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Cite: NAR/gkaa742 2020



PUL General Information

Literature Information

PUL ID

PUL0575

PubMed

20946531, Environ Microbiol. 2011 Feb;13(2):518-28. doi: 10.1111/j.1462-2920.2010.02355.x. Epub 2010 Oct 15.

Characterization method

microarray,growth assay,gene deletion mutant and growth assay

Genomic accession number

NZ_ABQA01000009.1

Nucelotide position range

6717-20398

Substrate

raffinose

Loci

EFME980_RS04995-EFME980_RS05050

Species

Enterococcus faecium/1352

Degradation or Biosynthesis

degradation

Gene Name

Locus Tag

Protein ID

Gene Position

GenBank Contig Range

EC Number

gtfA EFME980_RS04995 WP_002290364.1 0 - 1461 (-) NZ_ABQA01000009.1:6717-8178 2.4.1.7
- EFME980_RS05000 WP_002290365.1 1457 - 2441 (-) NZ_ABQA01000009.1:8174-9158 -
- EFME980_RS05005 WP_002290366.1 2521 - 2677 (-) NZ_ABQA01000009.1:9238-9394 -
- EFME980_RS05010 WP_002290367.1 2737 - 4921 (-) NZ_ABQA01000009.1:9454-11638 -
- EFME980_RS05015 WP_002290368.1 4960 - 5791 (-) NZ_ABQA01000009.1:11677-12508 -
- EFME980_RS05020 WP_002290370.1 5802 - 6675 (-) NZ_ABQA01000009.1:12519-13392 -
- EFME980_RS05025 WP_002290371.1 6684 - 7944 (-) NZ_ABQA01000009.1:13401-14661 -
- EFME980_RS05030 WP_002290372.1 8092 - 9403 (-) NZ_ABQA01000009.1:14809-16120 -
- EFME980_RS05035 WP_002290373.1 9434 - 10259 (-) NZ_ABQA01000009.1:16151-16976 -
- EFME980_RS05040 WP_008378728.1 10274 - 11171 (-) NZ_ABQA01000009.1:16991-17888 -
- EFME980_RS05045 WP_002290375.1 11253 - 12363 (-) NZ_ABQA01000009.1:17970-19080 -
- EFME980_RS05050 WP_002290378.1 12656 - 13682 (-) NZ_ABQA01000009.1:19373-20399 -

Cluster number

1

Gene name

Gene position

Gene type

Found by CGCFinder?

gtfA 1 - 1461 (-) CAZyme: GH13|GH13_18 Yes
- 1458 - 2441 (-) CAZyme: GH13_31|GH13 Yes
- 2522 - 2677 (-) other Yes
- 2738 - 4921 (-) CAZyme: GH36 Yes
- 4961 - 5791 (-) TC: gnl|TC-DB|Q00751|3.A.1.1.28 Yes
- 5803 - 6675 (-) TC: gnl|TC-DB|Q00750|3.A.1.1.28 Yes
- 6685 - 7944 (-) TC: gnl|TC-DB|Q00749|3.A.1.1.28 Yes
- 8093 - 9403 (-) CAZyme: GH4 Yes
- 9435 - 10259 (-) TC: gnl|TC-DB|Q93J92|3.A.1.1.36 Yes
- 11254 - 12363 (-) TC: gnl|TC-DB|Q9WZR7|3.A.1.1.40 Yes
- 12657 - 13682 (-) TF: DBD-Pfam|LacI,DBD-SUPERFAMILY|0044558 No

PUL ID

PUL0575

PubMed

20946531, Environ Microbiol. 2011 Feb;13(2):518-28. doi: 10.1111/j.1462-2920.2010.02355.x. Epub 2010 Oct 15.

Title

A genetic element present on megaplasmids allows Enterococcus faecium to use raffinose as carbon source.

Author

Zhang X, Vrijenhoek JE, Bonten MJ, Willems RJ, van Schaik W

Abstract

Enterococcus faecium is a commensal of the gastrointestinal tract of humans and animals. Since the 1990s, it has also emerged as a nosocomial pathogen. Little is known about carbon metabolism of E. faecium even though the ability to utilize different sugars could be an important factor in adapting to different ecological niches. In this study we identify an E. faecium gene cluster that is responsible for the metabolism of the alpha-galactoside sugar raffinose. Phenotypic testing of seven E. faecium isolates of which the genomes were previously sequenced showed that one isolate (strain E980) could grow on raffinose. Genome analysis identified a gene cluster containing two genes encoding alpha-galactosidases (termed agaA and agaB) that was uniquely present in E980. The agaA and agaB genes were significantly more frequently found in strains that are phylogenetically related to E980 and were more prevalent in surveillance isolates from hospital and community sources than in isolates from clinical infections. Disruption of the alpha-galactosidase gene agaB, but not of agaA, disabled growth on raffinose in strain E980. In all strains agaA and agaB are carried on megaplasmids that are between 150 and 300 kb in size. Filter-mating experiments showed that the megaplasmid of E980 can be transferred to a plasmidless recipient which then gains the ability to grow on raffinose. The observation that raffinose utilization by E. faecium is a trait carried by megaplasmids indicates that these megaplasmids can have important roles in shaping the competitive fitness of E. faecium in the environment, for example by expanding the metabolic repertoire of this organism.