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The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese.

Monnet C, Loux V, Gibrat JF, Spinnler E, Barbe V, Vacherie B, Gavory F, Gourbeyre E, Siguier P, Chandler M, Elleuch R, Irlinger F, Vallaeys T - PLoS ONE (2010)

Bottom Line: Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product.Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat.We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR782 Génie et microbiologie des procédés alimentaires, Thiverval-Grignon, France. monnet@grignon.inra.fr

ABSTRACT
Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+)/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.

Show MeSH
Catechol-type siderophore gene cluster in A. arilaitensis Re117.Genes are coloured as categorized: non-ribosomal siderophore peptide synthetase components and accessory proteins in blue, other siderophore biosynthesis proteins in orange, MbtH-like protein in dark purple, siderophore exporter in yellow, Fe3+/siderophore transport components in green and siderophore-interacting protein in grey. Triangles indicate the presence of putative IdeR (iron-dependent regulator) binding sites.
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pone-0015489-g003: Catechol-type siderophore gene cluster in A. arilaitensis Re117.Genes are coloured as categorized: non-ribosomal siderophore peptide synthetase components and accessory proteins in blue, other siderophore biosynthesis proteins in orange, MbtH-like protein in dark purple, siderophore exporter in yellow, Fe3+/siderophore transport components in green and siderophore-interacting protein in grey. Triangles indicate the presence of putative IdeR (iron-dependent regulator) binding sites.

Mentions: A catecholate or mixed catecholate-hydroxamate siderophore is presumably produced by A. arilaitensis. In contrast to A. aurescens TC1, Arthrobacter sp. FB24 and A. chlorophenolicus A6, the A. arilaitensis genome contains genes involved in the conversion of chorismate to the catecholate siderophore precursor 2,3-dihydroxybenzoate (AARI_32900-32920). The same gene cluster contains six non-ribosomal siderophore peptide synthetase components (AARI_32830-32870 and AARI_32890), which may be required for the modification of the basic siderophore structure (Figure 3). It also contains a gene encoding a putative L-ornithine 5-monooxygenase (AARI_32880), involved in the biosynthesis of pyoverdine, a mixed catecholate-hydroxamate siderophore produced by Pseudomonas aeruginosa [74], a MbtH-like protein (AARI_32820; Pfam family PF03621) which is a family of proteins found in many siderophore biosynthesis clusters, and a siderophore exporter (AARI_32810). The Fe3+/siderophore transport components AARI_32760-32770 and AARI_32790 are located in the same gene cluster and presumably transport the siderophore whose biosynthesis depends on the genes of this cluster. AARI_32780 is a siderophore-interacting protein that may be involved in removal of iron from the Fe3+/siderophore complex. A putative IdeR binding site is present upstream of AARI_32920 (sequence TTACATGAGGCTAACCTAA, position -58 relative to the translation start site) and another upstream of AARI_32790 (sequence TTACCATAGGCTACCCTTA, position -71 relative to the translation start site). Genes AARI_32760-32890 have a high G+C content (mean value of 69.1%, whereas the chromosome G+C content is 59.3%), probably reflecting recent horizontal transfer (see circle 12 of Figure 1, near position 3.7 Mbp).


The arthrobacter arilaitensis Re117 genome sequence reveals its genetic adaptation to the surface of cheese.

Monnet C, Loux V, Gibrat JF, Spinnler E, Barbe V, Vacherie B, Gavory F, Gourbeyre E, Siguier P, Chandler M, Elleuch R, Irlinger F, Vallaeys T - PLoS ONE (2010)

Catechol-type siderophore gene cluster in A. arilaitensis Re117.Genes are coloured as categorized: non-ribosomal siderophore peptide synthetase components and accessory proteins in blue, other siderophore biosynthesis proteins in orange, MbtH-like protein in dark purple, siderophore exporter in yellow, Fe3+/siderophore transport components in green and siderophore-interacting protein in grey. Triangles indicate the presence of putative IdeR (iron-dependent regulator) binding sites.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2991359&req=5

pone-0015489-g003: Catechol-type siderophore gene cluster in A. arilaitensis Re117.Genes are coloured as categorized: non-ribosomal siderophore peptide synthetase components and accessory proteins in blue, other siderophore biosynthesis proteins in orange, MbtH-like protein in dark purple, siderophore exporter in yellow, Fe3+/siderophore transport components in green and siderophore-interacting protein in grey. Triangles indicate the presence of putative IdeR (iron-dependent regulator) binding sites.
Mentions: A catecholate or mixed catecholate-hydroxamate siderophore is presumably produced by A. arilaitensis. In contrast to A. aurescens TC1, Arthrobacter sp. FB24 and A. chlorophenolicus A6, the A. arilaitensis genome contains genes involved in the conversion of chorismate to the catecholate siderophore precursor 2,3-dihydroxybenzoate (AARI_32900-32920). The same gene cluster contains six non-ribosomal siderophore peptide synthetase components (AARI_32830-32870 and AARI_32890), which may be required for the modification of the basic siderophore structure (Figure 3). It also contains a gene encoding a putative L-ornithine 5-monooxygenase (AARI_32880), involved in the biosynthesis of pyoverdine, a mixed catecholate-hydroxamate siderophore produced by Pseudomonas aeruginosa [74], a MbtH-like protein (AARI_32820; Pfam family PF03621) which is a family of proteins found in many siderophore biosynthesis clusters, and a siderophore exporter (AARI_32810). The Fe3+/siderophore transport components AARI_32760-32770 and AARI_32790 are located in the same gene cluster and presumably transport the siderophore whose biosynthesis depends on the genes of this cluster. AARI_32780 is a siderophore-interacting protein that may be involved in removal of iron from the Fe3+/siderophore complex. A putative IdeR binding site is present upstream of AARI_32920 (sequence TTACATGAGGCTAACCTAA, position -58 relative to the translation start site) and another upstream of AARI_32790 (sequence TTACCATAGGCTACCCTTA, position -71 relative to the translation start site). Genes AARI_32760-32890 have a high G+C content (mean value of 69.1%, whereas the chromosome G+C content is 59.3%), probably reflecting recent horizontal transfer (see circle 12 of Figure 1, near position 3.7 Mbp).

Bottom Line: Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product.Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat.We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.

View Article: PubMed Central - PubMed

Affiliation: INRA, UMR782 Génie et microbiologie des procédés alimentaires, Thiverval-Grignon, France. monnet@grignon.inra.fr

ABSTRACT
Arthrobacter arilaitensis is one of the major bacterial species found at the surface of cheeses, especially in smear-ripened cheeses, where it contributes to the typical colour, flavour and texture properties of the final product. The A. arilaitensis Re117 genome is composed of a 3,859,257 bp chromosome and two plasmids of 50,407 and 8,528 bp. The chromosome shares large regions of synteny with the chromosomes of three environmental Arthrobacter strains for which genome sequences are available: A. aurescens TC1, A. chlorophenolicus A6 and Arthrobacter sp. FB24. In contrast however, 4.92% of the A. arilaitensis chromosome is composed of ISs elements, a portion that is at least 15 fold higher than for the other Arthrobacter strains. Comparative genomic analyses reveal an extensive loss of genes associated with catabolic activities, presumably as a result of adaptation to the properties of the cheese surface habitat. Like the environmental Arthrobacter strains, A. arilaitensis Re117 is well-equipped with enzymes required for the catabolism of major carbon substrates present at cheese surfaces such as fatty acids, amino acids and lactic acid. However, A. arilaitensis has several specificities which seem to be linked to its adaptation to its particular niche. These include the ability to catabolize D-galactonate, a high number of glycine betaine and related osmolyte transporters, two siderophore biosynthesis gene clusters and a high number of Fe(3+)/siderophore transport systems. In model cheese experiments, addition of small amounts of iron strongly stimulated the growth of A. arilaitensis, indicating that cheese is a highly iron-restricted medium. We suggest that there is a strong selective pressure at the surface of cheese for strains with efficient iron acquisition and salt-tolerance systems together with abilities to catabolize substrates such as lactic acid, lipids and amino acids.

Show MeSH