The eLignin Microbial Database

A curated resource for microbial metabolism of lignin-derived aromatic compounds

brinkdp/eLignin 0 0

Pseudomonas putida KT2440

Kingdom
Bacteria
Phylum
Proteobacteria
Class
Gamma-proteobacteria
Type
Gram negative
Strain
KT2440
Origin (Details)
Soil
Origin (Category)
Soil
Genome Sequenced
Yes
Empirical Data

Utilizible (lignin-derived) carbon sources (17) Empirical

NB! Always check the primary references for the experimental details; "utilizable" does not necessarily equal "growth-supporting".

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Substrate Reference(s) Comment(s)
4-hydroxybenzoic acid Salvachúa et al (2015)
Ravi et al (2017) 		-
alkali lignin Salvachúa et al (2015) (from corn stover; ~25% lignin conversion, including Klason lignin and monomers)
benzoic acid Jiménez et al (2002)
Ravi et al (2017) 		-
caffeic acid Jiménez et al (2002) -
catechol Jiménez et al (2002) -
coniferyl alcohol Jiménez et al (2002) -
corn stover lignin Rodriguez2017 (base-catalyzed depolymerized corn stover)
ferulic acid Salvachúa et al (2015)
Ravi et al (2017) 		-
gallic acid Nogales et al (2010) -
p-coumaric acid Salvachúa et al (2015)
Ravi et al (2017) 		-
phenylheptanoate Jiménez et al (2002) -
phenylhexanoate Jiménez et al (2002) -
phenyloctanoate Jiménez et al (2002) -
protocatechuic acid Jiménez et al (2002) -
quinic acid Jiménez et al (2002) -
vanillic acid Salvachúa et al (2015)
Ravi et al (2017) 		-
vanillin Ravi et al (2017) -

Pathways (8) Empirical

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Pathway Name Reference(s)
benzoic acid Jiménez et al (2002)
beta-ketoadipate (all branches) Poblete-Castro et al (2012)
beta-ketoadipate: Catechol branch Jiménez et al (2002)
beta-ketoadipate: lower branch Jiménez et al (2002)
beta-ketoadipate: Protocatechuate branch Jiménez et al (2002)
coniferyl alcohol Jiménez et al (2002)
ferulic acid Jiménez et al (2002)
p-coumaric acid Jiménez et al (2002)

Enzymes (19) Empirical

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Enzyme Gene(s) Reference(s)
1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase Pp_benD Jiménez et al (2002)
2-hydroxymuconate-6-semialdehyde dehydrogenase - -
3-carboxy-cis,cis-muconate cycloisomerase - -
3-oxoadipate enol-lactonase - -
4-carboxymuconolactone decarboxylase - -
4-hydroxybenzoate 3-monooxygenase Pp_pobA Jiménez et al (2002)
4-oxalmesaconate hydratase - -
4-oxalomesaconate tautomerase - -
Benzoate 1,2-dioxygenase Pp_benA
Pp_benB 		Jiménez et al (2002)
catechol 1,2-dioxygenase Pp_catA Jiménez et al (2002)
Coniferyl alcohol dehydrogenase Pp_calA Jiménez et al (2002)
Coniferyl aldehyde dehydrogenase Pp_calB Jiménez et al (2002)
Feruloyl-CoA synthase - -
gallate dioxygenase - -
HMG aldolase - -
muconate cycloisomerase Pp_catB Jiménez et al (2002)
muconolactone isomerase Pp_catC Jiménez et al (2002)
Protocatechuate 3,4-dioxygenase - -
Vanillin dehydrogenase - -

Transporters (4) Empirical

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Transporter Reference
Pp_benKp Cowles et al (2000)
Pp_benFp Cowles et al (2000)
Pp_benE1p NISHIKAWA et al (2008)
Pp_benE2p NISHIKAWA et al (2008)

Genes (25) Empirical

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Gene Name Reference(s)
Pp_benA Jiménez et al (2002)
Pp_benB Jiménez et al (2002)
Pp_benD Jiménez et al (2002)
Pp_benE1 NISHIKAWA et al (2008)
Pp_benE2 NISHIKAWA et al (2008)
Pp_benF Cowles et al (2000)
Pp_benK Jiménez et al (2002)
Pp_calA Jiménez et al (2002)
Pp_calB Jiménez et al (2002)
Pp_catA Jiménez et al (2002)
Pp_catB Jiménez et al (2002)
Pp_catC Jiménez et al (2002)
Pp_fcs Jiménez et al (2002)
Pp_galA Nogales et al (2005)
Pp_galB Nogales et al (2010)
Pp_galC Nogales et al (2010)
Pp_galD Nogales et al (2010)
Pp_pcaB Jiménez et al (2002)
Pp_pcaC Jiménez et al (2002)
Pp_pcaD Jiménez et al (2002)
Pp_pcaG Jiménez et al (2002)
Pp_pcaH Jiménez et al (2002)
Pp_pobA Jiménez et al (2002)
Pp_vdh Jiménez et al (2002)
Pp_xylG Inoue et al (1995)
Predicted Relationships Hide predicted
The sections below contain relationships inferred from the empirical data above. They are computationally predicted and have not been independently verified. Learn more about data assumptions →
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Predicted pathways in Pseudomonas putida KT2440 Predicted

Inferred from reported utilizable carbon sources: if the organism can utilise a compound that enters a pathway as a reactant, it may carry that pathway. Not experimentally verified. What does this mean?

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Predicted pathway Funneling branch Inferred via substrate Reference
caffeic acid caffeic acid branch caffeic acid Jiménez et al (2002)
catechol meta-cleavage catechol meta-cleavage branch catechol Jiménez et al (2002)
guaiacol coniferyl branch vanillic acid Salvachúa et al (2015), Ravi et al (2017)
protocatechuate 2,3-cleavage protocatechuate 2,3-cleavage branch protocatechuic acid Jiménez et al (2002)
protocatechuate 4,5-cleavage beta-ketoadipate branch protocatechuic acid Jiménez et al (2002)
syringic acid I sinapyl branch gallic acid Nogales et al (2010)
vanillin I coniferyl branch vanillic acid, vanillin Salvachúa et al (2015), Ravi et al (2017)
vanillin II coniferyl branch vanillic acid, vanillin Salvachúa et al (2015), Ravi et al (2017)

Predicted enzymes in Pseudomonas putida KT2440 Predicted

Inferred from confirmed pathways: if the organism is confirmed to carry a pathway, enzymes known to catalyse reactions in that pathway are predicted to be present. The pathway used for each inference is shown. Not experimentally verified. What does this mean?

Predicted enzyme Inferred via pathway Reference
4-hydroxybenzaldehyde dehydrogenase p-coumaric acid Jiménez et al (2002)
caffeate coenzyme A ligase p-coumaric acid Jiménez et al (2002)
enoyl-CoA hydratase/lyase p-coumaric acid Jiménez et al (2002)
trans-feruloyl-CoA hydratase ferulic acid Jiménez et al (2002)

Culture Collections

Strain Depository ID
KT2440 ATCC 47054
KT2440 DSM 6125

Genome Sequencing

Strain Status Reference
KT2440 Yes Nelson et al (2002)
KT2440 Yes Belda et al (2016)

Other Databases

Database Comment
Pseudomonas Genome Database Genome sequence database
KEGG Pathway database
NCBI Genome sequence database
NCBI Taxonomy Taxonomy database

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