Bacterial lipoprotein maturation

A species-neutral bacterial envelope-biogenesis module for the ordered maturation of lipobox-containing prolipoproteins by Lgt diacylglyceryl transfer, LspA signal peptide cleavage, and Lnt or lineage-equivalent N-acylation where triacylated lipoproteins are produced. Pseudomonas putida KT2440 provides the current UniProt exemplars for the canonical diderm Lgt-LspA-Lnt route; Lol sorting and substrate-specific lipoprotein functions are downstream context outside this module.

MODULE:bacterial_lipoprotein_maturationDRAFTBiological Processmodules/bacterial_lipoprotein_maturation.yaml
lipoprotein biosynthetic processGO:0042158
GO:0042158
lipoprotein biosynthetic process
GO:0042158 is the biological-process term for formation of mature lipoproteins and covers the shared process context for Lgt, LspA, and Lnt.
UniPathway:UPA00664
UniPathway UPA00664
UPA00664 represents the Lgt diacylglyceryl-transfer substep of bacterial lipoprotein biosynthesis.
UniPathway:UPA00665
UniPathway UPA00665
UPA00665 represents the LspA signal-peptide-cleavage substep of bacterial lipoprotein biosynthesis.
UniPathway:UPA00666
UniPathway UPA00666
UPA00666 represents the Lnt N-acyl-transfer substep of bacterial lipoprotein biosynthesis.
file:modules/prolipoprotein_diacylglyceryl_transfer-deep-research-openscientist.md
OpenScientist module research for the Lgt step
OpenScientist supports UPA00664 as the first committed Lgt step and explicitly separates it from downstream LspA cleavage, Lnt N-acylation, and Lol sorting.
file:modules/apolipoprotein_n_acyltransferase-deep-research-openscientist.md
OpenScientist module research for the Lnt step
OpenScientist supports UPA00666 as the terminal Lnt N-acylation step of diderm bacterial lipoprotein maturation and separates it from upstream Lgt and LspA reactions.
file:projects/P_PUTIDA/deep-research/PSEPK__prolipoprotein_diacylglyceryl_transfer__upa00664-deep-research-openscientist.md
OpenScientist PSEPK UPA00664 satisfiability review
The species-aware UPA00664 review supports lgt/PP_5142/Q88CN8 as the single high-confidence KT2440 Lgt candidate and warns not to count the PP_4236 DsbE/CcmG-like protein as a second Lgt.
file:projects/P_PUTIDA/deep-research/PSEPK__apolipoprotein_n_acyltransferase__upa00666-deep-research-openscientist.md
OpenScientist PSEPK UPA00666 satisfiability review
The species-aware UPA00666 review supports lnt/PP_4790/Q88DN4 as the single high-confidence KT2440 Lnt candidate and notes intact neighboring Lgt, LspA, and Lol machinery.
file:projects/P_PUTIDA/deep-research/PSEPK__bacterial_lipoprotein_maturation__upa00665-deep-research-openscientist.md
OpenScientist PSEPK UPA00665 satisfiability review
The species-aware UPA00665 review supports lspA/PP_0604/Q88Q91 as the KT2440 signal-peptidase-II step and treats the lspA-only candidate list as a KEGG-boundary artifact, because the adjacent Lgt and Lnt steps are encoded by PP_5142 and PP_4790.
file:modules/bacterial_lipoprotein_maturation-deep-research-openscientist.md
OpenScientist module research for bacterial lipoprotein maturation
OpenScientist supports the reusable boundary as a strictly ordered Lgt-to-LspA-to-terminal-acylation maturation module, separates downstream Lol sorting and substrate-specific lipoprotein functions, and emphasizes that the terminal N-acylation chemistry is lineage-variable.
file:PSEPK/lgt/lgt-ai-review.yaml
Curated lgt review
The lgt review accepts phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activity, plasma membrane localization, and lipoprotein biosynthetic process.
file:PSEPK/lspA/lspA-ai-review.yaml
Curated lspA review
The lspA review accepts LspA's aspartic-type endopeptidase activity and plasma membrane localization, modifies broad proteolysis to lipoprotein biosynthetic process, and proposes a more specific lipoprotein signal peptidase activity term.
file:PSEPK/lnt/lnt-ai-review.yaml
Curated lnt review
The lnt review accepts or refines annotations to N-acyltransferase activity, plasma membrane localization, and lipoprotein biosynthetic process.

Reusable boundary: this module models maturation chemistry, not all proteins that later behave as mature lipoproteins. The canonical diderm route is Lgt-dependent diacylglyceryl transfer, LspA signal peptide cleavage, and Lnt N-acylation. Monoderm lineages can retain Lgt/LspA but use non-orthologous or variable terminal modification; those variants should be modeled explicitly rather than forcing Lnt where it is absent. The PSEPK instantiation is satisfiable with lgt/Q88CN8, lspA/Q88Q91, and lnt/Q88DN4 as local UniProt exemplars.

4Nodes
3Parts
0Variant Sets
0Variants
3Annotons
2Connections

Derived QC

Recommended-field compliance

52.4% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)
  • module.knowledge_gaps[1] · status (0/1)
  • module.knowledge_gaps[1] · provenance (0/1)
  • module.knowledge_gaps[2] · status (0/1)
  • module.knowledge_gaps[2] · provenance (0/1)
  • module.knowledge_gaps[3] · status (0/1)
  • module.knowledge_gaps[3] · provenance (0/1)
  • module.knowledge_gaps[4] · status (0/1)
  • module.knowledge_gaps[4] · provenance (0/1)

Module deep research

✓ present

  • bacterial_lipoprotein_maturation-deep-research-openscientist.md (openscientist)

Leaf nodes lacking representative members

✓ every leaf node grounds to a representative protein.

Template conformance

✓ every declared conforms_to bundle matches its template motif.

Reaction chaining (advisory)

✓ every PRECEDES step chains, or its break is acknowledged via chaining_status.

  • lgt_diacylglyceryl_transfer_step → lspa_signal_peptide_cleavage_step [NOT_CHECKED]
  • lspa_signal_peptide_cleavage_step → lnt_n_acylation_step [NOT_CHECKED]

Gene-review completeness (3/3 grounded genes reviewed)

3 complete review(s) · 3 with deep research · 0 missing review · 0 reviewed but lacking deep research

Gene Review Complete Deep research
lgt Q88CN8 ✓ ✓ ✓
lnt Q88DN4 ✓ ✓ ✓
lspA Q88Q91 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
plasma membraneGO:0005886
Bacterial lipoprotein maturationBiological Processbacterial_lipoprotein_maturation
lipoprotein biosynthetic processGO:0042158
Context
bacteriaNCBITaxon:2
plasma membraneGO:0005886

Connections

Part 1: Diacylglyceryl transfer to prolipoprotein cysteine
Lgt diacylglyceryl transferReactionlgt_diacylglyceryl_transfer_step

Lgt transfers a diacylglyceryl group from phosphatidylglycerol to the conserved cysteine of a lipobox-containing prolipoprotein.

Annotons

Lgt family: prolipoprotein diacylglyceryl transferase
lgt_diacylglyceryl_transferase
Participant: Family: prolipoprotein diacylglyceryl transferase family
Family:
prolipoprotein diacylglyceryl transferase familyInterPro:IPR001640
Representative Members: PSEPK lgt exemplarUniProtKB:Q88CN8

Function

phosphatidylglycerol-prolipoprotein diacylglyceryl transferase activityGO:0008961

Processes

lipoprotein biosynthetic processGO:0042158

Locations

plasma membraneGO:0005886

First committed lipidation step; creates the diacylglyceryl prolipoprotein substrate required by LspA.

Part 2: Signal peptide cleavage from diacylglyceryl-prolipoprotein
LspA signal peptide cleavageReactionlspa_signal_peptide_cleavage_step

LspA/signal peptidase II removes the signal peptide immediately N-terminal to the diacylglyceryl-modified lipobox cysteine.

Annotons

LspA family: signal peptidase II
lspa_signal_peptidase_ii
Participant: Family: lipoprotein signal peptidase family
Family:
lipoprotein signal peptidase familyPANTHER:PTHR33695
Representative Members: PSEPK lspA exemplarUniProtKB:Q88Q91

Function

aspartic-type endopeptidase activityGO:0004190

Processes

lipoprotein biosynthetic processGO:0042158

Locations

plasma membraneGO:0005886

Ordered middle step; acts after Lgt lipidation and before terminal N-acylation by Lnt or a lineage-specific equivalent.

Part 3: Terminal N-acylation of apolipoprotein
Lnt N-acylationReactionlnt_n_acylation_step

Lnt transfers an acyl chain from a glycerophospholipid donor to the N-terminal cysteine amino group of a diacylglyceryl apolipoprotein.

Annotons

Lnt family: apolipoprotein N-acyltransferase
lnt_n_acyltransferase
Participant: Family: apolipoprotein N-acyltransferase family
Family:
apolipoprotein N-acyltransferase familyInterPro:IPR004563
Representative Members: PSEPK lnt exemplarUniProtKB:Q88DN4

Function

apolipoprotein N-acyltransferase activityGO:0016747

Processes

lipoprotein biosynthetic processGO:0042158

Locations

plasma membraneGO:0005886

Terminal diderm lipoprotein-maturation step; creates the mature triacylated lipoprotein used by downstream envelope sorting systems.