Genome Sequence of Porphyromonas gingivalis Strain A7436

Chastain-Gross, Ryan P.; Xie, Gary; Bélanger, Myriam; Kumar, Dibyendu; Whitlock, Joan A.; Liu, Li; Farmerie, William G.; Daligault, Hajnalka E.; Han, Cliff; Brettin, Thomas; Progulske‐Fox, Ann

doi:10.1128/genomea.00927-15

Cited by 16 publications

(12 citation statements)

References 26 publications

(29 reference statements)

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“…Dowell, Jr., at the Centers for Disease Control and Prevention in Atlanta, GA, in the mid-1980s. Information source: http://www.ncbi.nlm.nih.gov/biosample/SAMN03366764 and Chastain-Gross et al ( 2015 )…”

Section: Methodsmentioning

confidence: 99%

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

Chen¹,

Siddiqui

Olsen

2017

Front. Cell. Infect. Microbiol.

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Currently, genome sequences of a total of 19 Porphyromonas gingivalis strains are available, including eight completed genomes (strains W83, ATCC 33277, TDC60, HG66, A7436, AJW4, 381, and A7A1-28) and 11 high-coverage draft sequences (JCVI SC001, F0185, F0566, F0568, F0569, F0570, SJD2, W4087, W50, Ando, and MP4-504) that are assembled into fewer than 300 contigs. The objective was to compare these genomes at both nucleotide and protein sequence levels in order to understand their phylogenetic and functional relatedness. Four copies of 16S rRNA gene sequences were identified in each of the eight complete genomes and one in the other 11 unfinished genomes. These 43 16S rRNA sequences represent only 24 unique sequences and the derived phylogenetic tree suggests a possible evolutionary history for these strains. Phylogenomic comparison based on shared proteins and whole genome nucleotide sequences consistently showed two groups with closely related members: one consisted of ATCC 33277, 381, and HG66, another of W83, W50, and A7436. At least 1,037 core/shared proteins were identified in the 19 P. gingivalis genomes based on the most stringent detecting parameters. Comparative functional genomics based on genome-wide comparisons between NCBI and RAST annotations, as well as additional approaches, revealed functions that are unique or missing in individual P. gingivalis strains, or species-specific in all P. gingivalis strains, when compared to a neighboring species P. asaccharolytica. All the comparative results of this study are available online for download at ftp://www.homd.org/publication_data/20160425/.

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Section: Methodsmentioning

confidence: 99%

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

Chen¹,

Siddiqui

Olsen

2017

Front. Cell. Infect. Microbiol.

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“…To date, inconsistent amino acid sequences of a Fur homolog in P. gingivalis laboratory strains and clinical isolates identified based on genome sequencing have been deposited in databases. Among them are examples of 166-amino-acid-long proteins in W83 (AAQ65662) and TDC60 (BAK25731) (Nelson et al, 2003; Watanabe et al, 2011) and 200-amino-acid-long proteins in A7436 (AKV64657), ATCC 33277 (BAG34022), and JCVI SC001 (EOA10344) (Naito et al, 2008; McLean et al, 2013; Chastain-Gross et al, 2015; Figure 1). Experimental analysis performed by Butler et al (2014) employed a 166-amino-acid-long version of the P. gingivalis Fur homolog (termed Har) but possessing the amino acid sequence derived from the ATCC 33277 strain.…”

Section: Resultsmentioning

confidence: 99%

“…(B) Amino acid sequences of PgFur protein versions identified in P. gingivalis strains. Start codon of the longest protein version (MDR) deposited in databases is shown in blue (e.g., BAG34022 in ATCC 33277, EOA10344 in JCVI SC001, AKV64657 in A7436) (Naito et al, 2008; McLean et al, 2013; Chastain-Gross et al, 2015), the shortest protein version (MIV) deposited in databases is shown in green (e.g., AAQ65662 in W83, BAK25731 in TDC60) (Nelson et al, 2003; Watanabe et al, 2011), and the protein version identified in this study (MAV) is shown in red. The entire sequence of the PgFur protein and its mRNA identified in this study is shadowed.…”

Section: Resultsmentioning

confidence: 99%

Porphyromonas gingivalis PgFur Is a Member of a Novel Fur Subfamily With Non-canonical Function

Śmiga

Bielecki

Olczak

et al. 2019

Front. Cell. Infect. Microbiol.

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Porphyromonas gingivalis , a keystone pathogen of chronic periodontitis, uses ferric uptake regulator homolog (PgFur) to regulate production of virulence factors. This study aimed to characterize PgFur protein in regard to its structure-function relationship. We experimentally identified the 5′ mRNA sequence encoding the 171-amino-acid-long PgFur protein in the A7436 strain and examined this PgFur version as a full-length protein. PgFur protein did not bind to the canonical Escherichia coli Fur box, but the wild-type phenotype of the mutant Δ pgfur strain was restored partially when expression of the ecfur gene was induced from the native pgfur promoter. The full-length PgFur protein contained one zinc atom per protein monomer, but did not bind iron, manganese, or heme. Single cysteine substitutions of CXXC motifs resulted in phenotypes similar to the mutant Δ pgfur strain. The modified proteins were produced in E. coli at significantly lower levels, were highly unstable, and did not bind zinc. The pgfur gene was expressed at the highest levels in bacteria cultured for 24 h in the absence of iron and heme or at higher levels in bacteria cultured for 10 h in the presence of protoporphyrin IX source. No influence of high availability of Fe 2+ , Zn 2+ , or Mn 2+ on pgfur gene expression was observed. Two chromosomal mutant strains producing protein lacking 4 ( pgfur Δ 4aa ) or 13 ( pgfur Δ 13aa ) C-terminal amino acid residues were examined in regard to importance of the C-terminal lysine-rich region. The pgfur Δ 13aa strain showed a phenotype typical for the mutant Δ pgfur strain, but both the wild-type PgFur protein and its truncated version bound zinc with similar ability. The Δ pgfur mutant strain produced higher amounts of HmuY protein compared with the wild-type strain, suggesting compromised regulation of its expression. Potential PgFur ligands, Fe 2+ , Mn 2+ , Zn 2+ , PPIX, or serum components, did not influence HmuY production in the Δ pgfur mutant strain. The mutant pgfur Δ 4aa and pgfur Δ 13aa strains exhibited affected HmuY protein production. PgFur, regardless of the presence of the C-terminal lysine-rich region, bound to the hmu operon promoter. Our data suggest that cooperation of PgFur with partners/cofactors and/or protein/DNA modifications would be required to accomplish its role played in an in vivo multilayer regulatory net...

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“…To assign the potential function of the PgRsp protein, first bioinformatics approaches were employed. Searching for PgRsp-encoding sequences in P. gingivalis strains revealed that amino acid sequences deposited in databases for several P. gingivalis strains (e.g., W83, AJW4, ATCC 33277, 381, HG66, A7A1-28) predicted a 207-amino-acid version of the PgRsp protein, whereas in the A7436 strain a 283-amino-acid protein was predicted [49]. Our theoretical approaches and preliminary analysis of the 5 UTR region of the mRNA encoding PgRsp using 5 RACE (data not shown) led us to the conclusion that in the A7436 strain the pgrsp gene encodes a 207-amino-acid long protein.…”

Section: Pgrsp-a Heme-binding Member Of a Novel Family Of Crp/fnr Supmentioning

confidence: 99%

PgRsp Is a Novel Redox-Sensing Transcription Regulator Essential for Porphyromonas gingivalis Virulence

Śmiga

Olczak

2019

Microorganisms

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Porphyromonas gingivalis is one of the etiological agents of chronic periodontitis. Both heme and oxidative stress impact expression of genes responsible for its survival and virulence. Previously we showed that P. gingivalis ferric uptake regulator homolog affects expression of a gene encoding a putative Crp/Fnr superfamily member, termed P. gingivalis redox-sensing protein (PgRsp). Although PgRsp binds heme and shows the highest similarity to proteins assigned to the CooA family, it could be a member of a novel, separate family of proteins with unknown function. Expression of the pgrsp gene is autoregulated and iron/heme dependent. Genes encoding proteins engaged in the oxidative stress response were upregulated in the pgrsp mutant (TO11) strain compared with the wild-type strain. The TO11 strain showed higher biomass production, biofilm formation, and coaggregation ability with Tannerella forsythia and Prevotella intermedia. We suggest that PgRsp may regulate production of virulence factors, proteases, Hmu heme acquisition system, and FimA protein. Moreover, we observed growth retardation of the TO11 strain under oxidative conditions and decreased survival ability of the mutant cells inside macrophages. We conclude that PgRsp protein may play a role in the oxidative stress response using heme as a ligand for sensing changes in redox status, thus regulating the alternative pathway of the oxidative stress response alongside OxyR.

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Genome Sequence of Porphyromonas gingivalis Strain A7436

Cited by 16 publications

References 26 publications

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

In silico Comparison of 19 Porphyromonas gingivalis Strains in Genomics, Phylogenetics, Phylogenomics and Functional Genomics

Porphyromonas gingivalis PgFur Is a Member of a Novel Fur Subfamily With Non-canonical Function

PgRsp Is a Novel Redox-Sensing Transcription Regulator Essential for Porphyromonas gingivalis Virulence

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