Bacterial putrescine biosynthesis by arginine and ornithine routes

A reusable bacterial module for putrescine supply through alternative amino-acid routes. In the two-reaction arginine/agmatine route, SpeA decarboxylates L-arginine to agmatine and SpeB hydrolyzes agmatine to putrescine. In the direct ornithine route, SpeC decarboxylates L-ornithine to putrescine. Organisms may encode either or both routes. Upstream amino-acid supply, downstream spermidine synthesis, uptake, and putrescine catabolism are outside the boundary.

MODULE:bacterial_putrescine_biosynthesisCOMPLETECONCRETEMetabolic Pathwaymodules/bacterial_putrescine_biosynthesis.yaml
putrescine biosynthetic processGO:0009446
PMID:12634339
Identification of the putrescine biosynthetic genes in Pseudomonas aeruginosa and characterization of agmatine deiminase and N-carbamoylputrescine amidohydrolase of the arginine decarboxylase pathway.
Same-genus genetics establishes arginine-derived and direct ornithine routes as alternative ways to supply putrescine.
Putrescine can be synthesized either directly from ornithine by ornithine decarboxylase (ODC; the speC product) or indirectly from arginine via arginine decarboxylase (ADC; the speA product).
PMID:28862813
Polyamine is a critical determinant of Pseudomonas chlororaphis O6 for GacS-dependent bacterial cell growth and biocontrol capacity.
Disrupting both SpeA and SpeC eliminated polyamine production in a related pseudomonad, supporting route redundancy.
Polyamine production was reduced in the speC mutant, and was eliminated in the speAspeC mutant.
PMID:40673658
The Pseudomonas aeruginosa Type VI secretion system toxin Tse8 evolved from a novel N-carbamoylputrescine amidohydrolase.
Direct agmatinase conversion is an established route from agmatine to putrescine.
There are currently three known routes from agmatine to putrescine, including direct conversion by agmatinase.
UniProtKB:Q88QC7
Pseudomonas putida KT2440 SpeA
Q88QC7 is the exact KT2440 biosynthetic arginine decarboxylase exemplar.
UniProtKB:Q88KU3
Pseudomonas putida KT2440 SpeB
Q88KU3 is the exact KT2440 candidate agmatinase exemplar.
UniProtKB:Q88PI6
Pseudomonas putida KT2440 SpeC
Q88PI6 is the exact KT2440 ornithine decarboxylase exemplar.
UniProtKB:P21170
Escherichia coli K-12 SpeA
Reviewed, experimentally supported biosynthetic arginine decarboxylase exemplar.
UniProtKB:P60651
Escherichia coli K-12 SpeB
Reviewed, experimentally supported agmatinase exemplar used as the orthology anchor.
UniProtKB:Q9HVQ3
Pseudomonas aeruginosa PAO1 SpeC
Same-genus ornithine decarboxylase exemplar with mutant evidence and a PAINT seed of the PTHR11482 ornithine decarboxylase node.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_putrescine_biosynthesis__ppu00330-deep-research-openscientist.md
OpenScientist PSEPK module, pathway, and taxon review
The report evaluates route satisfiability against the KT2440 proteome and separates core candidates from neighboring ppu00330 functions.

The route choice is modeled with variants rather than three optional linear steps: SpeA and SpeB are connected only inside the arginine/agmatine route, while SpeC is an independent alternative. The module is species-neutral; KT2440 proteins are exact exemplars rather than universal members. The lineage-variable AguA plus N-carbamoylputrescine-amidohydrolase route is not modeled here because the commissioned KT2440 review found AguA but no verified completing enzyme. PP_3019 remains an untested candidate, and convergently evolved AguY enzymes mean absence of a canonical AguB does not prove absence of activity. The consolidated OpenScientist module+ppu00330+ PSEPK report and its HTML/PDF artifacts were consumed; no separate gene-level or generic-module report files materialized in this worktree. Taxonomic scope: the module is bacterial rather than pan-domain. Plants use related ADCs (PTHR43295 SF1/SF2/SF7) but complete the arginine route mainly through agmatine iminohydrolase and N-carbamoylputrescine amidohydrolase (with a minor ARGAH agmatinase route), and eukaryotes generally rely on ODC, so those routes belong in polyamine_metabolism. Within Bacteria the exemplars carry the strongest available evidence: E. coli K-12 SpeA and SpeB (purified-enzyme assays) and P. aeruginosa PAO1 SpeC (mutant evidence), with P. putida KT2440 kept as one homology-grounded instance. The ornithine-route selector is the fold-type III ODC subfamily PTHR11482:SF6, which covers the Pseudomonas SpeC enzymes. The enterobacterial constitutive ODC SpeC (E. coli P21169) is a fold-type I enzyme of the Orn/Lys/Arg decarboxylase class-I family (PTHR45229) and is not selected here. Adding it would need a second family alternative with its own family and gene reviews; that is recorded as follow-up curation. Family reviews: PTHR43295 (SpeA) is coherent and grants arginine decarboxylase activity family-wide. PTHR11358 (SpeB) is heterogeneous, which is why the agmatinase step uses an ORTHOLOG_OF selector anchored on E. coli SpeB rather than a family. PTHR11482 grants ODC activity to SF6.

5Nodes
2Parts
1Variant Sets
2Variants
3Annotons
1Connections

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

Module deep research

✗ none found

No MODULE:bacterial_putrescine_biosynthesis deep-research report alongside the module YAML.

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Function consistency and core coverage

4 gene-function check(s) reflected in core functions · 0 conflict(s) · 0 evidence or coverage gap(s) (7 comparison(s))

Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.

AnnotonParticipantFunctionAssessment
spea_activity SpeA (Pseudomonas putida KT2440)
UniProtKB:Q88QC7
Family Representative 		arginine decarboxylase activity
GO:0008792 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
spea_activity SpeA (Escherichia coli K-12)
UniProtKB:P21170
Family Representative 		arginine decarboxylase activity
GO:0008792 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
speb_activity ORTHOLOG_OF
Gene 		agmatinase activity
GO:0008783 		Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews.
spec_activity SpeC (Pseudomonas putida KT2440)
UniProtKB:Q88PI6
Family Representative 		ornithine decarboxylase activity
GO:0004586 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
spec_activity SpeC (Pseudomonas aeruginosa PAO1)
UniProtKB:Q9HVQ3
Family Representative 		ornithine decarboxylase activity
GO:0004586 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
spea_activity bacterial biosynthetic arginine decarboxylase family
PANTHER:PTHR43295:SF9
Family 		arginine decarboxylase activity
GO:0008792 		Family Supported
Family review supports GO:0008792 FAMILY_WIDE. Asserted by bacterial_putrescine_biosynthesis for SF9 SpeA. Every cached Swiss-Prot member is an arginine decarboxylase and the PAINT IBD is placed at a node whose seeds cover both the bacterial and the plant subfamilies.
spec_activity ornithine decarboxylase 1-related family
PANTHER:PTHR11482:SF6
Family 		ornithine decarboxylase activity
GO:0004586 		Family Supported
Family review supports GO:0004586 for PANTHER:PTHR11482:SF6. ODC subfamilies, plus AZIN2 (SF4), whose review accepts weak ODC activity. bacterial_putrescine_biosynthesis selects SF6; polyamine_metabolism selects the base family, which also takes in AZIN1.

Gene-review completeness (6/6 grounded genes reviewed)

6 complete review(s) · 0 with deep research · 0 missing review · 6 reviewed but lacking deep research

Gene Review Complete Deep research
speA P21170 ✓ ✓ ✗
speA Q88QC7 ✓ ✓ ✗
speB P60651 ✓ ✓ ✗
speB Q88KU3 ✓ ✓ ✗
speC Q88PI6 ✓ ✓ ✗
speC Q9HVQ3 ✓ ✓ ✗

Details

Context
bacteriaNCBITaxon:2
Bacterial putrescine biosynthesis by arginine and ornithine routesMetabolic Pathwaybacterial_putrescine_biosynthesis
putrescine biosynthetic processGO:0009446
Context
bacteriaNCBITaxon:2
Variant set: Putrescine synthesis route from an amino-acid precursor by precursor and reaction sequence (One Or More)
Two-reaction arginine/agmatine routeMetabolic Pathwayarginine_agmatine_route

SpeA forms agmatine from L-arginine and SpeB hydrolyzes that intermediate directly to putrescine and urea.

Connections

SpeA supplies agmatine, the substrate hydrolyzed by SpeB.
Part 1: agmatine formation
SpeA arginine decarboxylationReactionspea_arginine_decarboxylation

Annotons

Biosynthetic arginine decarboxylase activity
spea_activity
Participant: Family: bacterial biosynthetic arginine decarboxylase family
Family:
bacterial biosynthetic arginine decarboxylase familyPANTHER:PTHR43295:SF9
Representative Members: SpeA (Pseudomonas putida KT2440)UniProtKB:Q88QC7 SpeA (Escherichia coli K-12)UniProtKB:P21170
Required Function:
arginine decarboxylase activityGO:0008792

Function

arginine decarboxylase activityGO:0008792
Substrates: L-arginineCHEBI:32682
Products: agmatineCHEBI:58145 carbon dioxideCHEBI:16526
Cofactors: pyridoxal 5'-phosphateCHEBI:597326 magnesium ionCHEBI:18420

Produces the intermediate consumed by SpeB.

Part 2: putrescine formation from agmatine
SpeB agmatine hydrolysisReactionspeb_agmatine_hydrolysis

Annotons

Agmatinase activity
speb_activity
Participant: Ortholog Of: SpeB (Pseudomonas putida KT2440)
Gene Product:
SpeB (Pseudomonas putida KT2440)UniProtKB:Q88KU3 Exact KT2440 candidate; PE 3, homology-supported.
Ortholog Of:
Escherichia coli K-12 SpeBUniProtKB:P60651
Required Function:
agmatinase activityGO:0008783
Orthologs of characterized SpeB retaining K01480 and EC 3.5.3.11. Q88KU3 is the exact KT2440 candidate; TIGR01230 alone is insufficient because the PP_4523 K12255 guanidinobutyrase paralog shares the family.

Function

agmatinase activityGO:0008783
Substrates: agmatineCHEBI:58145 waterCHEBI:15377
Products: putrescineCHEBI:326268 ureaCHEBI:16199
Cofactors: manganese ionCHEBI:29035

Completes direct conversion of agmatine to putrescine.

Direct ornithine routeReactionornithine_route

SpeC forms putrescine directly from L-ornithine in one reaction. The selector covers only the fold-type III ODC subfamily PTHR11482:SF6 (e.g. Pseudomonas SpeC); it does not match the fold-type I enterobacterial ornithine decarboxylases (E. coli SpeC P21169 and SpeF, PTHR45229), so the ornithine route of Enterobacteriaceae is outside what this variant selects.

Annotons

Ornithine decarboxylase activity
spec_activity
Participant: Family: ornithine decarboxylase 1-related family
Family:
ornithine decarboxylase 1-related familyPANTHER:PTHR11482:SF6
Representative Members: SpeC (Pseudomonas putida KT2440)UniProtKB:Q88PI6 SpeC (Pseudomonas aeruginosa PAO1)UniProtKB:Q9HVQ3
Required Function:
ornithine decarboxylase activityGO:0004586

Function

ornithine decarboxylase activityGO:0004586
Substrates: L-ornithineCHEBI:46911
Products: putrescineCHEBI:326268 carbon dioxideCHEBI:16526
Cofactors: pyridoxal 5'-phosphateCHEBI:597326

Provides an independent one-reaction route to putrescine.