1
|
Insertional Inactivation and Gene Complementation of Prevotella intermedia Type IX Secretion System Reveals Its Indispensable Roles in Black Pigmentation, Hemagglutination, Protease Activity of Interpain A, and Biofilm Formation. J Bacteriol 2022; 204:e0020322. [PMID: 35862729 PMCID: PMC9380532 DOI: 10.1128/jb.00203-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Prevotella intermedia, a Gram-negative oral anaerobic bacterium, is frequently isolated from the periodontal pockets of patients with chronic periodontitis. In recent years, the involvement of the bacterium in respiratory tract infections as well as in oral infections has been revealed. P. intermedia possesses several potent virulence factors, such as cysteine proteinase interpain A encoded by the inpA gene. The genome of P. intermedia carries genes of the type IX secretion system (T9SS), which enables the translocation of virulence factors across the outer membrane in several pathogens belonging to the phylum Bacteroidetes; however, it is still unclear whether the T9SS is functional in this microorganism. Recently, we performed targeted mutagenesis in the strain OMA14 of P. intermedia. Here, we successfully obtained mutants deficient in inpA and the T9SS component genes porK and porT. None of the mutants exhibited protease activity of interpain A. The porK and porT mutants, but not the inpA mutant, showed defects in colony pigmentation, hemagglutination, and biofilm formation. We also obtained a complemented strain for the porK gene that recovered all the above abilities. These results indicate that T9SS functions in P. intermedia and that interpain A is one of the T9SS cargo proteins. IMPORTANCE The virulence factors of periodontal pathogens such as Prevotella intermedia have not been elucidated. Using our established procedure, we succeeded in generating type IX secretion system mutants and gene complementation strains that might transfer virulence factors to the bacterial surface. The generated strains clearly indicate that T9SS in P. intermedia is essential for colonial pigmentation, hemagglutination, and biofilm formation. These results indicated that interpain A is a T9SS cargo protein.
Collapse
|
2
|
Li J, Gálvez EJC, Amend L, Almási É, Iljazovic A, Lesker TR, Bielecka AA, Schorr EM, Strowig T. A versatile genetic toolbox for Prevotella copri enables studying polysaccharide utilization systems. EMBO J 2021; 40:e108287. [PMID: 34676563 PMCID: PMC8634118 DOI: 10.15252/embj.2021108287] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 09/08/2021] [Accepted: 09/24/2021] [Indexed: 12/30/2022] Open
Abstract
Prevotella copri is a prevalent inhabitant of the human gut and has been associated with plant‐rich diet consumption and diverse health states. The underlying genetic basis of these associations remains enigmatic due to the lack of genetic tools. Here, we developed a novel versatile genetic toolbox for rapid and efficient genetic insertion and allelic exchange applicable to P. copri strains from multiple clades. Enabled by the genetic platform, we systematically investigated the specificity of polysaccharide utilization loci (PULs) and identified four highly conserved PULs for utilizing arabinan, pectic galactan, arabinoxylan, and inulin, respectively. Further genetic and functional analysis of arabinan utilization systems illustrate that P. copri has evolved two distinct types of arabinan‐processing PULs (PULAra) and that the type‐II PULAra is significantly enriched in individuals consuming a vegan diet compared to other diets. In summary, this genetic toolbox will enable functional genetic studies for P. copri in future.
Collapse
Affiliation(s)
- Jing Li
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eric J C Gálvez
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Hannover Medical School, Hannover, Germany
| | - Lena Amend
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Éva Almási
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Aida Iljazovic
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Agata A Bielecka
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Eva-Magdalena Schorr
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany.,Hannover Medical School, Hannover, Germany.,Centre for Individualized Infection Medicine, Hannover, Germany
| |
Collapse
|
3
|
Non-oral Prevotella stepping into the spotlight. Anaerobe 2021; 68:102321. [PMID: 33482304 DOI: 10.1016/j.anaerobe.2021.102321] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 01/12/2021] [Accepted: 01/14/2021] [Indexed: 02/07/2023]
Abstract
Species now affiliated to genus Prevotella have been known for decades as an integral part of human oral cavity microbiota. They were frequently isolated from patients with periodontitis or from dental root canals but also from healthy subjects. With the exception of Prevotella intermedia, they were considered opportunistic pathogens, as they were isolated also from various bacterial abscesses from the head, neck, breast, skin and various other body sites. Consequently, Prevotella were not in the focus of research activities. On the other hand, the four species found in the rumen never caused any disease and seemed early on to be numerous and important part of the rumen ecosystem indicating this genus harbored bacteria with enormously diverse habitats and lifestyles. The purpose of this review is to illustrate the main research themes performed in Prevotella on a path from less noted oral bacteria and from hard to cultivate and study rumen organisms to important mutualistic bacteria in guts of various mammals warranting major research efforts.
Collapse
|
4
|
Restriction-modification mediated barriers to exogenous DNA uptake and incorporation employed by Prevotella intermedia. PLoS One 2017; 12:e0185234. [PMID: 28934361 PMCID: PMC5608340 DOI: 10.1371/journal.pone.0185234] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 09/09/2017] [Indexed: 12/18/2022] Open
Abstract
Prevotella intermedia, a major periodontal pathogen, is increasingly implicated in human respiratory tract and cystic fibrosis lung infections. Nevertheless, the specific mechanisms employed by this pathogen remain only partially characterized and poorly understood, largely due to its total lack of genetic accessibility. Here, using Single Molecule, Real-Time (SMRT) genome and methylome sequencing, bisulfite sequencing, in addition to cloning and restriction analysis, we define the specific genetic barriers to exogenous DNA present in two of the most widespread laboratory strains, P. intermedia ATCC 25611 and P. intermedia Strain 17. We identified and characterized multiple restriction-modification (R-M) systems, some of which are considerably divergent between the two strains. We propose that these R-M systems are the root cause of the P. intermedia transformation barrier. Additionally, we note the presence of conserved Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) systems in both strains, which could provide a further barrier to exogenous DNA uptake and incorporation. This work will provide a valuable resource during the development of a genetic system for P. intermedia, which will be required for fundamental investigation of this organism’s physiology, metabolism, and pathogenesis in human disease.
Collapse
|
5
|
Olsen I, Tribble GD, Fiehn NE, Wang BY. Bacterial sex in dental plaque. J Oral Microbiol 2013; 5:20736. [PMID: 23741559 PMCID: PMC3672468 DOI: 10.3402/jom.v5i0.20736] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/07/2013] [Accepted: 05/10/2013] [Indexed: 11/14/2022] Open
Abstract
Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.
Collapse
Affiliation(s)
- Ingar Olsen
- Faculty of Dentistry, Department of Oral Biology, University of Oslo, Oslo, Norway
| | - Gena D. Tribble
- Department of Periodontics, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Nils-Erik Fiehn
- Faculty of Health Sciences, Department of International Health, Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Bing-Yan Wang
- Department of Periodontics, School of Dentistry, University of Texas Health Science Center at Houston, Houston, TX, USA
| |
Collapse
|
6
|
Chung D, Farkas J, Huddleston JR, Olivar E, Westpheling J. Methylation by a unique α-class N4-cytosine methyltransferase is required for DNA transformation of Caldicellulosiruptor bescii DSM6725. PLoS One 2012; 7:e43844. [PMID: 22928042 PMCID: PMC3425538 DOI: 10.1371/journal.pone.0043844] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/30/2012] [Indexed: 12/14/2022] Open
Abstract
Thermophilic microorganisms capable of using complex substrates offer special advantages for the conversion of lignocellulosic biomass to biofuels and bioproducts. Members of the gram-positive bacterial genus Caldicellulosiruptor are anaerobic thermophiles with optimum growth temperatures between 65°C and 78°C and are the most thermophilic cellulolytic organisms known. In fact, they efficiently use biomass non-pretreated as their sole carbon source and in successive rounds of application digest 70% of total switchgrass substrate. The ability to genetically manipulate these organisms is a prerequisite to engineering them for use in conversion of these complex substrates to products of interest as well as identifying gene products critical for their ability to utilize non-pretreated biomass. Here, we report the first example of DNA transformation of a member of this genus, C. bescii. We show that restriction of DNA is a major barrier to transformation (in this case apparently absolute) and that methylation with an endogenous unique α-class N4-Cytosine methyltransferase is required for transformation of DNA isolated from E. coli. The use of modified DNA leads to the development of an efficient and reproducible method for DNA transformation and the combined frequencies of transformation and recombination allow marker replacement between non-replicating plasmids and chromosomal genes providing the basis for rapid and efficient methods of genetic manipulation.
Collapse
Affiliation(s)
- Daehwan Chung
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Department of Energy, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Joel Farkas
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Department of Energy, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Jennifer R. Huddleston
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Department of Energy, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Estefania Olivar
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Department of Energy, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
| | - Janet Westpheling
- Department of Genetics, University of Georgia, Athens, Georgia, United States of America
- The BioEnergy Science Center, Department of Energy, Oak Ridge National Laboratory, Oak Ridge, Tennessee, United States of America
- * E-mail:
| |
Collapse
|
7
|
Chung DH, Huddleston JR, Farkas J, Westpheling J. Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes. J Ind Microbiol Biotechnol 2011; 38:1867-77. [PMID: 21604181 DOI: 10.1007/s10295-011-0976-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 04/07/2011] [Indexed: 11/27/2022]
Abstract
Potent HaeIII-like DNA restriction activity was detected in cell-free extracts of Caldicellulosiruptor bescii DSM 6725 using plasmid DNA isolated from Escherichia coli as substrate. Incubation of the plasmid DNA in vitro with HaeIII methyltransferase protected it from cleavage by HaeIII nuclease as well as cell-free extracts of C. bescii. The gene encoding the putative restriction enzyme was cloned and expressed in E. coli with a His-tag at the C-terminus. The purified protein was 38 kDa as predicted by the 981-bp nucleic acid sequence, was optimally active at temperatures between 75°C and 85°C, and was stable for more than 1 week when stored at 35°C. The cleavage sequence was determined to be 5'-GG/CC-3', indicating that CbeI is an isoschizomer of HaeIII. A search of the C. bescii genome sequence revealed the presence of both a HaeIII-like restriction endonuclease (Athe 2438) and DNA methyltransferase (Athe 2437). Preliminary analysis of other Caldicellulosiruptor species suggested that this restriction/modification activity is widespread in this genus. A phylogenetic analysis based on sequence alignment and conserved motif searches identified features of CbeI distinct from other members of this group and classified CbeI as a member of a novel subfamily of HaeIII-like enzymes.
Collapse
Affiliation(s)
- Dae-Hwan Chung
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | | | | | | |
Collapse
|
8
|
Tribble GD, Garza JJ, Yeung VL, Rigney TW, Dao DHV, Rodrigues PH, Walker CB, Smith CJ. Genetic analysis of mobile tetQ elements in oral Prevotella species. Anaerobe 2010; 16:604-9. [PMID: 20826220 DOI: 10.1016/j.anaerobe.2010.08.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Revised: 08/16/2010] [Accepted: 08/27/2010] [Indexed: 10/19/2022]
Abstract
Prevotella species are members of the bacterial oral flora and are opportunistic pathogens in polymicrobial infections of soft tissues. Antibiotic resistance to tetracyclines is common in these bacteria, and the gene encoding this resistance has been previously identified as tetQ. The tetQ gene is also found on conjugative transposons in the intestinal Bacteroides species; whether these related bacteria have transmitted tetQ to Prevotella is unknown. In this study, we describe our genetic analysis of mobile tetQ elements in oral Prevotella species. Our results indicate that the mobile elements encoding tetQ in oral species are distinct from those found in the Bacteroides. The intestinal bacteria may act as a reservoir for the tetQ gene, but Prevotella has incorporated this gene into an IS21-family transposon. This transposon is present in Prevotella species from more than one geographical location, implying that the mechanism of tetQ spread between oral Prevotella species is highly conserved.
Collapse
Affiliation(s)
- Gena D Tribble
- Department of Periodontics, University of Texas Health Science Center at Houston, 77030, USA.
| | | | | | | | | | | | | | | |
Collapse
|
9
|
Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed. Appl Microbiol Biotechnol 2009; 85:1301-13. [DOI: 10.1007/s00253-009-2349-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 11/06/2009] [Accepted: 11/07/2009] [Indexed: 10/20/2022]
|
10
|
Enhanced transformation efficiency of recalcitrant Bacillus cereus and Bacillus weihenstephanensis isolates upon in vitro methylation of plasmid DNA. Appl Environ Microbiol 2008; 74:7817-20. [PMID: 18952874 DOI: 10.1128/aem.01932-08] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Digestion patterns of chromosomal DNAs of Bacillus cereus and Bacillus weihenstephanensis strains suggest that Sau3AI-type restriction modification systems are widely present among the isolates tested. In vitro methylation of plasmid DNA was used to enhance poor plasmid transfer upon electroporation to recalcitrant strains that carry Sau3AI restriction barriers.
Collapse
|
11
|
Accetto T, Avgustin G. Expression of nuclease gene nucA, a member of an operon putatively involved in uracil removal from DNA and its subsequent reuse in Prevotella bryantii. Arch Microbiol 2008; 190:111-7. [PMID: 18427783 DOI: 10.1007/s00203-008-0372-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2008] [Revised: 04/04/2008] [Accepted: 04/07/2008] [Indexed: 10/22/2022]
Abstract
The genomic region of Prevotella bryantii TC1-1 that conferred an increased nucleolytic activity on Escherichia coli was characterized. It contains two divergent transcriptional units separated by an AT-rich promoter region. One unit is comprised of three genes involved in nucleotide metabolism. nucA, the first gene of this unit, whose product belongs to exonuclease/endonuclease/phosphatase Pfam family, was thought to be required for the increased nucleolytic activity and various expression strategies were employed to confirm its role. The nucA expression was only successful in cell free system where DNase and RNase activity was observed. Two genes downstream of nucA code for a putative uracil DNA glycosylase and uridine kinase which could be involved in the removal of misincorporated uracil from DNA and its reuse. Given that apurinic/apyrimidinic nuclease activity is required after uracil removal from DNA, it was somewhat surprising to find out that nucA, whose product belongs to protein family consisting mostly of apurinic/apyrimidinic nucleases, has no apurinic/apyrimidinic activity.
Collapse
Affiliation(s)
- Tomaz Accetto
- Zootechnical Department, Biotechnical Faculty, University of Ljubljana, Groblje 3, 1230, Domzale, Slovenia
| | | |
Collapse
|
12
|
Accetto T, Avguštin G. Studies on Prevotella nuclease using a system for the controlled expression of cloned genes in P. bryantii TC1-1. MICROBIOLOGY-SGM 2007; 153:2281-2288. [PMID: 17600072 DOI: 10.1099/mic.0.2007/005850-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Available tools for genetic analysis in the anaerobic rumen bacterium Prevotella bryantii are limited to only two known systems for gene delivery, and no genes, with the exception of plasmid maintenance and selection genes, have been successfully expressed from plasmids in any species of the genus Prevotella until now. It is shown here that nucB, a newly cloned nuclease gene from P. bryantii, can be controllably expressed from shuttle vector pRH3 in P. bryantii strain TC1-1, depending on the tetracycline concentration in the growth medium. nucB expression is also growth-medium dependent and this regulation presumably takes place at the translational level. His-tagged NucB was purified from P. bryantii TC1-1 culture supernatant and was shown to degrade DNA as well as RNA; it is most likely a minor 36 kDa P. bryantii non-specific nuclease.
Collapse
Affiliation(s)
- Tomaž Accetto
- University of Ljubljana, Biotechnical Faculty, Zootechnical Department, Chair for Microbiology and Microbial Biotechnology, 1230 Domžale, Slovenia
| | - Gorazd Avguštin
- University of Ljubljana, Biotechnical Faculty, Zootechnical Department, Chair for Microbiology and Microbial Biotechnology, 1230 Domžale, Slovenia
| |
Collapse
|