Table 2

Substrates converted by Arthrobacter sp. Rue61a
Carbon source, concentration Prediction from genome Growth in mineral medium/comments
Aromatic compounds
Benzoate, 2 mM incomplete
2-Nitrobenzoate, 2 mM absent
Anthranilate (2-aminobenzoate), 2 mM present, CoA thioester pathway +
3-Hydroxyanthranilate (2-amino-3-hydroxybenzoate), 2 mM absent –/cometabolic conversion
5-Hydroxyanthranilate (2-amino-5-hydroxybenzoate), 2 mM n.s. –/cometabolic conversion
Salicylate (2-hydroxybenzoate), 2 mM absent
3-Hydroxybenzoate, 2 mM n.s.
4-Hydroxybenzoate, 2 mM present, via protocatechuate +
Gentisate (2,5-dihydroxybenzoate), 2 mM n.s.
Protocatechuate (3,4-dihydroxybenzoate), 2 mM present, ortho pathway +
Vanillate (4-hydroxy-3-methoxybenzoate), 2 mM present +
Phenylethylamine, 2 mM incomplete
Phenylacetate, 2 mM incomplete –/cometabolic conversion
4-Hydroxyphenylacetate, 2 mM present, via homoprotocatechuate +
Homoprotocatechuate (3,4-dihydroxyphenylacetate), 2 mM present, meta pathway +
Tyrosine, 2 mM present, via 4-hydroxyphenylacetate and homoprotocatechuate +
4-Hydroxymandelate [2-hydroxy-2-(4-hydroxyphenyl)acetate], 2 mM incomplete
Phenol, 1 mM incomplete; possible monooxygenation –/no hydroxylation to catechol
Catechol, 1 mM incomplete –/cometabolic conversion to cis,cis-muconate within 1–2 days (cells pre-grown with protocatechuate) or 4–5 days (cells grown on other C sources)*
Styrene (ethenylbenzene), 1 mM incomplete –/cometabolic conversion
Biphenyl, 2 mM incomplete
4-Phenoxybenzoate, 1 mM n.s.
* by resting cells (OD600 nm ~20) pre-grown in MM supplemented with glucose as carbon source (0.5%), or with glucose plus 1 mM or 2 mM of either benzoate, anthranilate, biphenyl, homoprotocatechuate, protocatechuate, or catechol.
N-Heterocyclic compounds
Hypoxanthine and xanthine, 2 mM present +
Quinaldine (2-methylquinoline), 2 mM present +
1H-4-Oxoquinaldine, 1 mM present +
1H-3-Hydroxy-4-oxoquinaldine, 1 mM present +
Sugars (and -derivatives)
Glucose, 0.25% and 0.5% present +
Fructose, 0.5% present +
Galactose, 0.5% present +
L-Arabinose, 0.5% present +
Mannose, 0.5% present +
Ribose, 0.5% present +
Rhamnose, 0.5% incomplete +
Xylose, 0.5% present +
Lactose, 0.25% present +
Sucrose, 0.25% present +
Trehalose, 0.25% possibly via maltose +
Maltose, 0.25% n.s. +
D-Glucosamine, 0.5% present +
N-Acetyl-β-D-glucosamine, 0.5% present +
Alcohols and carboxylic acids
Ethanol (0.5% and 1%) present +
Glycerol (1%) present +
2-Chloroacetate, 1 mM, 3 mM, 10 mM n.s.
Acetate, 1 mM, 3 mM present +
Glycolate (2-hydroxyethanoic acid), 10 mM absent
Glyoxylate, 10 mM present +
Pyruvate, 40 mM present +
Glutarate, 10 mM absent
D-Gluconate, 0.5% present +
Lipids
Triacylglycerides: Tributyrin absent –/no zones of clearing on tributyrin plates
Monoacylglycerides: 1-Oleyl-rac-glycerol, 2 mM present +
Natural polymers
Starch present +/growth and zones of clearing on starch plates
Pectin n.s.
Lichenin n.s.
Carboxymethylcellulose n.s.
Chitin n.s.
Protein present +/growth and zones of clearing on skim milk plates
Amines, amides and related compounds
Choline (N,N,N-trimethylethanolammonium chloride), 0.2% via glycine betaine +
Glycine betaine (2-trimethylammonioacetate), 0.5% incomplete +
Creatinine (2-amino-1-methyl-5H-imidazol-4-one), 0.2% absent
Creatine [2-(1-methylcarbamimidamido)acetate], 0.2% present, via sarcosine +
Sarcosine [2-(methylamino)acetic acid], 0.5% present +
Putrescine (butane-1,4-diamine), 5 mM present, via 4-aminobutyrate +
Agmatine [N-(4-aminobutyl)guanidine sulfate], 15 mM incomplete, via putrescine +
Allantoin [(2,5-dioxo-4-imidazolidinyl)urea], 0.2% incomplete +
Taurine (2-aminoethanesulfonic acid), 10 mM incomplete
Nitrogen sources Prediction from genome Growth in mineral medium with glucose
Urea, 0.2% present +
Allantoin [(2,5-dioxo-4-imidazolidinyl)urea], 0.02%, 0.2% incomplete +
Creatine [2-(methylguanidino)ethanoic acid], 0.2% present +
Putrescine (butane-1,4-diamine), 5 mM present +
Agmatine [N-(4-aminobutyl)guanidine sulfate], 5 mM incomplete +
Taurine (2-aminoethanesulfonic acid), 5 mM absent
Sulfur source Prediction from genome Growth in mineral medium with glucose
Taurine (2-aminoethanesulfonic acid), 1 mM sulfite formation by taurine dioxygenase +

n.s., not specified.

Niewerth et al.

Niewerth et al. BMC Genomics 2012 13:534   doi:10.1186/1471-2164-13-534

Open Data