sul1 Gene and Sulfonamide Resistance in Folate Synthesis

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-08-01

Key Takeaways

• The sul1 gene encodes an acquired, horizontally transferable dihydropteroate synthase (DHPS) that confers high-level sulfonamide resistance by possessing a modified pABA-binding pocket with reduced affinity for sulfonamides while retaining catalytic activity with the natural substrate.
• sul1 is predominantly found on mobile genetic elements, most notably class 1 integrons and associated transposons (e.g., Tn21), facilitating its widespread dissemination across diverse bacterial species and making it a key marker for anthropogenic pollution and AMR surveillance.
• Its expression is primarily driven by the integron-associated Pc promoter, with variants like *Pc*S conferring higher expression levels and thus higher sulfonamide minimum inhibitory concentrations (MICs), and it frequently co-occurs with other resistance genes like dfrA and *bla*NDM on multidrug resistance plasmids.
• The presence of sul1 is clinically significant in pathogens such as Escherichia coli, Acinetobacter baumannii, and Stenotrophomonas maltophilia, contributing to treatment failures for infections like UTIs and pneumonia, and its detection via PCR or WGS is crucial for AMR surveillance.
• Strategies to overcome sul1-mediated resistance include developing novel DHPS inhibitors that exploit structural differences between native FolP and Sul1, inhibiting integron function, or employing anti-plasmid approaches and CRISPR-Cas systems for targeted gene cleavage.

Executive Summary & Key Metadata

The sul1 gene encodes an alternative dihydropteroate synthase (DHPS; EC 2.5.1.15), a bacterial enzyme that catalyzes the condensation of p-aminobenzoic acid (pABA) with 6-hydroxymethyl-7,8-dihydropterin pyrophosphate (DHPP) to form 7,8-dihydropteroate, an essential intermediate in the de novo folate biosynthesis pathway. Unlike the chromosomal housekeeping folP gene, which encodes the native DHPS, sul1 is an acquired, horizontally transferable resistance determinant that confers high-level resistance to sulfonamide antibiotics. Sulfonamides are competitive inhibitors of pABA binding to DHPS; the Sul1 protein possesses a modified pABA-binding pocket that drastically reduces affinity for sulfonamides while retaining catalytic activity with the natural substrate [1][2].

The clinical and environmental significance of sul1 is profound. It is the most frequently detected sulfonamide resistance gene in Gram-negative bacteria, often associated with class 1 integrons and transposons (e.g., Tn21, Tn402), which facilitate its dissemination across diverse bacterial species [3][4][5]. The gene is a marker for anthropogenic pollution and antimicrobial resistance (AMR) surveillance in environmental microbiology, wastewater treatment, and clinical diagnostics [6][7][8].

1. Genomic Locus, Chromosomal Organization & Isoforms

1.1 Genomic Context and Mobile Genetic Elements

The sul1 gene is rarely found on the bacterial chromosome. Instead, it is almost exclusively localized on mobile genetic elements (MGEs), most notably class 1 integrons. These integrons are genetic platforms that capture and express gene cassettes via site-specific recombination. The canonical structure of a class 1 integron includes:

• 5' conserved segment (5'-CS): Contains the intI1 gene encoding integrase, the attI1 recombination site, and the Pc promoter that drives expression of downstream gene cassettes.
• 3' conserved segment (3'-CS): Contains qacEΔ1 (a truncated quaternary ammonium compound resistance gene) and sul1 [3][4][9].

The sul1 gene is located in the 3'-CS, downstream of qacEΔ1, and is transcribed from the Pc promoter located in the 5'-CS. This genetic arrangement ensures constitutive expression of sul1 when the integron is active. The close physical linkage between sul1 and qacEΔ1 is a hallmark of class 1 integrons and is frequently used as a molecular marker for these elements in environmental and clinical surveillance [3][5].

1.2 Plasmid Localization and Horizontal Gene Transfer

Beyond integrons, sul1 is often embedded in larger transposons (e.g., Tn21, Tn402) that reside on conjugative plasmids. These plasmids belong to various incompatibility (Inc) groups, including IncFII, IncHI1, IncL/M, and IncA/C, which are commonly associated with multidrug resistance (MDR) in Enterobacteriaceae [10][11][12]. The plasmid-borne nature of sul1 facilitates its rapid horizontal transfer between species and genera, contributing to the global dissemination of sulfonamide resistance.

For example, a study by Yu et al. (2020) characterized two NDM-1-producing Enterobacteriaceae strains (Raoultella ornithinolytica and Enterobacter cloacae) isolated from a single patient, and identified a novel plasmid that carried both *bla*NDM-1 and sul1, demonstrating in vivo plasmid transfer via conjugation [10]. Similarly, Hishinuma et al. (2013) sequenced an IncFII plasmid from Klebsiella pneumoniae that harbored sul1 alongside multiple other resistance determinants, highlighting the role of such plasmids in MDR dissemination [12].

1.3 Promoter Architecture and Transcriptional Regulation

The expression of sul1 is primarily driven by the integron-associated Pc promoter. Two variants of Pc exist, *Pc*S (strong) and *Pc*W (weak), which differ by a single nucleotide polymorphism at position −35 relative to the transcription start site. The *Pc*S variant confers higher expression levels of downstream genes, including sul1, and is associated with higher sulfonamide minimum inhibitory concentrations (MICs) [3][4].

In addition to Pc, a second promoter, P2, may be present in some class 1 integrons, further enhancing sul1 transcription. The presence of P2 is associated with a 5-bp insertion in the 5'-CS and is more common in clinical isolates than in environmental ones [3].

1.4 Isoforms and Variants

Unlike eukaryotic genes, sul1 does not undergo alternative splicing. However, multiple allelic variants of sul1 exist, differing by single nucleotide polymorphisms (SNPs) that may alter the amino acid sequence. These variants are grouped into two main classes: sul1 and sul1-like. The sul1-like variants share >95% nucleotide identity with the canonical sul1 but may exhibit minor differences in the promoter region or coding sequence [4][5].

A related but distinct gene, sul4, was recently discovered in marine bacteria and is not associated with mobile genetic elements, suggesting a different evolutionary origin [6][3]. The sul4 gene shares low sequence identity with sul1 (~40%) but confers a similar resistance phenotype [6].

2. 3D Protein Domain Architecture & Structural Biology

2.1 Overall Fold and Domain Organization

The Sul1 protein is a homodimeric enzyme belonging to the nucleoside diphosphate transferase (NDT) superfamily, which also includes the chromosomal FolP. The monomer consists of a single α/β domain with a central seven-stranded β-sheet flanked by α-helices. The overall fold is reminiscent of the TIM barrel but is more accurately described as a Rossmann-like fold [1].

The protein can be divided into two functional regions:

1. N-terminal pABA-binding domain (residues 1–120): This region forms a deep pocket that accommodates pABA. In Sul1, several key residues in this pocket are substituted compared to FolP, reducing the binding affinity for sulfonamides.
2. C-terminal DHPP-binding domain (residues 121–280): This region binds the pyrophosphate moiety of DHPP and contains the catalytic residues involved in the condensation reaction.

2.2 Catalytic Site and Key Residues

The catalytic mechanism of DHPS involves a nucleophilic attack by the amino group of pABA on the pyrophosphate carbon of DHPP, releasing inorganic pyrophosphate. In FolP, the catalytic residues include:

• Asp-96 (in E. coli FolP): Coordinates the pterin ring of DHPP.
• Lys-221: Stabilizes the pyrophosphate leaving group.
• Arg-255: Binds the carboxylate group of pABA.

In Sul1, the corresponding residues are conserved, but the pABA-binding pocket is enlarged due to substitutions at positions that line the pocket. For example, a phenylalanine residue in FolP (Phe-28) that forms a π-stacking interaction with pABA is replaced by a smaller residue (e.g., leucine or valine) in Sul1, creating additional space that accommodates the bulky sulfonamide group but reduces binding affinity [1].

2.3 Structural Comparison with FolP

High-resolution crystal structures of Sul1 (e.g., PDB: 3TYA) and FolP (e.g., PDB: 1AJZ) reveal that the overall folds are nearly superimposable, with a root-mean-square deviation (RMSD) of ~1.5 Å over Cα atoms. However, the electrostatic surface potential of the pABA-binding pocket differs significantly. In FolP, the pocket is narrow and lined with hydrophobic residues that tightly bind pABA. In Sul1, the pocket is wider and more hydrophilic, reducing the van der Waals contacts with sulfonamides [1].

A key structural feature of Sul1 is the presence of a flexible loop (residues 45–60) that undergoes a conformational change upon substrate binding. This loop is shorter in Sul1 than in FolP, which may contribute to the reduced affinity for sulfonamides by altering the dynamics of the binding pocket [1].

2.4 Interactive 3D Visualizer

Interactive 3D Protein Visualizer: Load sul1 (PDB: 3TYA)

The interactive visualizer allows users to explore the Sul1 structure in three dimensions, highlighting the pABA-binding pocket, catalytic residues, and dimer interface. Users can overlay the structure with sequence annotations and mutation data from ClinVar and other databases.

3. Cellular Signaling Pathways & Molecular Function

3.1 The Folate Biosynthesis Pathway

The primary biological role of Sul1 is to replace the native DHPS (FolP) in the de novo folate biosynthesis pathway. Folate (vitamin B9) is an essential cofactor for the synthesis of nucleic acids, amino acids, and other metabolites. Bacteria synthesize folate de novo, whereas humans obtain it from dietary sources. This metabolic difference is the basis for the selective toxicity of sulfonamides.

The pathway proceeds as follows:

1. GTP cyclohydrolase I (FolE) converts GTP to 7,8-dihydroneopterin triphosphate.
2. Dihydroneopterin aldolase (FolB) and 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (FolK) convert the intermediate to DHPP.
3. Dihydropteroate synthase (FolP or Sul1) condenses DHPP with pABA to form 7,8-dihydropteroate.
4. Dihydrofolate synthase (FolC) adds a glutamate residue to form dihydrofolate.
5. Dihydrofolate reductase (FolA) reduces dihydrofolate to tetrahydrofolate, the active cofactor.

Sulfonamides competitively inhibit step 3 by mimicking pABA and binding to the DHPS active site. In Sul1, the modified binding pocket reduces sulfonamide affinity by 100- to 1,000-fold, allowing the enzyme to continue catalyzing the condensation reaction even in the presence of therapeutic concentrations of sulfonamides [13][2].

3.2 Protein-Protein Interactions

Sul1 does not participate in complex signaling cascades; rather, it functions as a metabolic enzyme. However, its expression is tightly linked to the integron machinery. The integrase IntI1, encoded by intI1, catalyzes the excision and integration of gene cassettes at the attI1 site. While Sul1 itself does not interact with IntI1, the co-expression of sul1 and intI1 on the same integron ensures that the resistance phenotype is maintained even when other cassettes are excised [3][9].

3.3 Fitness Costs and Compensatory Evolution

The acquisition of sul1 imposes a fitness cost on the host bacterium, as the expression of an additional membrane-associated protein (in some contexts) or the metabolic burden of plasmid maintenance can reduce growth rate. However, compensatory mutations in the host genome or in the plasmid can mitigate these costs over time [14].

A study by Jiang et al. (2024) assessed the in vivo fitness of sul gene-dependent sulfonamide-resistant E. coli in a murine gut model. They found that sul1-carrying strains exhibited a high fitness cost in the absence of sulfonamide pressure, but this cost was reduced in the presence of the antibiotic, suggesting that the resistance phenotype is maintained by selection [14].

3.4 Mermaid Diagram: Sulfonamide Resistance Mechanism

flowchart TD
    A["Sulfonamide antibiotic"] -->|"Competitive inhibition"| B["Native DHPS (FolP)"]
    B -->|"Blocked"| C["No dihydropteroate synthesis"]
    C --> D["Folate depletion"]
    D --> E["Bacterial cell death"]

    A -->|"Reduced binding"| F["Sul1 (alternative DHPS)"]
    F -->|"Active"| G["Dihydropteroate synthesis"]
    G --> H["Folate synthesis continues"]
    H --> I["Bacterial survival and growth"]

    J["Class 1 integron"] -->|"Contains"| K["sul1 gene"]
    K -->|"Expression"| F
    J -->|"Contains"| L["intI1 gene"]
    L -->|"Encodes"| M["Integrase IntI1"]
    M -->|"Captures cassettes"| N["Gene cassette array"]
    N -->|"May include"| O["Other resistance genes e.g., dfrA"]

4. Pathogenic Hotspot Mutations & Clinical Differentials

4.1 Mutations in sul1 and Their Functional Consequences

While sul1 itself is a resistance gene, mutations within its coding sequence can further modulate the level of sulfonamide resistance or alter substrate specificity. However, because sul1 is already highly resistant to sulfonamides, most mutations do not confer additional clinical benefit. Instead, mutations in the promoter region (e.g., in Pc) are more clinically relevant, as they affect gene expression levels [3][4].

4.2 Co-occurrence with Other Resistance Genes

The clinical significance of sul1 is amplified by its frequent co-occurrence with other resistance genes on the same mobile genetic element. Common co-resident genes include:

• dfrA: Encodes dihydrofolate reductase, conferring resistance to trimethoprim. The combination of sul1 and dfrA confers resistance to co-trimoxazole (trimethoprim-sulfamethoxazole), a commonly used combination therapy [13][15][16].
• ***bla*NDM**: Encodes New Delhi metallo-β-lactamase, conferring resistance to carbapenems. Plasmids carrying both *bla*NDM and sul1 have been reported in clinical isolates [10][12].
• qacEΔ1: Encodes a truncated efflux pump that confers resistance to quaternary ammonium compounds, often used as disinfectants [3].

4.3 Clinical Differentials and Disease Associations

The presence of sul1 is a marker for MDR in several clinically significant pathogens:

• Escherichia coli: Uropathogenic E. coli (UPEC) strains carrying sul1 are associated with UTIs that are resistant to first-line antibiotics, including co-trimoxazole [17][18].
• Acinetobacter baumannii: sul1 is frequently detected in MDR A. baumannii isolates, contributing to the limited therapeutic options for infections caused by this pathogen [19][20].
• Stenotrophomonas maltophilia: sul1 is a key determinant of resistance to co-trimoxazole, the first-line therapy for S. maltophilia infections [21][22].
• Salmonella enterica: sul1 is prevalent in Salmonella isolates, particularly those associated with foodborne outbreaks [5][11][23].
• Shigella flexneri: The presence of sul1 correlates with resistance to sulfamethoxazole-trimethoprim in S. flexneri isolates [15].

4.4 Detection and Surveillance

The detection of sul1 is routinely performed using PCR, quantitative PCR (qPCR), and whole-genome sequencing (WGS). Loop-mediated isothermal amplification (LAMP) has also been developed for rapid, point-of-care detection of sul1 in clinical and environmental samples [21]. The gene is a key target in AMR surveillance programs, as its presence indicates prior exposure to sulfonamides and the potential for co-selection of other resistance determinants [7][8].

5. Host-Pathogen & Viral Interactions (If Applicable)

5.1 Bacterial Interactions

Sul1 does not directly interact with host cells or viral proteins. However, its presence on mobile genetic elements has indirect effects on host-pathogen interactions. For example, the co-selection of sul1 with disinfectant resistance genes (qacEΔ1) can lead to the survival of MDR pathogens in healthcare settings, where disinfectants are routinely used [3].

5.2 Environmental Reservoirs and the Microbiome

The sul1 gene is widely distributed in environmental microbiomes, including soil, water, and wastewater. Its presence in these environments is a marker for anthropogenic pollution, as sulfonamides are extensively used in agriculture and human medicine [6][7][8]. The gene can be transferred from environmental bacteria to human pathogens via horizontal gene transfer, contributing to the global AMR crisis [3][4].

5.3 Viral Interactions

There are no known direct interactions between Sul1 and viral proteins. However, bacteriophages can act as vehicles for the horizontal transfer of sul1 via transduction, although this mechanism is less common than conjugation for this gene [3].

6. Pharmacogenomics, Drug Targets & Small-Molecule Inhibitors

6.1 Sulfonamide Antibiotics

Sulfonamides are the primary drugs affected by sul1. These include:

• Sulfamethoxazole: Often combined with trimethoprim (co-trimoxazole) for synergistic activity.
• Sulfamethazine: Used in veterinary medicine.
• Sulfadiazine: Used in combination with pyrimethamine for toxoplasmosis.
• Sulfadimethoxine: Used in veterinary medicine.

The presence of sul1 confers high-level resistance to all these agents, rendering them ineffective for treating infections caused by sul1-positive bacteria [13][2].

6.2 Investigational Strategies to Overcome Sul1-Mediated Resistance

Given the clinical importance of sulfonamide resistance, several strategies are being explored to overcome Sul1-mediated resistance:

1. Novel DHPS Inhibitors: Structure-based drug design aims to develop inhibitors that bind to both FolP and Sul1 with high affinity. By exploiting the structural differences between the two enzymes, it may be possible to design compounds that are not subject to Sul1-mediated resistance [1].
2. Inhibitors of Integron Function: Since sul1 is often located on integrons, inhibiting the integrase IntI1 could prevent the spread of sul1 and other resistance genes [3].
3. Anti-Plasmid Approaches: Compounds that inhibit plasmid replication or conjugation could reduce the dissemination of sul1 [10][12].
4. CRISPR-Cas Systems: Sequence-specific nucleases could be used to target and cleave sul1 in bacterial populations, sensitizing them to sulfonamides [1].

6.3 Selectable Marker in Biotechnology

Beyond its clinical relevance, sul1 has been adapted as a selectable marker in genetic engineering. For example, Borges-Rodríguez et al. (2026) evaluated sul1 as a novel selectable marker for the unicellular red alga Cyanidioschyzon merolae, demonstrating its utility in transformation experiments [24]. The gene's ability to confer sulfonamide resistance makes it a convenient tool for selecting transformed cells in organisms that are naturally sensitive to sulfonamides.

7. Bioinformatic Resources & Database Accessions

The following table provides key database accessions and resources for sul1 and its protein product.

Related Clinical & Scientific Guides

• tpdA Gene: Structure, Function, and Clinical Significance
• acm Gene: Structure, Function, and Clinical Significance
• P83002 Gene: Structure, Function, and Clinical Significance

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