1
|
Arend LNVS, Bergamo R, Rocha FB, Bail L, Ito C, Baura VA, Balsanelli E, Pothier JF, Rezzonico F, Pilonetto M, Smits THM, Tuon FF. Dissemination of NDM-producing bacteria in Southern Brazil. Diagn Microbiol Infect Dis 2023; 106:115930. [PMID: 37001228 DOI: 10.1016/j.diagmicrobio.2023.115930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 01/23/2023] [Accepted: 02/28/2023] [Indexed: 03/08/2023]
Abstract
BACKGROUND The dissemination of NDM-1 carbapenemases (New Delhi Metallo-β-lactamase) is a global public health problem, mainly in developing countries. The aim of this study was to characterize the spread of NDM-producing bacteria in the Southern Brazilian states analyzing epidemiological, molecular, and antimicrobial susceptibility aspects. METHODS A total of 10,684 carbapenem-resistant isolates of Enterobacterales, Pseudomonas spp. and Acinetobacter spp. obtained from several hospitals in eight cities in Southern Brazil were screened, and 486 NDM-producing bacteria were selected. RESULTS The incidence varied from 0.5 to 77 cases/100.000 habitants. ST11, ST15, ST340 and ST674 were the most common in K. pneumoniae. A total of 5 plasmids were identified in one K. pneumoniae strain: Col440I, Col440II, IncFIA(HI1), IncFIB(K), IncFIB(pQil)/ IncFII(K), and IncR. CONCLUSIONS The number of patients with NDM-producing bacteria has increased in Southern Brazil, whose gene is present in different plasmids, explaining the expansion of this enzyme.
Collapse
Affiliation(s)
- Lavinia N V S Arend
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil; Public Health Central Laboratory-State of Paraná-LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, Paraná, Brazil
| | | | - Fabiano B Rocha
- CGLAB General Coordination of Laboratories of Public Health, Ministry of Health, Brasilia, Federal District, Brazil
| | - Larissa Bail
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Carmen Ito
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil
| | - Valter A Baura
- Laboratory of Biochemistry, Polytechnic Center, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Eduardo Balsanelli
- Laboratory of Biochemistry, Polytechnic Center, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Joël F Pothier
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Fabio Rezzonico
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Marcelo Pilonetto
- Public Health Central Laboratory-State of Paraná-LACEN/PR, Molecular Bacteriology Division, São José Dos Pinhais, Paraná, Brazil; Core for Advanced Molecular Investigation, Graduate Program in Health Sciences, School of Medicine, Pontifícia Universidade Católica Do Paraná, Curitiba, Paraná, Brazil
| | - Theo H M Smits
- Environmental Genomics and Systems Biology Research Group, Institute of Natural Resource Sciences (IUNR), Zurich University of Applied Sciences ZHAW, Wädenswil, Switzerland
| | - Felipe Francisco Tuon
- Laboratory of Emerging Infectious Diseases, School of Medicine, Pontifícia Universidade Católica do Paraná, Curitiba, Paraná, Brazil.
| |
Collapse
|
2
|
Huergo LF, Conzentino M, Gonçalves MV, Gernet MV, Reis RA, Pedrosa FO, Baura VA, Pires A, Gerhardt ECM, Tuleski TR, Balsanelli E, Guizelini D, Souza EM, Chandra G, Cruz LM. The microbiome of a shell mound: ancient anthropogenic waste as a source of Streptomyces degrading recalcitrant polysaccharides. World J Microbiol Biotechnol 2021; 37:210. [PMID: 34719741 DOI: 10.1007/s11274-021-03174-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 06/25/2021] [Accepted: 10/18/2021] [Indexed: 10/20/2022]
Abstract
Metagenome amplicon DNA sequencing and traditional cell culture techniques are helping to uncover the diversity and the biotechnological potential of prokaryotes in different habitats around the world. It has also had a profound impact on microbial taxonomy in the last decades. Here we used metagenome 16S rDNA amplicon sequencing to reveal the microbiome composition of different layers of an anthropogenic soil collected at a shell mound Sambaqui archeological site. The Samabaqui soil microbiome is mainly composed by phyla Acidobacteria, Rokubacteria, Proteobacteria and Thaumarchaeota. Using culture-dependent analysis we obtained few Streptomyces isolates from the Sambaqui soil. One of the isolates, named Streptomyces sp. S3, was able to grow in minimal medium containing recalcitrant polysaccharides including chitin, xylan, carboxymethylcellulose or microcrystalline cellulose as sole carbon sources. The activities of enzymes degrading these compounds were confirmed in cell free supernatants. The genome sequence revealed not only an arsenal of genes related to polysaccharides degradation but also biosynthetic gene clusters which may be involved in the production of biotechnologically interesting secondary metabolites.
Collapse
Affiliation(s)
| | | | | | | | | | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Valter A Baura
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Araceli Pires
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | | | - Thalita R Tuleski
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Dieval Guizelini
- Programa de Pós-graduação em Bioinformática, UFPR, Curitiba, PR, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Govind Chandra
- Department of Molecular Microbiology, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Leonardo M Cruz
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| |
Collapse
|
3
|
Souza FFC, Mathai PP, Pauliquevis T, Balsanelli E, Pedrosa FO, Souza EM, Baura VA, Monteiro RA, Cruz LM, Souza RAF, Andreae MO, Barbosa CGG, de Angelis IH, Sánchez-Parra B, Pӧhlker C, Weber B, Ruff E, Reis RA, Godoi RHM, Sadowsky MJ, Huergo LF. Influence of seasonality on the aerosol microbiome of the Amazon rainforest. Sci Total Environ 2021; 760:144092. [PMID: 33341626 DOI: 10.1016/j.scitotenv.2020.144092] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/14/2020] [Accepted: 11/22/2020] [Indexed: 06/12/2023]
Abstract
The Amazon rainforest is the world's largest tropical forest, and this biome may be a significant contributor to primary biological aerosol (PBA) emissions on a global scale. These aerosols also play a pivotal role in modulating ecosystem dynamics, dispersing biological material over geographic barriers and influencing climate through radiation absorption, light scattering, or acting as cloud condensation nuclei. Despite their importance, there are limited studies investigating the effect of environmental variables on the bioaerosol composition in the Amazon rainforest. Here we present a 16S rRNA gene-based amplicon sequencing approach to investigate the bacterial microbiome in aerosols of the Amazon rainforest during distinct seasons and at different heights above the ground. Our data revealed that seasonal changes in temperature, relative humidity, and precipitation are the primary drivers of compositional changes in the Amazon rainforest aerosol microbiome. Interestingly, no significant differences were observed in the bacterial community composition of aerosols collected at ground and canopy levels. The core airborne bacterial families present in Amazon aerosol were Enterobacteriaceae, Beijerinckiaceae, Polyangiaceae, Bacillaceae and Ktedonobacteraceae. By correlating the bacterial taxa identified in the aerosol with literature data, we speculate that the phyllosphere may be one possible source of airborne bacteria in the Amazon rainforest. Results of this study indicate that the aerosol microbiota of the Amazon Rainforest are fairly diverse and principally impacted by seasonal changes in temperature and humidity.
Collapse
Affiliation(s)
| | - Prince P Mathai
- Biotechnology Institute, University of Minnesota, St. Paul, MN, USA
| | | | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Fabio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Valter A Baura
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Rose A Monteiro
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Leonardo M Cruz
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Rodrigo A F Souza
- Meteorology Department, State University of Amazonas - UEA, Manaus, AM, Brazil
| | - Meinrat O Andreae
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany; Scripps Institution of Oceanography, University of San Diego, La Jolla, CA, USA
| | - Cybelli G G Barbosa
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | | | | | - Christopher Pӧhlker
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Bettina Weber
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany; Institut für Biologie, University of Graz, Graz, Austria
| | - Emil Ruff
- Ecosystems Center, Marine Biological Laboratory, Woods Hole, USA; J Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, USA
| | | | | | | | | |
Collapse
|
4
|
Bombassaro A, Schneider GX, Costa FF, Leão ACR, Soley BS, Medeiros F, da Silva NM, Lima BJFS, Castro RJA, Bocca AL, Baura VA, Balsanelli E, Pankievicz VCS, Hrysay NMC, Scola RH, Moreno LF, Azevedo CMPS, Souza EM, Gomes RR, de Hoog S, Vicente VA. Genomics and Virulence of Fonsecaea pugnacius, Agent of Disseminated Chromoblastomycosis. Front Genet 2020; 11:822. [PMID: 32849816 PMCID: PMC7417343 DOI: 10.3389/fgene.2020.00822] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [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: 11/13/2019] [Accepted: 07/08/2020] [Indexed: 11/16/2022] Open
Abstract
Among agents of chromoblastomycosis, Fonsecaea pugnacius presents a unique type of infection because of its secondary neurotropic dissemination from a chronic cutaneous case in an immunocompetent patient. Neurotropism occurs with remarkable frequency in the fungal family Herpotrichiellaceae, possibly associated with the ability of some species to metabolize aromatic hydrocarbons. In an attempt to understand this new disease pattern, were conducted genomic analysis of Fonsecaea pugnacius (CBS 139214) performed with de novo assembly, gene prediction, annotation and mitochondrial genome assembly, supplemented with animal infection models performed with Tenebrio molitor in Mus musculus lineages BALB/c and C57BL/6. The genome draft of 34.8 Mb was assembled with a total of 12,217 protein-coding genes. Several proteins, enzymes and metabolic pathways related to extremotolerance and virulence were recognized. The enzyme profiles of black fungi involved in chromoblastomycosis and brain infection were analyzed with the Carbohydrate-Active Enzymes (CAZY) and peptidases database (MEROPS). The capacity of the fungus to survive inside Tenebrio molitor animal model was confirmed by histopathological analysis and by presence of melanin and hyphae in host tissue. Although F. pugnacius was isolated from brain in a murine model following intraperitoneal infection, cytokine levels were not statistically significant, indicating a profile of an opportunistic agent. A dual ecological ability can be concluded from presence of metabolic pathways for nutrient scavenging and extremotolerance, combined with a capacity to infect human hosts.
Collapse
Affiliation(s)
- Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Gabriela X Schneider
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Flávia F Costa
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Aniele C R Leão
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna S Soley
- Pharmacology Post-graduation Program, Department of Pharmacology, Federal University of Paraná, Curitiba, Brazil
| | - Fernanda Medeiros
- Graduation in Biology Sciences, Federal University of Paraná, Curitiba, Brazil
| | - Nickolas M da Silva
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Bruna J F S Lima
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | | | - Anamélia L Bocca
- Department of Cell Biology, University of Brasilia, Brasilia, Brazil
| | - Valter A Baura
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Nyvia M C Hrysay
- Service of Neuromuscular and Demyelinating Diseases, Complex Histochemistry-Immunity Laboratory, Hospital of Clinics, Federal University of Paraná, Curitiba, Brazil
| | - Rosana H Scola
- Service of Neuromuscular and Demyelinating Diseases, Complex Histochemistry-Immunity Laboratory, Hospital of Clinics, Federal University of Paraná, Curitiba, Brazil
| | - Leandro F Moreno
- Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | | | - Emanuel M Souza
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Sybren de Hoog
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Center of Expertise in Mycology of Radboud University Medical Center/Canisius Wilhelmina Hospital, Nijmegen, Netherlands
| | - Vânia A Vicente
- Microbiology, Parasitology and Pathology Post-graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Engineering Bioprocess and Biotechnology Post-graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| |
Collapse
|
5
|
Souza FFC, Rissi DV, Pedrosa FO, Souza EM, Baura VA, Monteiro RA, Balsanelli E, Cruz LM, Souza RAF, Andreae MO, Reis RA, Godoi RHM, Huergo LF. Uncovering prokaryotic biodiversity within aerosols of the pristine Amazon forest. Sci Total Environ 2019; 688:83-86. [PMID: 31229831 DOI: 10.1016/j.scitotenv.2019.06.218] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 06/11/2019] [Accepted: 06/14/2019] [Indexed: 06/09/2023]
Abstract
Biological aerosols (bioaerosol) are atmospheric particles that act as a dispersion unit of living organisms across the globe thereby affecting the biogeographic distribution of organisms. Despite their importance, there is virtually no knowledge about bioaerosols emitted by pristine forests. Here we provide the very first survey of the prokaryotic community of a bioaerosol collected inside pristine Amazon forest at 2 m above ground. Total atmospheric particles were collected at the Amazon Tall Tower Observatory, subjected to metagenomic DNA extraction and the prokaryotic diversity was determined by 16S rRNA gene amplicon sequencing. A total of 271,577 reads of 250 bp of the 16S rRNA gene amplicon were obtained. Only 27% of the reads could be classified using the 16S SILVA database. Most belonged to Proteobacteria, Actinobacteria and Firmicutes which is in good agreement with other bioaerosol studies. Further inspection of the reads using Blast searches and the 18S SILVA database revealed that most of the dataset was composed of Fungi sequences. The identified microbes suggest that the atmosphere may act as an important gateway to interchange bacteria between plants, soil and water ecosystems.
Collapse
Affiliation(s)
| | - Daniel V Rissi
- Department of Livestock Microbial Ecology, Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Fabio O Pedrosa
- Programa de pós-graduação em Bioinformática, SEPTI, UFPR, Curitiba, PR, Brazil; Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Emanuel M Souza
- Programa de pós-graduação em Bioinformática, SEPTI, UFPR, Curitiba, PR, Brazil; Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Valter A Baura
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Rose A Monteiro
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Leonardo M Cruz
- Programa de pós-graduação em Bioinformática, SEPTI, UFPR, Curitiba, PR, Brazil; Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Rodrigo A F Souza
- Meteorology Department, State University of Amazonas - UEA, Manaus, AM, Brazil
| | | | | | | | - Luciano F Huergo
- Setor Litoral, UFPR, Matinhos, PR, Brazil; Programa de pós-graduação em Bioinformática, SEPTI, UFPR, Curitiba, PR, Brazil; Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
| |
Collapse
|
6
|
Huergo LF, Rissi DV, Elias AS, Gonçalves MV, Gernet MV, Barreto F, Dahmer GW, Reis RA, Pedrosa FO, Souza EM, Monteiro RA, Baura VA, Balsanelli E, Cruz LM. Influence of ancient anthropogenic activities on the mangrove soil microbiome. Sci Total Environ 2018; 645:1-9. [PMID: 30015113 DOI: 10.1016/j.scitotenv.2018.07.094] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 07/07/2018] [Accepted: 07/08/2018] [Indexed: 06/08/2023]
Abstract
Mangroves are highly productive ecosystems located at the transition between the terrestrial and marine environments. Mangroves play an important role in carbon storage, nutrient cycling and support for the marine food web. Mangrove soils are formed by fine particles rich in organic carbon and are subject to constant fluctuations in oxygen, salinity and nutrient availability due to fresh water flux and tidal variations. Microbes play an important role in nutrient cycling in mangrove soils; however, studies on the mangrove soil microbiome are scarce. Here we compare the microbiome of pristine mangrove soil located in an environmentally protected area in Guaratuba, Southern Brazil, with the microbiome of mangrove soil affected by the presence of carbonaceaous debris eroding from an archeological site known as Sambaqui. We show that although the Sambaqui site has a major effect on soil chemistry, increasing the soil pH by 2.6 units, only minor changes in the soil microbiome were detected indicating resilience of the microbial community to pH variations. The high alpha diversity indexes and predicted metabolic potential suggest that the mangrove soil microbiome not only provides important ecological services but also may host a broad range of microbes and genes of biotechnological interest.
Collapse
Affiliation(s)
| | - Daniel V Rissi
- Programa de pós-graduação em Bioinformática, SEPTI, UFPR, Curitiba, PR, Brazil
| | | | | | | | | | | | | | - Fábio O Pedrosa
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Emanuel M Souza
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Rose A Monteiro
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Valter A Baura
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Eduardo Balsanelli
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Leonardo M Cruz
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil.
| |
Collapse
|
7
|
Klassen LMB, Chequin A, Manica GCM, Biembengut IV, Toledo MB, Baura VA, de O Pedrosa F, Ramos EAS, Costa FF, de Souza EM, Klassen G. MMP9 gene expression regulation by intragenic epigenetic modifications in breast cancer. Gene 2017; 642:461-466. [PMID: 29162512 DOI: 10.1016/j.gene.2017.11.054] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 07/21/2017] [Revised: 11/10/2017] [Accepted: 11/17/2017] [Indexed: 12/19/2022]
Abstract
Breast cancer is the most frequently diagnosed cancer and the leading cause of cancer death among women worldwide. Metastasis remains a major challenge for the clinical management and prognosis of patients with cancer. The metalloprotease MMP-9 plays a critical role in the first step of metastasis through extracellular matrix degradation. In this study, our goal was to determine the effect of epigenetic mechanisms in the promoter and intragenic region of this gene and to correlate it to the levels of expression of MMP9 in breast cancer cell lines. We have identified that MMP9 was highly expressed in the breast cancer cell lines MCF7 and MDA-MB-436 after 5-aza-2'-deoxycytidine (5-azadC) treatment. Sequencing of the promoter region as well as the CGI intronic CpG islands showed a specific sequence in CGI2, between CpGs 12-30 that was demethylated after 5-azadC treatment. This specific region was studied in breast cancer samples that revealed similar results with demethylation in positive MMP-9 breast cancer samples. Furthermore, the histone methylation marker of open chromatin (H3K4me3) was found in the promoter and intronic regions of MMP9 after 5-azadC treatment. Taken together these results showed a mechanism of DNA methylation and gene expression regulation by epigenetic marks present in the intronic DNA region of MMP9.
Collapse
Affiliation(s)
| | - Andressa Chequin
- Basic Pathology Department, Federal University of Parana, Brazil
| | | | | | - Mariana B Toledo
- Basic Pathology Department, Federal University of Parana, Brazil
| | - Valter A Baura
- Biochemistry and Molecular Biology Department, Federal University of Parana, Brazil
| | - Fábio de O Pedrosa
- Biochemistry and Molecular Biology Department, Federal University of Parana, Brazil
| | - Edneia A S Ramos
- Basic Pathology Department, Federal University of Parana, Brazil
| | - Fabrício F Costa
- Genomic Sciences and Biotechnology Program, UCB, Brasília, Brazil
| | - Emanuel M de Souza
- Biochemistry and Molecular Biology Department, Federal University of Parana, Brazil
| | - Giseli Klassen
- Basic Pathology Department, Federal University of Parana, Brazil.
| |
Collapse
|
8
|
Tadra-Sfeir MZ, Faoro H, Camilios-Neto D, Brusamarello-Santos L, Balsanelli E, Weiss V, Baura VA, Wassem R, Cruz LM, De Oliveira Pedrosa F, Souza EM, Monteiro RA. Genome wide transcriptional profiling of Herbaspirillum seropedicae SmR1 grown in the presence of naringenin. Front Microbiol 2015; 6:491. [PMID: 26052319 PMCID: PMC4440368 DOI: 10.3389/fmicb.2015.00491] [Citation(s) in RCA: 15] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 05/04/2015] [Indexed: 11/13/2022] Open
Abstract
Herbaspirillum seropedicae is a diazotrophic bacterium which associates endophytically with economically important gramineae. Flavonoids such as naringenin have been shown to have an effect on the interaction between H. seropedicae and its host plants. We used a high-throughput sequencing based method (RNA-Seq) to access the influence of naringenin on the whole transcriptome profile of H. seropedicae. Three hundred and four genes were downregulated and seventy seven were upregulated by naringenin. Data analysis revealed that genes related to bacterial flagella biosynthesis, chemotaxis and biosynthesis of peptidoglycan were repressed by naringenin. Moreover, genes involved in aromatic metabolism and multidrug transport efllux were actived.
Collapse
Affiliation(s)
- Michelle Z Tadra-Sfeir
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Helisson Faoro
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil ; Instituto Carlos Chagas, Fundação Oswaldo Cruz, Fiocruz-PR Curitiba, Brazil
| | - Doumit Camilios-Neto
- Department of Biochemistry and Biotechnology, Universidade Estadual de Londrina Londrina, Brazil
| | - Liziane Brusamarello-Santos
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Eduardo Balsanelli
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Vinicius Weiss
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Valter A Baura
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Roseli Wassem
- Department of Genetics, Universidade Federal do Paraná Curitiba, Brazil
| | - Leonardo M Cruz
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Fábio De Oliveira Pedrosa
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Emanuel M Souza
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| | - Rose A Monteiro
- Nitrogen Fixation group, Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná Curitiba, Brazil
| |
Collapse
|
9
|
Marin AM, Souza EM, Pedrosa FO, Souza LM, Sassaki GL, Baura VA, Yates MG, Wassem R, Monteiro RA. Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1. Microbiology (Reading) 2012; 159:167-175. [PMID: 23125118 DOI: 10.1099/mic.0.061135-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Several bacteria are able to degrade flavonoids either to use them as carbon sources or as a detoxification mechanism. Degradation pathways have been proposed for several bacteria, but the genes responsible are not known. We identified in the genome of the endophyte Herbaspirillum seropedicae SmR1 an operon potentially associated with the degradation of aromatic compounds. We show that this operon is involved in naringenin degradation and that its expression is induced by naringenin and chrysin, two closely related flavonoids. Mutation of fdeA, the first gene of the operon, and fdeR, its transcriptional activator, abolished the ability of H. seropedicae to degrade naringenin.
Collapse
Affiliation(s)
- A M Marin
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - E M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - F O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - L M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - G L Sassaki
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - V A Baura
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - M G Yates
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| | - R Wassem
- Department of Genetics, Universidade Federal do Paraná, CP 19071, 81531-980, Curitiba, PR, Brazil
| | - R A Monteiro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-980, Curitiba, PR, Brazil
| |
Collapse
|
10
|
Monteiro RA, Balsanelli E, Tuleski T, Faoro H, Cruz LM, Wassem R, Baura VA, Tadra-Sfeir MZ, Weiss V, DaRocha WD, Muller-Santos M, Chubatsu LS, Huergo LF, Pedrosa FO, Souza EM. Genomic comparison of the endophyte Herbaspirillum seropedicaeSmR1 and the phytopathogen Herbaspirillum rubrisubalbicansM1 by suppressive subtractive hybridization and partial genome sequencing. FEMS Microbiol Ecol 2012; 80:441-51. [PMID: 22268687 DOI: 10.1111/j.1574-6941.2012.01309.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 12/23/2011] [Accepted: 01/11/2012] [Indexed: 12/28/2022] Open
Affiliation(s)
- Rose A. Monteiro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Thalita Tuleski
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Helison Faoro
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Leonardo M. Cruz
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Roseli Wassem
- Department of Genetics; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Valter A. Baura
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Michelle Z. Tadra-Sfeir
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Vinícius Weiss
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Wanderson D. DaRocha
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Marcelo Muller-Santos
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Leda S. Chubatsu
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Luciano F. Huergo
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Fábio O. Pedrosa
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| | - Emanuel M. Souza
- Department of Biochemistry and Molecular Biology; Universidade Federal do Paraná; Curitiba; PR; Brazil
| |
Collapse
|
11
|
Pedrosa FO, Monteiro RA, Wassem R, Cruz LM, Ayub RA, Colauto NB, Fernandez MA, Fungaro MHP, Grisard EC, Hungria M, Madeira HMF, Nodari RO, Osaku CA, Petzl-Erler ML, Terenzi H, Vieira LGE, Steffens MBR, Weiss VA, Pereira LFP, Almeida MIM, Alves LR, Marin A, Araujo LM, Balsanelli E, Baura VA, Chubatsu LS, Faoro H, Favetti A, Friedermann G, Glienke C, Karp S, Kava-Cordeiro V, Raittz RT, Ramos HJO, Ribeiro EMSF, Rigo LU, Rocha SN, Schwab S, Silva AG, Souza EM, Tadra-Sfeir MZ, Torres RA, Dabul ANG, Soares MAM, Gasques LS, Gimenes CCT, Valle JS, Ciferri RR, Correa LC, Murace NK, Pamphile JA, Patussi EV, Prioli AJ, Prioli SMA, Rocha CLMSC, Arantes OMN, Furlaneto MC, Godoy LP, Oliveira CEC, Satori D, Vilas-Boas LA, Watanabe MAE, Dambros BP, Guerra MP, Mathioni SM, Santos KL, Steindel M, Vernal J, Barcellos FG, Campo RJ, Chueire LMO, Nicolás MF, Pereira-Ferrari L, Silva JLDC, Gioppo NMR, Margarido VP, Menck-Soares MA, Pinto FGS, Simão RDCG, Takahashi EK, Yates MG, Souza EM. Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses. PLoS Genet 2011; 7:e1002064. [PMID: 21589895 PMCID: PMC3093359 DOI: 10.1371/journal.pgen.1002064] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Accepted: 03/18/2011] [Indexed: 01/28/2023] Open
Abstract
The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.
Collapse
|
12
|
Oliveira MA, Baura VA, Aquino B, Huergo LF, Kadowaki MA, Chubatsu LS, Souza EM, Dixon R, Pedrosa FO, Wassem R, Monteiro RA. Role of conserved cysteine residues in Herbaspirillum seropedicae NifA activity. Res Microbiol 2009; 160:389-95. [DOI: 10.1016/j.resmic.2009.06.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2009] [Revised: 05/29/2009] [Accepted: 06/10/2009] [Indexed: 11/24/2022]
|
13
|
Noindorf L, Rego FGM, Baura VA, Monteiro RA, Wassem R, Cruz LM, Rigo LU, Souza EM, Steffens MBR, Pedrosa FO, Chubatsu LS. Characterization of the orf1glnKamtB operon of Herbaspirillum seropedicae. Arch Microbiol 2005; 185:55-62. [PMID: 16331441 DOI: 10.1007/s00203-005-0066-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [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: 08/19/2005] [Revised: 10/21/2005] [Accepted: 11/11/2005] [Indexed: 10/25/2022]
Abstract
Herbaspirillum seropedicae is an endophytic nitrogen-fixing bacterium that colonizes economically important grasses. In this organism, the amtB gene is co-transcribed with two other genes: glnK that codes for a PII-like protein and orf1 that codes for a probable periplasmatic protein of unknown function. The expression of the orf1glnKamtB operon is increased under nitrogen-limiting conditions and is dependent on NtrC. An amtB mutant failed to transport methylammonium. Post-translational control of nitrogenase was also partially impaired in this mutant, since a complete switch-off of nitrogenase after ammonium addition was not observed. This result suggests that the AmtB protein is involved in the signaling pathway for the reversible inactivation of nitrogenase in H. seropedicae.
Collapse
Affiliation(s)
- Lilian Noindorf
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP 19046, 81531-990, Curitiba, Brazil
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Araujo MS, Baura VA, Souza EM, Benelli EM, Rigo LU, Steffens MBR, Pedrosa FO, Chubatsu LS. In vitro uridylylation of the Azospirillum brasilense N-signal transducing GlnZ protein. Protein Expr Purif 2004; 33:19-24. [PMID: 14680957 DOI: 10.1016/j.pep.2003.08.024] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [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: 06/30/2003] [Revised: 08/12/2003] [Indexed: 11/24/2022]
Abstract
Azospirillum brasilense is a diazotroph which associates with important agricultural crops. The nitrogen fixation process in this organism is highly regulated by ammonium and oxygen, and involves several proteins including the two PII-like proteins, GlnB and GlnZ. Although these proteins are structurally very similar, they play different roles in the control of nitrogen fixation. In this work, we describe the expression, purification, and uridylylation of the GlnZ protein of A. brasilense strain FP2. The amplified glnZ gene was sub-cloned and expressed as a His-tagged fusion protein. After purification, we obtained 30-40 mg of purified GlnZ per liter of culture. This protein was purified to 99% purity and assayed for in vitro uridylylation using a partially purified Escherichia coli GlnD as a source of uridylylyl-transferase activity. Analyses of the uridylylation reactions in non-denaturing and denaturing polyacrylamide gel electrophoresis showed that up to 74% of GlnZ monomers were modified after 30 min reaction. This covalent modification is strictly dependent on ATP and 2-ketoglutarate, while glutamine acts as an inhibitor and promotes deuridylylation.
Collapse
Affiliation(s)
- Mariana S Araujo
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, CP19046, Curitiba, PR 81531-990, Brazil
| | | | | | | | | | | | | | | |
Collapse
|