Database Authors
Anamika Kothari1, Suzanne Paley1, Anahit Penesyan2, Brendan Wilson-Mortier2, Amanda Mackie2, Ron Caspi1, Ian Paulsen2, Peter D Karp1
1SRI International, 2Macquarie University
Summary The Gram-positive bacterium Enterococcus faecalis is a natural inhabitant of the mammalian gastrointestinal tract and is commonly found in soil, sewage, water, and food, frequently through fecal contamination. It can withstand oxidative stress, desiccation, extremes of temperature and pH, and it has high endogenous resistance to salinity, bile acids, detergents, and antibiotics [Klare01]. It is also an opportunistic pathogen that is becoming increasingly resistant to antimicrobial agents due to acquisition of resistance-conferring mobile genetic elements. Enterococci are resistant to cephalosporins, clindamycin, tetracycline, penicillinase-resistant penicillins such as oxacillin, and vancomycin [Tailor93, Huycke98]. In the past decades Enterococcus faecalis strains have emerged as the second to third most common cause of nosocomial infections, including urinary tract and soft tissue infections, bacteremia, and endocarditis [Murray90].

Enterococcus faecalis was originally isolated in 1906 under the name Streptococcus faecalis [Andrewes06]. In the following years the term Enterococcus was used frequently as a separate generic designation outside the Streptococci. However, a classification scheme proposed in 1937 separated Streptococci into four divisions, one of which was the enterococci [Sherman37]. It was only in 1984, after DNA-DNA and DNA-rRNA hybridizations showed that S. faecalis was distantly related to streptococci, that the organism was transferred to a new genus that was named Enterococcus [Schleifer84].

Enterococcus faecalis OG1RF is a rifampicin and fusidic acid-resistant derivative of E. faecalis OG1 (originally named 2Sa), which was isolated from human saliva [Gold75, Oliver77, Dunny78]. E. faecalis OG1RF is used widely in experimental analyses as it encodes less antimicrobial resistance determinants and is more amenable to genetic manipulation than its highly virulent and vancomycin-resistant counterpart E. faecalis V583 [Paulsen03, Bourgogne08]. This PGDB has benefited from ortholog propagation from the Tier 2 database for E. faecalis V583, as well as minimal manual curation of unique features, including its CRISPR system.

This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp11, Karp16] component of Pathway Tools software version 28.5 and MetaCyc [Caspi18] version 28.1 on 12-Apr-2024.

We thank Professor Jose Lemos and his team (University of Florida) and Professor Kimberly Kline and her team (University of Geneva) for their assistance in identifying recent advancements in E. faecalis research and relevant data collections for this PGDB.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NC_0173162,5822,49874102,739,625NCBI Assembly:GCF_000172575.2
Ortholog data available?Yes
Database Contents
Genes2,582
Pathways214
Enzymatic Reactions1,210
Transport Reactions72
Polypeptides2,501
Protein Complexes100
Enzymes661
Transporters265
Compounds961
Transcription Units1,603
tRNAs58
Protein Features3,417
GO Terms4,158
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Lactobacillales
Enterococcaceae
Enterococcus
Enterococcus faecalis
Enterococcus faecalis OG1RF
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603002
NCBI BioProjectPRJNA224116
NCBI-Taxonomy474186
Annotation ProviderNCBI RefSeq
Annotation Date2023-06-20
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.5
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Andrewes06: Andrewes FW, Horder TJ (1906). "A study of the Streptococci pathogenic for man." The Lancet 168(4333);708-713.

Bourgogne08: Bourgogne A, Garsin DA, Qin X, Singh KV, Sillanpaa J, Yerrapragada S, Ding Y, Dugan-Rocha S, Buhay C, Shen H, Chen G, Williams G, Muzny D, Maadani A, Fox KA, Gioia J, Chen L, Shang Y, Arias CA, Nallapareddy SR, Zhao M, Prakash VP, Chowdhury S, Jiang H, Gibbs RA, Murray BE, Highlander SK, Weinstock GM (2008). "Large scale variation in Enterococcus faecalis illustrated by the genome analysis of strain OG1RF." Genome Biol 9(7);R110. PMID: 18611278

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Dunny78: Dunny GM, Brown BL, Clewell DB (1978). "Induced cell aggregation and mating in Streptococcus faecalis: evidence for a bacterial sex pheromone." Proc Natl Acad Sci U S A 75(7);3479-83. PMID: 98769

Gold75: Gold OG, Jordan HV, van Houte J (1975). "The prevalence of enterococci in the human mouth and their pathogenicity in animal models." Arch Oral Biol 20(7);473-7. PMID: 807189

Huycke98: Huycke MM, Sahm DF, Gilmore MS (1998). "Multiple-drug resistant enterococci: the nature of the problem and an agenda for the future." Emerg Infect Dis 4(2);239-49. PMID: 9621194

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Klare01: Klare I, Werner G, Witte W (2001). "Enterococci. Habitats, infections, virulence factors, resistances to antibiotics, transfer of resistance determinants." Contrib Microbiol 8;108-22. PMID: 11764728

Murray90: Murray BE (1990). "The life and times of the Enterococcus." Clin Microbiol Rev 3(1);46-65. PMID: 2404568

Oliver77: Oliver DR, Brown BL, Clewell DB (1977). "Analysis of plasmid deoxyribonucleic acid in a cariogenic strain of Streptococcus faecalis: an approach to identifying genetic determinants on cryptic plasmids." J Bacteriol 130(2);759-65. PMID: 122512

Paulsen03: Paulsen IT, Banerjei L, Myers GS, Nelson KE, Seshadri R, Read TD, Fouts DE, Eisen JA, Gill SR, Heidelberg JF, Tettelin H, Dodson RJ, Umayam L, Brinkac L, Beanan M, Daugherty S, DeBoy RT, Durkin S, Kolonay J, Madupu R, Nelson W, Vamathevan J, Tran B, Upton J, Hansen T, Shetty J, Khouri H, Utterback T, Radune D, Ketchum KA, Dougherty BA, Fraser CM (2003). "Role of mobile DNA in the evolution of vancomycin-resistant Enterococcus faecalis." Science 299(5615);2071-4. PMID: 12663927

Schleifer84: Schleifer K H, Kilpper-Balz R (1984). "Transfer of Streptococcus faecalis and Streptococcus faecium to the Genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov." International Journal of Systematic Bacteriology 34(1);31-34.

Sherman37: Sherman JM (1937). "THE STREPTOCOCCI." Bacteriol Rev 1(1);3-97. PMID: 16350049

Tailor93: Tailor SA, Bailey EM, Rybak MJ (1993). "Enterococcus, an emerging pathogen." Ann Pharmacother 27(10);1231-42. PMID: 8251694

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