Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003684 damaged DNA binding	IEA GO_REF:0000104	MARK AS OVER ANNOTATED	Summary: Compatible with mismatch recognition but too broad when mismatched DNA binding and ATP-dependent DNA damage sensor activity are available. Reason: The specific mismatch-sensor terms capture the core activity.
GO:0003690 double-stranded DNA binding	IEA GO_REF:0000118	MARK AS OVER ANNOTATED	Summary: MutS acts on duplex DNA, but this generic binding term loses the mismatch specificity that defines its function. Reason: GO:0030983 is the informative substrate-specific term.
GO:0005524 ATP binding	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: Retain as non-core. ATP binding is required for the MutS conformational cycle, but the integrated sensor term is more informative. Reason: Correct mechanistic property subsumed by GO:0140664.
GO:0005829 cytosol	IEA GO_REF:0000118	ACCEPT	Summary: Accept as the leaf-level location of the soluble bacterial mismatch sensor. Reason: Consistent with the reviewed protein record and chromosomal DNA substrate.
GO:0006298 mismatch repair	IEA GO_REF:0000120	ACCEPT	Summary: Accept. KT2440 recombineering experiments directly tested permanent mutS deletion and established a MutS-dependent hierarchy of mismatch correction. Reason: Core biological process with direct organism-specific genetic support. Supporting Evidence: PMID:31599106 permanent deletion of mutS or transient loss of mutL activity
GO:0030983 mismatched DNA binding	IEA GO_REF:0000120	ACCEPT	Summary: Accept as the substrate-specific recognition function of MutS. Reason: MutS is the mismatch-recognition component, unlike downstream MutL. Supporting Evidence: file:PSEPK/mutS/mutS-uniprot.txt mismatch recognition step
GO:0140664 ATP-dependent DNA damage sensor activity	IEA GO_REF:0000002	ACCEPT	Summary: Accept as the most informative integrated molecular function. MutS couples recognition of mismatched DNA to an ATP-dependent signaling transition that initiates repair. Reason: Captures both lesion sensing and the essential ATPase-driven switch.

Core Functions

MutS recognizes mismatches in duplex DNA and couples recognition to an ATP-dependent signaling-clamp transition that recruits downstream mismatch-repair machinery.

Molecular Function:

ATP-dependent DNA damage sensor activity

Directly Involved In:

mismatch repair

Cellular Locations:

cytosol

Supporting Evidence:

file:PSEPK/mutS/mutS-uniprot.txt
mismatch recognition step
PMID:31599106
permanent deletion of mutS or transient loss of mutL activity

Binds mismatched duplex DNA as the substrate-recognition step that precedes the ATP-dependent signaling transition.

Molecular Function:

mismatched DNA binding

Directly Involved In:

mismatch repair

Cellular Locations:

cytosol

Supporting Evidence:

file:PSEPK/mutS/mutS-uniprot.txt
mismatch recognition step

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000104

Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features

GO_REF:0000118

TreeGrafter-generated GO annotations

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

file:PSEPK/mutS/mutS-uniprot.txt

UniProtKB entry for PSEPK MutS (Q88ME7)

"This protein is involved in the repair of mismatches in DNA."
"mismatch recognition step"

PMID:31599106

Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene.

"permanent deletion of mutS or transient loss of mutL activity"
"data unequivocally established the hierarchy"

Suggested Experiments

Experiment: Measure binding, ATPase activity, and sliding-clamp formation on matched duplexes and the mismatch classes ranked by the KT2440 recombineering study.

Hypothesis: KT2440 MutS ATPase switching differs quantitatively across mismatch classes.

Type: purified-protein mismatch recognition and ATPase assay

Deep Research

Falcon

(mutS-deep-research-falcon.md)

Research Report: Functional Annotation of **mutS** (UniProt: **Q88ME7**; locus **PP_1626**) in *Pseudomonas putida* KT2440 Falcon Edison Scientific Literature 28 citations 2 artifacts 2026-06-11T21:28:13.877826

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000024 Figure 3 on page 4 reports the mutation frequencies and fold-changes for the pS2311M and pS2514M conditional mutator devices. Speci (image/png)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Functional Annotation of mutS (UniProt: Q88ME7; locus PP_1626) in Pseudomonas putida KT2440

1. Target verification (gene/protein identity)

The target protein is MutS, a canonical DNA mismatch repair (MMR) mismatch-recognition ATPase in Pseudomonas putida strain KT2440 (gene mutS, locus PP_1626, UniProt Q88ME7). P. putida KT2440 is reported to encode mutS and mutL but lacks a bona fide mutH homolog, indicating an “abridged” bacterial MMR architecture relative to E. coli’s MutS/MutL/MutH pathway. (aparicio2020mismatchrepairhierarchy pages 1-2)

2. Key concepts & current mechanistic understanding (2024-focused)

2.1 Definition: what MutS does

MutS is the initiating sensor of post-replicative mismatch repair, detecting replication errors (base–base mismatches and small insertion–deletion loops, IDLs), and then coordinating recruitment/activation of downstream repair factors (notably MutL-family proteins) to remove the error-containing nascent strand segment and restore the correct sequence. (waters2024newdiscoverieson pages 8-9, zarb2024singlemoleculeprobing pages 20-28)

2.2 Substrate specificity (mismatch types)

MutS recognizes single-base mismatches and small IDLs, with strong preference for single-base IDLs over larger loops (larger IDLs are inefficiently recognized/processed by MutS alone, implying different handling or reduced repair). (zarb2024singlemoleculeprobing pages 57-61, zarb2024singlemoleculeprobing pages 61-65)

2.3 Core MutS catalytic cycle: ATP/ADP-driven conformational switching and sliding clamp

Recent single-molecule kinetic work (largely in E. coli MutS, used here as mechanistic inference for bacterial MutS family members) supports a nucleotide-state model:

Scanning state: MutS in an ADP-bound/open conformation scans dsDNA for helix distortions from mismatches. (zarb2024singlemoleculeprobing pages 57-61)
Mismatch recognition: mismatch binding is ATP-independent in the sense that MutS can bind mismatches without ATP, but ATP strongly enhances productive transitions. Binding induces a sharp DNA bend/kink (≈ 60°) and involves localized mismatch-contact residues including a conserved Phe-X-Glu motif. (zarb2024singlemoleculeprobing pages 15-20)
Activation and “sliding clamp” formation: after mismatch binding, ADP→ATP exchange and binding of two ATP molecules per MutS dimer triggers a conformational change into a ring-like sliding clamp that releases the mismatch site and diffuses along dsDNA, facilitating recruitment/loading of MutL. (zarb2024singlemoleculeprobing pages 20-28, zarb2024singlemoleculeprobing pages 57-61)
Resetting: the sliding-clamp state is long-lived on dsDNA; ATP hydrolysis and reopening/reset is associated with encountering ssDNA regions, gaps, or DNA breaks, returning MutS to a scanning-competent state. (zarb2024singlemoleculeprobing pages 57-61)

Quantitative kinetic parameters from single-molecule measurements illustrate nucleotide control. For example, for a CC mismatch, the conformational-change rate k2 was reported as 0.007 ± 0.001 s⁻¹ with 1 mM ADP versus 0.57 ± 0.01 s⁻¹ with 1 mM ATP, highlighting strong ATP dependence and ADP dampening; clamp-formation rate is reduced by physiologic ADP levels. (zarb2024singlemoleculeprobing pages 52-57, zarb2024singlemoleculeprobing pages 57-61)

2.4 “Action-at-a-distance” in MMR: how mismatch recognition communicates with distant incision sites (2024 expert synthesis)

A key unresolved/active research area is how mismatch detection by MutS leads to strand incision/excision at sites that may be distant from the mismatch. A 2024 review synthesizes evidence into three non-exclusive model classes:

Tracking/sliding: ATP-bound MutS (and/or MutL) moves along DNA as a sliding clamp, creating a distribution of repair factors along the DNA that enables incision at a distance. (collingwood2024actionatadistanceindna pages 1-3, collingwood2024actionatadistanceindna pages 4-6)
DNA looping/loop extrusion: ATP-dependent translocation could extrude DNA loops, bridging mismatch and incision sites. (collingwood2024actionatadistanceindna pages 4-6, collingwood2024actionatadistanceindna pages 1-3)
Oligomerization/bridging: MutS can remain mismatch-bound while MutL-family assemblies bridge the gap, potentially altering DNA topology and facilitating incision. (collingwood2024actionatadistanceindna pages 4-6, collingwood2024actionatadistanceindna pages 1-3)

Crucially, this review contrasts E. coli’s MutH-dependent pathway with MutH-lacking systems where MutL-family proteins provide endonuclease activity to create nicks on the nascent strand, requiring robust long-range communication mechanisms. This distinction is directly relevant to P. putida KT2440, which lacks MutH. (collingwood2024actionatadistanceindna pages 3-4, aparicio2020mismatchrepairhierarchy pages 1-2)

3. Pseudomonas putida KT2440/EM42-specific functional evidence

3.1 Pathway context in P. putida: abridged MutS/MutL system

In P. putida KT2440, MMR is described as comprising MutS and MutL homologs without MutH, motivating empirical measurement of mismatch-type sensitivity in this organism. (aparicio2020mismatchrepairhierarchy pages 1-2)

3.2 Organism-specific mismatch recognition/repair hierarchy

Using ssDNA recombineering of pyrF under wild-type conditions, ΔmutS, and transient MutL inhibition (dominant-negative mutL E36K), a mismatch-recognition hierarchy was established for P. putida:

A:G < C:C < G:A < C:A, A:A, G:G, T:T, T:G, A:C, C:T < G:T, T:C. (aparicio2020mismatchrepairhierarchy pages 1-2)

This is a key, direct P. putida-specific functional annotation point: MutS-dependent MMR does not correct all mismatches equally; rather, mismatch identity strongly affects whether introduced base substitutions are rejected or tolerated. (aparicio2020mismatchrepairhierarchy pages 1-2)

4. Cellular localization and interaction partners (with organism-specific caveats)

4.1 Where MutS acts in the cell

Direct imaging or subcellular localization measurements for MutS in P. putida KT2440 were not found in the retrieved corpus. However, based on conserved bacterial MutS biochemistry, its site of action is intracellular on chromosomal DNA (nucleoid-associated) during/after replication when mismatches arise. (zarb2024singlemoleculeprobing pages 20-28, waters2024newdiscoverieson pages 8-9)

4.2 Interaction partners and pathway components

P. putida sources explicitly describe MutS recruiting MutL as an initiating step (canonical MMR). (fernandezcabezon2021spatiotemporalmanipulationof pages 2-3)

Because P. putida lacks MutH, its strand incision is expected to be MutL-mediated (endonuclease-capable MutL systems) or reliant on pre-existing discontinuities, consistent with the broader MutH-lacking MMR paradigm described in 2024 expert synthesis. (collingwood2024actionatadistanceindna pages 3-4, collingwood2024actionatadistanceindna pages 1-3)

A P. putida KT2440 study discussing MMR notes that strand discrimination “could involve the beta clamp of the replication machinery,” citing prior work (in other bacteria) connecting replication clamps to MMR positioning, but this is not direct biochemical evidence in P. putida. (aparicio2020mismatchrepairhierarchy pages 8-9)

5. Recent developments and latest research (prioritizing 2023–2024)

5.1 2024: Mechanistic models for long-range communication in MMR

The 2024 Biomolecules review emphasizes that “action-at-a-distance” remains incompletely explained and that multiple mechanisms likely coexist, with organism-specific differences between bacterial and eukaryotic systems and between MutH-dependent vs MutH-lacking pathways. (collingwood2024actionatadistanceindna pages 4-6, collingwood2024actionatadistanceindna pages 3-4)

5.2 2024: Single-molecule quantification of nucleotide effects on MutS clamp formation

Recent single-molecule work quantifies how ATP promotes mismatch binding and sliding-clamp formation, while physiologic ADP buffers/dampens clamp formation and conformational changes, providing a kinetic basis for how cellular nucleotide pools can tune MMR initiation. (zarb2024singlemoleculeprobing pages 52-57, zarb2024singlemoleculeprobing pages 57-61)

5.3 2024: Review-level synthesis of early recruitment/regulation

A 2024 review of early DNA damage response steps summarizes the widely accepted MMR recruitment cascade in which MutS-family sensors detect replication errors, then recruit MutL-family proteins whose nuclease activity (in MutH-lacking systems) can be activated in coordination with replication-associated clamps (e.g., PCNA in eukaryotes), followed by excision and resynthesis. (waters2024newdiscoverieson pages 8-9)

6. Current applications and real-world implementations (with quantitative results)

6.1 Controllable “mutator devices” in P. putida KT2440 (synthetic biology; 2021 foundational implementation)

A demonstrated real-world implementation for P. putida is spatiotemporal manipulation of MMR to accelerate evolution/phenotype emergence using inducible expression of a dominant-negative mutL E36K allele on broad-host-range plasmids.

Quantitative outcomes (mutation frequency readouts in rpoB and rpsL via antibiotic resistance):

Cyclohexanone-inducible device pS2311M: up to 438-fold increase in rifampicin-resistant mutants and 10-fold increase in streptomycin-resistant mutants vs control (early exponential induction condition). (fernandezcabezon2021spatiotemporalmanipulationof pages 3-4, fernandezcabezon2021spatiotemporalmanipulationof media 45d6effd)
Thermoinducible device pS2514M: 45-fold increase in rifampicin-resistant mutants and 14-fold increase in streptomycin-resistant mutants vs control (under the described induction protocol). (fernandezcabezon2021spatiotemporalmanipulationof pages 3-4, fernandezcabezon2021spatiotemporalmanipulationof media 45d6effd)

The same work cites prior evidence that a ΔmutS KT2440 derivative has ~1000-fold higher frequency of rifampicin-resistant mutants than wild type, illustrating the strong constitutive mutator phenotype expected when MutS is removed. (fernandezcabezon2021spatiotemporalmanipulationof pages 8-8)

These mutator devices were used to accelerate emergence of selectable phenotypes (e.g., antibiotic resistance) and to revert a synthetic uracil auxotrophy, and were positioned as tools to support adaptive laboratory evolution and metabolic cell factory optimization. (fernandezcabezon2021spatiotemporalmanipulationof pages 1-2)

6.2 Genome engineering / recombineering workflows using transient MMR suppression

A P. putida recombineering study explicitly frames permanent ΔmutS or transient MMR suppression (dominant-negative MutL) as a strategy to enable “bias-free” incorporation of base substitutions during ssDNA recombineering, supporting strain engineering methods for precise single-nucleotide changes. (aparicio2020mismatchrepairhierarchy pages 1-2, aparicio2020mismatchrepairhierarchy pages 8-9)

7. Interpretation for functional annotation of Q88ME7 (MutS) in P. putida KT2440

7.1 Primary molecular function

MutS (Q88ME7) functions as a DNA mismatch-recognition ATPase that initiates MMR by detecting mismatches/small IDLs in dsDNA and transitioning (ATP-driven) into a sliding clamp state that recruits MutL-family proteins to trigger downstream incision/excision and repair synthesis. (zarb2024singlemoleculeprobing pages 20-28, zarb2024singlemoleculeprobing pages 57-61)

7.2 Biological processes/pathways

MutS participates in replication fidelity maintenance through the DNA mismatch repair pathway, thereby suppressing spontaneous mutation accumulation; disabling MMR (ΔmutS or dominant-negative MutL) yields strong mutator phenotypes, directly demonstrated in P. putida KT2440 by large increases in antibiotic-resistant mutants. (fernandezcabezon2021spatiotemporalmanipulationof pages 3-4, fernandezcabezon2021spatiotemporalmanipulationof pages 8-8)

7.3 Cellular compartment

MutS action is best annotated as cytoplasmic / nucleoid-associated (DNA-bound), acting on chromosomal DNA. Direct P. putida-specific localization measurements were not identified in the retrieved sources, so this localization is inferred from conserved MutS family mechanism. (zarb2024singlemoleculeprobing pages 20-28, waters2024newdiscoverieson pages 8-9)

7.4 P. putida-specific nuance: mismatch preference matters

For P. putida, experimental evidence indicates that mismatch identity strongly controls repair sensitivity, yielding a specific mismatch hierarchy that should be considered when interpreting mutation spectra, designing recombineering oligos, or engineering directed evolution schemes. (aparicio2020mismatchrepairhierarchy pages 1-2)

8. Summary table (evidence map)

Topic	Concise finding	Quantitative / specific details	Key citations, DOI/URL, year
Verified target identity	Target matches MutS DNA mismatch repair protein: UniProt Q88ME7, gene mutS, ordered locus PP_1626, organism Pseudomonas putida KT2440; literature on P. putida MMR consistently treats MutS as the mismatch-recognition factor acting with MutL in an abridged, MutH-lacking bacterial MMR system. Conserved family/domain assignment is consistent with a canonical MutS DNA mismatch repair family ATPase/sliding-clamp protein.	P. putida encodes MutS and MutL but lacks a bona fide MutH homolog; therefore pathway inference should follow MutH-independent bacterial MMR, not the full E. coli 3-protein methyl-directed pathway.	(aparicio2020mismatchrepairhierarchy pages 1-2, collingwood2024actionatadistanceindna pages 3-4) Aparicio et al., Environ. Microbiol. DOI: https://doi.org/10.1111/1462-2920.14814 (2020); Collingwood et al., Biomolecules DOI: https://doi.org/10.3390/biom14111442 (2024)
Core MutS mechanism	MutS is the primary mismatch sensor. It scans dsDNA in an ADP-bound/open state, binds mismatches or small IDLs, then undergoes ADP→ATP exchange; binding of two ATP molecules converts the dimer to a closed/sliding-clamp state that leaves the mismatch and diffuses on DNA to recruit/load MutL. ATP hydrolysis resets the complex after encountering ssDNA/gaps or breaks.	MutS binds mismatched DNA with ~10–20-fold higher affinity than matched DNA; ATP can enhance mismatch binding up to ~29-fold for some mismatches; ADP reduces clamp-formation kinetics; example for CC mismatch: k2 = 0.007 ± 0.001 s⁻¹ with 1 mM ADP vs 0.57 ± 0.01 s⁻¹ with 1 mM ATP. DNA is kinked by ~60° upon mismatch recognition.	(zarb2024singlemoleculeprobing pages 57-61, zarb2024singlemoleculeprobing pages 20-28, zarb2024singlemoleculeprobing pages 61-65, zarb2024singlemoleculeprobing pages 15-20, zarb2024singlemoleculeprobing pages 52-57) Zarb (2024, single-molecule thesis/manuscript in retrieved corpus); Waters & Spratt, DOI: https://doi.org/10.3390/ijms25031676 (2024)
P. putida mismatch-recognition hierarchy	In P. putida, MMR shows a clear mismatch-recognition hierarchy rather than equal correction of all mismatches. This hierarchy was inferred by ssDNA recombineering in WT, ΔmutS, and transient mutL E36K inhibition backgrounds.	Reported hierarchy: A:G < C:C < G:A < C:A, A:A, G:G, T:T, T:G, A:C, C:T < G:T, T:C. This is the key organism-specific specificity result available for KT2440/EM42-related strains.	(aparicio2020mismatchrepairhierarchy pages 1-2) Aparicio et al., DOI: https://doi.org/10.1111/1462-2920.14814 (2020)
P. putida mutator phenotypes / MMR perturbation	Conditional inhibition of MMR in P. putida was implemented with plasmid-borne dominant-negative mutL E36K devices; these transiently elevate mutation frequency and accelerate phenotype emergence. A cited KT2440 ΔmutS strain shows a much stronger constitutive mutator phenotype.	KT2440/pS2311M: 438-fold increase in RifR and 10-fold increase in StrR vs control when induction ended in early exponential phase. KT2440/pS2514M: 45-fold RifR and 14-fold StrR increases. A cited prior study found ΔmutS KT2440 ~1000-fold higher RifR frequency vs WT. Mutation frequencies were reported as mutants per 10⁹ viable cells.	(fernandezcabezon2021spatiotemporalmanipulationof pages 3-4, fernandezcabezon2021spatiotemporalmanipulationof pages 8-8, fernandezcabezon2021spatiotemporalmanipulationof pages 4-5, fernandezcabezon2021spatiotemporalmanipulationof pages 1-2, fernandezcabezon2021spatiotemporalmanipulationof pages 6-7) Fernández-Cabezón et al., ACS Synth. Biol. DOI: https://doi.org/10.1021/acssynbio.1c00031 (2021)
Action-at-a-distance models	Recent expert synthesis concludes that communication between a mismatch-bound MutS complex and distant incision/excision sites can be explained by three non-exclusive model classes: tracking/sliding, DNA looping, and oligomerization/bridging. In MutH-lacking bacteria, MutL-family endonuclease activity substitutes for MutH-mediated nicking.	Sliding-clamp models: ATP-bound MutS diffuses away from the mismatch and recruits MutL. Looping models: ATP-driven translocation/extrusion brings distant sites together. Oligomerization models: MutS remains mismatch-bound while MutL/other factors bridge distance. Review emphasizes that mechanisms likely differ by organism and may coexist.	(collingwood2024actionatadistanceindna pages 4-6, collingwood2024actionatadistanceindna pages 3-4, collingwood2024actionatadistanceindna pages 1-3, collingwood2024actionatadistanceindna pages 12-14) Collingwood et al., Biomolecules DOI: https://doi.org/10.3390/biom14111442 (2024)
Pathway context and localization	Functional localization is intracellular, chromosome-associated (nucleoid/DNA-bound): MutS acts on newly replicated genomic DNA where replication errors arise, then coordinates with MutL and downstream excision/resynthesis factors. For P. putida, localization is inferred from conserved bacterial MutS biochemistry and organism-specific MMR genetics rather than direct localization imaging in the retrieved sources.	In canonical bacterial descriptions, downstream factors include MutL, helicase/excision factors such as UvrD and exonucleases, followed by DNA polymerase and ligase. In MutH-lacking systems, strand discrimination relies on MutL endonuclease/nicks or pre-existing discontinuities rather than MutH cleavage at hemimethylated GATC sites.	(aparicio2020mismatchrepairhierarchy pages 1-2, aparicio2020mismatchrepairhierarchy pages 12-13, collingwood2024actionatadistanceindna pages 3-4, collingwood2024actionatadistanceindna pages 1-3, waters2024newdiscoverieson pages 8-9) Aparicio et al., DOI: https://doi.org/10.1111/1462-2920.14814 (2020); Collingwood et al., DOI: https://doi.org/10.3390/biom14111442 (2024); Waters & Spratt, DOI: https://doi.org/10.3390/ijms25031676 (2024)

Table: This table condenses the verified identity, conserved mechanism, organism-specific mismatch preferences, quantitative mutator phenotypes, and current mechanistic models relevant to Pseudomonas putida KT2440 MutS (Q88ME7/PP_1626). It separates direct P. putida evidence from broader bacterial MutS mechanism needed for functional annotation.

9. Key limitations of available evidence for this specific protein

Direct MutS localization/interaction experiments in P. putida KT2440 (e.g., imaging at the replisome, co-IP with β-clamp) were not present in the retrieved corpus; thus, localization is annotated primarily by conserved mechanism with explicit caveats. (aparicio2020mismatchrepairhierarchy pages 8-9)
Some P. putida-specific quantitative results for ΔmutS (e.g., full mutation rate estimates, genome-wide spectra) are indicated to exist in supporting materials (e.g., “mutational activity” in supplementary figures) but were not extractable from the provided excerpts. (aparicio2020mismatchrepairhierarchy pages 13-14)

References (URLs and publication dates as available)

Aparicio T. et al. “Mismatch repair hierarchy of Pseudomonas putida…” Environmental Microbiology Nov 2020. https://doi.org/10.1111/1462-2920.14814 (aparicio2020mismatchrepairhierarchy pages 1-2)
Fernández-Cabezón L. et al. “Spatiotemporal manipulation of the mismatch repair system of Pseudomonas putida…” ACS Synthetic Biology Apr 2021. https://doi.org/10.1021/acssynbio.1c00031 (fernandezcabezon2021spatiotemporalmanipulationof pages 3-4)
Collingwood B.W. et al. “Action-At-A-Distance in DNA Mismatch Repair…” Biomolecules Nov 2024. https://doi.org/10.3390/biom14111442 (collingwood2024actionatadistanceindna pages 4-6)
Waters K.L., Spratt D.E. “New Discoveries on Protein Recruitment…” International Journal of Molecular Sciences Jan 2024. https://doi.org/10.3390/ijms25031676 (waters2024newdiscoverieson pages 8-9)

References

(aparicio2020mismatchrepairhierarchy pages 1-2): Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, and Víctor de Lorenzo. Mismatch repair hierarchy of pseudomonas putida revealed by mutagenic ssdna recombineering of the pyrf gene. Environmental Microbiology, 22:45-58, Nov 2020. URL: https://doi.org/10.1111/1462-2920.14814, doi:10.1111/1462-2920.14814. This article has 23 citations and is from a domain leading peer-reviewed journal.
(waters2024newdiscoverieson pages 8-9): Kelly L. Waters and Donald E. Spratt. New discoveries on protein recruitment and regulation during the early stages of the dna damage response pathways. International Journal of Molecular Sciences, 25:1676, Jan 2024. URL: https://doi.org/10.3390/ijms25031676, doi:10.3390/ijms25031676. This article has 15 citations.
(zarb2024singlemoleculeprobing pages 20-28): J Zarb. Single molecule probing of mismatch type and sequence dependence of dna mismatch repair by muts. Unknown journal, 2024.
(zarb2024singlemoleculeprobing pages 57-61): J Zarb. Single molecule probing of mismatch type and sequence dependence of dna mismatch repair by muts. Unknown journal, 2024.
(zarb2024singlemoleculeprobing pages 61-65): J Zarb. Single molecule probing of mismatch type and sequence dependence of dna mismatch repair by muts. Unknown journal, 2024.
(zarb2024singlemoleculeprobing pages 15-20): J Zarb. Single molecule probing of mismatch type and sequence dependence of dna mismatch repair by muts. Unknown journal, 2024.
(zarb2024singlemoleculeprobing pages 52-57): J Zarb. Single molecule probing of mismatch type and sequence dependence of dna mismatch repair by muts. Unknown journal, 2024.
(collingwood2024actionatadistanceindna pages 1-3): Bryce W. Collingwood, Scott J. Witte, and Carol M. Manhart. Action-at-a-distance in dna mismatch repair: mechanistic insights and models for how dna and repair proteins facilitate long-range communication. Biomolecules, 14:1442, Nov 2024. URL: https://doi.org/10.3390/biom14111442, doi:10.3390/biom14111442. This article has 1 citations.
(collingwood2024actionatadistanceindna pages 4-6): Bryce W. Collingwood, Scott J. Witte, and Carol M. Manhart. Action-at-a-distance in dna mismatch repair: mechanistic insights and models for how dna and repair proteins facilitate long-range communication. Biomolecules, 14:1442, Nov 2024. URL: https://doi.org/10.3390/biom14111442, doi:10.3390/biom14111442. This article has 1 citations.
(collingwood2024actionatadistanceindna pages 3-4): Bryce W. Collingwood, Scott J. Witte, and Carol M. Manhart. Action-at-a-distance in dna mismatch repair: mechanistic insights and models for how dna and repair proteins facilitate long-range communication. Biomolecules, 14:1442, Nov 2024. URL: https://doi.org/10.3390/biom14111442, doi:10.3390/biom14111442. This article has 1 citations.
(fernandezcabezon2021spatiotemporalmanipulationof pages 2-3): Lorena Fernández-Cabezón, Antonin Cros, and Pablo I. Nikel. Spatiotemporal manipulation of the mismatch repair system of pseudomonas putida accelerates phenotype emergence. Apr 2021. URL: https://doi.org/10.1021/acssynbio.1c00031, doi:10.1021/acssynbio.1c00031. This article has 28 citations and is from a domain leading peer-reviewed journal.
(aparicio2020mismatchrepairhierarchy pages 8-9): Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, and Víctor de Lorenzo. Mismatch repair hierarchy of pseudomonas putida revealed by mutagenic ssdna recombineering of the pyrf gene. Environmental Microbiology, 22:45-58, Nov 2020. URL: https://doi.org/10.1111/1462-2920.14814, doi:10.1111/1462-2920.14814. This article has 23 citations and is from a domain leading peer-reviewed journal.
(fernandezcabezon2021spatiotemporalmanipulationof pages 3-4): Lorena Fernández-Cabezón, Antonin Cros, and Pablo I. Nikel. Spatiotemporal manipulation of the mismatch repair system of pseudomonas putida accelerates phenotype emergence. Apr 2021. URL: https://doi.org/10.1021/acssynbio.1c00031, doi:10.1021/acssynbio.1c00031. This article has 28 citations and is from a domain leading peer-reviewed journal.
(fernandezcabezon2021spatiotemporalmanipulationof media 45d6effd): Lorena Fernández-Cabezón, Antonin Cros, and Pablo I. Nikel. Spatiotemporal manipulation of the mismatch repair system of pseudomonas putida accelerates phenotype emergence. Apr 2021. URL: https://doi.org/10.1021/acssynbio.1c00031, doi:10.1021/acssynbio.1c00031. This article has 28 citations and is from a domain leading peer-reviewed journal.
(fernandezcabezon2021spatiotemporalmanipulationof pages 8-8): Lorena Fernández-Cabezón, Antonin Cros, and Pablo I. Nikel. Spatiotemporal manipulation of the mismatch repair system of pseudomonas putida accelerates phenotype emergence. Apr 2021. URL: https://doi.org/10.1021/acssynbio.1c00031, doi:10.1021/acssynbio.1c00031. This article has 28 citations and is from a domain leading peer-reviewed journal.
(fernandezcabezon2021spatiotemporalmanipulationof pages 1-2): Lorena Fernández-Cabezón, Antonin Cros, and Pablo I. Nikel. Spatiotemporal manipulation of the mismatch repair system of pseudomonas putida accelerates phenotype emergence. Apr 2021. URL: https://doi.org/10.1021/acssynbio.1c00031, doi:10.1021/acssynbio.1c00031. This article has 28 citations and is from a domain leading peer-reviewed journal.
(fernandezcabezon2021spatiotemporalmanipulationof pages 4-5): Lorena Fernández-Cabezón, Antonin Cros, and Pablo I. Nikel. Spatiotemporal manipulation of the mismatch repair system of pseudomonas putida accelerates phenotype emergence. Apr 2021. URL: https://doi.org/10.1021/acssynbio.1c00031, doi:10.1021/acssynbio.1c00031. This article has 28 citations and is from a domain leading peer-reviewed journal.
(fernandezcabezon2021spatiotemporalmanipulationof pages 6-7): Lorena Fernández-Cabezón, Antonin Cros, and Pablo I. Nikel. Spatiotemporal manipulation of the mismatch repair system of pseudomonas putida accelerates phenotype emergence. Apr 2021. URL: https://doi.org/10.1021/acssynbio.1c00031, doi:10.1021/acssynbio.1c00031. This article has 28 citations and is from a domain leading peer-reviewed journal.
(collingwood2024actionatadistanceindna pages 12-14): Bryce W. Collingwood, Scott J. Witte, and Carol M. Manhart. Action-at-a-distance in dna mismatch repair: mechanistic insights and models for how dna and repair proteins facilitate long-range communication. Biomolecules, 14:1442, Nov 2024. URL: https://doi.org/10.3390/biom14111442, doi:10.3390/biom14111442. This article has 1 citations.
(aparicio2020mismatchrepairhierarchy pages 12-13): Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, and Víctor de Lorenzo. Mismatch repair hierarchy of pseudomonas putida revealed by mutagenic ssdna recombineering of the pyrf gene. Environmental Microbiology, 22:45-58, Nov 2020. URL: https://doi.org/10.1111/1462-2920.14814, doi:10.1111/1462-2920.14814. This article has 23 citations and is from a domain leading peer-reviewed journal.
(aparicio2020mismatchrepairhierarchy pages 13-14): Tomas Aparicio, Akos Nyerges, István Nagy, Csaba Pal, Esteban Martínez‐García, and Víctor de Lorenzo. Mismatch repair hierarchy of pseudomonas putida revealed by mutagenic ssdna recombineering of the pyrf gene. Environmental Microbiology, 22:45-58, Nov 2020. URL: https://doi.org/10.1111/1462-2920.14814, doi:10.1111/1462-2920.14814. This article has 23 citations and is from a domain leading peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

aparicio2020mismatchrepairhierarchy pages 1-2
zarb2024singlemoleculeprobing pages 57-61
zarb2024singlemoleculeprobing pages 15-20
fernandezcabezon2021spatiotemporalmanipulationof pages 2-3
aparicio2020mismatchrepairhierarchy pages 8-9
waters2024newdiscoverieson pages 8-9
fernandezcabezon2021spatiotemporalmanipulationof pages 8-8
fernandezcabezon2021spatiotemporalmanipulationof pages 1-2
aparicio2020mismatchrepairhierarchy pages 13-14
fernandezcabezon2021spatiotemporalmanipulationof pages 3-4
collingwood2024actionatadistanceindna pages 4-6
zarb2024singlemoleculeprobing pages 20-28
zarb2024singlemoleculeprobing pages 61-65
zarb2024singlemoleculeprobing pages 52-57
collingwood2024actionatadistanceindna pages 1-3
collingwood2024actionatadistanceindna pages 3-4
fernandezcabezon2021spatiotemporalmanipulationof pages 4-5
fernandezcabezon2021spatiotemporalmanipulationof pages 6-7
collingwood2024actionatadistanceindna pages 12-14
aparicio2020mismatchrepairhierarchy pages 12-13
https://doi.org/10.1111/1462-2920.14814
https://doi.org/10.3390/biom14111442
https://doi.org/10.3390/ijms25031676
https://doi.org/10.1021/acssynbio.1c00031
https://doi.org/10.1111/1462-2920.14814,
https://doi.org/10.3390/ijms25031676,
https://doi.org/10.3390/biom14111442,
https://doi.org/10.1021/acssynbio.1c00031,

📚 Additional Documentation

Notes

(mutS-notes.md)

mutS curation notes

MutS (Q88ME7; PP_1626) is the experimentally supported mismatch-recognition
component of KT2440 MMR. The direct study used permanent mutS deletion and
resolved a hierarchy of corrected mismatch classes
PMID:31599106.

The core functions retain both mismatched-DNA binding and ATP-dependent DNA
damage sensor activity: the first captures substrate recognition, while the
second captures the ATP-driven signaling transition. Generic damaged-DNA and
duplex-DNA binding terms were marked over-annotated.

📄 View Raw YAML

id: Q88ME7
gene_symbol: mutS
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: >-
  MutS is the cytosolic ATP-dependent mismatch sensor that initiates
  post-replicative DNA mismatch repair. It recognizes base-pair mismatches and
  small insertion/deletion loops in duplex DNA, then uses its ATPase cycle to
  form a signaling clamp and recruit MutL for downstream strand incision and
  excision. In Pseudomonas putida KT2440, MutS and MutL constitute the two
  conserved recognition/incision components of a MutH-independent mismatch
  repair system.
existing_annotations:
  - term:
      id: GO:0003684
      label: damaged DNA binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000104
    qualifier: enables
    review:
      summary: >-
        Compatible with mismatch recognition but too broad when mismatched DNA
        binding and ATP-dependent DNA damage sensor activity are available.
      action: MARK_AS_OVER_ANNOTATED
      reason: The specific mismatch-sensor terms capture the core activity.
  - term:
      id: GO:0003690
      label: double-stranded DNA binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000118
    qualifier: enables
    review:
      summary: >-
        MutS acts on duplex DNA, but this generic binding term loses the
        mismatch specificity that defines its function.
      action: MARK_AS_OVER_ANNOTATED
      reason: GO:0030983 is the informative substrate-specific term.
  - term:
      id: GO:0005524
      label: ATP binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    qualifier: enables
    review:
      summary: >-
        Retain as non-core. ATP binding is required for the MutS conformational
        cycle, but the integrated sensor term is more informative.
      action: KEEP_AS_NON_CORE
      reason: Correct mechanistic property subsumed by GO:0140664.
  - term:
      id: GO:0005829
      label: cytosol
    evidence_type: IEA
    original_reference_id: GO_REF:0000118
    qualifier: located_in
    review:
      summary: Accept as the leaf-level location of the soluble bacterial mismatch sensor.
      action: ACCEPT
      reason: Consistent with the reviewed protein record and chromosomal DNA substrate.
  - term:
      id: GO:0006298
      label: mismatch repair
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    qualifier: involved_in
    review:
      summary: >-
        Accept. KT2440 recombineering experiments directly tested permanent
        mutS deletion and established a MutS-dependent hierarchy of mismatch
        correction.
      action: ACCEPT
      reason: Core biological process with direct organism-specific genetic support.
      supported_by:
        - reference_id: PMID:31599106
          supporting_text: "permanent deletion of mutS or transient loss of mutL activity"
  - term:
      id: GO:0030983
      label: mismatched DNA binding
    evidence_type: IEA
    original_reference_id: GO_REF:0000120
    qualifier: enables
    review:
      summary: Accept as the substrate-specific recognition function of MutS.
      action: ACCEPT
      reason: MutS is the mismatch-recognition component, unlike downstream MutL.
      supported_by:
        - reference_id: file:PSEPK/mutS/mutS-uniprot.txt
          supporting_text: "mismatch recognition step"
  - term:
      id: GO:0140664
      label: ATP-dependent DNA damage sensor activity
    evidence_type: IEA
    original_reference_id: GO_REF:0000002
    qualifier: enables
    review:
      summary: >-
        Accept as the most informative integrated molecular function. MutS
        couples recognition of mismatched DNA to an ATP-dependent signaling
        transition that initiates repair.
      action: ACCEPT
      reason: Captures both lesion sensing and the essential ATPase-driven switch.
references:
  - id: GO_REF:0000002
    title: Gene Ontology annotation through association of InterPro records with GO terms
    findings: []
  - id: GO_REF:0000104
    title: Electronic Gene Ontology annotations created by transferring manual GO annotations between related proteins based on shared sequence features
    findings: []
  - id: GO_REF:0000118
    title: TreeGrafter-generated GO annotations
    findings: []
  - id: GO_REF:0000120
    title: Combined Automated Annotation using Multiple IEA Methods
    findings: []
  - id: file:PSEPK/mutS/mutS-uniprot.txt
    title: UniProtKB entry for PSEPK MutS (Q88ME7)
    findings:
      - supporting_text: "This protein is involved in the repair of mismatches in DNA."
      - supporting_text: "mismatch recognition step"
  - id: PMID:31599106
    title: Mismatch repair hierarchy of Pseudomonas putida revealed by mutagenic ssDNA recombineering of the pyrF gene.
    findings:
      - supporting_text: "permanent deletion of mutS or transient loss of mutL activity"
        reference_section_type: ABSTRACT
      - supporting_text: "data unequivocally established the hierarchy"
        reference_section_type: ABSTRACT
    reference_review:
      relevance: HIGH
      correctness: VERIFIED
      review_notes: >-
        PubMed and the cached abstract were checked. The study directly tests
        KT2440 MutS-dependent correction across mismatch classes.
core_functions:
  - description: >-
      MutS recognizes mismatches in duplex DNA and couples recognition to an
      ATP-dependent signaling-clamp transition that recruits downstream
      mismatch-repair machinery.
    molecular_function:
      id: GO:0140664
      label: ATP-dependent DNA damage sensor activity
    directly_involved_in:
      - id: GO:0006298
        label: mismatch repair
    locations:
      - id: GO:0005829
        label: cytosol
    supported_by:
      - reference_id: file:PSEPK/mutS/mutS-uniprot.txt
        supporting_text: "mismatch recognition step"
      - reference_id: PMID:31599106
        supporting_text: "permanent deletion of mutS or transient loss of mutL activity"
  - description: >-
      Binds mismatched duplex DNA as the substrate-recognition step that
      precedes the ATP-dependent signaling transition.
    molecular_function:
      id: GO:0030983
      label: mismatched DNA binding
    directly_involved_in:
      - id: GO:0006298
        label: mismatch repair
    locations:
      - id: GO:0005829
        label: cytosol
    supported_by:
      - reference_id: file:PSEPK/mutS/mutS-uniprot.txt
        supporting_text: "mismatch recognition step"
proposed_new_terms: []
suggested_questions:
  - question: >-
      Which mismatch classes most strongly stabilize the KT2440 MutS signaling
      clamp, and does the beta clamp recruit MutS at replication forks?
suggested_experiments:
  - hypothesis: KT2440 MutS ATPase switching differs quantitatively across mismatch classes.
    description: >-
      Measure binding, ATPase activity, and sliding-clamp formation on matched
      duplexes and the mismatch classes ranked by the KT2440 recombineering
      study.
    experiment_type: purified-protein mismatch recognition and ATPase assay

mutS

Gene Description

Existing Annotations Review

Core Functions

MutS recognizes mismatches in duplex DNA and couples recognition to an ATP-dependent signaling-clamp transition that recruits downstream mismatch-repair machinery.

Binds mismatched duplex DNA as the substrate-recognition step that precedes the ATP-dependent signaling transition.

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Research Report: Functional Annotation of mutS (UniProt: Q88ME7; locus PP_1626) in Pseudomonas putida KT2440

1. Target verification (gene/protein identity)

2. Key concepts & current mechanistic understanding (2024-focused)

2.1 Definition: what MutS does

2.2 Substrate specificity (mismatch types)

2.3 Core MutS catalytic cycle: ATP/ADP-driven conformational switching and sliding clamp

2.4 “Action-at-a-distance” in MMR: how mismatch recognition communicates with distant incision sites (2024 expert synthesis)

3. Pseudomonas putida KT2440/EM42-specific functional evidence

3.1 Pathway context in P. putida: abridged MutS/MutL system

3.2 Organism-specific mismatch recognition/repair hierarchy

4. Cellular localization and interaction partners (with organism-specific caveats)

4.1 Where MutS acts in the cell

4.2 Interaction partners and pathway components

5. Recent developments and latest research (prioritizing 2023–2024)

5.1 2024: Mechanistic models for long-range communication in MMR

5.2 2024: Single-molecule quantification of nucleotide effects on MutS clamp formation

5.3 2024: Review-level synthesis of early recruitment/regulation

6. Current applications and real-world implementations (with quantitative results)

6.1 Controllable “mutator devices” in P. putida KT2440 (synthetic biology; 2021 foundational implementation)

6.2 Genome engineering / recombineering workflows using transient MMR suppression

7. Interpretation for functional annotation of Q88ME7 (MutS) in P. putida KT2440

7.1 Primary molecular function

7.2 Biological processes/pathways

7.3 Cellular compartment

7.4 P. putida-specific nuance: mismatch preference matters

8. Summary table (evidence map)

9. Key limitations of available evidence for this specific protein

References (URLs and publication dates as available)

Artifacts

Citations

📚 Additional Documentation

Notes

mutS curation notes

📄 View Raw YAML