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Costa FDF, Souza RSCD, Voidaleski MF, Gomes RR, Reis GF, Lima BJFDS, Candido GZ, Geraldo MR, Soares JMB, Schneider GX, Trindade EDS, Bini IH, Moreno LF, Bombassaro A, Queiroz-Telles F, Raittz RT, Quan Y, Arruda P, Attili-Angelis D, de Hoog S, Vicente VA. Sugarcane: an unexpected habitat for black yeasts in Chaetothyriales. IMA Fungus 2023; 14:20. [PMID: 37794500 PMCID: PMC10552356 DOI: 10.1186/s43008-023-00124-7] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 08/22/2023] [Indexed: 10/06/2023] Open
Abstract
Sugarcane (Saccharum officinarum, Poaceae) is cultivated on a large scale in (sub)tropical regions such as Brazil and has considerable economic value for sugar and biofuel production. The plant is a rich substrate for endo- and epiphytic fungi. Black yeasts in the family Herpotrichiellaceae (Chaetothyriales) are colonizers of human-dominated habitats, particularly those rich in toxins and hydrocarbon pollutants, and may cause severe infections in susceptible human hosts. The present study assessed the diversity of Herpotrichiellaceae associated with sugarcane, using in silico identification and selective isolation. Using metagenomics, we identified 5833 fungal sequences, while 639 black yeast-like isolates were recovered in vitro. In both strategies, the latter fungi were identified as members of the genera Cladophialophora, Exophiala, and Rhinocladiella (Herpotrichiellaceae), Cyphellophora (Cyphellophoraceae), and Knufia (Trichomeriaceae). In addition, we discovered new species of Cladophialophora and Exophiala from sugarcane and its rhizosphere. The first environmental isolation of Cladophialophora bantiana is particularly noteworthy, because this species up to now is exclusively known from the human host where it mostly causes fatal brain disease in otherwise healthy patients.
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Affiliation(s)
- Flávia de F Costa
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Rafael S C de Souza
- Molecular Biology and Genetics Engineering Center, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Morgana F Voidaleski
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Renata R Gomes
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Guilherme F Reis
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Bruna J F de S Lima
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Giovanna Z Candido
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Marlon R Geraldo
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Jade M B Soares
- Biological Sciences Graduation, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Gabriela X Schneider
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | | | - Israel H Bini
- Department of Cell Biology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Leandro F Moreno
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Flávio Queiroz-Telles
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil
- Clinical Hospital of the Federal University of Paraná, Federal University of Paraná, Curitiba, Paraná, Brazil
| | - Roberto T Raittz
- Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, Brazil
| | - Yu Quan
- Center of Expertise in Mycology of Radboud, University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands
| | - Paulo Arruda
- Molecular Biology and Genetics Engineering Center, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
- Genetics and Evolution Department, Biology Institute, State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Derlene Attili-Angelis
- Division of Microbial Resources (DRM/CPQBA), State University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Sybren de Hoog
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.
- Center of Expertise in Mycology of Radboud, University Medical Center / Canisius Wilhelmina Hospital, Nijmegen, The Netherlands.
| | - Vania A Vicente
- Engineering Bioprocess and Biotechnology Post-Graduation Program, Department of Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Paraná, Brazil.
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Paraná, Brazil.
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2
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Perico CP, De Pierri CR, Neto GP, Fernandes DR, Pedrosa FO, de Souza EM, Raittz RT. Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin. Front Microbiol 2022; 13:1037455. [PMID: 36620039 PMCID: PMC9814972 DOI: 10.3389/fmicb.2022.1037455] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022] Open
Abstract
Brazil was the epicenter of worldwide pandemics at the peak of its second wave. The genomic/proteomic perspective of the COVID-19 pandemic in Brazil could provide insights to understand the global pandemics behavior. In this study, we track SARS-CoV-2 molecular information in Brazil using real-time bioinformatics and data science strategies to provide a comparative and evolutive panorama of the lineages in the country. SWeeP vectors represented the Brazilian and worldwide genomic/proteomic data from Global Initiative on Sharing Avian Influenza Data (GISAID) between February 2020 and August 2021. Clusters were analyzed and compared with PANGO lineages. Hierarchical clustering provided phylogenetic and evolutionary analyses of the lineages, and we tracked the P.1 (Gamma) variant origin. The genomic diversity based on Chao's estimation allowed us to compare richness and coverage among Brazilian states and other representative countries. We found that epidemics in Brazil occurred in two moments with different genetic profiles. The P.1 lineages emerged in the second wave, which was more aggressive. We could not trace the origin of P.1 from the variants present in Brazil. Instead, we found evidence pointing to its external source and a possible recombinant event that may relate P.1 to a B.1.1.28 variant subset. We discussed the potential application of the pipeline for emerging variants detection and the PANGO terminology stability over time. The diversity analysis showed that the low coverage and unbalanced sequencing among states in Brazil could have allowed the silent entry and dissemination of P.1 and other dangerous variants. This study may help to understand the development and consequences of variants of concern (VOC) entry.
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Affiliation(s)
- Camila P Perico
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
| | - Camilla R De Pierri
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Brazil
| | - Giuseppe Pasqualato Neto
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
| | - Danrley R Fernandes
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
| | - Fabio O Pedrosa
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Brazil
| | - Emanuel M de Souza
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Department of Biochemistry and Molecular Biology, Federal University of Paraná, Curitiba, Brazil
| | - Roberto T Raittz
- Laboratory of Artificial Intelligence Applied to Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
- Graduate Program in Bioinformatics, Professional and Technological Education Sector (SEPT), Federal University of Paraná, Curitiba, Brazil
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3
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Faoro H, Oliveira WK, Weiss VA, Tadra-Sfeir MZ, Cardoso RL, Balsanelli E, Brusamarello-Santos LCC, Camilios-Neto D, Cruz LM, Raittz RT, Marques ACQ, LiPuma J, Fadel-Picheth CMT, Souza EM, Pedrosa FO. Genome comparison between clinical and environmental strains of Herbaspirillum seropedicae reveals a potential new emerging bacterium adapted to human hosts. BMC Genomics 2019; 20:630. [PMID: 31375067 PMCID: PMC6679464 DOI: 10.1186/s12864-019-5982-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [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: 02/22/2019] [Accepted: 07/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Herbaspirillum seropedicae is an environmental β-proteobacterium that is capable of promoting the growth of economically relevant plants through biological nitrogen fixation and phytohormone production. However, strains of H. seropedicae have been isolated from immunocompromised patients and associated with human infections and deaths. In this work, we sequenced the genomes of two clinical strains of H. seropedicae, AU14040 and AU13965, and compared them with the genomes of strains described as having an environmental origin. RESULTS Both genomes were closed, indicating a single circular chromosome; however, strain AU13965 also carried a plasmid of 42,977 bp, the first described in the genus Herbaspirillum. Genome comparison revealed that the clinical strains lost the gene sets related to biological nitrogen fixation (nif) and the type 3 secretion system (T3SS), which has been described to be essential for interactions with plants. Comparison of the pan-genomes of clinical and environmental strains revealed different sets of accessorial genes. However, antimicrobial resistance genes were found in the same proportion in all analyzed genomes. The clinical strains also acquired new genes and genomic islands that may be related to host interactions. Among the acquired islands was a cluster of genes related to lipopolysaccharide (LPS) biosynthesis. Although highly conserved in environmental strains, the LPS biosynthesis genes in the two clinical strains presented unique and non-orthologous genes within the genus Herbaspirillum. Furthermore, the AU14040 strain cluster contained the neuABC genes, which are responsible for sialic acid (Neu5Ac) biosynthesis, indicating that this bacterium could add it to its lipopolysaccharide. The Neu5Ac-linked LPS could increase the bacterial resilience in the host aiding in the evasion of the immune system. CONCLUSIONS Our findings suggest that the lifestyle transition from environment to opportunist led to the loss and acquisition of specific genes allowing adaptations to colonize and survive in new hosts. It is possible that these substitutions may be the starting point for interactions with new hosts.
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Affiliation(s)
- Helisson Faoro
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil. .,Graduate Program on Bioinformatics, Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, 81520-260, Brazil. .,Laboratory of Gene Expression Regulation, Instituto Carlos Chagas, FIOCRUZ, Algacyr Munhoz Mader street, 3775, Curitiba, Paraná, 81350-010, Brazil.
| | - Willian K Oliveira
- Graduate Program on Bioinformatics, Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, 81520-260, Brazil.,Laboratory of Gene Expression Regulation, Instituto Carlos Chagas, FIOCRUZ, Algacyr Munhoz Mader street, 3775, Curitiba, Paraná, 81350-010, Brazil
| | - Vinicius A Weiss
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil.,Graduate Program on Bioinformatics, Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, 81520-260, Brazil
| | - Michelle Z Tadra-Sfeir
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil
| | - Rodrigo L Cardoso
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil
| | - Liziane C C Brusamarello-Santos
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil
| | - Doumit Camilios-Neto
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil.,Department of Biochemistry and Biothecnology, Universidade Estadual de Londrina, Celso Garcia Cid street, Londrina, Paraná, 86057-970, Brazil
| | - Leonardo M Cruz
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil
| | - Roberto T Raittz
- Graduate Program on Bioinformatics, Universidade Federal do Paraná, Alcides Viera Arcoverde street 1225, Curitiba, Paraná, 81520-260, Brazil
| | - Ana C Q Marques
- Department of Clinical Analyses, Universidade Federal do Paraná, Av. Lothário Meissner 632, Curitiba, Paraná, 80210-170, Brazil
| | - John LiPuma
- Department of Pediatrics, University of Michigan, 1500 E. Medical Center Dr, Ann Arbor, MI, 48109, USA
| | - Cyntia M T Fadel-Picheth
- Department of Clinical Analyses, Universidade Federal do Paraná, Av. Lothário Meissner 632, Curitiba, Paraná, 80210-170, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Coronel Francisco H. dos Santos street, Curitiba, Paraná, 81531-980, Brazil.
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4
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Vicente VA, Weiss VA, Bombassaro A, Moreno LF, Costa FF, Raittz RT, Leão AC, Gomes RR, Bocca AL, Fornari G, de Castro RJA, Sun J, Faoro H, Tadra-Sfeir MZ, Baura V, Balsanelli E, Almeida SR, Dos Santos SS, Teixeira MDM, Soares Felipe MS, do Nascimento MMF, Pedrosa FO, Steffens MB, Attili-Angelis D, Najafzadeh MJ, Queiroz-Telles F, Souza EM, De Hoog S. Comparative Genomics of Sibling Species of Fonsecaea Associated with Human Chromoblastomycosis. Front Microbiol 2017; 8:1924. [PMID: 29062304 PMCID: PMC5640708 DOI: 10.3389/fmicb.2017.01924] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 08/02/2017] [Accepted: 09/21/2017] [Indexed: 01/16/2023] Open
Abstract
Fonsecaea and Cladophialophora are genera of black yeast-like fungi harboring agents of a mutilating implantation disease in humans, along with strictly environmental species. The current hypothesis suggests that those species reside in somewhat adverse microhabitats, and pathogenic siblings share virulence factors enabling survival in mammal tissue after coincidental inoculation driven by pathogenic adaptation. A comparative genomic analysis of environmental and pathogenic siblings of Fonsecaea and Cladophialophora was undertaken, including de novo assembly of F. erecta from plant material. The genome size of Fonsecaea species varied between 33.39 and 35.23 Mb, and the core genomes of those species comprises almost 70% of the genes. Expansions of protein domains such as glyoxalases and peptidases suggested ability for pathogenicity in clinical agents, while the use of nitrogen and degradation of phenolic compounds was enriched in environmental species. The similarity of carbohydrate-active vs. protein-degrading enzymes associated with the occurrence of virulence factors suggested a general tolerance to extreme conditions, which might explain the opportunistic tendency of Fonsecaea sibling species. Virulence was tested in the Galleria mellonella model and immunological assays were performed in order to support this hypothesis. Larvae infected by environmental F. erecta had a lower survival. Fungal macrophage murine co-culture showed that F. erecta induced high levels of TNF-α contributing to macrophage activation that could increase the ability to control intracellular fungal growth although hyphal death were not observed, suggesting a higher level of extremotolerance of environmental species.
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Affiliation(s)
- Vania A Vicente
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Vinícius A Weiss
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Amanda Bombassaro
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | - Leandro F Moreno
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Flávia F Costa
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil
| | - Roberto T Raittz
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil
| | - Aniele C Leão
- Bioprocess Engineering and Biotechnology, Federal University of Paraná, Curitiba, Brazil.,Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,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
| | - Anamelia L Bocca
- Department of Cell Biology, University of Brasília, Brasilia, Brazil
| | - Gheniffer Fornari
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil
| | | | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, China
| | - Helisson Faoro
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Valter Baura
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Eduardo Balsanelli
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Sandro R Almeida
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Suelen S Dos Santos
- Department of Clinical and Toxicological Analysis, Faculty of Pharmaceutical Sciences, University of São Paulo, Sao Paulo, Brazil
| | - Marcus de Melo Teixeira
- Department of Cell Biology, University of Brasília, Brasilia, Brazil.,Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Maria S Soares Felipe
- Department of Genomic Sciences and Biotechnology, Catholic University of Brasília, Brasilia, Brazil
| | | | - Fabio O Pedrosa
- Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | - Maria B Steffens
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, Federal University of Paraná, Curitiba, Brazil
| | | | - Mohammad J Najafzadeh
- Department of Parasitology and Mycology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Flávio Queiroz-Telles
- Microbiology, Parasitology and Pathology Post-Graduation Program, Department of Basic Pathology, Federal University of Paraná, Curitiba, Brazil.,Clinical Hospital of the Federal University of Paraná, Curitiba, Brazil
| | - Emanuel M Souza
- Laboratory of Bioinformatics, Sector of Technological and Professional Education, Federal University of Paraná, Curitiba, Brazil.,Department of Biochemistry, 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.,CBS-KNAW Fungal Biodiversity Centre, Utrecht, Netherlands.,Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
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5
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Sanchuki HBS, Gravina F, Rodrigues TE, Gerhardt ECM, Pedrosa FO, Souza EM, Raittz RT, Valdameri G, de Souza GA, Huergo LF. Dynamics of the Escherichia coli proteome in response to nitrogen starvation and entry into the stationary phase. Biochim Biophys Acta Proteins Proteom 2016; 1865:344-352. [PMID: 27939605 DOI: 10.1016/j.bbapap.2016.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/02/2016] [Accepted: 12/06/2016] [Indexed: 01/31/2023]
Abstract
Nitrogen is needed for the biosynthesis of biomolecules including proteins and nucleic acids. In the absence of fixed nitrogen prokaryotes such as E. coli immediately ceases growth. Ammonium is the preferred nitrogen source for E. coli supporting the fastest growth rates. Under conditions of ammonium limitation, E. coli can use alternative nitrogen sources to supply ammonium ions and this reprogramming is led by the induction of the NtrC regulon. Here we used label free proteomics to determine the dynamics of E. coli proteins expression in response to ammonium starvation in both the short (30min) and the longer (60min) starvation. Protein abundances and post-translational modifications confirmed that activation of the NtrC regulon acts as the first line of defense against nitrogen starvation. The ribosome inactivating protein Rmf was induced shortly after ammonium exhaustion and this was preceded by induction of other ribosome inactivating proteins such as Hpf and RaiA supporting the hypothesis that ribosome shut-down is a key process during nitrogen limitation stress. The proteomic data revealed that growth arrest due to nitrogen starvation correlates with the accumulation of proteins involved in DNA condensation, RNA and protein catabolism and ribosome hibernation. Collectively, these proteome adaptations will result in metabolic inactive cells which are likely to exhibit multidrug tolerance.
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Affiliation(s)
| | - Fernanda Gravina
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil
| | - Thiago E Rodrigues
- Departamento de Bioquímica e Biologia Molecular, 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
| | - Roberto T Raittz
- Setor de Educação Profissional e Tecnológica, UFPR, Curitiba, PR, Brazil
| | - Glaucio Valdameri
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Departamento de Análises Clínicas, UFPR, Curitiba, PR, Brazil
| | - Gustavo A de Souza
- Department of Immunology, University of Oslo and Oslo University Hospital, The Proteomics Core Facility, Rikshospitalet, Oslo, Norway; Instituto do Cérebro, UFRN, Natal, RN, Brazil
| | - Luciano F Huergo
- Departamento de Bioquímica e Biologia Molecular, UFPR, Curitiba, PR, Brazil; Setor Litoral, UFPR, Matinhos, PR, Brazil.
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6
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Guizelini D, Raittz RT, Cruz LM, Souza EM, Steffens MBR, Pedrosa FO. GFinisher: a new strategy to refine and finish bacterial genome assemblies. Sci Rep 2016; 6:34963. [PMID: 27721396 PMCID: PMC5056350 DOI: 10.1038/srep34963] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [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: 06/14/2016] [Accepted: 09/20/2016] [Indexed: 01/10/2023] Open
Abstract
Despite the development in DNA sequencing technology, improving the number and the length of reads, the process of reconstruction of complete genome sequences, the so called genome assembly, is still complex. Only 13% of the prokaryotic genome sequencing projects have been completed. Draft genome sequences deposited in public databases are fragmented in contigs and may lack the full gene complement. The aim of the present work is to identify assembly errors and improve the assembly process of bacterial genomes. The biological patterns observed in genomic sequences and the application of a priori information can allow the identification of misassembled regions, and the reorganization and improvement of the overall de novo genome assembly. GFinisher starts generating a Fuzzy GC skew graphs for each contig in an assembly and follows breaking down the contigs in critical points in order to reassemble and close them using jFGap. This has been successfully applied to dataset from 96 genome assemblies, decreasing the number of contigs by up to 86%. GFinisher can easily optimize assemblies of prokaryotic draft genomes and can be used to improve the assembly programs based on nucleotide sequence patterns in the genome. The software and source code are available at http://gfinisher.sourceforge.net/.
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Affiliation(s)
- Dieval Guizelini
- Department of Biochemistry and Molecular Biology, Federal University of Parana (UFPR), Curitiba, PR, Brazil.,Graduate Program in Bioinformatics, Sector of Professional and Technological Education, Federal University of Parana (UFPR), Curitiba, PR, Brazil
| | - Roberto T Raittz
- Graduate Program in Bioinformatics, Sector of Professional and Technological Education, Federal University of Parana (UFPR), Curitiba, PR, Brazil
| | - Leonardo M Cruz
- Department of Biochemistry and Molecular Biology, Federal University of Parana (UFPR), Curitiba, PR, Brazil.,Graduate Program in Bioinformatics, Sector of Professional and Technological Education, Federal University of Parana (UFPR), Curitiba, PR, Brazil
| | - Emanuel M Souza
- Department of Biochemistry and Molecular Biology, Federal University of Parana (UFPR), Curitiba, PR, Brazil.,Graduate Program in Bioinformatics, Sector of Professional and Technological Education, Federal University of Parana (UFPR), Curitiba, PR, Brazil
| | - Maria B R Steffens
- Department of Biochemistry and Molecular Biology, Federal University of Parana (UFPR), Curitiba, PR, Brazil.,Graduate Program in Bioinformatics, Sector of Professional and Technological Education, Federal University of Parana (UFPR), Curitiba, PR, Brazil
| | - Fabio O Pedrosa
- Department of Biochemistry and Molecular Biology, Federal University of Parana (UFPR), Curitiba, PR, Brazil.,Graduate Program in Bioinformatics, Sector of Professional and Technological Education, Federal University of Parana (UFPR), Curitiba, PR, Brazil
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Otemaier KR, Steffens MBR, Raittz RT, Brawerman A, Marchaukoski JN. Biosom: gene synonym analysis by self-organizing map. Genet Mol Res 2015; 14:1461-8. [PMID: 25730085 DOI: 10.4238/2015.february.20.1] [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] [Indexed: 11/03/2022]
Abstract
There are several guidelines for gene nomenclature, but they are not always applied to the names of newly identified genes. The lack of standardization in naming genes generates inconsistent databases with errors such as genes with the same function and different names, genes with different functions and the same name, and use of an abbreviated name. This paper presents a methodology for predicting synonyms in a given gene nomenclature, thereby detecting and minimizing naming redundancy and inconsistency and facilitating the annotation of new genes and data mining in public databases. To identify gene synonyms, i.e., gene ambiguity, the methodology proposed begins by grouping genes according to their names using a Kohonen self-organizing map artificial neural network. Afterwards, it identifies the groups generated employing the Matrix-U technique. The employment of such techniques allows one to infer the synonyms of genes, to predict probable hypothetical gene names and to point out possible errors in a database record. Many mistakes related to gene nomenclature were detected in this research, demonstrating the importance of predicting synonyms. The methodology developed is applicable for describing hypothetical, putative and other types of genes without a known function. Moreover, it can also indicate a possible function for genes after grouping them.
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Affiliation(s)
- K R Otemaier
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - M B R Steffens
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - R T Raittz
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - A Brawerman
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil
| | - J N Marchaukoski
- Programa de Pós-Graduação em Bioinformática, Universidade Federal do Paraná, Curitiba, PR, Brasil
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Piro VC, Faoro H, Weiss VA, Steffens MBR, Pedrosa FO, Souza EM, Raittz RT. FGAP: an automated gap closing tool. BMC Res Notes 2014; 7:371. [PMID: 24938749 PMCID: PMC4091766 DOI: 10.1186/1756-0500-7-371] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [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: 02/27/2014] [Accepted: 06/09/2014] [Indexed: 12/01/2022] Open
Abstract
Background The fast reduction of prices of DNA sequencing allowed rapid accumulation of genome data. However, the process of obtaining complete genome sequences is still very time consuming and labor demanding. In addition, data produced from various sequencing technologies or alternative assemblies remain underexplored to improve assembly of incomplete genome sequences. Findings We have developed FGAP, a tool for closing gaps of draft genome sequences that takes advantage of different datasets. FGAP uses BLAST to align multiple contigs against a draft genome assembly aiming to find sequences that overlap gaps. The algorithm selects the best sequence to fill and eliminate the gap. Conclusions FGAP reduced the number of gaps by 78% in an E. coli draft genome assembly using two different sequencing technologies, Illumina and 454. Using PacBio long reads, 98% of gaps were solved. In human chromosome 14 assemblies, FGAP reduced the number of gaps by 35%. All the inserted sequences were validated with a reference genome using QUAST. The source code and a web tool are available at http://www.bioinfo.ufpr.br/fgap/.
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Affiliation(s)
| | | | | | | | | | | | - Roberto T Raittz
- Laboratory of Bioinformatics, Professional and Technological Education Sector, Federal University of Paraná, Curitiba, PR, Brazil, Rua Dr, Alcides Vieira Arcoverde 1225, Curitiba, Paraná, Brazil.
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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.
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