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Moreira S, Chyou TY, Wade J, Brown C. Diversification of the Rho transcription termination factor in bacteria. Nucleic Acids Res 2024; 52:8979-8997. [PMID: 38966992 PMCID: PMC11347177 DOI: 10.1093/nar/gkae582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 06/17/2024] [Accepted: 06/24/2024] [Indexed: 07/06/2024] Open
Abstract
Correct termination of transcription is essential for gene expression. In bacteria, factor-dependent termination relies on the Rho factor, that classically has three conserved domains. Some bacteria also have a functional insertion region. However, the variation in Rho structure among bacteria has not been analyzed in detail. This study determines the distribution, sequence conservation, and predicted features of Rho factors with diverse domain architectures by analyzing 2730 bacterial genomes. About half (49.8%) of the species analyzed have the typical Escherichia coli like Rho while most of the other species (39.8%) have diverse, atypical forms of Rho. Besides conservation of the main domains, we describe a duplicated RNA-binding domain present in specific species and novel variations in the bicyclomycin binding pocket. The additional regions observed in Rho proteins exhibit remarkable diversity. Commonly, however, they have exceptional amino acid compositions and are predicted to be intrinsically disordered, to undergo phase separation, or have prion-like behavior. Phase separation has recently been shown to play roles in Rho function and bacterial fitness during harsh conditions in one species and this study suggests a more widespread role. In conclusion, diverse atypical Rho factors are broadly distributed among bacteria, suggesting additional cellular roles.
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Affiliation(s)
- Sofia M Moreira
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Te-yuan Chyou
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
| | - Joseph T Wade
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
- Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, NY 12222, USA
| | - Chris M Brown
- Department of Biochemistry, University of Otago, Dunedin, Otago 9054, New Zealand
- Genetics Otago, University of Otago, Dunedin, Otago 9054, New Zealand
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2
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Intrinsic and Rho-dependent termination cooperate for efficient transcription termination at 3’ untranslated regions. Biochem Biophys Res Commun 2022; 628:123-132. [DOI: 10.1016/j.bbrc.2022.08.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 08/10/2022] [Accepted: 08/22/2022] [Indexed: 11/22/2022]
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3
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Merker Breyer G, Malvessi Cattani A, Silveira Schrank I, Maboni Siqueira F. The influence of regulatory elements on Mycoplasma hyopneumoniae 7448 transcriptional response during oxidative stress and heat shock. Mol Biol Rep 2021; 49:139-147. [PMID: 34676505 DOI: 10.1007/s11033-021-06851-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/15/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND The comprehension of genome organization and gene modulation is essential for understanding pathogens' infection mechanisms. Mycoplasma hyopneumoniae 7448 genome is organized in transcriptional units (TUs), which are flanked by regulatory elements such as putative promoters, terminators and repetitive sequences. Yet the relationship between the presence of these elements and bacterial responses during stress conditions remains unclear. Thus, in this study, in silico and RT-qPCR analyses were associated to determine the effect of regulatory elements in gene expression regulation upon heat shock and oxidative stress conditions. METHODS AND RESULTS Thirteen TU's organizational profiles were found based on promoters and terminators distribution. Differential expression in genes sharing the same TUs was observed, suggesting the activity of internal regulatory elements. Moreover, 88.8% of tested genes were differentially expressed under oxidative stress in comparison to the control condition, being 81.3% of them surrounded by their own regulatory elements. Similarly, under heat shock, 44.4% of the genes showed regulation when compared to control condition, being 75.0% of them surrounded by their own regulatory elements. CONCLUSIONS Altogether, this data suggests the activity of internal regulatory elements in gene modulation of M. hyopneumoniae 7448 transcription.
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Affiliation(s)
- Gabriela Merker Breyer
- Laboratory of Veterinary Bacteriology, Veterinary Pathology Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Amanda Malvessi Cattani
- Graduate Program in Cell and Molecular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Irene Silveira Schrank
- Graduate Program in Cell and Molecular Biology, Biotechnology Center, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil
| | - Franciele Maboni Siqueira
- Laboratory of Veterinary Bacteriology, Veterinary Pathology Department, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS, Brazil.
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4
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Maes D, Boyen F, Devriendt B, Kuhnert P, Summerfield A, Haesebrouck F. Perspectives for improvement of Mycoplasma hyopneumoniae vaccines in pigs. Vet Res 2021; 52:67. [PMID: 33964969 PMCID: PMC8106180 DOI: 10.1186/s13567-021-00941-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 04/23/2021] [Indexed: 12/21/2022] Open
Abstract
Mycoplasma hyopneumoniae (M. hyopneumoniae) is one of the primary agents involved in the porcine respiratory disease complex, economically one of the most important diseases in pigs worldwide. The pathogen adheres to the ciliated epithelium of the trachea, bronchi, and bronchioles, causes damage to the mucosal clearance system, modulates the immune system and renders the animal more susceptible to other respiratory infections. The pathogenesis is very complex and not yet fully understood. Cell-mediated and likely also mucosal humoral responses are considered important for protection, although infected animals are not able to rapidly clear the pathogen from the respiratory tract. Vaccination is frequently practiced worldwide to control M. hyopneumoniae infections and the associated performance losses, animal welfare issues, and treatment costs. Commercial vaccines are mostly bacterins that are administered intramuscularly. However, the commercial vaccines provide only partial protection, they do not prevent infection and have a limited effect on transmission. Therefore, there is a need for novel vaccines that confer a better protection. The present paper gives a short overview of the pathogenesis and immune responses following M. hyopneumoniae infection, outlines the major limitations of the commercial vaccines and reviews the different experimental M. hyopneumoniae vaccines that have been developed and tested in mice and pigs. Most experimental subunit, DNA and vector vaccines are based on the P97 adhesin or other factors that are important for pathogen survival and pathogenesis. Other studies focused on bacterins combined with novel adjuvants. Very few efforts have been directed towards the development of attenuated vaccines, although such vaccines may have great potential. As cell-mediated and likely also humoral mucosal responses are important for protection, new vaccines should aim to target these arms of the immune response. The selection of proper antigens, administration route and type of adjuvant and carrier molecule is essential for success. Also practical aspects, such as cost of the vaccine, ease of production, transport and administration, and possible combination with vaccines against other porcine pathogens, are important. Possible avenues for further research to develop better vaccines and to achieve a more sustainable control of M. hyopneumoniae infections are discussed.
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Affiliation(s)
- Dominiek Maes
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Filip Boyen
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Bert Devriendt
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Artur Summerfield
- Institute of Virology and Immunology, Sensemattstrasse 293, Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
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Gale GAR, Wang B, McCormick AJ. Evaluation and Comparison of the Efficiency of Transcription Terminators in Different Cyanobacterial Species. Front Microbiol 2021; 11:624011. [PMID: 33519785 PMCID: PMC7843447 DOI: 10.3389/fmicb.2020.624011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/13/2022] Open
Abstract
Cyanobacteria utilize sunlight to convert carbon dioxide into a wide variety of secondary metabolites and show great potential for green biotechnology applications. Although cyanobacterial synthetic biology is less mature than for other heterotrophic model organisms, there are now a range of molecular tools available to modulate and control gene expression. One area of gene regulation that still lags behind other model organisms is the modulation of gene transcription, particularly transcription termination. A vast number of intrinsic transcription terminators are now available in heterotrophs, but only a small number have been investigated in cyanobacteria. As artificial gene expression systems become larger and more complex, with short stretches of DNA harboring strong promoters and multiple gene expression cassettes, the need to stop transcription efficiently and insulate downstream regions from unwanted interference is becoming more important. In this study, we adapted a dual reporter tool for use with the CyanoGate MoClo Assembly system that can quantify and compare the efficiency of terminator sequences within and between different species. We characterized 34 intrinsic terminators in Escherichia coli, Synechocystis sp. PCC 6803, and Synechococcus elongatus UTEX 2973 and observed significant differences in termination efficiencies. However, we also identified five terminators with termination efficiencies of >96% in all three species, indicating that some terminators can behave consistently in both heterotrophic species and cyanobacteria.
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Affiliation(s)
- Grant A. R. Gale
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
- School of Biological Sciences, Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, United Kingdom
| | - Alistair J. McCormick
- School of Biological Sciences, Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, United Kingdom
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Li G, Obeng E, Shu J, Shu J, Chen J, Wu Y, He Y. Genomic Variability and Post-translational Protein Processing Enhance the Immune Evasion of Mycoplasma hyopneumoniae and Its Interaction With the Porcine Immune System. Front Immunol 2020; 11:510943. [PMID: 33117335 PMCID: PMC7575705 DOI: 10.3389/fimmu.2020.510943] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 08/27/2020] [Indexed: 11/23/2022] Open
Abstract
Mycoplasma hyopneumoniae (M. hyopneumoniae, Mhp) is a geographically widespread and economically devastating pathogen that colonizes ciliated epithelium; the infection of Mhp can damnify the mucociliary functions as well as leading to Mycoplasma pneumonia of swine (MPS). MPS is a chronic respiratory infectious disease with high infectivity, and the mortality can be increased by secondary infections as the host immunity gets down-regulated during Mhp infection. The host immune responses are regarded as the main driving force for the disease development, while MPS is prone to attack repeatedly in farms even with vaccination or other treatments. As one of the smallest microorganisms with limited genome scale and metabolic pathways, Mhp can use several mechanisms to achieve immune evasion effect and derive enough nutrients from its host, indicating that there is a strong interaction between Mhp and porcine organism. In this review, we summarized the immune evasion mechanisms from genomic variability and post-translational protein processing. Besides, Mhp can induce the immune cells apoptosis by reactive oxygen species production, excessive nitric oxide (NO) release and caspase activation, and stimulate the release of cytokines to regulate inflammation. This article seeks to provide some new points to reveal the complicated interaction between the pathogen and host immune system with Mhp as a typical example, further providing some new strategies for the vaccine development against Mhp infection.
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Affiliation(s)
- Gaojian Li
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Enoch Obeng
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jinqi Shu
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Jianhong Shu
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China.,Zhejiang Hom-Sun Biosciences Co., Ltd., Shaoxing, China
| | - Jian Chen
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yuehong Wu
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
| | - Yulong He
- Department of Biopharmacy, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, China
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Fritsch TE, Siqueira FM, Schrank IS. Global analysis of sRNA target genes in Mycoplasma hyopneumoniae. BMC Genomics 2018; 19:767. [PMID: 30352553 PMCID: PMC6199787 DOI: 10.1186/s12864-018-5136-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 10/01/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Small RNAs (sRNAs) are noncoding molecules that regulate different cellular activities in several bacteria. The role of sRNAs in gene expression regulation is poorly characterized in the etiological agent of porcine enzootic pneumonia Mycoplasma hyopneumoniae. We performed a global analysis of the sRNAs, sRNA target genes and regulatory elements previously identified in their genome and analyzed the expression of some sRNAs and their target genes by quantitative RT-PCR (qPCR) in three different culture conditions. RESULTS Seven of the 145 sRNA target genes are organized as monocistronic genes (mCs) while the other 138 sRNA target genes are organized into transcriptional units (TU). The identification of transcriptional regulatory elements (promoter motif, DNA repeat sequence or intrinsic terminator) was verified in 116 of the 145 sRNA target genes. Moreover, the 29 sRNA target genes without regulatory elements revealed the presence of at least one regulatory element in the boundaries of the TU or in other internal genes of the TU. We verified that 16 sRNAs showed differential expression, seven in heat shock condition and 14 in oxidative stress condition. Analysis of the differential expression of the sRNA target genes showed that the tested sRNAs possibly regulate gene expression. The sRNA target genes were up- or down-regulated possibly in response to sRNA only under oxidative stress condition. Moreover, the sRNA target genes are involved in diverse processes of the cell, some of which could be linked to transcription processes and cell homeostasis. CONCLUSION Our results indicate that bacterial sRNAs could regulate a number of targets with various outcomes, and different correlations between the levels of sRNA transcripts and their target gene mRNAs were found, which suggest that the regulation of gene expression via sRNAs may play an important role in mycoplasma.
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Affiliation(s)
- Tiago Ebert Fritsch
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Franciele Maboni Siqueira
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
| | - Irene Silveira Schrank
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS Brazil
- Departamento de Biologia Molecular e Biotecnologia – Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves 9500, P. 43421, C.P. 15005, CEP, Porto Alegre, RS 91501-970 Brazil
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8
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Sýkora M, Pospíšek M, Novák J, Mrvová S, Krásný L, Vopálenský V. Transcription apparatus of the yeast virus-like elements: Architecture, function, and evolutionary origin. PLoS Pathog 2018; 14:e1007377. [PMID: 30346988 PMCID: PMC6211774 DOI: 10.1371/journal.ppat.1007377] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 11/01/2018] [Accepted: 10/03/2018] [Indexed: 11/19/2022] Open
Abstract
Extrachromosomal hereditary elements such as organelles, viruses, and plasmids are important for the cell fitness and survival. Their transcription is dependent on host cellular RNA polymerase (RNAP) or intrinsic RNAP encoded by these elements. The yeast Kluyveromyces lactis contains linear cytoplasmic DNA virus-like elements (VLEs, also known as linear plasmids) that bear genes encoding putative non-canonical two-subunit RNAP. Here, we describe the architecture and identify the evolutionary origin of this transcription machinery. We show that the two RNAP subunits interact in vivo, and this complex interacts with another two VLE-encoded proteins, namely the mRNA capping enzyme and a putative helicase. RNAP, mRNA capping enzyme and the helicase also interact with VLE-specific DNA in vivo. Further, we identify a promoter sequence element that causes 5' mRNA polyadenylation of VLE-specific transcripts via RNAP slippage at the transcription initiation site, and structural elements that precede the termination sites. As a result, we present a first model of the yeast virus-like element transcription initiation and intrinsic termination. Finally, we demonstrate that VLE RNAP and its promoters display high similarity to poxviral RNAP and promoters of early poxviral genes, respectively, thereby pointing to their evolutionary origin.
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Affiliation(s)
- Michal Sýkora
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Pospíšek
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail: (MP); (VV)
| | - Josef Novák
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Silvia Mrvová
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Libor Krásný
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Václav Vopálenský
- Department of Genetics and Microbiology, Faculty of Science, Charles University, Prague, Czech Republic
- * E-mail: (MP); (VV)
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Cattani AM, Siqueira FM, Guedes RLM, Schrank IS. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation. PLoS One 2016; 11:e0168626. [PMID: 28005945 PMCID: PMC5179023 DOI: 10.1371/journal.pone.0168626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/02/2016] [Indexed: 12/15/2022] Open
Abstract
Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.
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Affiliation(s)
- Amanda Malvessi Cattani
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Franciele Maboni Siqueira
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Rafael Lucas Muniz Guedes
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | - Irene Silveira Schrank
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Centro de Biotecnologia, Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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