function that comprise the differences in structure and gene content from the other Nocardia genomes. In addition, a lot of the N. seriolae UTF1-specific genes were assigned to the ABC transport system. Because of limited resources in ocean environments, these N. seriolae UTF1 specific ABC transporters might facilitate adaptation strategies essential for marine environment survival. Thus, the availability of the complete N. seriolae UTF1 genome sequence will provide a valuable resource for comparative genomic studies of N. seriolae isolates, as well as provide new insights into the ecological and functional diversity of the genus Nocardia.
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Affiliation(s)
- Motoshige Yasuike
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Issei Nishiki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yuki Iwasaki
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Yoji Nakamura
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Atushi Fujiwara
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
- * E-mail: (AF); (MY)
| | - Yoshiko Shimahara
- Research Center of Fish Diseases, National Research Institute of Aquaculture, Japan Fisheries Research and Education Agency, Saiki, Oita, Japan
| | - Takashi Kamaishi
- Fisheries Agency, Ministry of Agriculture, Forestry and Fisheries, Chiyoda-ku, Tokyo, Japan
| | | | - Satoshi Nagai
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Takanori Kobayashi
- Headquarters, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
| | - Masaya Katoh
- Research Center for Bioinformatics and Biosciences, National Research Institute of Fisheries Science, Japan Fisheries Research and Education Agency, Yokohama, Kanagawa, Japan
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Rudramurthy SM, Honnavar P, Kaur H, Samanta P, Ray P, Ghosh A, Chakrabarti A. Molecular identification of clinical Nocardia isolates from India. J Med Microbiol 2015. [DOI: 10.1099/jmm.0.000143] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Shivaprakash M. Rudramurthy
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Prasanna Honnavar
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Harsimran Kaur
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Palash Samanta
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Pallab Ray
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Anup Ghosh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Arunaloke Chakrabarti
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, Chandigarh, India
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Luo Q, Hiessl S, Poehlein A, Daniel R, Steinbüchel A. Insights into the microbial degradation of rubber and gutta-percha by analysis of the complete genome of Nocardia nova SH22a. Appl Environ Microbiol 2014; 80:3895-907. [PMID: 24747905 PMCID: PMC4054215 DOI: 10.1128/aem.00473-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 04/14/2014] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequence of Nocardia nova SH22a was determined in light of the remarkable ability of rubber and gutta-percha (GP) degradation of this strain. The genome consists of a circular chromosome of 8,348,532 bp with a G+C content of 67.77% and 7,583 predicted protein-encoding genes. Functions were assigned to 72.45% of the coding sequences. Among them, a large number of genes probably involved in the metabolism of xenobiotics and hardly degradable compounds, as well as genes that participate in the synthesis of polyketide- and/or nonribosomal peptide-type secondary metabolites, were detected. Based on in silico analyses and experimental studies, such as transposon mutagenesis and directed gene deletion studies, the pathways of rubber and GP degradation were proposed and the relationship between both pathways was unraveled. The genes involved include, inter alia, genes participating in cell envelope synthesis (long-chain-fatty-acid-AMP ligase and arabinofuranosyltransferase), β-oxidation (α-methylacyl-coenzyme A [α-methylacyl-CoA] racemase), propionate catabolism (acyl-CoA carboxylase), gluconeogenesis (phosphoenolpyruvate carboxykinase), and transmembrane substrate uptake (Mce [mammalian cell entry] transporter). This study not only improves our insights into the mechanism of microbial degradation of rubber and GP but also expands our knowledge of the genus Nocardia regarding metabolic diversity.
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Affiliation(s)
- Quan Luo
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Sebastian Hiessl
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany
| | - Anja Poehlein
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Rolf Daniel
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Göttingen, Germany
| | - Alexander Steinbüchel
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Münster, Germany King Abdulaziz University, Faculty of Biology, Jeddah, Saudi Arabia
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Komaki H, Ichikawa N, Hosoyama A, Takahashi-Nakaguchi A, Matsuzawa T, Suzuki KI, Fujita N, Gonoi T. Genome based analysis of type-I polyketide synthase and nonribosomal peptide synthetase gene clusters in seven strains of five representative Nocardia species. BMC Genomics 2014; 15:323. [PMID: 24884595 PMCID: PMC4035055 DOI: 10.1186/1471-2164-15-323] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2013] [Accepted: 04/15/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Actinobacteria of the genus Nocardia usually live in soil or water and play saprophytic roles, but they also opportunistically infect the respiratory system, skin, and other organs of humans and animals. Primarily because of the clinical importance of the strains, some Nocardia genomes have been sequenced, and genome sequences have accumulated. Genome sizes of Nocardia strains are similar to those of Streptomyces strains, the producers of most antibiotics. In the present work, we compared secondary metabolite biosynthesis gene clusters of type-I polyketide synthase (PKS-I) and nonribosomal peptide synthetase (NRPS) among genomes of representative Nocardia species/strains based on domain organization and amino acid sequence homology. RESULTS Draft genome sequences of Nocardia asteroides NBRC 15531(T), Nocardia otitidiscaviarum IFM 11049, Nocardia brasiliensis NBRC 14402(T), and N. brasiliensis IFM 10847 were read and compared with published complete genome sequences of Nocardia farcinica IFM 10152, Nocardia cyriacigeorgica GUH-2, and N. brasiliensis HUJEG-1. Genome sizes are as follows: N. farcinica, 6.0 Mb; N. cyriacigeorgica, 6.2 Mb; N. asteroides, 7.0 Mb; N. otitidiscaviarum, 7.8 Mb; and N. brasiliensis, 8.9 - 9.4 Mb. Predicted numbers of PKS-I, NRPS, and PKS-I/NRPS hybrid clusters ranged between 4-11, 7-13, and 1-6, respectively, depending on strains, and tended to increase with increasing genome size. Domain and module structures of representative or unique clusters are discussed in the text. CONCLUSION We conclude the following: 1) genomes of Nocardia strains carry as many PKS-I and NRPS gene clusters as those of Streptomyces strains, 2) the number of PKS-I and NRPS gene clusters in Nocardia strains varies substantially depending on species, and N. brasiliensis strains carry the largest numbers of clusters among the species studied, 3) the seven Nocardia strains studied in the present work have seven common PKS-I and/or NRPS clusters, some of whose products are yet to be studied, and 4) different N. brasiliensis strains have some different gene clusters of PKS-I/NRPS, although the rest of the clusters are common within the N. brasiliensis strains. Genome sequencing suggested that Nocardia strains are highly promising resources in the search of novel secondary metabolites.
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Affiliation(s)
| | | | | | | | | | | | | | - Tohru Gonoi
- Medical Mycology Research Center (MMRC), Chiba University, Chuo-ku, Chiba 260-8673, Japan.
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Luo Q, Hiessl S, Steinbüchel A. Functional diversity of Nocardia in metabolism. Environ Microbiol 2013; 16:29-48. [PMID: 23981049 DOI: 10.1111/1462-2920.12221] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/12/2013] [Accepted: 07/19/2013] [Indexed: 11/29/2022]
Abstract
Bacteria affiliated in the genus Nocardia are aerobic and Gram-positive actinomycetes that are widely found in aquatic and terrestrial habitats. As occasional pathogens, several of them cause infection diseases called 'nocardiosis' affecting lungs, central nervous system, cutaneous tissues and others. In addition, members of the genus Nocardia exhibit an enormous metabolic versatility. On one side, many secondary metabolites have been isolated from members of this genus that exhibit various biological activities such as antimicrobial, antitumor, antioxidative and immunosuppressive activities. On the other side, many species are capable of degrading or converting aliphatic and aromatic toxic hydrocarbons, natural or synthetic polymers, and other widespread environmental pollutants. Because of these valuable properties and the application potential, Nocardia species have attracted much interest in academia and industry in recent years. A solid basis of genetic tools including a set of shuttle vectors and an efficient electroporation method for further genetic and metabolic engineering studies has been established to conduct efficient research. Associated with the increasing data of nocardial genome sequences, the functional diversity of Nocardia will be much faster and better understood.
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Affiliation(s)
- Quan Luo
- Institut für Molekulare Mikrobiologie und Biotechnologie, Westfälische Wilhelms-Universität Münster, Corrensstraße 3, 48149, Münster, Germany
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