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_maturationCOMPLETECONCRETEMetabolic 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:ECOLI/queF/queF-uniprot.txt
UniProtKB entry for ECOLI QueF
Q46920 is a reviewed NADPH-dependent preQ1 synthase assigned Rhea 13409 and EC 1.7.1.13 with experimental evidence, and is highly specific for preQ0.
file:ECOLI/tgt/tgt-uniprot.txt
UniProtKB entry for ECOLI Tgt
P0A847 is a reviewed zinc-dependent tRNA-guanine transglycosylase assigned Rhea 24104 and EC 2.4.2.29 with experimental evidence.
file:ECOLI/queA/queA-uniprot.txt
UniProtKB entry for ECOLI QueA
P0A7F9 is a reviewed S-adenosylmethionine:tRNA ribosyltransferase-isomerase assigned Rhea 32155 and EC 2.4.99.17 with experimental evidence, and follows an ordered bi-ter mechanism.
file:ECOLI/queG/queG-uniprot.txt
UniProtKB entry for ECOLI QueG
P39288 is assigned epoxyqueuosine reductase activity, Rhea 32159, cob(II)alamin and two [4Fe-4S] clusters, and its deletion accumulates epoxyqueuosine while lacking queuosine.
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:8323579
tRNA-guanine transglycosylase from Escherichia coli. Overexpression, purification and quaternary structure.
Escherichia coli K-12 is the organism in which the ordered steps of this module were established experimentally, so its QueF, Tgt, QueA and QueG are carried as reviewed exemplars beside the Pseudomonas putida KT2440 set.
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, and Acinetobacter baylyi ADP1 encodes both. Ontology note: GO:0008479 formally defines free-queuine insertion (RHEA:16633), while the GOC-maintained IPR004803 and MF_00168 rules apply it to bacterial preQ1-inserting Tgt. The module keeps GO:0008479 as the established bacterial mapping, uses a preQ1-specific preferred term and Rhea 24104 for the exact chemistry, and the Tgt gene reviews carry a proposed bacterial preQ1 transglycosylase term. Family note: PTHR46499 also contains archaeal tRNA-guanine(15) transglycosylases in the same subfamily (SF1) and archaeosine synthases in SF2, so its family review scopes GO:0008479 to SF1 rather than family-wide; HAMAP MF_00168 and NCBIfam TIGR00430 are the discriminating signatures for bacterial Tgt. That restriction is the source of the single remaining module_validator warning (FAMILY_SCOPE_RESTRICTED on tgt_activity): the family grounding is correct for both Tgt representatives, and the scope is narrowed truthfully rather than widened to silence the check. PAINT has no node-level annotations for PTHR36701, so the QueH descriptor asserts no ancestral node.

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

Derived QC

Recommended-field compliance

100.0% recommended fields populated

All recommended fields populated.

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.

Function consistency and core coverage

10 gene-function check(s) reflected in core functions · 0 conflict(s) · 1 evidence or coverage gap(s) (15 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
quef_activity QueF (Escherichia coli K-12)
UniProtKB:Q46920
Family Representative 		preQ1 synthase activity
GO:0033739 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
quef_activity QueF (Pseudomonas putida KT2440)
UniProtKB:Q88KX9
Family Representative 		preQ1 synthase activity
GO:0033739 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tgt_activity Tgt (Escherichia coli K-12)
UniProtKB:P0A847
Family Representative 		bacterial tRNA-guanosine(34) preQ1 transglycosylase activity
GO:0008479 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
tgt_activity Tgt (Pseudomonas putida KT2440)
UniProtKB:Q88PL7
Family Representative 		bacterial tRNA-guanosine(34) preQ1 transglycosylase activity
GO:0008479 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
quea_activity QueA (Escherichia coli K-12)
UniProtKB:P0A7F9
Family Representative 		S-adenosylmethionine:tRNA ribosyltransferase-isomerase activity
GO:0051075 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
quea_activity QueA (Pseudomonas putida KT2440)
UniProtKB:Q88PL8
Family Representative 		S-adenosylmethionine:tRNA ribosyltransferase-isomerase activity
GO:0051075 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
queg_activity QueG (Escherichia coli K-12)
UniProtKB:P39288
Family Representative 		epoxyqueuosine reductase activity
GO:0052693 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
queg_activity QueG (Pseudomonas putida KT2440)
UniProtKB:Q88DC7
Family Representative 		epoxyqueuosine reductase activity
GO:0052693 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
queh_activity QueH (Thermotoga maritima)
UniProtKB:Q9WZJ0
Family Representative 		epoxyqueuosine reductase activity
GO:0052693 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
queh_activity QueH (Acinetobacter baylyi ADP1)
UniProtKB:Q6FAK7
Family Representative 		epoxyqueuosine reductase activity
GO:0052693 		Core Supported
The GO molecular function is reflected in core_functions (exact term or a reviewed subclass).
quef_activity QueF preQ1 synthase family
PANTHER:PTHR34354
Family 		preQ1 synthase activity
GO:0033739 		Family Supported
Family review supports GO:0033739 FAMILY_WIDE. Single subfamily of type 2 QueF enzymes. Accepted as core by the E. coli and P. putida gene reviews, and asserted by the queuosine maturation module.
tgt_activity bacterial Tgt family
PANTHER:PTHR46499
Family 		bacterial tRNA-guanosine(34) preQ1 transglycosylase activity
GO:0008479 		Family Scope Restricted
GO:0008479 is SUBFAMILY_ONLY; this family grounding does not establish the allowed subfamily scope. GOC applies this term to bacterial Tgt (preQ1 insertion; InterPro2GO IPR004803). It holds for the Tgt members of SF1, including the E. coli and P. putida references, where it is accepted as core. It does not hold for the archaeal tRNA-guanine(15) transglycosylases in the same subfamily or for SF2 archaeosine synthases. A preQ1-specific bacterial term has been proposed in the gene reviews.
quea_activity QueA family
PANTHER:PTHR30307
Family 		S-adenosylmethionine:tRNA ribosyltransferase-isomerase activity
GO:0051075 		Family Supported
Family review supports GO:0051075 FAMILY_WIDE. Single QueA subfamily. Accepted as core by the E. coli and P. putida gene reviews, and asserted by the queuosine maturation module.
queg_activity QueG epoxyqueuosine reductase family
PANTHER:PTHR30002
Family 		epoxyqueuosine reductase activity
GO:0052693 		Family Supported
Family review supports GO:0052693 FAMILY_WIDE. Single QueG subfamily. Accepted as core by the E. coli and P. putida gene reviews, and asserted by the queuosine maturation module. The one uncharacterized Geobacillus member is named as an unknown protein rather than excluded.
queh_activity QueH epoxyqueuosine reductase family
PANTHER:PTHR36701:SF1
Family 		epoxyqueuosine reductase activity
GO:0052693 		Family Supported
Family review supports GO:0052693 FAMILY_WIDE. Single subfamily. Genes from eight phylogenetically distant members of this family, including the Thermotoga reference, each restored queuosine in an E. coli queG deletion, so the activity is family-wide rather than lineage-specific. Both reviewed members accept it as core, and the queuosine maturation module asserts it for the QueH route.

Gene-review completeness (10/10 grounded genes reviewed)

10 complete review(s) · 1 with deep research · 0 missing review · 9 reviewed but lacking deep research

Gene Review Complete Deep research
queA P0A7F9 ✓ ✓ ✗
queA Q88PL8 ✓ ✓ ✗
queF Q46920 ✓ ✓ ✗
queF Q88KX9 ✓ ✓ ✗
queG P39288 ✓ ✓ ✗
queG Q88DC7 ✓ ✓ ✗
queH Q6FAK7 ✓ ✓ ✗
queH Q9WZJ0 ✓ ✓ ✗
tgt P0A847 ✓ ✓ ✗
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 (Escherichia coli K-12)UniProtKB:Q46920 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 (Escherichia coli K-12)UniProtKB:P0A847 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 (Escherichia coli K-12)UniProtKB:P0A7F9 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 (Escherichia coli K-12)UniProtKB:P39288 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 current PTHR36701 PAINT refresh resolves no node-level annotations, so no ancestral PTN is asserted and no empty local slice is retained.
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.