1
|
Raynaud S, Le Pabic H, Felden B. Selective recovery of RNAs from bacterial pathogens after their internalization by human host cells. Methods 2018; 143:4-11. [PMID: 29709561 DOI: 10.1016/j.ymeth.2018.04.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 04/25/2018] [Accepted: 04/26/2018] [Indexed: 12/28/2022] Open
Abstract
Selective RNA extractions are required when studying bacterial gene expression within complex mixtures of pathogens and human cells, during adhesion, internalization and survival within the host. New technologies should be developed and implemented to enrich the amount of bacterial RNAs since the majority of RNAs are from the eukaryotic host cells, requiring high read depth coverage to capture the bacterial transcriptomes in dual-RNAseq studies. This will improve our understanding about bacterial adaptation to the host cell defenses, and about how they will adapt to an intracellular life. Here we present an RNA extraction protocol to selectively enrich the lowest bacterial RNA fraction from a mixture of human and bacterial cells, using zirconium beads, with minimal RNA degradation. Zirconium beads have higher capacity to extract bacterial RNAs than glass beads after pathogen internalization. We optimized the beads size and composition for an optimal bacterial lysis and RNA extraction. The protocol was validated on two human cell lines, differentiated macrophages and osteoblasts, with either Gram-positive (Staphylococcus aureus) or -negative (Salmonella typhimurium) bacteria. Relative to other published protocols, yield of total RNA recovery was significantly improved, while host cell infection was performed with a lower bacterial inoculum. Within the host, bacterial RNA recovery yields were about six-fold lower than an RNA extraction from pure bacteria, but the quality of the RNA recovered was essentially similar. Bacterial RNA recovery was more efficient for S. aureus than for S. typhimurium, probably due to their higher protection by the Gram-positive cell walls during the early step of eukaryotic cell lysis. These purified bacterial RNAs allow subsequent genes expression studies in the course of host cell-bacteria interactions.
Collapse
Affiliation(s)
- Simon Raynaud
- Univ Rennes, Inserm, BRM [Bacterial Regulatory RNAs and Medicine] UMR_S 1230, F-35000 Rennes, France
| | - Hélène Le Pabic
- Univ Rennes, Inserm, BRM [Bacterial Regulatory RNAs and Medicine] UMR_S 1230, F-35000 Rennes, France
| | - Brice Felden
- Univ Rennes, Inserm, BRM [Bacterial Regulatory RNAs and Medicine] UMR_S 1230, F-35000 Rennes, France.
| |
Collapse
|
2
|
Tanner SA, Chassard C, Rigozzi E, Lacroix C, Stevens MJA. Bifidobacterium thermophilum RBL67 impacts on growth and virulence gene expression of Salmonella enterica subsp. enterica serovar Typhimurium. BMC Microbiol 2016; 16:46. [PMID: 26988691 PMCID: PMC4797131 DOI: 10.1186/s12866-016-0659-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 03/02/2016] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Bifidobacterium thermophilum RBL67 (RBL67), a human fecal isolate and health promoting candidate shows antagonistic and protective effects against Salmonella and Listeria spec. in vitro. However, the underlying mechanisms fostering these effects remain unknown. In this study, the interactions of RBL67 and Salmonella enterica subsp. enterica serovar Typhimurium N-15 (N-15) were explored by global transcriptional analysis. RESULTS Growth experiments were performed in a complex nutritive medium with controlled pH of 6.0 and suitable for balanced growth of both RBL67 and N-15. RBL67 growth was slightly enhanced in presence of N-15. Conversely, N-15 showed reduced growth in the presence of RBL67. Transcriptional analyses revealed higher expression of stress genes and amino acid related function in RBL67 in co-culture with N-15 when compared to mono-culture. Repression of the PhoP regulator was observed in N-15 in presence of RBL67. Further, RBL67 activated virulence genes located on the Salmonella pathogenicity islands 1 and 2. Flagellar genes, however, were repressed by RBL67. Sequential expression of flagellar, SPI 1 and fimbrial genes is essential for Salmonella infection. Our data revealed that RBL67 triggers expression of SPI 1 and fimbrial determinants prematurely, potentially leading to redundant energy expenditure. In the competitive environment of the gut such energy expenditure could lead to enhanced clearing of Salmonella. CONCLUSION Our study provides first insights into probiotic-pathogen interactions on global transcriptional level and suggests that deregulation of virulence gene expression might be an additional protective mechanism of probiotica against infections of the host.
Collapse
Affiliation(s)
- Sabine A. Tanner
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Christophe Chassard
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
- />Present Address: Institut National de la Recherche Agronomique, UR 545 URF, 15000 Aurillac, France
| | - Eugenia Rigozzi
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Christophe Lacroix
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
| | - Marc J. A. Stevens
- />Laboratory of Food Biotechnology, ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, Zurich, Switzerland
| |
Collapse
|
3
|
Pronk LM, Sanderson KE. Intervening sequences in rrl genes and fragmentation of 23S rRNA in genera of the family Enterobacteriaceae. J Bacteriol 2001; 183:5782-7. [PMID: 11544246 PMCID: PMC95475 DOI: 10.1128/jb.183.19.5782-5787.2001] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) in the rrl genes for 23S rRNA are transcribed but later removed by RNase III without religation during RNA processing, leading to fragmented rRNA. We examined about 240 strains of the family Enterobacteriaceae for presence of IVSs using PCR. No IVSs were detected in strains belonging to Escherichia, Shigella, Enterobacter, Erwinia, Ewingella, Hafnia, Kluyvera, Morganella, Pantoea, or Serratia. Previously unreported IVSs were detected in Klebsiella oxytoca, Citrobacter amalonaticus, and Providencia stuartii; previously reported IVSs are in species of Salmonella, Proteus, Providencia, and Yersinia. The sporadic distribution of IVSs indicates lateral genetic transfer of IVSs.
Collapse
Affiliation(s)
- L M Pronk
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | | |
Collapse
|
4
|
Miller WL, Pabbaraju K, Sanderson KE. Fragmentation of 23S rRNA in strains of Proteus and Providencia results from intervening sequences in the rrn (rRNA) genes. J Bacteriol 2000; 182:1109-17. [PMID: 10648538 PMCID: PMC94388 DOI: 10.1128/jb.182.4.1109-1117.2000] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Intervening sequences (IVSs) were originally identified in the rrl genes for 23S rRNA (rrl genes, for large ribosomal subunit, part of rrn operon encoding rRNA) of Salmonella enterica serovars Typhimurium LT2 and Arizonae. These sequences are transcribed but later removed during RNase III processing of the rRNA, resulting in fragmentation of the 23S species; IVSs are uncommon, but have been reported in at least 10 bacterial genera. Through PCR amplification of IVS-containing regions of the rrl genes we showed that most Proteus and Providencia strains contain IVSs similar to those of serovar Typhimurium in distribution and location in rrl genes. By extraction and Northern blotting of rRNA, we also found that these IVSs result in rRNA fragmentation. We report the first finding of two very different sizes of IVS (113 bp and 183 to 187 bp) in different rrl genes in the same strain, in helix 25 of Proteus and Providencia spp.; IVSs from helix 45 are 113 to 123 bp in size. Analysis of IVS sequence and postulated secondary structure reveals striking similarities of Proteus and Providencia IVSs to those of serovar Typhimurium, with the stems of the smaller IVSs from helix 25 being similar to those of Salmonella helix 25 IVSs and with both the stem and the central loop domain of helix 45 IVSs being similar. Thus, IVSs of related sequences are widely distributed throughout the Enterobacteriaceae, in Salmonella, Yersinia, Proteus, and Providencia spp., but we did not find them in Escherichia coli, Citrobacter, Enterobacter, Klebsiella, or Morganella spp.; the sporadic distribution of IVSs of related sequence indicates that lateral genetic transfer has occurred.
Collapse
Affiliation(s)
- W L Miller
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada T2N 1N4
| | | | | |
Collapse
|
5
|
Mattatall NR, Daines DA, Liu SL, Sanderson KE. Salmonella typhi contains identical intervening sequences in all seven rrl genes. J Bacteriol 1996; 178:5323-6. [PMID: 8752356 PMCID: PMC178335 DOI: 10.1128/jb.178.17.5323-5326.1996] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Salmonella typhi Ty2 rrl genes contain intervening sequences (IVSs) in helix-25 but not in helix-45 on the basis of observed 23S rRNA fragmentation caused by IVS excision. We have confirmed this and shown all seven IVSs to be identical by isolating genomic DNA fragments containing each of the seven rrl genes from S. typhi Ty2 by use of pulsed-field gel electrophoresis; each rrl gene was amplified by PCR in the helix-25 and helix-45 regions and cycle sequenced. Thirty independent wild-type S. typhi strains, tested by genomic PCR and DraI restriction, also have seven rrl genes with helix-25 IVSs and no helix-45 IVSs. We propose that IVS homogeneity in S. typhi occurs because gene conversion drives IVS sequence maintenance and because adaptation to human hosts results in limited clonal diversity.
Collapse
Affiliation(s)
- N R Mattatall
- Salmonella Genetic Stock Centre, Department of Biological Sciences, University of Calgary, Alberta, Canada
| | | | | | | |
Collapse
|
6
|
Mattatall NR, Sanderson KE. Salmonella typhimurium LT2 possesses three distinct 23S rRNA intervening sequences. J Bacteriol 1996; 178:2272-8. [PMID: 8636028 PMCID: PMC177935 DOI: 10.1128/jb.178.8.2272-2278.1996] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The rrl genes for 23S rRNA of Salmonella typhimurium LT2 are known to carry intervening sequences (IVSs) at two sites, helix-25 and helix-45, which are excised by RNase III during rRNA maturation, resulting in rRNA which is fragmented but nevertheless functional. We isolated DNA fragments containing the seven rrl genes from BlnI, I-CeuI, and SpeI genomic digests following pulsed-field gel electrophoresis and used these DNA fragments as templates for PCRs utilizing primers upstream and downstream of helix-25 and helix-45. Variance in amplicon length and cycle sequencing indicated that rrlG and rrlH have IVSs in helix-25 of approximately 110 bp which are only 56% identical. rrnA, rrnB, rrnC, rrnD, rrnE, and rrnH have IVSs of approximately 90 bp in helix-45, and all have the same nucleotide sequence. Twenty-one independent wild-type strains of S. typhimurium from Salmonella Reference Collection A were analyzed for IVSs by using PCRs with genomic DNAs and by denaturing agarose electrophoresis of RNAs. Many strains resemble LT2, but some have no IVSs in helix-25 and others have IVSs in helix-45 in all seven rrl genes. However, the IVSs in individual wild-type lines are relatively stable, for several LT2 isolates separated over many years by many single-colony isolations are indistinguishable from one another, with the exception of line LB5010, which differs by one helix-25 IVS. We postulate that IVSs have entered strain LT2 by three independent lateral-transfer events and that the IVS in helix-45 was dispersed to and maintained in the same sequence in six of the seven rrl genes by the mechanism of gene conversion.
Collapse
Affiliation(s)
- N R Mattatall
- Salmonella Genetic Stock Centre, Uniersity of Calgary, Alberta, Canada.
| | | |
Collapse
|
7
|
Linton D, Clewley JP, Burnens A, Owen RJ, Stanley J. An intervening sequence (IVS) in the 16S rRNA gene of the eubacterium Helicobacter canis. Nucleic Acids Res 1994; 22:1954-8. [PMID: 7518076 PMCID: PMC308106 DOI: 10.1093/nar/22.11.1954] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
PCR amplicons enlarged by approximately 250bp were generated from the 16S rRNA (rrs) genes of certain strains of the recently described Helicobacter species, H. canis. The DNA sequence of the rrs gene of one such strain was determined, and it was shown that an intervening sequence (IVS) of 235bp followed nucleotide 199 in the rrs sequence. In four other H. canis strains, identical or similar IVSs were found, always at the same location in the rrs gene. The secondary structures of the RNA transcripts of the IVSs were predicted. They were characterised by the presence of a conserved stem-loop structure, a potential recognition site for RNA processing enzymes. Ribosomal RNA was compared from a strain of H. canis with and without the IVS-containing rrs gene. In the former 16S rRNA appeared as two fragments, whose sizes were consistent with cleavage at either side of the IVS, and which were not subsequently religated. The IVS sequence was not represented elsewhere in the H. canis genome. Its evolutionary significance is discussed.
Collapse
Affiliation(s)
- D Linton
- National Collection of Type Cultures, Virus Reference Division, Central Public Health Laboratory, London, UK
| | | | | | | | | |
Collapse
|
8
|
Sunday GJ, Gillespie MJ, Motley ST, Zambon JJ. Atypical structure of the 23S ribosomal RNA molecule in certain oral bacteria. J Dent Res 1991; 70:961-5. [PMID: 1710629 DOI: 10.1177/00220345910700061001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Ribosomal RNA (rRNA) isolated from Wolinella recta and seven related bacteria was examined by agarose gel electrophoresis. The 23S rRNA molecule could not be detected in W. recta, Wolinella curva, Bacteroides gracilis, or Bacteroides ureolyticus. In place of the 23S molecule, there were three smaller molecules of approximately 1700, 650, and 600 bases designated 23S alpha, 23S beta, and 23S delta, respectively. An intact 23S rRNA molecule could be isolated from Wolinella succinogenes, Campylobacter concisus, and Campylobacter sputorum. The cleavage sites of the W. recta 23S rRNA molecule were located by direct RNA sequence analysis and were found to be in similar locations, nucleotides 546 and 1180, as cleavage sites described in other prokaryotes. The presence or absence of the 23S rRNA molecule may be a useful marker for these micro-organisms.
Collapse
Affiliation(s)
- G J Sunday
- Department of Oral Biology, School of Dental Medicine, State University of New York, Buffalo 14214
| | | | | | | |
Collapse
|
9
|
Skurnik M, Toivanen P. Intervening sequences (IVSs) in the 23S ribosomal RNA genes of pathogenic Yersinia enterocolitica strains. The IVSs in Y. enterocolitica and Salmonella typhimurium have a common origin. Mol Microbiol 1991; 5:585-93. [PMID: 1710756 DOI: 10.1111/j.1365-2958.1991.tb00729.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The 23S ribosomal RNA (rRNA) was shown to be in two fragments in pathogenic Yersinia enterocolitica. The cleavage site in the structural gene of the 23S rRNA was occupied by an intervening sequence (IVS) of about 100 nucleotides, analogous to IVSs found in salmonellae (Burgin et al., 1990). Nucleotide sequences of IVSs of several Y. enterocolitica strains revealed that the IVSs of the highly virulent Y. enterocolitica serotypes strains, and the IVS of Salmonella typhimurium were about 90% similar. On the other hand, the IVSs of the highly and the poorly virulent Y. enterocolitica serotypes were only about 60% similar. These results give the impression that at some point during the IVS evolution, the highly virulent Y. enterocolitica and S. typhimurium both received their IVSs at about the same time from the same source, and that the poorly virulent serotypes received their IVSs earlier. We also found that strain LB5010, derived by extended mutagenization of S. typhimurium LT2, had lost the IVSs originally present in LT2, and that this loss had created a new 'hairpin loop' which substituted for the original 'hairpin loop'.
Collapse
Affiliation(s)
- M Skurnik
- Department of Medical Microbiology, Turku University, Finland
| | | |
Collapse
|
10
|
Selander RK, Beltran P, Smith NH, Barker RM, Crichton PB, Old DC, Musser JM, Whittam TS. Genetic population structure, clonal phylogeny, and pathogenicity of Salmonella paratyphi B. Infect Immun 1990; 58:1891-901. [PMID: 2341183 PMCID: PMC258740 DOI: 10.1128/iai.58.6.1891-1901.1990] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Genetic diversity and relationships among 123 strains of Salmonella paratyphi B (serotype 1,4,[5],12:b:[1,2]) were estimated from an assessment of electrophoretically demonstrable allelic variation at 24 chromosomal enzyme gene loci. Fourteen electrophoretic types, marking clones, were distinguished, the phylogeny of the clonal lineages was reconstructed, and biotype and other phenotypic characters were mapped onto this structure. Most d-tartrate-negative strains are members of an abundant, globally distributed clone (Pb 1) that is polymorphic for many biotype characters (including d-tartrate utilization), bacteriophage type, rRNA pattern, and colicin M and phage ES18 sensitivity. This clone is largely responsible for S. paratyphi B enteric fever in humans. In contrast, d-tartrate-positive strains (formerly known as S. java) occurred in all seven of the clonal lineages identified by population genetic analysis, although most d-tartrate-positive isolates belong to only two clones (Pb 3 and Pb 4), which vary in frequency geographically. Monophasic strains represent four closely related clones forming a distinctive phylogenetic lineage. The Kauffmann hypothesis of convergence in serotype among distantly related cell lineages through recombination (via phage transduction or other means) may account for the considerable genotypic diversity among clones of S. paratyphi B. Pb 4, Pb 6, and Pb 7 are more closely allied with clones of S. typhimurium and S. saintpaul than with other clones of S. paratyphi B. Sensitivity or resistance to colicin M and phage ES18 and the electrophoretic pattern of the rRNA, which were incorporated into a recently proposed scheme for the identification of types of S. paratyphi B, individually or in combination fail to mark clones or other meaningful phylogenetic subdivisions.
Collapse
Affiliation(s)
- R K Selander
- Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Hsu D, Pan MJ, Zee YC, LeFebvre RB. Unique ribosome structure of Leptospira interrogans is composed of four rRNA components. J Bacteriol 1990; 172:3478-80. [PMID: 2345155 PMCID: PMC209161 DOI: 10.1128/jb.172.6.3478-3480.1990] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
All known ribosomes of procaryotic organisms are made up of three rRNA components that are 23, 16, and 5S in size. We now report that in some Leptospira interrogans strains, the classical 23S rRNA is further processed to generate 14 and 17S rRNAs. This processing step was previously known to occur only in some eucaryotes and in a small group of procaryotes. The implications of this finding are discussed.
Collapse
Affiliation(s)
- D Hsu
- Department of Veterinary Microbiology and Immunology, School of Veterinary Medicine, University of California, Davis 95616
| | | | | | | |
Collapse
|
12
|
|