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Olczak T, Śmiga M, Antonyuk SV, Smalley JW. Hemophore-like proteins of the HmuY family in the oral and gut microbiome: unraveling the mystery of their evolution. Microbiol Mol Biol Rev 2024; 88:e0013123. [PMID: 38305743 PMCID: PMC10966948 DOI: 10.1128/mmbr.00131-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024] Open
Abstract
SUMMARY Heme (iron protoporphyrin IX, FePPIX) is the main source of iron and PPIX for host-associated pathogenic bacteria, including members of the Bacteroidota (formerly Bacteroidetes) phylum. Porphyromonas gingivalis, a keystone oral pathogen, uses a unique heme uptake (Hmu) system, comprising a hemophore-like protein, designated as the first member of the novel HmuY family. Compared to classical, secreted hemophores utilized by Gram-negative bacteria or near-iron transporter domain-based hemophores utilized by Gram-positive bacteria, the HmuY family comprises structurally similar proteins that have undergone diversification during evolution. The best characterized are P. gingivalis HmuY and its homologs from Tannerella forsythia (Tfo), Prevotella intermedia (PinO and PinA), Bacteroides vulgatus (Bvu), and Bacteroides fragilis (BfrA, BfrB, and BfrC). In contrast to the two histidine residues coordinating heme iron in P. gingivalis HmuY, Tfo, PinO, PinA, Bvu, and BfrA preferentially use two methionine residues. Interestingly, BfrB, despite conserved methionine residue, binds the PPIX ring without iron coordination. BfrC binds neither heme nor PPIX in keeping with the lack of conserved histidine or methionine residues used by other members of the HmuY family. HmuY competes for heme binding and heme sequestration from host hemoproteins with other members of the HmuY family to increase P. gingivalis competitiveness. The participation of HmuY in the host immune response confirms its relevance in relation to the survival of P. gingivalis and its ability to induce dysbiosis not only in the oral microbiome but also in the gut microbiome or other host niches, leading to local injuries and involvement in comorbidities.
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Affiliation(s)
- Teresa Olczak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Michał Śmiga
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Svetlana V. Antonyuk
- Molecular Biophysics Group, Institute of Systems, Molecular and Integrative Biology, Faculty of Health and Life Sciences, the University of Liverpool, Liverpool, United Kingdom
| | - John W. Smalley
- Institute of Life Course and Medical Sciences, School of Dentistry, the University of Liverpool, Liverpool, United Kingdom
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A quantitative framework reveals traditional laboratory growth is a highly accurate model of human oral infection. Proc Natl Acad Sci U S A 2022; 119:2116637119. [PMID: 34992142 PMCID: PMC8764681 DOI: 10.1073/pnas.2116637119] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 01/08/2023] Open
Abstract
Bacterial behavior and virulence during human infection is difficult to study and largely unknown, as our vast knowledge of infection microbiology is primarily derived from studies using in vitro and animal models. Here, we characterize the physiology of Porphyromonas gingivalis, a periodontal pathogen, in its native environment using 93 published metatranscriptomic datasets from periodontally healthy and diseased individuals. P. gingivalis transcripts were more abundant in samples from periodontally diseased patients but only above 0.1% relative abundance in one-third of diseased samples. During human infection, P. gingivalis highly expressed genes encoding virulence factors such as fimbriae and gingipains (proteases) and genes involved in growth and metabolism, indicating that P. gingivalis is actively growing during disease. A quantitative framework for assessing the accuracy of model systems showed that 96% of P. gingivalis genes were expressed similarly in periodontitis and in vitro midlogarithmic growth, while significantly fewer genes were expressed similarly in periodontitis and in vitro stationary phase cultures (72%) or in a murine abscess infection model (85%). This high conservation in gene expression between periodontitis and logarithmic laboratory growth is driven by overall low variance in P. gingivalis gene expression, relative to other pathogens including Pseudomonas aeruginosa and Staphylococcus aureus Together, this study presents strong evidence for the use of simple test tube growth as the gold standard model for studying P. gingivalis biology, providing biological relevance for the thousands of laboratory experiments performed with logarithmic phase P. gingivalis Furthermore, this work highlights the need to quantitatively assess the accuracy of model systems.
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Ryan D, Prezza G, Westermann AJ. An RNA-centric view on gut Bacteroidetes. Biol Chem 2020; 402:55-72. [PMID: 33544493 DOI: 10.1515/hsz-2020-0230] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/21/2020] [Indexed: 01/26/2023]
Abstract
Bacteria employ noncoding RNAs to maintain cellular physiology, adapt global gene expression to fluctuating environments, sense nutrients, coordinate their interaction with companion microbes and host cells, and protect themselves against bacteriophages. While bacterial RNA research has made fundamental contributions to biomedicine and biotechnology, the bulk of our knowledge of RNA biology stems from the study of a handful of aerobic model species. In comparison, RNA research is lagging in many medically relevant obligate anaerobic species, in particular the numerous commensal bacteria comprising our gut microbiota. This review presents a guide to RNA-based regulatory mechanisms in the phylum Bacteroidetes, focusing on the most abundant bacterial genus in the human gut, Bacteroides spp. This includes recent case reports on riboswitches, an mRNA leader, cis- and trans-encoded small RNAs (sRNAs) in Bacteroides spp., and a survey of CRISPR-Cas systems across Bacteroidetes. Recent work from our laboratory now suggests the existence of hundreds of noncoding RNA candidates in Bacteroides thetaiotaomicron, the emerging model organism for functional microbiota research. Based on these collective observations, we predict mechanistic and functional commonalities and differences between Bacteroides sRNAs and those of other model bacteria, and outline open questions and tools needed to boost Bacteroidetes RNA research.
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Affiliation(s)
- Daniel Ryan
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
| | - Gianluca Prezza
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
| | - Alexander J Westermann
- Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany.,Institute of Molecular Infection Biology (IMIB), University of Würzburg, Josef-Schneider-Str. 2/D15, D-97080, Würzburg, Germany
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Romero-Lastra P, Sánchez MC, Llama-Palacios A, Figuero E, Herrera D, Sanz M. Gene expression of Porphyromonas gingivalis ATCC 33277 when growing in an in vitro multispecies biofilm. PLoS One 2019; 14:e0221234. [PMID: 31437202 PMCID: PMC6706054 DOI: 10.1371/journal.pone.0221234] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Accepted: 08/01/2019] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND AND OBJECTIVE Porphyromonas gingivalis, an oral microorganism residing in the subgingival biofilm, may exert diverse pathogenicity depending on the presence of specific virulence factors, but its gene expression has not been completely established. This investigation aims to compare the transcriptomic profile of this pathogen when growing within an in vitro multispecies biofilm or in a planktonic state. MATERIALS AND METHODS P. gingivalis ATCC 33277 was grown in anaerobiosis within multi-well culture plates at 37°C under two conditions: (a) planktonic samples (no hydroxyapatite discs) or (b) within a multispecies-biofilm containing Streptococcus oralis, Actinomyces naeslundii, Veillonella parvula, Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans deposited on hydroxyapatite discs. Scanning Electron Microscopy (SEM) and Confocal Laser Scanning Microscopy (CLSM) combined with Fluorescence In Situ Hybridization (FISH) were used to verify the formation of the biofilm and the presence of P. gingivalis. Total RNA was extracted from both the multispecies biofilm and planktonic samples, then purified and, with the use of a microarray, its differential gene expression was analyzed. A linear model was used for determining the differentially expressed genes using a filtering criterion of two-fold change (up or down) and a significance p-value of <0.05. Differential expression was confirmed by Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR). RESULTS SEM verified the development of the multispecies biofilm and FISH confirmed the incorporation of P. gingivalis. The microarray demonstrated that, when growing within the multispecies biofilm, 19.1% of P. gingivalis genes were significantly and differentially expressed (165 genes were up-regulated and 200 down-regulated), compared with planktonic growth. These genes were mainly involved in functions related to the oxidative stress, cell envelope, transposons and metabolism. The results of the microarray were confirmed by RT-qPCR. CONCLUSION Significant transcriptional changes occurred in P. gingivalis when growing in a multispecies biofilm compared to planktonic state.
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Affiliation(s)
- Patricia Romero-Lastra
- Laboratory of Dental Research, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - María C. Sánchez
- Laboratory of Dental Research, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - Arancha Llama-Palacios
- Laboratory of Dental Research, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - Elena Figuero
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
- * E-mail:
| | - David Herrera
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
| | - Mariano Sanz
- ETEP Research Group, Faculty of Odontology, Complutense University of Madrid, Madrid, Spain
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Śmiga M, Stępień P, Olczak M, Olczak T. PgFur participates differentially in expression of virulence factors in more virulent A7436 and less virulent ATCC 33277 Porphyromonas gingivalis strains. BMC Microbiol 2019; 19:127. [PMID: 31185896 PMCID: PMC6558696 DOI: 10.1186/s12866-019-1511-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 06/04/2019] [Indexed: 12/19/2022] Open
Abstract
Background Porphyromonas gingivalis is considered a keystone pathogen responsible for chronic periodontitis. Although several virulence factors produced by this bacterium are quite well characterized, very little is known about regulatory mechanisms that allow different strains of P. gingivalis to efficiently survive in the hostile environment of the oral cavity, a typical habitat characterized by low iron and heme concentrations. The aim of this study was to characterize P. gingivalis Fur homolog (PgFur) in terms of its role in production of virulence factors in more (A7436) and less (ATCC 33277) virulent strains. Results Expression of a pgfur depends on the growth phase and iron/heme concentration. To better understand the role played by the PgFur protein in P. gingivalis virulence under low- and high-iron/heme conditions, a pgfur-deficient ATCC 33277 strain (TO16) was constructed and its phenotype compared with that of a pgfur A7436-derived mutant strain (TO6). In contrast to the TO6 strain, the TO16 strain did not differ in the growth rate and hemolytic activity compared with the ATCC 33277 strain. However, both mutant strains were more sensitive to oxidative stress and they demonstrated changes in the production of lysine- (Kgp) and arginine-specific (Rgp) gingipains. In contrast to the wild-type strains, TO6 and TO16 mutant strains produced larger amounts of HmuY protein under high iron/heme conditions. We also demonstrated differences in production of glycoconjugates between the A7436 and ATCC 33277 strains and we found evidence that PgFur protein might regulate glycosylation process. Moreover, we revealed that PgFur protein plays a role in interactions with other periodontopathogens and is important for P. gingivalis infection of THP-1-derived macrophages and survival inside the cells. Deletion of the pgfur gene influences expression of many transcription factors, including two not yet characterized transcription factors from the Crp/Fnr family. We also observed lower expression of the CRISPR/Cas genes. Conclusions We show here for the first time that inactivation of the pgfur gene exerts a different influence on the phenotype of the A7436 and ATCC 33277 strains. Our findings further support the hypothesis that PgFur regulates expression of genes encoding surface virulence factors and/or genes involved in their maturation. Electronic supplementary material The online version of this article (10.1186/s12866-019-1511-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Michał Śmiga
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14A St, 50-383, Wrocław, Poland
| | - Paulina Stępień
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14A St, 50-383, Wrocław, Poland
| | - Mariusz Olczak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14A St, 50-383, Wrocław, Poland
| | - Teresa Olczak
- Laboratory of Medical Biology, Faculty of Biotechnology, University of Wrocław, F. Joliot-Curie 14A St, 50-383, Wrocław, Poland.
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Ralston MT, Papoutsakis ET. RNAseq‐based transcriptome assembly of
Clostridium acetobutylicum
for functional genome annotation and discovery. AIChE J 2018. [DOI: 10.1002/aic.16396] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Matthew T. Ralston
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
- Center for Bioinformatics and Computational Biology University of Delaware Newark DE 19711
| | - Eleftherios T. Papoutsakis
- Dept. of Chemical and Biomolecular Engineering University of Delaware Newark DE 19711
- Molecular Biotechnology Laboratory, Delaware Biotechnology Institute University of Delaware Newark DE 19711
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Zhuang K, Jiang Y, Feng X, Li L, Dang F, Zhang W, Man C. Transcriptomic response to GABA-producing Lactobacillus plantarum CGMCC 1.2437T induced by L-MSG. PLoS One 2018; 13:e0199021. [PMID: 29894506 PMCID: PMC5997328 DOI: 10.1371/journal.pone.0199021] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Accepted: 05/30/2018] [Indexed: 12/14/2022] Open
Abstract
Gamma-aminobutyric acid (GABA) is an inhibitory neurotransmitter found in the central nervous system of mammals. A range of bacterial species can synthesize GABA, including Lactobacillus plantarum of which L-monosodium glutamate (L-MSG) is an inducer of its production. In order to synthesize GABA in high concentrations, L-MSG was utilized as the single inducing factor, a chemically defined medium (CDM) was used as the fermentation substrate, with L. plantarum CGMCC 1.2437T cultured in medium supplemented with or without L-MSG. High-throughput transcriptome sequencing was used to explore the differential genes expression of bacterial cells at 36 h of fermentation, where the GABA concentration of CDM with L-MSG reached the peak value and was 7.7 times higher than that of medium without L-MSG at the same timepoint. A total of 87 genes showed significant differential expression induced by L-MSG: of these, 69 were up-regulated genes and 18 were down-regulated. The up-regulated genes were assigned to biological processes and molecular function, while the down-regulated genes covered biological process, cellular process and molecular function. Interrogation of results using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, indicated carbohydrate metabolism, fatty acid synthesis and amino acid metabolism were closely associated with GABA synthesis induced by L-MSG. This study provides insights into L. plantarum-mediated GABA fermentation at the molecular level and will provide a new approach for further studies related to GABA production by the other Lactic acid bacteria.
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Affiliation(s)
- Kejin Zhuang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Technology, Northeast Agricultural University, Harbin, China
| | - Yujun Jiang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiaohan Feng
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Technology, Northeast Agricultural University, Harbin, China
| | - Li Li
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Technology, Northeast Agricultural University, Harbin, China
| | - Fangfang Dang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Technology, Northeast Agricultural University, Harbin, China
| | - Wei Zhang
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Technology, Northeast Agricultural University, Harbin, China
| | - Chaoxin Man
- Key Laboratory of Dairy Science, Ministry of Education, College of Food Science and Technology, Northeast Agricultural University, Harbin, China
- * E-mail:
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8
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Deng ZL, Sztajer H, Jarek M, Bhuju S, Wagner-Döbler I. Worlds Apart - Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions. Front Microbiol 2018; 9:124. [PMID: 29467738 PMCID: PMC5807917 DOI: 10.3389/fmicb.2018.00124] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 01/18/2018] [Indexed: 12/28/2022] Open
Abstract
Periodontitis is a worldwide prevalent oral disease which results from dysbiosis of the periodontal microbiome. Some of the most active microbial players, e.g., Porphyromonas gingivalis, Treponema denticola, and Fusobacterium nucleatum, have extensively been studied in the laboratory, but it is unclear to which extend these findings can be transferred to in vivo conditions. Here we show that the transcriptional profiles of P. gingivalis, T. denticola, and F. nucleatum in the periodontal niche are distinct from those in single laboratory culture and exhibit functional similarities. GO (gene ontology) term enrichment analysis showed up-regulation of transporters, pathogenicity related traits and hemin/heme uptake mechanisms for all three species in vivo. Differential gene expression analysis revealed that cysteine proteases, transporters and hemin/heme-binding proteins were highly up-regulated in the periodontal niche, while genes involved in DNA modification were down-regulated. The data suggest strong interactions between those three species regarding protein degradation, iron up-take, and mobility in vivo, explaining their enhanced synergistic pathogenicity. We discovered a strikingly high frequency of Single Nucleotide Polymorphisms (SNPs) in vivo. For F. nucleatum we discovered a total of 127,729 SNPs in periodontal niche transcripts, which were found in similar frequency in health and disease and covered the entire genome, suggesting continuous evolution in the host. We conclude that metabolic interactions shape gene expression in vivo. Great caution is required when inferring pathogenicity of microbes from laboratory data, and microdiversity is an important adaptive trait of natural communities.
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Affiliation(s)
- Zhi-Luo Deng
- Research Group Microbial Communication, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Helena Sztajer
- Research Group Microbial Communication, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Michael Jarek
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Sabin Bhuju
- Genome Analytics, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Irene Wagner-Döbler
- Research Group Microbial Communication, Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
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Acuña-Amador L, Primot A, Cadieu E, Roulet A, Barloy-Hubler F. Genomic repeats, misassembly and reannotation: a case study with long-read resequencing of Porphyromonas gingivalis reference strains. BMC Genomics 2018; 19:54. [PMID: 29338683 PMCID: PMC5771137 DOI: 10.1186/s12864-017-4429-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 12/29/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota. We successfully identify the genetic loci responsible for assembly breaks and misassemblies and demonstrate the importance and usefulness of long-read sequencing and curated reannotation. RESULTS We showed that the fragmentation in Bacteroidia draft genomes assembled from massively parallel sequencing linearly correlates with genomic repeats of the same or greater size than the reads. We also demonstrated that some of these repeats, especially the long ones, correspond to misassembled loci in three reference Porphyromonas gingivalis genomes marked as circularized (thus complete or finished). We prove that even at modest coverage (30X), long-read resequencing together with PCR contiguity verification (rrn operons and an integrative and conjugative element or ICE) can be used to identify and correct the wrongly combined or assembled regions. Finally, although time-consuming and labor-intensive, consistent manual biocuration of three P. gingivalis strains allowed us to compare and correct the existing genomic annotations, resulting in a more accurate interpretation of the genomic differences among these strains. CONCLUSIONS In this study, we demonstrate the usefulness and importance of long-read sequencing in verifying published genomes (even when complete) and generating assemblies for new bacterial strains/species with high genomic plasticity. We also show that when combined with biological validation processes and diligent biocurated annotation, this strategy helps reduce the propagation of errors in shared databases, thus limiting false conclusions based on incomplete or misleading information.
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Affiliation(s)
- Luis Acuña-Amador
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.,Laboratorio de Investigación en Bacteriología Anaerobia, Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Aline Primot
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France
| | - Alain Roulet
- GenoToul Genome & Transcriptome (GeT-PlaGe), INRA, US1426, Castanet-Tolosan, France
| | - Frédérique Barloy-Hubler
- Institut de Génétique et Développement de Rennes, CNRS, UMR6290, Université de Rennes 1, Rennes, France.
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10
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Romero-Lastra P, Sánchez MC, Ribeiro-Vidal H, Llama-Palacios A, Figuero E, Herrera D, Sanz M. Comparative gene expression analysis of Porphyromonas gingivalis ATCC 33277 in planktonic and biofilms states. PLoS One 2017; 12:e0174669. [PMID: 28369099 PMCID: PMC5378342 DOI: 10.1371/journal.pone.0174669] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/13/2017] [Indexed: 11/24/2022] Open
Abstract
Background and objective Porphyromonas gingivalis is a keystone pathogen in the onset and progression of periodontitis. Its pathogenicity has been related to its presence and survival within the subgingival biofilm. The aim of the present study was to compare the genome-wide transcription activities of P. gingivalis in biofilm and in planktonic growth, using microarray technology. Material and methods P. gingivalis ATCC 33277 was incubated in multi-well culture plates at 37°C for 96 hours under anaerobic conditions using an in vitro static model to develop both the planktonic and biofilm states (the latter over sterile ceramic calcium hydroxyapatite discs). The biofilm development was monitored by Confocal Laser Scanning Microscopy (CLSM) and Scanning Electron Microscopy (SEM). After incubation, the bacterial cells were harvested and total RNA was extracted and purified. Three biological replicates for each cell state were independently hybridized for transcriptomic comparisons. A linear model was used for determining differentially expressed genes and reverse transcription quantitative polymerase chain reaction (RT-qPCR) was used to confirm differential expression. The filtering criteria of ≥ ±2 change in gene expression and significance p-values of <0.05 were selected. Results A total of 92 out of 1,909 genes (4.8%) were differentially expressed by P. gingivalis growing in biofilm compared to planktonic. The 54 up-regulated genes in biofilm growth were mainly related to cell envelope, transport, and binding or outer membranes proteins. Thirty-eight showed decreased expression, mainly genes related to transposases or oxidative stress. Conclusion The adaptive response of P. gingivalis in biofilm growth demonstrated a differential gene expression.
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Affiliation(s)
- P. Romero-Lastra
- Laboratory of Dental Research, University Complutense, Madrid, Spain
| | - MC. Sánchez
- Laboratory of Dental Research, University Complutense, Madrid, Spain
| | - H. Ribeiro-Vidal
- Laboratory of Dental Research, University Complutense, Madrid, Spain
| | - A. Llama-Palacios
- Laboratory of Dental Research, University Complutense, Madrid, Spain
| | - E. Figuero
- Laboratory of Dental Research, University Complutense, Madrid, Spain
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group, University Complutense, Madrid, Spain
| | - D. Herrera
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group, University Complutense, Madrid, Spain
| | - M. Sanz
- ETEP (Etiology and Therapy of Periodontal Diseases) Research Group, University Complutense, Madrid, Spain
- * E-mail:
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Comprehensive Transcriptome Profiles of Streptococcus mutans UA159 Map Core Streptococcal Competence Genes. mSystems 2016; 1:mSystems00038-15. [PMID: 27822519 PMCID: PMC5069739 DOI: 10.1128/msystems.00038-15] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 03/10/2016] [Indexed: 12/15/2022] Open
Abstract
In Streptococcus mutans, an oral colonizer associated with dental caries, development of competence for natural genetic transformation is triggered by either of two types of peptide pheromones, competence-stimulating peptides (CSPs) (18 amino acids [aa]) or SigX-inducing peptides (XIPs) (7 aa). Competence induced by CSP is a late response to the pheromone that requires the response regulator ComE and the XIP-encoding gene comS. XIP binds to ComR to allow expression of the alternative sigma factor SigX and the effector genes it controls. While these regulatory links are established, the precise set of effectors controlled by each regulator is poorly defined. To improve the definition of all three regulons, we used a high-resolution tiling array to map global changes in gene expression in the early and late phases of the CSP response. The early phase of the CSP response was limited to increased gene expression at four loci associated with bacteriocin production and immunity. In the late phase, upregulated regions expanded to a total of 29 loci, including comS and genes required for DNA uptake and recombination. The results indicate that the entire late response to CSP depends on the expression of comS and that the immediate transcriptional response to CSP, mediated by ComE, is restricted to just four bacteriocin-related loci. Comparison of the new data with published transcriptome data permitted the identification of all of the operons in each regulon: 4 for ComE, 2 for ComR, and 21 for SigX. Finally, a core set of 27 panstreptococcal competence genes was identified within the SigX regulon by comparison of transcriptome data from diverse streptococcal species. IMPORTANCES. mutans has the hard surfaces of the oral cavity as its natural habitat, where it depends on its ability to form biofilms in order to survive. The comprehensive identification of S. mutans regulons activated in response to peptide pheromones provides an important basis for understanding how S. mutans can transition from individual to social behavior. Our study placed 27 of the 29 transcripts activated during competence within three major regulons and revealed a core set of 27 panstreptococcal competence-activated genes within the SigX regulon.
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12
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Kim J, Pérez-Pantoja D, Silva-Rocha R, Oliveros JC, de Lorenzo V. High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2. Environ Microbiol 2015; 18:3327-3341. [PMID: 26373670 DOI: 10.1111/1462-2920.13054] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/30/2015] [Accepted: 09/12/2015] [Indexed: 11/28/2022]
Abstract
Pseudomonas putida mt-2 metabolizes m-xylene and other aromatic compounds through the enzymes encoded by the xyl operons of the TOL plasmid pWW0 along with other chromosomally encoded activities. Tiling arrays of densely overlapping oligonucleotides were designed to cover every gene involved in this process, allowing dissection of operon structures and exposing the interplay of plasmid and chromosomal functions. All xyl sequences were transcribed in response to aromatic substrates and the 3'-termini of both upper and lower mRNA operons extended beyond their coding regions, i.e. the 3'-end of the lower operon mRNA penetrated into the convergent xylS regulatory gene. Furthermore, xylR mRNA for the master m-xylene responsive regulator of the system was decreased by aromatic substrates, while the cognate upper operon mRNA was evenly stable throughout its full length. RNA sequencing confirmed these data at a single nucleotide level and refined the formerly misannotated xylL sequence. The chromosomal ortho route for degradation of benzoate (the ben, cat clusters and some pca genes) was activated by this aromatic, but not by the TOL substrates, toluene or m-xylene. We advocate this scenario as a testbed of natural retroactivity between a pre-existing metabolic network and a new biochemical pathway implanted through gene transfer.
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Affiliation(s)
- Juhyun Kim
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Danilo Pérez-Pantoja
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Rafael Silva-Rocha
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Juan Carlos Oliveros
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnologia-CSIC, Campus de Cantoblanco, Madrid, Spain.
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13
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Arjunan P, El-Awady A, Dannebaum RO, Kunde-Ramamoorthy G, Cutler CW. High-throughput sequencing reveals key genes and immune homeostatic pathways activated in myeloid dendritic cells by Porphyromonas gingivalis 381 and its fimbrial mutants. Mol Oral Microbiol 2015; 31:78-93. [PMID: 26466817 DOI: 10.1111/omi.12131] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2015] [Indexed: 12/14/2022]
Abstract
The human microbiome consists of highly diverse microbial communities that colonize our skin and mucosal surfaces, aiding in maintenance of immune homeostasis. The keystone pathogen Porphyromonas gingivalis induces a dysbiosis and disrupts immune homeostasis through as yet unclear mechanisms. The fimbrial adhesins of P. gingivalis facilitate biofilm formation, invasion of and dissemination by blood dendritic cells; hence, fimbriae may be key factors in disruption of immune homeostasis. In this study we employed RNA-sequencing transcriptome profiling to identify differentially expressed genes (DEGs) in human monocyte-derived dendritic cells (MoDCs) in response to in vitro infection/exposure by Pg381 or its isogenic mutant strains that solely express minor-Mfa1 fimbriae (DPG3), major-FimA fimbriae (MFI) or are deficient in both fimbriae (MFB) relative to uninfected control. Our results yielded a total of 479 DEGs that were at least two-fold upregulated and downregulated in MoDCs significantly (P ≤ 0.05) by all four strains and certain DEGs that were strain-specific. Interestingly, the gene ontology biological and functional analysis shows that the upregulated genes in DPG3-induced MoDCs were more significant than other strains and associated with inflammation, immune response, anti-apoptosis, cell proliferation, and other homeostatic functions. Both transcriptome and quantitative polymerase chain reaction results show that DPG3, which solely expresses Mfa1, increased ZNF366, CD209, LOX1, IDO1, IL-10, CCL2, SOCS3, STAT3 and FOXO1 gene expression. In conclusion, we have identified key DC-mediated immune homeostatic pathways that could contribute to dysbiosis in periodontal infection with P. gingivalis.
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Affiliation(s)
- P Arjunan
- Department of Periodontics, Georgia Regents University, Augusta, GA, USA
| | - A El-Awady
- Department of Periodontics, Georgia Regents University, Augusta, GA, USA
| | - R O Dannebaum
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA
| | - G Kunde-Ramamoorthy
- Department of Energy, Joint Genome Institute, Walnut Creek, CA, USA.,Department of Biochemistry, National University of Singapore, Singapore
| | - C W Cutler
- Department of Periodontics, Georgia Regents University, Augusta, GA, USA
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Klein BA, Chen T, Scott JC, Koenigsberg AL, Duncan MJ, Hu LT. Identification and characterization of a minisatellite contained within a novel miniature inverted-repeat transposable element (MITE) of Porphyromonas gingivalis. Mob DNA 2015; 6:18. [PMID: 26448788 PMCID: PMC4596501 DOI: 10.1186/s13100-015-0049-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 09/23/2015] [Indexed: 12/26/2022] Open
Abstract
Background Repetitive regions of DNA and transposable elements have been found to constitute large percentages of eukaryotic and prokaryotic genomes. Such elements are known to be involved in transcriptional regulation, host-pathogen interactions and genome evolution. Results We identified a minisatellite contained within a miniature inverted-repeat transposable element (MITE) in Porphyromonas gingivalis. The P. gingivalis minisatellite and associated MITE, named ‘BrickBuilt’, comprises a tandemly repeating twenty-three nucleotide DNA sequence lacking spacer regions between repeats, and with flanking ‘leader’ and ‘tail’ subunits that include small inverted-repeat ends. Forms of the BrickBuilt MITE are found 19 times in the genome of P. gingivalis strain ATCC 33277, and also multiple times within the strains W83, TDC60, HG66 and JCVI SC001. BrickBuilt is always located intergenically ranging between 49 and 591 nucleotides from the nearest upstream and downstream coding sequences. Segments of BrickBuilt contain promoter elements with bidirectional transcription capabilities. Conclusions We performed a bioinformatic analysis of BrickBuilt utilizing existing whole genome sequencing, microarray and RNAseq data, as well as performing in vitro promoter probe assays to determine potential roles, mechanisms and regulation of the expression of these elements and their affect on surrounding loci. The multiplicity, localization and limited host range nature of MITEs and MITE-like elements in P. gingivalis suggest that these elements may play an important role in facilitating genome evolution as well as modulating the transcriptional regulatory system. Electronic supplementary material The online version of this article (doi:10.1186/s13100-015-0049-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brian A Klein
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111 USA ; Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Tsute Chen
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Jodie C Scott
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Andrea L Koenigsberg
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111 USA
| | - Margaret J Duncan
- Department of Microbiology, The Forsyth Institute, Cambridge, MA 02142 USA
| | - Linden T Hu
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111 USA
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15
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Zhang Z, Shen T, Rui B, Zhou W, Zhou X, Shang C, Xin C, Liu X, Li G, Jiang J, Li C, Li R, Han M, You S, Yu G, Yi Y, Wen H, Liu Z, Xie X. CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. Nucleic Acids Res 2014; 43:D549-57. [PMID: 25392417 PMCID: PMC4383945 DOI: 10.1093/nar/gku1137] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The Central Carbon Metabolic Flux Database (CeCaFDB, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. It encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information gathered from hundreds of journal articles. In addition to its comprehensive literature-derived data, the CeCaFDB supports a common text search function among the data and interactive visualization of the curated flux distributions with compartmentation information based on the Cytoscape Web API, which facilitates data interpretation. The CeCaFDB offers four modules to calculate a similarity score or to perform an alignment between the flux distributions. One of the modules was built using an inter programming algorithm for flux distribution alignment that was specifically designed for this study. Based on these modules, the CeCaFDB also supports an extensive flux distribution comparison function among the curated data. The CeCaFDB is strenuously designed to address the broad demands of biochemists, metabolic engineers, systems biologists and members of the -omics community.
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Affiliation(s)
- Zhengdong Zhang
- College of Computer Science and Technology, Guizhou University, Guiyang, Guizhou 550025, P.R. China
| | - Tie Shen
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Bin Rui
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Wenwei Zhou
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Xiangfei Zhou
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Chuanyu Shang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Chenwei Xin
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Xiaoguang Liu
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Gang Li
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Jiansi Jiang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Chao Li
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Ruiyuan Li
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Mengshu Han
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Shanping You
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Guojun Yu
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Yin Yi
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Han Wen
- School of Life Sciences, Anhui Agricultural University, Hefei, Anhui 230026, P. R. China
| | - Zhijie Liu
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
| | - Xiaoyao Xie
- Key Laboratory of Information and Computing Science Guizhou Province, Guizhou Normal University, Guiyang, Guizhou 563000, P. R. China
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16
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Billis K, Billini M, Tripp HJ, Kyrpides NC, Mavromatis K. Comparative transcriptomics between Synechococcus PCC 7942 and Synechocystis PCC 6803 provide insights into mechanisms of stress acclimation. PLoS One 2014; 9:e109738. [PMID: 25340743 PMCID: PMC4207680 DOI: 10.1371/journal.pone.0109738] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 08/13/2014] [Indexed: 12/13/2022] Open
Abstract
Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803 are model cyanobacteria from which the metabolism and adaptive responses of other cyanobacteria are inferred. Using stranded and 5' enriched libraries, we measured the gene expression response of cells transferred from reference conditions to stress conditions of decreased inorganic carbon, increased salinity, increased pH, and decreased illumination at 1-h and 24-h after transfer. We found that the specific responses of the two strains were by no means identical. Transcriptome profiles allowed us to improve the structural annotation of the genome i.e. identify possible missed genes (including anti-sense), alter gene coordinates and determine transcriptional units (operons). Finally, we predicted associations between proteins of unknown function and biochemical pathways by revealing proteins of known functions that are co-regulated with the unknowns. Future studies of these model organisms will benefit from the cataloging of their responses to environmentally relevant stresses, and improvements in their genome annotations found here.
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Affiliation(s)
- Konstantinos Billis
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- Department of Genetics, Development and Molecular Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Maria Billini
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Group of Prokaryotic Cell Biology, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- Faculty of Biology, Philipps-Universität, Marburg, Germany
| | - H. James Tripp
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
| | - Nikos C. Kyrpides
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Konstantinos Mavromatis
- Microbial Genome and Metagenome Program, DOE-Joint Genome Institute, Walnut Creek, California, United States of America
- Computational Biology Group, Celgene Corp, San Francisco, California, United States of America
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17
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Ciuraszkiewicz J, Śmiga M, Mackiewicz P, Gmiterek A, Bielecki M, Olczak M, Olczak T. Fur homolog regulatesPorphyromonas gingivalisvirulence under low-iron/heme conditions through a complex regulatory network. Mol Oral Microbiol 2014; 29:333-53. [DOI: 10.1111/omi.12077] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/30/2014] [Indexed: 12/22/2022]
Affiliation(s)
- J. Ciuraszkiewicz
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - M. Śmiga
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - P. Mackiewicz
- Department of Genomics; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - A. Gmiterek
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - M. Bielecki
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - M. Olczak
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
| | - T. Olczak
- Laboratory of Biochemistry; Faculty of Biotechnology; University of Wroclaw; Wroclaw Poland
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18
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Transcriptome dynamics-based operon prediction in prokaryotes. BMC Bioinformatics 2014; 15:145. [PMID: 24884724 PMCID: PMC4235196 DOI: 10.1186/1471-2105-15-145] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Accepted: 04/22/2014] [Indexed: 11/21/2022] Open
Abstract
Background Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. Results In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. Conclusion We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.
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19
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Ohara-Nemoto Y, Rouf SMA, Naito M, Yanase A, Tetsuo F, Ono T, Kobayakawa T, Shimoyama Y, Kimura S, Nakayama K, Saiki K, Konishi K, Nemoto TK. Identification and characterization of prokaryotic dipeptidyl-peptidase 5 from Porphyromonas gingivalis. J Biol Chem 2014; 289:5436-48. [PMID: 24398682 PMCID: PMC3937620 DOI: 10.1074/jbc.m113.527333] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2013] [Revised: 12/22/2013] [Indexed: 11/06/2022] Open
Abstract
Porphyromonas gingivalis, a Gram-negative asaccharolytic anaerobe, is a major causative organism of chronic periodontitis. Because the bacterium utilizes amino acids as energy and carbon sources and incorporates them mainly as dipeptides, a wide variety of dipeptide production processes mediated by dipeptidyl-peptidases (DPPs) should be beneficial for the organism. In the present study, we identified the fourth P. gingivalis enzyme, DPP5. In a dpp4-7-11-disrupted P. gingivalis ATCC 33277, a DPP7-like activity still remained. PGN_0756 possessed an activity indistinguishable from that of the mutant, and was identified as a bacterial orthologue of fungal DPP5, because of its substrate specificity and 28.5% amino acid sequence identity with an Aspergillus fumigatus entity. P. gingivalis DPP5 was composed of 684 amino acids with a molecular mass of 77,453, and existed as a dimer while migrating at 66 kDa on SDS-PAGE. It preferred Ala and hydrophobic residues, had no activity toward Pro at the P1 position, and no preference for hydrophobic P2 residues, showed an optimal pH of 6.7 in the presence of NaCl, demonstrated Km and kcat/Km values for Lys-Ala-MCA of 688 μM and 11.02 μM(-1) s(-1), respectively, and was localized in the periplasm. DPP5 elaborately complemented DPP7 in liberation of dipeptides with hydrophobic P1 residues. Examinations of DPP- and gingipain gene-disrupted mutants indicated that DPP4, DPP5, DPP7, and DPP11 together with Arg- and Lys-gingipains cooperatively liberate most dipeptides from nutrient oligopeptides. This is the first study to report that DPP5 is expressed not only in eukaryotes, but also widely distributed in bacteria and archaea.
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Affiliation(s)
- Yuko Ohara-Nemoto
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, and
| | - Shakh M. A. Rouf
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, and
| | - Mariko Naito
- the Division of Microbiology and Oral Infection, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588
| | - Amie Yanase
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, and
| | - Fumi Tetsuo
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, and
| | - Toshio Ono
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, and
| | - Takeshi Kobayakawa
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, and
| | - Yu Shimoyama
- the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, and
| | - Shigenobu Kimura
- the Division of Molecular Microbiology, Iwate Medical University, Iwate 028-3694, and
| | - Koji Nakayama
- the Division of Microbiology and Oral Infection, Department of Molecular Microbiology and Immunology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki 852-8588
| | - Keitarou Saiki
- the Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo 102-8159, Japan
| | - Kiyoshi Konishi
- the Department of Microbiology, Nippon Dental University School of Life Dentistry at Tokyo, Tokyo 102-8159, Japan
| | - Takayuki K. Nemoto
- From the Department of Oral Molecular Biology, Course of Medical and Dental Sciences, and
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20
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Pfeifer-Sancar K, Mentz A, Rückert C, Kalinowski J. Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique. BMC Genomics 2013; 14:888. [PMID: 24341750 PMCID: PMC3890552 DOI: 10.1186/1471-2164-14-888] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 12/03/2013] [Indexed: 01/16/2023] Open
Abstract
Background The use of RNAseq to resolve the transcriptional organization of an organism was established in recent years and also showed the complexity and dynamics of bacterial transcriptomes. The aim of this study was to comprehensively investigate the transcriptome of the industrially relevant amino acid producer and model organism Corynebacterium glutamicum by RNAseq in order to improve its genome annotation and to describe important features for transcription and translation. Results RNAseq data sets were obtained by two methods, one that focuses on 5′-ends of primary transcripts and another that provides the overall transcriptome with an improved resolution of 3′-ends of transcripts. Subsequent data analysis led to the identification of more than 2,000 transcription start sites (TSSs), the definition of 5′-UTRs (untranslated regions) for annotated protein-coding genes, operon structures and many novel transcripts located between or in antisense orientation to protein-coding regions. Interestingly, a high number of mRNAs (33%) is transcribed as leaderless transcripts. From the data, consensus promoter and ribosome binding site (RBS) motifs were identified and it was shown that the majority of genes in C. glutamicum are transcribed monocistronically, but operons containing up to 16 genes are also present. Conclusions The comprehensive transcriptome map of C. glutamicum established in this study represents a major step forward towards a complete definition of genetic elements (e.g. promoter regions, gene starts and stops, 5′-UTRs, RBSs, transcript starts and ends) and provides the ideal basis for further analyses on transcriptional regulatory networks in this organism. The methods developed are easily applicable for other bacteria and have the potential to be used also for quantification of transcriptomes, replacing microarrays in the near future.
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Affiliation(s)
| | | | | | - Jörn Kalinowski
- Microbial Genomics and Biotechnology, Center for Biotechnology, Bielefeld University, Universitätsstraße 27, 33615, Bielefeld, Germany.
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21
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Tribble GD, Kerr JE, Wang BY. Genetic diversity in the oral pathogen Porphyromonas gingivalis: molecular mechanisms and biological consequences. Future Microbiol 2013; 8:607-20. [PMID: 23642116 DOI: 10.2217/fmb.13.30] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Porphyromonas gingivalis is a Gram-negative anaerobic bacterium that colonizes the human oral cavity. It is implicated in the development of periodontitis, a chronic periodontal disease affecting half of the adult population in the USA. To survive in the oral cavity, these bacteria must colonize dental plaque biofilms in competition with other bacterial species. Long-term survival requires P. gingivalis to evade host immune responses, while simultaneously adapting to the changing physiology of the host and to alterations in the plaque biofilm. In reflection of this highly variable niche, P. gingivalis is a genetically diverse species and in this review the authors summarize genetic diversity as it relates to pathogenicity in P. gingivalis. Recent studies revealing a variety of mechanisms by which adaptive changes in genetic content can occur are also reviewed. Understanding the genetic plasticity of P. gingivalis will provide a better framework for understanding the host-microbe interactions associated with periodontal disease.
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Affiliation(s)
- Gena D Tribble
- Department of Periodontics, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX 77054, USA.
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22
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Li S, Dong X, Su Z. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics 2013; 14:520. [PMID: 23899370 PMCID: PMC3734233 DOI: 10.1186/1471-2164-14-520] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Accepted: 07/27/2013] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads. RESULTS To fill these gaps, we have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM (http://bioinfolab.uncc.edu/TruHmm_package/) for assembling full length transcripts. We found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases. CONCLUSIONS As has been demonstrated in many other prokaryotes, E. coli K12 also has a highly complex and dynamic transcriptomes under different culture conditions and growth phases. Such complex and dynamic transcriptomes might play important roles in the physiology of the bacterium. TruHMM is a highly accurate and robust algorithm for assembling full-length transcripts in prokaryotes using directional RNA-seq short reads.
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Affiliation(s)
- Shan Li
- Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA
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Abstract
UNLABELLED In contrast to the rapidly increasing knowledge on genome content and diversity of bacterial viruses, insights in intracellular phage development and its impact on bacterial physiology are very limited. We present a multifaceted study combining quantitative PCR (qPCR), microarray, RNA-seq, and two-dimensional gel electrophoresis (2D-GE), to obtain a global overview of alterations in DNA, RNA, and protein content in Pseudomonas aeruginosa PAO1 cells upon infection with the strictly lytic phage LUZ19. Viral genome replication occurs in the second half of the phage infection cycle and coincides with degradation of the bacterial genome. At the RNA level, there is a sharp increase in viral mRNAs from 23 to 60% of all transcripts after 5 and 15 min of infection, respectively. Although microarray analysis revealed a complex pattern of bacterial up- and downregulated genes, the accumulation of viral mRNA clearly coincides with a general breakdown of abundant bacterial transcripts. Two-dimensional gel electrophoretic analyses shows no bacterial protein degradation during phage infection, and seven stress-related bacterial proteins appear. Moreover, the two most abundantly expressed early and late-early phage proteins, LUZ19 gene product 13 (Gp13) and Gp21, completely inhibit P. aeruginosa growth when expressed from a single-copy plasmid. Since Gp13 encodes a predicted GNAT acetyltransferase, this observation points at a crucial but yet unexplored level of posttranslational viral control during infection. IMPORTANCE Massive genome sequencing has led to important insights into the enormous genetic diversity of bacterial viruses (bacteriophages). However, for nearly all known phages, information on the impact of the phage infection on host physiology and intracellular phage development is scarce. This aspect of phage research should be revitalized, as phages evolved genes which can shut down or redirect bacterial processes in a very efficient way, which can be exploited towards antibacterial design. In this context, we initiated a study of the human opportunistic pathogen Pseudomonas aeruginosa under attack by one its most common predators, the Phikmvlikevirus. By analyzing various stages of infection at different levels, this study uncovers new features of phage infection, representing a cornerstone for future studies on members of this phage genus.
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Hirano T, Beck DAC, Wright CJ, Demuth DR, Hackett M, Lamont RJ. Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis. Mol Oral Microbiol 2012. [PMID: 23194602 DOI: 10.1111/omi.12007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The periodontal pathogen Porphyromonas gingivalis experiences a number of environmental conditions in the oral cavity, and must monitor and respond to a variety of environmental cues. However, the organism possesses only five full two-component systems, one of which is the hybrid system GppX. To investigate the regulon controlled by GppX we performed RNA-Seq on a ΔGppX mutant. Fifty-three genes were upregulated and 37 genes were downregulated in the ΔGppX mutant. Pathway analyses revealed no systemic function for GppX under nutrient-replete conditions; however, over 40% of the differentially abundant genes were annotated as encoding hypothetical proteins indicating a novel role for GppX. Abundance of small RNA was, in general, not affected by the absence of GppX. To further define the role of GppX with respect to regulation of a hypothetical protein observed with the greatest significant relative abundance change relative to a wild-type control, PGN_0151, we constructed a series of strains in which the ΔgppX mutation was complemented with a GppX protein containing specific domain and phosphotransfer mutations. The transmembrane domains, the DNA-binding domain and the phosphotransfer residues were all required for regulation of PGN_0151. In addition, binding of GppX to the PGN_0151 promoter regions was confirmed by an electrophoretic mobility shift assay. Both the ΔGppX mutant and a ΔPGN_0151 mutant were deficient in monospecies biofilm formation, suggesting a role for the GppX-PGN_0151 regulon in colonization and survival of the organism.
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Affiliation(s)
- T Hirano
- Center for Oral Health and Systemic Disease, School of Dentistry, University of Louisville, Louisville, KY, USA
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Klein BA, Tenorio EL, Lazinski DW, Camilli A, Duncan MJ, Hu LT. Identification of essential genes of the periodontal pathogen Porphyromonas gingivalis. BMC Genomics 2012; 13:578. [PMID: 23114059 PMCID: PMC3547785 DOI: 10.1186/1471-2164-13-578] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 10/24/2012] [Indexed: 01/09/2023] Open
Abstract
Background Porphyromonas gingivalis is a Gram-negative anaerobic bacterium associated with periodontal disease onset and progression. Genetic tools for the manipulation of bacterial genomes allow for in-depth mechanistic studies of metabolism, physiology, interspecies and host-pathogen interactions. Analysis of the essential genes, protein-coding sequences necessary for survival of P. gingivalis by transposon mutagenesis has not previously been attempted due to the limitations of available transposon systems for the organism. We adapted a Mariner transposon system for mutagenesis of P. gingivalis and created an insertion mutant library. By analyzing the location of insertions using massively-parallel sequencing technology we used this mutant library to define genes essential for P. gingivalis survival under in vitro conditions. Results In mutagenesis experiments we identified 463 genes in P. gingivalis strain ATCC 33277 that are putatively essential for viability in vitro. Comparing the 463 P. gingivalis essential genes with previous essential gene studies, 364 of the 463 are homologues to essential genes in other species; 339 are shared with more than one other species. Twenty-five genes are known to be essential in P. gingivalis and B. thetaiotaomicron only. Significant enrichment of essential genes within Cluster of Orthologous Groups ‘D’ (cell division), ‘I’ (lipid transport and metabolism) and ‘J’ (translation/ribosome) were identified. Previously, the P. gingivalis core genome was shown to encode 1,476 proteins out of a possible 1,909; 434 of 463 essential genes are contained within the core genome. Thus, for the species P. gingivalis twenty-two, seventy-seven and twenty-three percent of the genome respectively are devoted to essential, core and accessory functions. Conclusions A Mariner transposon system can be adapted to create mutant libraries in P. gingivalis amenable to analysis by next-generation sequencing technologies. In silico analysis of genes essential for in vitro growth demonstrates that although the majority are homologous across bacterial species as a whole, species and strain-specific subsets are apparent. Understanding the putative essential genes of P. gingivalis will provide insights into metabolic pathways and niche adaptations as well as clinical therapeutic strategies.
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Affiliation(s)
- Brian A Klein
- Department of Molecular Biology and Microbiology, Tufts University Sackler School of Biomedical Sciences, Boston, MA 02111, USA
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Lasa I, Toledo-Arana A, Gingeras TR. An effort to make sense of antisense transcription in bacteria. RNA Biol 2012; 9:1039-44. [PMID: 22858676 PMCID: PMC3551857 DOI: 10.4161/rna.21167] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Analysis of bacterial transcriptomes have shown the existence of a genome-wide process of overlapping transcription due to the presence of antisense RNAs, as well as mRNAs that overlapped in their entire length or in some portion of the 5′- and 3′-UTR regions. The biological advantages of such overlapping transcription are unclear but may play important regulatory roles at the level of transcription, RNA stability and translation. In a recent report, the human pathogen Staphylococcus aureus is observed to generate genome-wide overlapping transcription in the same bacterial cells leading to a collection of short RNA fragments generated by the endoribonuclease III, RNase III. This processing appears most prominently in Gram-positive bacteria. The implications of both the use of pervasive overlapping transcription and the processing of these double stranded templates into short RNAs are explored and the consequences discussed.
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Affiliation(s)
- Iñigo Lasa
- Laboratory of Microbial Biofilms, Idab-CSIC-Universidad Pública de Navarra-Gobierno de Navarra, Pamplona, Spain.
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Hirano T, Beck DAC, Demuth DR, Hackett M, Lamont RJ. Deep sequencing of Porphyromonas gingivalis and comparative transcriptome analysis of a LuxS mutant. Front Cell Infect Microbiol 2012; 2:79. [PMID: 22919670 PMCID: PMC3422912 DOI: 10.3389/fcimb.2012.00079] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Accepted: 05/21/2012] [Indexed: 01/10/2023] Open
Abstract
Porphyromonas gingivalis is a major etiological agent in chronic and aggressive forms of periodontal disease. The organism is an asaccharolytic anaerobe and is a constituent of mixed species biofilms in a variety of microenvironments in the oral cavity. P. gingivalis expresses a range of virulence factors over which it exerts tight control. High-throughput sequencing technologies provide the opportunity to relate functional genomics to basic biology. In this study we report qualitative and quantitative RNA-Seq analysis of the transcriptome of P. gingivalis. We have also applied RNA-Seq to the transcriptome of a ΔluxS mutant of P. gingivalis deficient in AI-2-mediated bacterial communication. The transcriptome analysis confirmed the expression of all predicted ORFs for strain ATCC 33277, including 854 hypothetical proteins, and allowed the identification of hitherto unknown transcriptional units. Twelve non-coding RNAs were identified, including 11 small RNAs and one cobalamin riboswitch. Fifty-seven genes were differentially regulated in the LuxS mutant. Addition of exogenous synthetic 4,5-dihydroxy-2,3-pentanedione (DPD, AI-2 precursor) to the ΔluxS mutant culture complemented expression of a subset of genes, indicating that LuxS is involved in both AI-2 signaling and non-signaling dependent systems in P. gingivalis. This work provides an important dataset for future study of P. gingivalis pathophysiology and further defines the LuxS regulon in this oral pathogen.
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Affiliation(s)
- Takanori Hirano
- Center for Oral Health and Systemic Disease, School of Dentistry, University of Louisville Louisville, KY, USA
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