Porphyromonas gingivalis W50 Heme-excess vs Heme-limitation
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ABSTRACT:
ORGANISM(S): Porphyromonas gingivalis
PROVIDER: GSE13375 | GEO | 2008/11/19
SECONDARY ACCESSION(S): PRJNA109799
REPOSITORIES: GEO
Similar Datasets
Project description:Transcription profiling of P. gingivalis W50 grown in continuous culture under conditions of heme-excess and heme-limitation. Reference design (using Cy5 labelled genomic DNA as the reference) to compare two conditions: heme-excess vs heme-limitation. Three samples for each condition, independently grown.
2010-05-16 | E-GEOD-13375 | biostudies-arrayexpress
Project description:Porphyromonas gingivalis is an anaerobic, Gram-negative oral pathogen associated with chronic periodontitis. P. gingivalis has an obligate requirement for heme which it obtains from the host. Heme availability has been linked to disease initiation and progression. In this study we used continuous culture of the bacterium to determine the effect of heme limitation and excess on the P. gingivalis proteome. Four biological replicates of whole cell lysate (WCL) and outer membrane vesicle (OMV) samples were digested with trypsin and analysed by tandem mass spectrometry and MaxQuant label-free quantification. In total, 1211 proteins were quantified with 108 and 49 proteins significantly changing in abundance more than 1.5-fold (p<0.05) in the WCLs and OMVs respectively. The proteins most upregulated in response to heme limitation were those involved in binding and transporting heme while the four proteins most upregulated in the heme excess condition constitute a putative heme efflux system. In general, the protein abundance ratios obtained for OMVs and WCLs agreed, indicating that changes to the OM protein composition are passed on to OMVs, however 16 proteins were preferentially packaged into OMVs in one condition more than the other. In particular, moonlighting cytoplasmic proteins were preferentially associated with OMVs under heme excess.
2018-05-18 | PXD009730 | Pride
Project description:Porphyromonas gingivalis W50 Heme-excess vs Heme-limitation
| PRJNA109799 | ENA
Project description:Porphyromonas gingivalis is a major pathogen associated with the microbial biofilm-mediated disease chronic periodontitis. P. gingivalis has an obligate requirement for iron and protoporphyrin IX which it satisfies by transporting heme and iron liberated from the human host. The level of cellular iron in P. gingivalis affects the expression of a distinct iron-associated regulon of 64 genes and low iron invokes an iron sparing response. Iron homeostasis is usually mediated in Gram-negative bacteria at the transcriptional level by the Ferric Uptake Regulator (Fur). There is a single predicted P. gingivalis Fur superfamily orthologue named Har (heme associated regulator) that lacks the conserved metal binding residues found in other Fur orthologues. We show that Har binds both heme and ferrous iron resulting in a conformational change in the protein. Har was unable to complement the Escherichia coli H1780 fur mutant and there was no change in cellular metal content in a P. gingivalis Har mutant compared with the wild-type. The Har regulon of 44 genes is not predicted to play a role in iron homeostasis. Together these data indicated that Har does not regulate iron homeostasis in P. gingivalis. However, Har was required for heme-responsive biofilm development and its regulon overlapped P. gingivalis regulons previously identified after growth in heme limitation or as a homotypic biofilm. P. gingivalis is unique as an iron-dependent Gram-negative bacterium with a single heme-binding Fur superfamily orthologue, Har, that does not regulate iron homeostasis.
2015-04-01 | GSE37099 | GEO
Project description:Porphyromonas gingivalis is a major pathogen associated with the microbial biofilm-mediated disease chronic periodontitis. P. gingivalis has an obligate requirement for iron and protoporphyrin IX which it satisfies by transporting heme and iron liberated from the human host. The level of cellular iron in P. gingivalis affects the expression of a distinct iron-associated regulon of 64 genes and low iron invokes an iron sparing response. Iron homeostasis is usually mediated in Gram-negative bacteria at the transcriptional level by the Ferric Uptake Regulator (Fur). There is a single predicted P. gingivalis Fur superfamily orthologue named Har (heme associated regulator) that lacks the conserved metal binding residues found in other Fur orthologues. We show that Har binds both heme and ferrous iron resulting in a conformational change in the protein. Har was unable to complement the Escherichia coli H1780 fur mutant and there was no change in cellular metal content in a P. gingivalis Har mutant compared with the wild-type. The Har regulon of 44 genes is not predicted to play a role in iron homeostasis. Together these data indicated that Har does not regulate iron homeostasis in P. gingivalis. However, Har was required for heme-responsive biofilm development and its regulon overlapped P. gingivalis regulons previously identified after growth in heme limitation or as a homotypic biofilm. P. gingivalis is unique as an iron-dependent Gram-negative bacterium with a single heme-binding Fur superfamily orthologue, Har, that does not regulate iron homeostasis. Paired samples were compared on the same microarray using a two-colour system. A total of 6 paired microarray hybridizations were performed representing 6 biological replicates, where a balanced dye design was used, with the overall analysis including three microarrays where P. gingivalis 33277 samples were labeled with Cy3 and the paired ECR455 samples were labeled with Cy5 and three other microarrays where samples were labeled with the opposite combination of fluorophores.
2015-04-01 | E-GEOD-37099 | biostudies-arrayexpress
Project description:Porphyromonas gingivalis is one of the main etiological agents responsible for initiating and progressing periodontal diseases in humans. P. gingivalis does not synthesize heme, and it uses host hemoproteins as a source of this molecule. The main heme uptake mechanism utilized by P. gingivalis is the Hmu system composed of six proteins where HmuY (hemophore-like protein) and HmuR (TonB-dependant outer membrane heme receptor) play a crucial role in heme supply. The second heme uptake mechanism is the Hus system composed of four proteins, with HusA (hemophore-like protein) and HusB (TonB-dependant outer membrane receptor) supporting heme uptake. Heme and iron starvation influence the P. gingivalis phenotype, therefore the aim was to determine the influence of deletion of HmuY and HmuR (ΔhmuYR strain) or HusA and HusB (ΔhusAB strain) encoding genes on P. gingivalis gene expression.
2024-12-31 | GSE275439 | GEO
Project description:Porphyromonas gingivalis is an anaerobic, asaccharolytic, gram-negative bacterium that has essential requirements for both iron and protoporphyrin IX, which it preferentially obtains as heme. A combination of large-scale quantitative proteomic analysis using stable isotope labeling strategies and mass spectrometry, together with transcriptomic analysis using custom-made DNA microarrays, was used to identify changes in P. gingivalis W50 protein and transcript abundances on changing from heme-excess to heme-limited continuous culture. This approach identified 160 genes and 70 proteins that were differentially regulated by heme availability, with broad agreement between the transcriptomic and proteomic data. A change in abundance of the enzymes of the aspartate and glutamate catabolic pathways was observed with heme limitation, which was reflected in organic acid end product levels of the culture fluid. These results demonstrate a shift from an energy-efficient anaerobic respiration to a less efficient process upon heme limitation. Heme limitation also resulted in an increase in abundance of a protein, PG1374, which we have demonstrated, by insertional inactivation, to have a role in epithelial cell invasion. The greater abundance of a number of transcripts/proteins linked to invasion of host cells, the oxidative stress response, iron/heme transport, and virulence of the bacterium indicates that there is a broad response of P. gingivalis to heme availability.
| S-EPMC2632107 | biostudies-literature
Project description:Porphyromonas gingivalis is one of the main etiological agents responsible for initiating and progressing periodontal diseases in humans. P. gingivalis does not synthesize heme, and it uses host hemoproteins as a source of this molecule. The main heme uptake mechanism utilized by P. gingivalis is the Hmu system composed of six proteins where HmuY (hemophore-like protein) and HmuR (TonB-dependant outer membrane heme receptor) play a crucial role in heme supply. The second heme uptake mechanism is the Hus system composed of four proteins, with HusA (hemophore-like protein) and HusB (TonB-dependant outer membrane receptor), having a supporting role in heme uptake. Heme and iron starvation influence the P. gingivalis phenotype, therefore the aim was to determine the influence of deletion of HmuY and HmuR (ΔhmuYR strain) or HusA and HusB (ΔhusAB strain) encoding genes on P. gingivalis phenotype including the impact on protein production in response to the analyzed deletion. The mutant strains were constructed in wild-type A7436 P. gingivalis strain. Bacteria were grown in basal medium (BM) supplemented with 7.7 µM heme. After analysis of bacteria lysates with SDS-PAGE and CBB G-250 staining, in ΔhmuYR a protein (~45 kDa) was detected produced in higher amounts, than in the wild-type and the ΔhusAB strains. The gel band of interest, as well as its corresponding sections in the WT lanes were excised for bottom-up LC-MS analysis, and the protein was identified as FimA.
2024-12-28 | PXD054703 | Pride
Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization
2008-10-09 | GSE13128 | GEO
Project description:Genotyping studies suggest that there is genetic variability among P. gingivalis strains, however the extent of variability remains unclear, and the regions of variability have only partially been identified. We previously used heteroduplex analysis of the ribosomal operon intergenic spacer region (ISR) to type P. gingivalis strains in several diverse populations, identifying 6 predominant heteroduplex types and many minor ones. In addition we used ISR sequence analysis to determine the relatedness of P. gingivalis strains to one another, and demonstrated a link between ISR sequence phylogeny and the disease-associated phenotype of P. gingivalis strains. The availability of whole genome microarrays based on the genomic sequence of strain W83 has allowed a more comprehensive analysis of P. gingivalis strain variability, using the entire genome. The objectives of this study were to define the phylogeny of P. gingivalis strains using the entire genome, to compare the phylogeny based on genome content to the phylogeny based on a single locus (ISR), and to identify genes that are associated with the strongly disease-associated strain W83 that could be important for virulence. Keywords: Comparative genomic hybridization Comparative genomic analysis of 7 clinically prevalent P. gingivalis strains was performed, using whole genome microarrays based on the sequence of strain W83. Strain W83 was the reference strains and there were 6 test strains. Flip-dye replicates were performed.
2010-05-18 | E-GEOD-13128 | biostudies-arrayexpress