Bacterial preQ1 incorporation and queuosine maturation

A reusable bacterial pathway that converts preQ0 to the mature queuosine modification at wobble position 34 of tRNA(Asp), tRNA(Asn), tRNA(His), and tRNA(Tyr). QueF reduces preQ0 to preQ1, Tgt exchanges guanine-34 for preQ1, QueA transfers and rearranges the ribose moiety of S-adenosylmethionine to form epoxyqueuosine, and either QueG or the nonhomologous QueH family reduces epoxyqueuosine to queuosine.

MODULE:bacterial_preq1_incorporation_queuosine_maturationDRAFTCONCRETEMetabolic Pathwaymodules/bacterial_preq1_incorporation_queuosine_maturation.yaml
tRNA queuosine(34) biosynthetic processGO:0008616
GO:0008616
tRNA queuosine(34) biosynthetic process
GO:0008616 captures formation of queuosine at position 34 through the four reactions in this module.
UniPathway:UPA00392
tRNA-queuosine biosynthesis
The four PSEPK proteins carry UniPathway UPA00392 membership.
file:PSEPK/queF/queF-uniprot.txt
UniProtKB entry for PSEPK QueF
Q88KX9 is a reviewed NADPH-dependent preQ1 synthase assigned Rhea 13409.
file:PSEPK/tgt/tgt-uniprot.txt
UniProtKB entry for PSEPK Tgt
Q88PL7 is a reviewed tRNA-guanine transglycosylase assigned Rhea 24104.
file:PSEPK/queA/queA-uniprot.txt
UniProtKB entry for PSEPK QueA
Q88PL8 is a reviewed S-adenosylmethionine:tRNA ribosyltransferase-isomerase assigned Rhea 32155.
file:PSEPK/queG/queG-uniprot.txt
UniProtKB entry for PSEPK QueG
Q88DC7 is assigned epoxyqueuosine reductase activity and Rhea 32159.
file:modules/bacterial_preq1_incorporation_queuosine_maturation-deep-research-openscientist.md
Reusable-module research for bacterial queuosine maturation
The pathway has the ordered core QueF, Tgt, QueA, and a final QueG or QueH epoxyqueuosine reductase, while preQ0 synthesis and salvage are outside this module boundary.
PMID:34652139
Epoxyqueuosine Reductase QueH in the Biosynthetic Pathway to tRNA Queuosine Is a Unique Metalloenzyme.
QueH is a structurally distinct, cobalamin-independent replacement or supplement for QueG that catalyzes the terminal epoxyqueuosine-reduction step.
PMID:28128549
Identification of a Novel Epoxyqueuosine Reductase Family by Comparative Genomics.
Double-deletion and heterologous-complementation experiments establish DUF208/QueH as a nonorthologous QueG replacement, while Acinetobacter baylyi demonstrates that both families can coexist.
UniProtKB:Q9WZJ0
Reviewed Thermotoga maritima QueH exemplar
Q9WZJ0 is a reviewed QueH epoxyqueuosine reductase in InterPro IPR003828 and PANTHER PTHR36701.

This module begins with preQ0 supplied by upstream 7-deazaguanine biosynthesis and ends with mature Q34-tRNA. QueF therefore belongs here as the committed preQ1-supply reaction, but FolE/QueD/QueE/QueC and GTP supply are outside the boundary. The eukaryotic queuine-salvage route is also outside this bacterial module. Generic electron-donor regeneration and synthesis of the cobalamin and iron-sulfur cofactors used by QueG or the iron-sulfur cofactor used by QueH are supporting context, not pathway parts. Pseudomonas putida KT2440 implements the terminal step with QueG; QueH is retained as a reusable nonhomologous alternative.

7Nodes
4Parts
1Variant Sets
2Variants
5Annotons
3Connections

Derived QC

Recommended-field compliance

60.0% recommended fields populated
  • module.knowledge_gaps[0] · status (0/1)
  • module.knowledge_gaps[0] · provenance (0/1)

Module deep research

✓ present

  • bacterial_preq1_incorporation_queuosine_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.

Gene-review completeness (4/6 grounded genes reviewed)

4 complete review(s) · 1 with deep research · 2 missing review · 3 reviewed but lacking deep research

Gene Review Complete Deep research
QueH (Acinetobacter baylyi ADP1) Q6FAK7 ✗ — —
QueH (Thermotoga maritima) Q9WZJ0 ✗ — —
queA Q88PL8 ✓ ✓ ✗
queF Q88KX9 ✓ ✓ ✗
queG Q88DC7 ✓ ✓ ✗
tgt Q88PL7 ✓ ✓ ✓

Details

Context
bacteriaNCBITaxon:2
Bacterial preQ1 incorporation and queuosine maturationMetabolic Pathwaybacterial_preq1_incorporation_queuosine_maturation
tRNA queuosine(34) biosynthetic processGO:0008616
Context
bacteriaNCBITaxon:2

Connections

QueF supplies preQ1 to Tgt.
Tgt produces the preQ1-tRNA consumed by QueA.
QueA produces the epoxyqueuosine-tRNA consumed by QueG or QueH.
Part 1: preQ1 formation
QueF-dependent preQ1 formationReactionquef_preq1_formation

Annotons

QueF preQ1 synthase activity
quef_activity
Participant: Family: QueF preQ1 synthase family
Family:
QueF preQ1 synthase familyPANTHER:PTHR34354
Representative Members: QueF (Pseudomonas putida KT2440)UniProtKB:Q88KX9

Function

preQ1 synthase activityGO:0033739
Substrates: 7-cyano-7-carbaguanine (preQ0) NADPH
Products: 7-aminomethyl-7-carbaguanine (preQ1) NADP+

Processes

tRNA queuosine(34) biosynthetic processGO:0008616

Supplies preQ1 for base exchange into target tRNAs.

Part 2: preQ1 incorporation at tRNA position 34
Tgt-dependent preQ1-tRNA formationReactiontgt_preq1_incorporation

Annotons

Tgt tRNA-guanine transglycosylase activity
tgt_activity
Participant: Family: bacterial Tgt family
Family:
bacterial Tgt familyPANTHER:PTHR46499
Representative Members: Tgt (Pseudomonas putida KT2440)UniProtKB:Q88PL7

Function

bacterial tRNA-guanosine(34) preQ1 transglycosylase activityGO:0008479
Substrates: preQ1 guanosine(34)-containing target tRNA
Products: preQ1-modified tRNA guanine

Processes

tRNA queuosine(34) biosynthetic processGO:0008616

Covalently installs preQ1 at the anticodon wobble position.

Part 3: epoxyqueuosine formation
QueA-dependent epoxyqueuosine formationReactionquea_epoxyqueuosine_formation

Annotons

QueA SAM:tRNA ribosyltransferase-isomerase activity
quea_activity
Participant: Family: QueA family
Family:
QueA familyPANTHER:PTHR30307
Representative Members: QueA (Pseudomonas putida KT2440)UniProtKB:Q88PL8

Function

S-adenosylmethionine:tRNA ribosyltransferase-isomerase activityGO:0051075
Substrates: preQ1-modified tRNA S-adenosyl-L-methionine
Products: epoxyqueuosine-modified tRNA adenine L-methionine

Processes

tRNA queuosine(34) biosynthetic processGO:0008616

Builds the cyclopentenediol-containing epoxyqueuosine intermediate.

Part 4: epoxyqueuosine reduction
QueG- or QueH-dependent queuosine formationReactionepoxyqueuosine_reduction

QueG and QueH are nonhomologous solutions for the same terminal reaction. At least one route is required, and some genomes may encode both families.

Variant set: Epoxyqueuosine reductase family variants by enzyme family (One Or More)
Cobalamin-dependent QueG routeReactionqueg_epoxyqueuosine_reductase_variant

Annotons

QueG epoxyqueuosine reductase activity
queg_activity
Participant: Family: QueG epoxyqueuosine reductase family
Family:
QueG epoxyqueuosine reductase familyPANTHER:PTHR30002
Representative Members: QueG (Pseudomonas putida KT2440)UniProtKB:Q88DC7

Function

epoxyqueuosine reductase activityGO:0052693
Substrates: epoxyqueuosine-modified tRNA reduced electron donor
Products: queuosine-modified tRNA oxidized electron donor water

Processes

tRNA queuosine(34) biosynthetic processGO:0008616

Completes mature Q34 formation through the cobalamin-dependent QueG route.

Cobalamin-independent QueH routeReactionqueh_epoxyqueuosine_reductase_variant

Annotons

QueH epoxyqueuosine reductase activity
queh_activity
Participant: Family: QueH epoxyqueuosine reductase family
Family:
QueH epoxyqueuosine reductase familyPANTHER:PTHR36701:SF1 The local PTHR36701 PAINT export contains no node-level annotations, so no ancestral PTN is asserted.
Representative Members: QueH (Thermotoga maritima)UniProtKB:Q9WZJ0 QueH (Acinetobacter baylyi ADP1)UniProtKB:Q6FAK7

Function

epoxyqueuosine reductase activityGO:0052693
Substrates: epoxyqueuosine-modified tRNA reduced electron donor
Products: queuosine-modified tRNA oxidized electron donor water

Processes

tRNA queuosine(34) biosynthetic processGO:0008616

Completes mature Q34 formation through the cobalamin-independent QueH route.