GO Term	Evidence	Action	Reason
GO:0006304 DNA modification	IEA GO_REF:0000002	MODIFY	Summary: Too general - DNA modification occurs, but the biological function is specifically antirestriction, not just general DNA modification Proposed replacements: symbiont-mediated evasion of host restriction-modification system Supporting Evidence: PMID:3029954 The darA and darB gene products are found in the phage head and protect any DNA packaged into a phage head, including transduced chromosomal markers, from restriction
GO:0008168 methyltransferase activity	IEA GO_REF:0000043	MODIFY	Summary: Too general - DarB has a methyltransferase domain, but specifically acts on DNA Proposed replacements: DNA-methyltransferase activity Supporting Evidence: GO_REF:0000043 UniProtKB keyword mapping and InterPro domain IPR011639 (Type II methyltransferase M.TaqI-like domain) indicate DNA methyltransferase activity
GO:0032259 methylation	IEA GO_REF:0000043	KEEP AS NON CORE	Summary: Too general and not the core biological process - methylation may occur but the key function is antirestriction defense Reason: While DarB has a methyltransferase domain suggesting methylation activity, the primary biological function is antirestriction. Methylation is a molecular mechanism, not the biological role
GO:0005737 cytoplasm	NAS	NEW	Summary: Added to align core_functions with existing annotations. Reason: Core function term not present in existing_annotations.

Deep Research

Falcon

(darB-deep-research-falcon.md)

Research Report: Functional Annotation of **darB'** (UniProt **Q9XJG2**) from **Punavirus P1** Falcon Edison Scientific Literature 21 citations 2 artifacts 2026-05-22T22:04:55.247521

Edison artifact artifact-00 (text/markdown)

## Context ID: pqac-00000007 Figure 3B illustrates how phage P1 evades bacterial restriction-modification (R-M) systems. Phage P1 co-injects DarA and DarB prote (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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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 darB' (UniProt Q9XJG2) from Punavirus P1

Executive summary (identity verification and evidence limits)

The UniProt entry provided (Q9XJG2) describes DarB′, annotated as a “DNA methylase homolog DarB′” (fragment) from Punavirus P1, with predicted domains consistent with a SAM-dependent DNA methyltransferase superfamily (DNA_Protect_Modify; TaqI-like MTase domain; Eco57I/PF07669). However, within the full-text literature retrieved here, I could not find any primary publication that explicitly mentions UniProt Q9XJG2 or Punavirus P1 darB′. The available peer-reviewed literature instead discusses bacteriophage P1 “DarB/DarA” proteins as virion-delivered anti-restriction factors, and only notes methyltransferase-like features for DarB as a bioinformatic signature rather than a biochemically validated activity. Therefore, organism-specific claims about Punavirus P1 DarB′ are limited to the UniProt metadata supplied by the user, and functional conclusions rely on (i) direct evidence for P1 DarB-like proteins and (ii) domain-level inference from characterized SAM-dependent DNA methyltransferases. (anton2025biologyofhostdependent pages 32-35, zaworski2022reassemblingacannon pages 13-14)

1) Key concepts and definitions (current understanding)

Host-dependent restriction–modification systems distinguish “self” from “non-self” DNA largely via epigenetic DNA modification (often methylation). In the canonical model, a methyltransferase transfers a methyl group from S-adenosylmethionine (SAM/AdoMet) to DNA bases (commonly N6-A, N4-C, or C5-C), and a restriction function preferentially attacks DNA lacking the protective modification pattern. (Anton et al., EcoSal Plus, publication date Dec 2025, https://doi.org/10.1128/ecosalplus.esp-0014-2022) (anton2025biologyofhostdependent pages 3-6)

Phage anti-restriction strategies

Phages can evade RM-like defenses using several strategies, including: (i) chemical modification of their DNA, (ii) removing restriction motifs, (iii) degrading/perturbing SAM pools, or (iv) protein-mediated occlusion/shielding of restriction sites on incoming phage DNA. A well-known example is phage P1 DarA/DarB, described as being co-injected with DNA to shield restriction sites (“restriction-site occlusion”). (Kang et al., Biophysics Reports, Jan 2025, https://doi.org/10.52601/bpr.2025.240070) (kang2025bacterialrestrictionmodificationsystems pages 8-9)

2) Target-gene context and identity check: darB′ (Q9XJG2)

What is confidently known for Q9XJG2 (from the provided UniProt entry)

Organism: Punavirus P1
Gene name: darB′
Description: “DNA methylase homolog DarB′” (fragment)
Domains (predicted): DNA_Protect_Modify; TaqI-like methyltransferase domain; SAM-dependent methyltransferase superfamily; Eco57I (PF07669)

What the literature supports for DarB-like proteins (phage P1)

Several sources describe phage P1 DarA/DarB as virion-associated proteins that are delivered early during infection and protect phage DNA against host restriction systems by shielding/occluding restriction sites (notably in a cis-acting manner on DNA packaged in the virion). (kang2025bacterialrestrictionmodificationsystems pages 8-9, anton2025biologyofhostdependent pages 32-35)

A schematic depiction of this “restriction-site shielding” mechanism for P1 DarA/DarB is shown in Figure 3B of Kang et al. 2025. (kang2025bacterialrestrictionmodificationsystems media 9a53130f)

3) Primary function: what reaction is catalyzed and what is substrate specificity?

3.1 Direct evidence for DarB/DarB′ enzymatic methyltransferase activity

No direct biochemical reaction has been demonstrated for DarB (or DarB′) in the retrieved evidence. The most specific statement found is that injected DarB was noted to contain a “bioinformatic signature of methyltransferase”, while also stating that how it acts against diverse RM systems remains unresolved. (Zaworski et al., PLOS Genetics, Apr 4, 2022, https://doi.org/10.1371/journal.pgen.1009943) (zaworski2022reassemblingacannon pages 13-14)

Thus, for Q9XJG2 (Punavirus P1 DarB′), substrate specificity (DNA motif), modified base (m6A/m4C/m5C), and catalytic activity remain unverified in the available literature set. (zaworski2022reassemblingacannon pages 13-14)

3.2 Domain-based inference: what a SAM-dependent DNA MTase “would do”

Given the UniProt-provided domain annotations (SAM-dependent MTase superfamily; TaqI-like; Eco57I-like), the most plausible inferred biochemical function is DNA base methylation using SAM/AdoMet as the methyl donor, as is typical for SAM-dependent DNA methyltransferases. (anton2025biologyofhostdependent pages 3-6)

A representative experimentally characterized adenine DNA methyltransferase (M.EcoGII) installs N6-methyladenine (m6dA) on DNA using SAM and contains hallmark SAM-dependent MTase motifs (including an FxGxG AdoMet-binding motif and a DPPY catalytic motif). (Murray et al., Nucleic Acids Research, online Dec 2017, https://doi.org/10.1093/nar/gkx1191) (murray2017thenonspecificadenine pages 6-8)

Importantly, this supports only family-level inference—it does not establish that Q9XJG2 performs the same chemistry, nor what sequence motif it targets. (murray2017thenonspecificadenine pages 6-8, anton2025biologyofhostdependent pages 3-6)

4) Biological processes, pathways, and localization

4.1 Biological role: anti-restriction / DNA protection during entry

The P1 dar system is described as a virion-head–incorporated set of proteins (DarA, DarB, Ulx, DdrB, DdrA, Hdf) that confer protection against several Type I HDRM systems and BREX, acting only in cis on DNA that is packaged within the virion. This cis-only behavior supports a model in which the Dar proteins physically obstruct host restriction machinery from accessing the entering phage genome. (Anton et al., EcoSal Plus, Dec 2025, https://doi.org/10.1128/ecosalplus.esp-0014-2022) (anton2025biologyofhostdependent pages 32-35)

Kang et al. similarly describe DarA/DarB as co-injected proteins that occlude restriction sites on the P1 genome to avoid destruction by host RM. (Kang et al., Biophysics Reports, Jan 2025, https://doi.org/10.52601/bpr.2025.240070) (kang2025bacterialrestrictionmodificationsystems pages 8-9)

4.2 Localization

For P1 DarB-like proteins, the best-supported localization is:
- Virion-associated (packaged in the phage head) prior to infection, and
- Intracellular, bound to/associated with incoming phage DNA immediately after injection, consistent with a DNA-shielding role. (anton2025biologyofhostdependent pages 32-35, kang2025bacterialrestrictionmodificationsystems media 9a53130f)

For Punavirus P1 DarB′ (Q9XJG2), no direct localization experiments were retrieved; thus, localization is inferred by homology/functional analogy to Dar systems and by the DNA protection-modification functional theme. (anton2025biologyofhostdependent pages 32-35)

5) Recent developments (prioritizing 2023–2024)

Direct 2023–2024 papers on Punavirus P1 DarB′ (Q9XJG2) were not found in the retrieved literature set. Nonetheless, recent high-impact work clarifies broader phage–methyltransferase–defense conflicts relevant to interpreting DarB′-like domain predictions.

5.1 2024 mechanistic advance: phage Ocr inhibits a BREX methyltransferase

Li et al. provide in vitro characterization of a BREX methyltransferase (E-BrxX) and show that the phage protein Ocr inhibits BrxX by acting as a DNA mimic, forming a stable complex and preventing substrate recognition and methylation. This is a contemporary example of phage counter-defense targeting methyltransferase-centered bacterial defense systems. (Li et al., Nucleic Acids Research, Jul 2024, https://doi.org/10.1093/nar/gkae608) (li2024ocrmediatedsuppressionof pages 1-2)

Quantitative data from this 2024 study include:
- In vitro methylation assay conditions: 2 μM BrxX, 10 μM DNA, 150 μM SAM, 37°C for 30 min. (li2024ocrmediatedsuppressionof pages 8-9)
- Kinetic parameters: Km(DNA) = 3.41 ± 0.74 μM; Km(SAM) = 380.01 ± 52.61 μM, suggesting relatively low SAM affinity in vitro. (li2024ocrmediatedsuppressionof pages 6-7)
- Inhibition potency: IC50(Ocr) = 1.17 ± 0.07 μM; binding affinity reported as extremely tight (KD < 10−12 M). (li2024ocrmediatedsuppressionof pages 8-9)

These results demonstrate how phage proteins can antagonize methyltransferase-based defense systems, and they provide a methodological template (activity assays, kinetics, structural mechanism) that could be applied to experimental validation of DarB′-like proteins. (li2024ocrmediatedsuppressionof pages 8-9, li2024ocrmediatedsuppressionof pages 6-7)

5.2 2023 context: genome-encoded defense and methyltransferase functions in phage–host interactions

A 2023 proteomic/genomic study of lytic phages infecting Klebsiella pneumoniae reports that phage genomes encode diverse defense-related proteins, including those associated with restriction-modification system interactions and methyltransferases, reflecting the broad prevalence of such functions in phage–bacteria conflict. (Bleriot et al., Microbiology Spectrum, Apr 2023, https://doi.org/10.1128/spectrum.03974-22) (kang2025bacterialrestrictionmodificationsystems pages 8-9)

6) Current applications and real-world implementations

6.1 Engineering/selection of phages for therapeutic use

Phage therapy development must contend with bacterial DNA defense systems (including RM-like and BREX-like systems). Mechanistic studies showing that phage proteins can inhibit methyltransferase-centered defenses (e.g., Ocr–BrxX) provide concrete molecular targets and design principles for engineering phages or selecting naturally resistant phages. (li2024ocrmediatedsuppressionof pages 1-2)

6.2 Enzymes and reagents for epigenetics and mapping

SAM-dependent methyltransferases are widely used as molecular biology tools and as probes for methylation biology; while not specific to DarB′, the demonstrated activity/motif logic for adenine MTases (e.g., M.EcoGII) illustrates how phage-derived MTases can be leveraged for mapping base modifications and studying restriction sensitivity changes. (murray2017thenonspecificadenine pages 6-8)

7) Expert opinion and synthesis (authoritative sources)

Authoritative reviews emphasize that phage anti-restriction encompasses both DNA modification strategies and protein-mediated physical shielding, and that the P1 dar system is a prototypic example of virion-delivered protection acting in cis on packaged DNA. At the same time, reviews explicitly note that the precise mechanism of Dar-mediated evasion remains unclear and that dependencies among dar proteins (for virion incorporation) complicate phenotype interpretation. (Anton et al., EcoSal Plus, Dec 2025, https://doi.org/10.1128/ecosalplus.esp-0014-2022) (anton2025biologyofhostdependent pages 32-35)

8) Key statistics and data points from recent studies

BREX prevalence: BREX systems occur in ~10% of bacterial/archaeal genomes; Type I comprises ~55% of BREX systems. (Li et al., NAR, Jul 2024, https://doi.org/10.1093/nar/gkae608) (li2024ocrmediatedsuppressionof pages 1-2)
Ocr inhibition of BrxX (2024): IC50 1.17 ± 0.07 μM; KD reported < 10−12 M; Km(DNA) 3.41 ± 0.74 μM; Km(SAM) 380.01 ± 52.61 μM. (li2024ocrmediatedsuppressionof pages 8-9, li2024ocrmediatedsuppressionof pages 6-7)
Dar system mode of action (qualitative, but experimentally grounded in prior work synthesized by reviews): dar acts in cis on virion-packaged DNA and is consistent with physical obstruction of host defense proteins. (anton2025biologyofhostdependent pages 32-35)

Evidence summary table

Topic	Key points	Evidence strength (direct/indirect/inference)	Key citations (context IDs)
identity/organism	Target to annotate is UniProt Q9XJG2, described by the user as darB' from Punavirus P1, a fragment with DNA_Protect_Modify, TaqI-like methyltransferase, SAM-dependent MTase superfamily, and Eco57I/PF07669 domain assignments. Literature retrieved in the available evidence discusses bacteriophage P1 DarB/DarAB anti-restriction proteins, but does not directly validate the specific Punavirus P1 UniProt entry; therefore symbol-level ambiguity remains and annotation must be cautious.	Indirect/inference	Provided by user (UniProt)
role in anti-restriction	Multiple reviews state that phage P1 DarA and DarB are packaged/co-injected with phage DNA and protect the incoming genome from host restriction systems by shielding/occluding restriction sites; Dar functions in cis on DNA packaged in the virion and has activity against several Type I systems and BREX.	Direct for P1 DarB function in literature; indirect for Q9XJG2	(kang2025bacterialrestrictionmodificationsystems pages 8-9, anton2025biologyofhostdependent pages 32-35, kang2025bacterialrestrictionmodificationsystems media 9a53130f)
evidence for methyltransferase activity	Available literature does not directly demonstrate DarB enzymatic methyltransferase activity. One source notes only that injected DarB contains a bioinformatic “signature of methyltransferase,” while emphasizing that its action against diverse RM systems remains unelucidated. No direct catalytic assay, modified base measurement, or target motif for DarB was identified in the retrieved evidence.	Indirect/inference	(zaworski2022reassemblingacannon pages 13-14)
mechanism hypotheses	Best-supported current hypothesis is protein-mediated physical obstruction of host HDRM/BREX access to entering phage DNA. Reviews note Dar proteins may need one another for virion incorporation, complicating mutant interpretation, and the exact molecular mechanism remains unresolved. An alternative speculative hypothesis is interference with integrity/assembly of restricting complexes rather than direct DNA methylation.	Indirect/inference	(anton2025biologyofhostdependent pages 32-35, zaworski2022reassemblingacannon pages 13-14, kang2025bacterialrestrictionmodificationsystems media 9a53130f)
enzymatic reaction (general SAM-dependent DNA MTases)	For SAM-dependent DNA methyltransferases in general, the reaction is transfer of a methyl group from SAM/AdoMet to DNA bases, commonly N6 of adenine, N4 of cytosine, or C5 of cytosine. A representative adenine MTase (M.EcoGII) uses SAM and contains conserved FxGxG AdoMet-binding and DPPY catalytic motifs; phage-encoded MTases are broadly recognized as anti-restriction/DNA-protection factors. These facts support only family-level functional inference for Q9XJG2, not direct proof of DarB' activity or specificity.	Inference from homologous/family MTases	(murray2017thenonspecificadenine pages 6-8, anton2025biologyofhostdependent pages 3-6, fomenkov2020plasmidreplicationassociatedsinglestrandspecific pages 5-6)
quantitative data/stats	Recent quantitative context comes from related phage-defense methyltransferase systems rather than DarB itself: BREX occurs in ~10% of bacterial/archaeal genomes and Type I BREX accounts for ~55% of BREX systems; BrxX assays used 2 μM enzyme, 10 μM DNA, 150 μM SAM, with DNA Km 3.41 ± 0.74 μM, SAM Km 380.01 ± 52.61 μM, Ocr inhibition IC50 1.17 ± 0.07 μM, and Ocr-BrxX KD below 10^-12 M. These data illustrate contemporary mechanistic work on phage–methyltransferase conflicts but are not measurements for DarB'.	Indirect/contextual	(li2024ocrmediatedsuppressionof pages 8-9, li2024ocrmediatedsuppressionof pages 6-7, li2024ocrmediatedsuppressionof pages 1-2)
key limitations	No retrieved primary study directly characterizes UniProt Q9XJG2 from Punavirus P1. The literature predominantly covers P1 DarA/DarB anti-restriction phenotypes rather than DarB' biochemistry. No direct evidence in the retrieved set establishes catalytic reaction, methyl-acceptor base, recognition motif, localization beyond virion-associated delivery, or whether the UniProt fragment is active. Therefore the safest annotation is anti-restriction/DNA-protection protein with putative methyltransferase-like features inferred from domains.	Direct statement about evidence gap plus inference	(anton2025biologyofhostdependent pages 32-35, zaworski2022reassemblingacannon pages 13-14)

Table: This table summarizes what the available evidence supports for DarB/DarB' relevant to UniProt Q9XJG2. It distinguishes direct evidence for phage P1 anti-restriction function from weaker, domain-based inferences about methyltransferase activity and highlights major evidence gaps.

9) Proposed functional annotation for Q9XJG2 (Punavirus P1 darB′)

Most defensible primary function (given evidence constraints)

DarB′ (Q9XJG2) is best annotated as a putative phage DNA protection/anti-restriction factor, with predicted SAM-dependent DNA methyltransferase-like domains but without direct biochemical validation of methyltransferase activity or motif specificity in the current evidence set. (zaworski2022reassemblingacannon pages 13-14, anton2025biologyofhostdependent pages 32-35)

Likely biological process and localization

By analogy to the well-described P1 dar system, DarB′-like proteins are most consistent with early infection, intracellular association with incoming phage DNA, either by physically shielding restriction sites or (if enzymatically active) by installing protective methylation marks. The strongest direct support is for the protein-mediated shielding model in P1. (kang2025bacterialrestrictionmodificationsystems pages 8-9, anton2025biologyofhostdependent pages 32-35, kang2025bacterialrestrictionmodificationsystems media 9a53130f)

10) Key gaps and what would resolve them (experimental priorities)

The critical missing data for Q9XJG2 are (i) direct demonstration of methyltransferase activity, (ii) identification of modified base (m6A/m4C/m5C), (iii) recognition motif and/or specificity, and (iv) confirmation that the UniProt “fragment” is catalytically competent. The 2024 BrxX work provides a modern experimental template (SAM-dependent activity assays, kinetics, inhibition/complex formation, and structural approaches) that could be adapted for DarB′. (li2024ocrmediatedsuppressionof pages 8-9, li2024ocrmediatedsuppressionof pages 6-7, li2024ocrmediatedsuppressionof pages 1-2)

References

(anton2025biologyofhostdependent pages 32-35): Brian P. Anton, Robert Blumenthal, James B. Eaglesham, Iwona Mruk, Richard J. Roberts, Shuang-yong Xu, Peter R. Weigele, and Elisabeth A. Raleigh. Biology of host-dependent restriction-modification in prokaryotes. EcoSal Plus, Dec 2025. URL: https://doi.org/10.1128/ecosalplus.esp-0014-2022, doi:10.1128/ecosalplus.esp-0014-2022. This article has 8 citations.
(zaworski2022reassemblingacannon pages 13-14): Julie Zaworski, Oyut Dagva, Julius Brandt, Chloé Baum, Laurence Ettwiller, Alexey Fomenkov, and Elisabeth A. Raleigh. Reassembling a cannon in the dna defense arsenal: genetics of stysa, a brex phage exclusion system in salmonella lab strains. PLOS Genetics, 18:e1009943, Apr 2022. URL: https://doi.org/10.1371/journal.pgen.1009943, doi:10.1371/journal.pgen.1009943. This article has 20 citations and is from a domain leading peer-reviewed journal.
(anton2025biologyofhostdependent pages 3-6): Brian P. Anton, Robert Blumenthal, James B. Eaglesham, Iwona Mruk, Richard J. Roberts, Shuang-yong Xu, Peter R. Weigele, and Elisabeth A. Raleigh. Biology of host-dependent restriction-modification in prokaryotes. EcoSal Plus, Dec 2025. URL: https://doi.org/10.1128/ecosalplus.esp-0014-2022, doi:10.1128/ecosalplus.esp-0014-2022. This article has 8 citations.
(kang2025bacterialrestrictionmodificationsystems pages 8-9): Haoyang Kang, Ang Gao, and Yalan Zhu. Bacterial restriction-modification systems: mechanisms of defense against phage infection. Biophysics Reports, 11:1, Jan 2025. URL: https://doi.org/10.52601/bpr.2025.240070, doi:10.52601/bpr.2025.240070. This article has 8 citations.
(kang2025bacterialrestrictionmodificationsystems media 9a53130f): Haoyang Kang, Ang Gao, and Yalan Zhu. Bacterial restriction-modification systems: mechanisms of defense against phage infection. Biophysics Reports, 11:1, Jan 2025. URL: https://doi.org/10.52601/bpr.2025.240070, doi:10.52601/bpr.2025.240070. This article has 8 citations.
(murray2017thenonspecificadenine pages 6-8): Iain A Murray, Richard D Morgan, Yvette Luyten, Alexey Fomenkov, Ivan R. Corrêa, Nan Dai, Mohammed B Allaw, Xing Zhang, Xiaodong Cheng, and Richard J Roberts. The non-specific adenine dna methyltransferase m.ecogii. Nucleic Acids Research, 46:840-848, Dec 2017. URL: https://doi.org/10.1093/nar/gkx1191, doi:10.1093/nar/gkx1191. This article has 44 citations and is from a highest quality peer-reviewed journal.
(li2024ocrmediatedsuppressionof pages 1-2): Shen Li, Tianhao Xu, Xinru Meng, Yujuan Yan, Ying Zhou, Lei Duan, Yulong Tang, Li Zhu, and Litao Sun. Ocr-mediated suppression of brxx unveils a phage counter-defense mechanism. Nucleic Acids Research, 52:8580-8594, Jul 2024. URL: https://doi.org/10.1093/nar/gkae608, doi:10.1093/nar/gkae608. This article has 9 citations and is from a highest quality peer-reviewed journal.
(li2024ocrmediatedsuppressionof pages 8-9): Shen Li, Tianhao Xu, Xinru Meng, Yujuan Yan, Ying Zhou, Lei Duan, Yulong Tang, Li Zhu, and Litao Sun. Ocr-mediated suppression of brxx unveils a phage counter-defense mechanism. Nucleic Acids Research, 52:8580-8594, Jul 2024. URL: https://doi.org/10.1093/nar/gkae608, doi:10.1093/nar/gkae608. This article has 9 citations and is from a highest quality peer-reviewed journal.
(li2024ocrmediatedsuppressionof pages 6-7): Shen Li, Tianhao Xu, Xinru Meng, Yujuan Yan, Ying Zhou, Lei Duan, Yulong Tang, Li Zhu, and Litao Sun. Ocr-mediated suppression of brxx unveils a phage counter-defense mechanism. Nucleic Acids Research, 52:8580-8594, Jul 2024. URL: https://doi.org/10.1093/nar/gkae608, doi:10.1093/nar/gkae608. This article has 9 citations and is from a highest quality peer-reviewed journal.
(fomenkov2020plasmidreplicationassociatedsinglestrandspecific pages 5-6): Alexey Fomenkov, Zhiyi Sun, Iain A Murray, Cristian Ruse, Colleen McClung, Yoshiharu Yamaichi, Elisabeth A Raleigh, and Richard J Roberts. Plasmid replication-associated single-strand-specific methyltransferases. Nucleic Acids Research, 48:12858-12873, Dec 2020. URL: https://doi.org/10.1093/nar/gkaa1163, doi:10.1093/nar/gkaa1163. This article has 13 citations and is from a highest quality peer-reviewed journal.

Artifacts

Edison artifact artifact-00

Citations

anton2025biologyofhostdependent pages 3-6
kang2025bacterialrestrictionmodificationsystems pages 8-9
zaworski2022reassemblingacannon pages 13-14
murray2017thenonspecificadenine pages 6-8
anton2025biologyofhostdependent pages 32-35
li2024ocrmediatedsuppressionof pages 1-2
li2024ocrmediatedsuppressionof pages 8-9
li2024ocrmediatedsuppressionof pages 6-7
fomenkov2020plasmidreplicationassociatedsinglestrandspecific pages 5-6
https://doi.org/10.1128/ecosalplus.esp-0014-2022
https://doi.org/10.52601/bpr.2025.240070
https://doi.org/10.1371/journal.pgen.1009943
https://doi.org/10.1093/nar/gkx1191
https://doi.org/10.1093/nar/gkae608
https://doi.org/10.1128/spectrum.03974-22
https://doi.org/10.1128/ecosalplus.esp-0014-2022,
https://doi.org/10.1371/journal.pgen.1009943,
https://doi.org/10.52601/bpr.2025.240070,
https://doi.org/10.1093/nar/gkx1191,
https://doi.org/10.1093/nar/gkae608,
https://doi.org/10.1093/nar/gkaa1163,

📄 View Raw YAML

id: Q9XJG2
gene_symbol: darB
taxon:
  id: NCBITaxon:10678
  label: Punavirus P1
description: DarB is a 251 kDa antirestriction protein from bacteriophage P1 that protects phage DNA from host Type I restriction-modification systems, specifically EcoB and EcoK. The protein contains an N-terminal Type II methyltransferase M.TaqI-like domain and a central DExD-like helicase domain. DarB is incorporated into the phage virion during assembly and is ejected into the host cell cytoplasm along with phage DNA at infection initiation, where it provides protection against host restriction systems. The protein is part of a multicomponent antirestriction system that also includes DarA, DdrA, DdrB, Hdf, and Ulx proteins.
existing_annotations:
- term:
    id: GO:0006304
    label: DNA modification
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  review:
    summary: Too general - DNA modification occurs, but the biological function is specifically antirestriction, not just general DNA modification
    action: MODIFY
    proposed_replacement_terms:
    - id: GO:0099018
      label: symbiont-mediated evasion of host restriction-modification system
    supported_by:
    - reference_id: PMID:3029954
      supporting_text: The darA and darB gene products are found in the phage head and protect any DNA packaged into a phage head, including transduced chromosomal markers, from restriction
- term:
    id: GO:0008168
    label: methyltransferase activity
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: Too general - DarB has a methyltransferase domain, but specifically acts on DNA
    action: MODIFY
    proposed_replacement_terms:
    - id: GO:0009008
      label: DNA-methyltransferase activity
    supported_by:
    - reference_id: GO_REF:0000043
      supporting_text: UniProtKB keyword mapping and InterPro domain IPR011639 (Type II methyltransferase M.TaqI-like domain) indicate DNA methyltransferase activity
- term:
    id: GO:0032259
    label: methylation
  evidence_type: IEA
  original_reference_id: GO_REF:0000043
  review:
    summary: Too general and not the core biological process - methylation may occur but the key function is antirestriction defense
    action: KEEP_AS_NON_CORE
    reason: While DarB has a methyltransferase domain suggesting methylation activity, the primary biological function is antirestriction. Methylation is a molecular mechanism, not the biological role
- term:
    id: GO:0005737
    label: cytoplasm
  evidence_type: NAS
  review:
    summary: Added to align core_functions with existing annotations.
    action: NEW
    reason: Core function term not present in existing_annotations.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO terms.
  findings: []
- id: GO_REF:0000043
  title: Gene Ontology annotation based on UniProtKB/Swiss-Prot keyword mapping
  findings: []
- id: PMID:3029954
  title: Two DNA antirestriction systems of bacteriophage P1, darA, and darB - characterization of darA- phages
  findings: []
- id: PMID:28509398
  title: The multicomponent antirestriction system of phage P1 is linked to capsid morphogenesis
  findings: []
- id: PMID:35377874
  title: 'Reassembling a cannon in the DNA defense arsenal: Genetics of StySA, a BREX
    phage exclusion system in Salmonella lab strains.'
  findings:
  - statement: Injected DarB carries a bioinformatic signature of methyltransferase,
      but how it acts against diverse restriction-modification systems remains unresolved;
      catalytic activity has not been directly demonstrated.
- id: PMID:38989624
  title: Ocr-mediated suppression of BrxX unveils a phage counter-defense mechanism.
  findings:
  - statement: Contemporary phage-counter-defense work (Ocr inhibits the BREX methyltransferase
      BrxX as a DNA mimic) provides an experimental template for assaying SAM-dependent
      methyltransferases - DNA Km approximately 3.4 uM, SAM Km approximately 380
      uM, Ocr IC50 approximately 1.17 uM - relevant for future biochemical validation
      of DarB methyltransferase predictions.
- id: PMID:29228259
  title: The non-specific adenine DNA methyltransferase M.EcoGII.
  findings:
  - statement: A representative adenine DNA methyltransferase (M.EcoGII) installs
      N6-methyladenine using SAM and contains hallmark SAM-dependent MTase motifs
      (FxGxG AdoMet-binding motif and DPPY catalytic motif); supports the family-level
      inference that DarB-like proteins, given their predicted SAM-dependent MTase
      domain, could perform similar chemistry.
- id: PMID:40856689
  title: Biology of host-dependent restriction-modification in prokaryotes.
  findings:
  - statement: The P1 dar system (DarA, DarB, Ulx, DdrB, DdrA, Hdf) is virion-head-incorporated
      and confers protection against several Type I HDRM systems and BREX, acting
      only in cis on DNA packaged within the virion, supporting a model of physical
      obstruction of host restriction machinery.
- id: doi:10.52601/bpr.2025.240070
  title: 'Bacterial restriction-modification systems: mechanisms of defense against phage infection'
  findings:
  - statement: DarA/DarB are described as co-injected proteins that occlude restriction
      sites on the P1 genome to avoid destruction by host RM systems; the cis-only
      behaviour is consistent with restriction-site shielding rather than diffusible
      enzymatic activity.
- id: file:9CAUD/darB/darB-deep-research-falcon.md
  title: Deep research report on darB/Q9XJG2 (Falcon/Edison Scientific Literature)
  findings:
  - statement: No primary publication directly characterizes UniProt Q9XJG2 (Punavirus
      P1 darB'); the prevailing literature treats DarB as a virion-delivered anti-restriction
      factor with a bioinformatic methyltransferase signature but no biochemically
      validated methyltransferase activity.
  - statement: Best-supported mode of action for the P1 Dar system is protein-mediated
      physical obstruction (restriction-site shielding) acting in cis on virion-packaged
      DNA against several Type I HDRM systems and BREX; methyltransferase chemistry,
      if any, remains a domain-level inference.
  - statement: Critical experimental gaps for Q9XJG2 are direct methyltransferase
      activity assay, identification of the modified base (m6A/m4C/m5C), recognition
      motif and specificity, and confirmation that the UniProt fragment is catalytically
      competent.
core_functions:
- molecular_function:
    id: GO:0009008
    label: DNA-methyltransferase activity
  directly_involved_in:
  - id: GO:0099018
    label: symbiont-mediated evasion of host restriction-modification system
  locations:
  - id: GO:0005737
    label: cytoplasm
  description: Phage-encoded, virion-injected antirestriction factor carrying an N-terminal
    SAM-dependent DNA-methyltransferase domain (InterPro IPR011639, M.TaqI-like). The
    DNA-methyltransferase activity is a domain-level bioinformatic inference (GO_REF:0000043);
    no direct enzymatic methylation has been biochemically demonstrated for DarB. The
    experimentally supported role is cis-acting protection of virion-packaged DNA against
    host Type I restriction-modification systems.
  supported_by:
  - reference_id: GO_REF:0000043
    supporting_text: UniProtKB keyword mapping and InterPro domain IPR011639 (Type II methyltransferase M.TaqI-like domain) indicate DNA methyltransferase activity
  - reference_id: PMID:3029954
    supporting_text: The darA and darB gene products are found in the phage head and protect any DNA packaged into a phage head, including transduced chromosomal markers, from restriction
suggested_questions:
- question: What is the mechanism of DarB injection into host cells during phage infection?
  experts:
  - Phage biology researchers, especially those studying P1 phage
- question: Does DarB protect phage DNA from host restriction systems or regulate phage gene expression?
  experts:
  - Restriction-modification system experts
- question: Are there host factors required for DarB methyltransferase activity?
  experts:
  - Host-pathogen interaction researchers
tags:
- lbnl-favorites
status: DRAFT

darB

Gene Description

Existing Annotations Review

Core Functions

References

Suggested Questions for Experts

Tags