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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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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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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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Siqueira FM, de Morais GL, Higashi S, Beier LS, Breyer GM, de Sá Godinho CP, Sagot MF, Schrank IS, Zaha A, de Vasconcelos ATR. Mycoplasma non-coding RNA: identification of small RNAs and targets. BMC Genomics 2016; 17:743. [PMID: 27801290 PMCID: PMC5088518 DOI: 10.1186/s12864-016-3061-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Background Bacterial non-coding RNAs act by base-pairing as regulatory elements in crucial biological processes. We performed the identification of trans-encoded small RNAs (sRNA) from the genomes of Mycoplama hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis, which are Mycoplasma species that have been identified in the porcine respiratory system. Results A total of 47, 15 and 11 putative sRNAs were predicted in M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively. A comparative genomic analysis revealed the presence of species or lineage specific sRNA candidates. Furthermore, the expression profile of some M. hyopneumoniae sRNAs was determined by a reverse transcription amplification approach, in three different culture conditions. All tested sRNAs were transcribed in at least one condition. A detailed investigation revealed a differential expression profile for two M. hyopneumoniae sRNAs in response to oxidative and heat shock stress conditions, suggesting that their expression is influenced by environmental signals. Moreover, we analyzed sRNA-mRNA hybrids and accessed putative target genes for the novel sRNA candidates. The majority of the sRNAs showed interaction with multiple target genes, some of which could be linked to pathogenesis and cell homeostasis activity. Conclusion This study contributes to our knowledge of Mycoplasma sRNAs and their response to environmental changes. Furthermore, the mRNA target prediction provides a perspective for the characterization and comprehension of the function of the sRNA regulatory mechanisms. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3061-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Franciele Maboni Siqueira
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Guilherme Loss de Morais
- Laboratório Nacional de Computação Científica (LNCC), Laboratório de Bioinformática (LABINFO), Petrópolis, Rio de Janeiro, Brazil
| | - Susan Higashi
- Inria Grenoble Rhône-Alpes, 38330, Montbonnot Saint-Martin, France.,Université Lyon 1, Villeurbanne, France.,CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France
| | - Laura Scherer Beier
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Gabriela Merker Breyer
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Caio Padoan de Sá Godinho
- Laboratório Nacional de Computação Científica (LNCC), Laboratório de Bioinformática (LABINFO), Petrópolis, Rio de Janeiro, Brazil
| | - Marie-France Sagot
- Inria Grenoble Rhône-Alpes, 38330, Montbonnot Saint-Martin, France.,Université Lyon 1, Villeurbanne, France.,CNRS, UMR5558, Laboratoire de Biométrie et Biologie Évolutive, F-69622, Villeurbanne, France
| | - Irene Silveira Schrank
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Arnaldo Zaha
- Centro de Biotecnologia (CBiot), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil.
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Fritsch TE, Siqueira FM, Schrank IS. Intrinsic terminators in Mycoplasma hyopneumoniae transcription. BMC Genomics 2015; 16:273. [PMID: 25886614 PMCID: PMC4411717 DOI: 10.1186/s12864-015-1468-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Accepted: 03/17/2015] [Indexed: 11/24/2022] Open
Abstract
Background Mycoplasma hyopneumoniae, an important pathogen of swine, exhibits a low guanine and cytosine (GC) content genome. M. hyopneumoniae genome is organised in long transcriptional units and promoter sequences have been mapped upstream of all transcription units. These analysis provided insights into the gene organisation and transcription initiation at the genome scale. However, the presence of transcriptional terminator sequences in the M. hyopneumoniae genome is poorly understood. Results In silico analyses demonstrated the presence of putative terminators in 82% of the 33 monocistronic units (mCs) and in 74% of the 116 polycistronic units (pCs) considering different classes of terminators. The functional activity of 23 intrinsic terminators was confirmed by RT-PCR and qPCR. Analysis of all terminators found by three software algorithms, combined with experimental results, allowed us to propose a pattern of RNA hairpin formation during the termination process and to predict the location of terminators in the M. hyopneumoniae genome sequence. Conclusions The stem-loop structures of intrinsic terminators of mycoplasma diverge from the pattern of terminators found in other bacteria due the low content of guanine and cytosine. In M. hyopneumoniae, transcription can end after a transcriptional unit and before its terminator sequence and can also continue past the terminator sequence with RNA polymerases gradually releasing the RNA. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1468-6) contains supplementary material, which is available to authorized users.
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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, Porto Alegre, RS, CEP 91501-970, Brazil.
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Chou WC, Ma Q, Yang S, Cao S, Klingeman DM, Brown SD, Xu Y. Analysis of strand-specific RNA-seq data using machine learning reveals the structures of transcription units in Clostridium thermocellum. Nucleic Acids Res 2015; 43:e67. [PMID: 25765651 PMCID: PMC4446414 DOI: 10.1093/nar/gkv177] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 02/22/2015] [Indexed: 12/31/2022] Open
Abstract
Identification of transcription units (TUs) encoded in a bacterial genome is essential to elucidation of transcriptional regulation of the organism. To gain a detailed understanding of the dynamically composed TU structures, we have used four strand-specific RNA-seq (ssRNA-seq) datasets collected under two experimental conditions to derive the genomic TU organization of Clostridium thermocellum using a machine-learning approach. Our method accurately predicted the genomic boundaries of individual TUs based on two sets of parameters measuring the RNA-seq expression patterns across the genome: expression-level continuity and variance. A total of 2590 distinct TUs are predicted based on the four RNA-seq datasets. Among the predicted TUs, 44% have multiple genes. We assessed our prediction method on an independent set of RNA-seq data with longer reads. The evaluation confirmed the high quality of the predicted TUs. Functional enrichment analyses on a selected subset of the predicted TUs revealed interesting biology. To demonstrate the generality of the prediction method, we have also applied the method to RNA-seq data collected on Escherichia coli and achieved high prediction accuracies. The TU prediction program named SeqTU is publicly available at https://code.google.com/p/seqtu/. We expect that the predicted TUs can serve as the baseline information for studying transcriptional and post-transcriptional regulation in C. thermocellum and other bacteria.
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Affiliation(s)
- Wen-Chi Chou
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, GA 30602, USA BioEnergy Science Center, TN 37831, USA
| | - Qin Ma
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, GA 30602, USA BioEnergy Science Center, TN 37831, USA
| | - Shihui Yang
- BioEnergy Science Center, TN 37831, USA Biosciences Division, Oak Ridge National Laboratory, TN 37831, USA National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Sha Cao
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, GA 30602, USA
| | - Dawn M Klingeman
- BioEnergy Science Center, TN 37831, USA Biosciences Division, Oak Ridge National Laboratory, TN 37831, USA
| | - Steven D Brown
- BioEnergy Science Center, TN 37831, USA Biosciences Division, Oak Ridge National Laboratory, TN 37831, USA
| | - Ying Xu
- Computational Systems Biology Lab, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, GA 30602, USA BioEnergy Science Center, TN 37831, USA College of Computer Science and Technology and School of Public Health, Jilin University, Changchun, Jilin 130012, China
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Siqueira FM, Gerber AL, Guedes RLM, Almeida LG, Schrank IS, Vasconcelos ATR, Zaha A. Unravelling the transcriptome profile of the Swine respiratory tract mycoplasmas. PLoS One 2014; 9:e110327. [PMID: 25333523 PMCID: PMC4198240 DOI: 10.1371/journal.pone.0110327] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 09/11/2014] [Indexed: 11/18/2022] Open
Abstract
The swine respiratory ciliary epithelium is mainly colonized by Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis. While colonization by M. flocculare is virtually asymptomatic, M. hyopneumoniae and M. hyorhinis infections may cause respiratory disease. Information regarding transcript structure and gene abundance provides valuable insight into gene function and regulation, which has not yet been analyzed on a genome-wide scale in these Mycoplasma species. In this study, we report the construction of transcriptome maps for M. hyopneumoniae, M. flocculare and M. hyorhinis, which represent data for conducting comparative studies on the transcriptional repertory. For each species, three cDNA libraries were generated, yielding averages of 415,265, 695,313 and 93,578 reads for M. hyopneumoniae, M. flocculare and M. hyorhinis, respectively, with an average read length of 274 bp. The reads mapping showed that 92%, 98% and 96% of the predicted genes were transcribed in the M. hyopneumoniae, M. flocculare and M. hyorhinis genomes, respectively. Moreover, we showed that the majority of the genes are co-expressed, confirming the previously predicted transcription units. Finally, our data defined the RNA populations in detail, with the map transcript boundaries and transcription unit structures on a genome-wide scale.
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Affiliation(s)
- Franciele Maboni Siqueira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Biológicas – Bioquímica, UFRGS, Porto Alegre, Brazil
| | - Alexandra Lehmkuhl Gerber
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | - Rafael Lucas Muniz Guedes
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | - Luiz Gonzaga Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | - Irene Silveira Schrank
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil
| | | | - Arnaldo Zaha
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, UFRGS, Porto Alegre, Brazil
- * E-mail:
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Genome organization in Mycoplasma hyopneumoniae: identification of promoter-like sequences. Mol Biol Rep 2014; 41:5395-402. [DOI: 10.1007/s11033-014-3411-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Accepted: 05/11/2014] [Indexed: 11/26/2022]
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Simionatto S, Marchioro SB, Maes D, Dellagostin OA. Mycoplasma hyopneumoniae: from disease to vaccine development. Vet Microbiol 2013; 165:234-42. [PMID: 23680109 DOI: 10.1016/j.vetmic.2013.04.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 02/02/2023]
Abstract
Mycoplasma hyopneumoniae is the etiological agent of swine enzootic pneumonia (EP), a disease that affects swine production worldwide. Vaccination is the most cost-effective strategy for the control and prevention of the disease. Despite efforts to control M. hyopneumoniae infection, significant economic losses in pig production continue to occur. The results of genome-based research have the potential to help understand the biology and pathogenesis of M. hyopneumoniae, and contribute to the development of more effective vaccines and diagnostic tests. In this review, the characteristics of M. hyopneumoniae related to pathogenesis and control measures will be discussed. Special emphasis will be placed on vaccination strategies that have been proposed with the use of reverse vaccinology approaches.
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Affiliation(s)
- Simone Simionatto
- Núcleo de Biotecnologia, Centro de Desenvolvimento Tecnológico, Universidade Federal de Pelotas, RS, Brazil.
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Siqueira FM, Thompson CE, Virginio VG, Gonchoroski T, Reolon L, Almeida LG, da Fonsêca MM, de Souza R, Prosdocimi F, Schrank IS, Ferreira HB, de Vasconcelos ATR, Zaha A. New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis. BMC Genomics 2013; 14:175. [PMID: 23497205 PMCID: PMC3610235 DOI: 10.1186/1471-2164-14-175] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 03/08/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative agent of enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences of M. flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts. RESULTS The overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although M. flocculare and M. hyopneumoniae display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in M. flocculare and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species. CONCLUSIONS The comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors. M. hyopneumoniae and M. flocculare display many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. The M. hyorhinis genome contains differences in some components involved in metabolism and evasion of the host's immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis in the hyopneumoniae clade.
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Affiliation(s)
- Franciele Maboni Siqueira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Biológicas - Bioquímica. UFRGS, Porto Alegre, Brazil
| | - Claudia Elizabeth Thompson
- Laboratório de Bioinformática. Laboratório Nacional de Computação Científica. Petrópolis, Rio de Janeiro, Brazil
| | - Veridiana Gomes Virginio
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular. Centro de Biotecnologia UFRGS, Porto Alegre, Brazil
| | - Taylor Gonchoroski
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
| | - Luciano Reolon
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular. Centro de Biotecnologia UFRGS, Porto Alegre, Brazil
| | - Luiz Gonzaga Almeida
- Laboratório de Bioinformática. Laboratório Nacional de Computação Científica. Petrópolis, Rio de Janeiro, Brazil
| | - Marbella Maria da Fonsêca
- Laboratório de Bioinformática. Laboratório Nacional de Computação Científica. Petrópolis, Rio de Janeiro, Brazil
| | - Rangel de Souza
- Laboratório de Bioinformática. Laboratório Nacional de Computação Científica. Petrópolis, Rio de Janeiro, Brazil
| | - Francisco Prosdocimi
- Departamento de Bioquímica Médica. Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Irene Silveira Schrank
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular. Centro de Biotecnologia UFRGS, Porto Alegre, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências. UFRGS, Porto Alegre, Brazil
| | - Henrique Bunselmeyer Ferreira
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular. Centro de Biotecnologia UFRGS, Porto Alegre, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências. UFRGS, Porto Alegre, Brazil
| | | | - Arnaldo Zaha
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil
- Programa de Pós-Graduação em Biologia Celular e Molecular. Centro de Biotecnologia UFRGS, Porto Alegre, Brazil
- Programa de Pós-Graduação em Ciências Biológicas - Bioquímica. UFRGS, Porto Alegre, Brazil
- Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências. UFRGS, Porto Alegre, Brazil
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Weber SDS, Sant'Anna FH, Schrank IS. Unveiling Mycoplasma hyopneumoniae promoters: sequence definition and genomic distribution. DNA Res 2012; 19:103-15. [PMID: 22334569 PMCID: PMC3325076 DOI: 10.1093/dnares/dsr045] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Several Mycoplasma species have had their genome completely sequenced, including four strains of the swine pathogen Mycoplasma hyopneumoniae. Nevertheless, little is known about the nucleotide sequences that control transcriptional initiation in these microorganisms. Therefore, with the objective of investigating the promoter sequences of M. hyopneumoniae, 23 transcriptional start sites (TSSs) of distinct genes were mapped. A pattern that resembles the σ70 promoter −10 element was found upstream of the TSSs. However, no −35 element was distinguished. Instead, an AT-rich periodic signal was identified. About half of the experimentally defined promoters contained the motif 5′-TRTGn-3′, which was identical to the −16 element usually found in Gram-positive bacteria. The defined promoters were utilized to build position-specific scoring matrices in order to scan putative promoters upstream of all coding sequences (CDSs) in the M. hyopneumoniae genome. Two hundred and one signals were found associated with 169 CDSs. Most of these sequences were located within 100 nucleotides of the start codons. This study has shown that the number of promoter-like sequences in the M. hyopneumoniae genome is more frequent than expected by chance, indicating that most of the sequences detected are probably biologically functional.
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Affiliation(s)
- Shana de Souto Weber
- Centro de Biotecnologia, Programa de Pós-graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
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