ArnE is a small multi-pass inner-membrane subunit of the undecaprenyl phosphate-alpha-L-Ara4N flippase. Together with ArnF, ArnE moves the lipid-linked 4-amino-4-deoxy-L-arabinose donor from the cytoplasmic leaflet to the periplasmic leaflet of the inner membrane, enabling ArnT to transfer L-Ara4N onto lipid A and thereby reducing the negative charge of the outer membrane lipopolysaccharide during polymyxin-resistance lipid A modification.
Definition: Enables the directional transport of a lipid from one leaflet of a membrane to the other leaflet with undecaprenyl phosphate-alpha-L-Ara4N as the transported substrate.
Justification: ArnE/ArnF moves undecaprenyl phosphate-alpha-L-Ara4N from the cytoplasmic leaflet to the periplasmic leaflet. GO:0140303 is the correct existing parent because GO's flippase and floppase terms currently sit under ATPase-coupled intramembrane lipid transporter activity and therefore make an unsupported ATP-coupling claim for this small SMR/DMT-family system. A child for undecaprenyl-phosphate-L-Ara4N flippase activity would capture the ArnE/ArnF activity more exactly without asserting a coupling mechanism.
Parent term: intramembrane lipid transporter activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005886 plasma membrane | IBA GO_REF:0000033 | ACCEPT | Summary: ArnE is an integral E. coli inner-membrane protein; for a bacterial protein this compartment is represented by GO:0005886 'plasma membrane'. The phylogenetic annotation is consistent with UniProt's subcellular localization and with experimental C-terminal topology analysis of the E. coli inner membrane proteome. Reason: This IBA annotation correctly places ArnE at the inner membrane where the ArnE/ArnF flippase acts. Yan et al. describe PmrL/ArnE and PmrM/ArnF as small hydrophobic inner-membrane proteins, and Daley et al. experimentally mapped E. coli inner-membrane protein topology by C-terminal GFP/PhoA tagging. GO uses 'plasma membrane' for the bacterial cytoplasmic membrane. Supporting Evidence: PMID:17928292 PmrL and PmrM are small, hydrophobic, inner membrane proteins with many of the characteristics of small multidrug resistance transporters PMID:15919996 Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins |
| GO:0005886 plasma membrane | IDA PMID:15919996 Global topology analysis of the Escherichia coli inner membr... | ACCEPT | Summary: ArnE localization to the E. coli inner membrane was included in the global topology analysis that experimentally established C-terminal topology for 601 inner-membrane proteins using alkaline phosphatase and GFP fusions. Reason: This is a direct experimental localization row for ArnE's bacterial plasma membrane location and agrees with ArnE's membrane-spanning topology and lipid-linked-donor flippase role in the inner membrane. Supporting Evidence: PMID:15919996 Using C-terminal tagging with the alkaline phosphatase and green fluorescent protein, we established the periplasmic or cytoplasmic locations of the C termini for 601 inner membrane proteins |
| GO:0005886 plasma membrane | IEA GO_REF:0000120 | ACCEPT | Summary: The automated UniProt localization row to plasma membrane is correct; ArnE is a multi-pass inner-membrane protein. Reason: UniProt annotates ArnE as a cell inner membrane multi-pass membrane protein, and the experimental topology evidence independently supports the same bacterial plasma-membrane localization. Supporting Evidence: PMID:15919996 Global topology analysis of the Escherichia coli inner membrane proteome |
| GO:0009103 lipopolysaccharide biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: ArnE participates in LPS biosynthesis through the L-Ara4N lipid A modification pathway. It acts after formation of undecaprenyl phosphate-alpha-L-Ara4N and before ArnT transfers L-Ara4N to lipid A. Reason: Lipid A is the lipid component of lipopolysaccharide, and the ArnE flippase subunit is required to deliver the lipid-linked L-Ara4N donor to the periplasmic face of the inner membrane for lipid A modification. The UniRule/UniPathway electronic row is therefore biologically consistent with the experimentally established arnE phenotype. Supporting Evidence: PMID:17928292 Modification of lipid A with the 4-amino-4-deoxy-L-arabinose (L-Ara4N) moiety is required for resistance to polymyxin and cationic antimicrobial peptides in Escherichia coli and Salmonella typhimurium |
| GO:0009245 lipid A biosynthetic process | IEA GO_REF:0000104 | ACCEPT | Summary: ArnE acts in the modification branch that converts lipid A into L-Ara4N-modified lipid A. The step is a late lipid A modification rather than de novo Kdo2-lipid A assembly, but it is conventionally grouped with lipid A biosynthesis. Reason: Deleting arnE largely abolishes the L-Ara4N-modified lipid A species formed in the polymyxin-resistant pmrAc background. This validates ArnE's placement in lipid A biosynthesis in the broad GOA/UniProt sense. Supporting Evidence: PMID:17928292 In the pmrL or pmrM deletion mutants, over 95% of each of the L-Ara4N-modified lipid A species was missing |
| GO:0010041 response to iron(III) ion | IEP PMID:15322361 A Genome-wide view of the Escherichia coli BasS-BasR two-com... | MARK AS OVER ANNOTATED | Summary: The arn/yfbE operon is transcriptionally induced by external iron in a BasS-BasR-dependent manner, and arnE therefore has expression evidence linked to Fe(III). ArnE's direct gene-product role is nevertheless lipid A donor flipping, not Fe(III) sensing, detoxification, or transport. Reason: This IEP row records a real transcriptional response, but it overstates ArnE's function. ArnE is induced as part of the BasS-BasR arn regulon and executes the L-Ara4N lipid A modification effector pathway downstream; the protein itself does not do the sensing or other direct work of the iron response. Supporting Evidence: PMID:15322361 First we showed that the hypothetical yfbE operon that appears to be implicated in the modification of lipopolysaccharides is regulated at the level of transcription in response to external iron PMID:15322361 BasS-BasR system is essential for this iron-dependent induction of yfbE |
| GO:0010041 response to iron(III) ion | IGI PMID:12139617 Fe(III)-mediated cellular toxicity. | MARK AS OVER ANNOTATED | Summary: The PmrA/PmrB system protects Enterobacteriaceae from Fe(III)-mediated toxicity, and in E. coli its BasS-BasR/PmrA homolog induces the arn operon. This connects arnE to the Fe(III)-induced lipid A modification regulon indirectly rather than making ArnE itself an iron-response protein. Reason: The genetic Fe(III) phenotype is mediated through PmrA/PmrB regulation of envelope-modification effectors. For arnE, the effector activity remains intramembrane flipping of undecaprenyl phosphate-alpha-L-Ara4N for L-Ara4N lipid A modification; neither the Chamnongpol abstract nor the direct ArnE flippase evidence establishes a molecular role in Fe(III) sensing or detoxification. Supporting Evidence: PMID:12139617 Fe(III) exhibits microbicidal activity towards strains of Salmonella enterica, Escherichia coli and Klebsiella pneumoniae defective in the Fe(III)-responding PmrA/PmrB signal transduction system PMID:15322361 BasS-BasR system is essential for this iron-dependent induction of yfbE |
| GO:0016020 membrane | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro transfers a generic membrane annotation from the ArnE SMR/EamA domain architecture. This is correct for an inner-membrane flippase subunit. Reason: The term is broad but true; ArnE is a multi-pass membrane protein in the inner membrane. More specific rows to GO:0005886 capture the bacterial plasma-membrane localization. Supporting Evidence: PMID:17928292 PmrL and PmrM are small, hydrophobic, inner membrane proteins with many of the characteristics of small multidrug resistance transporters |
| GO:0022857 transmembrane transporter activity | IEA GO_REF:0000120 | MODIFY | Summary: Automated family/domain mappings annotate ArnE to the broad SMR/DMT parent activity. ArnE does support transport, but the demonstrated ArnE/ArnF activity is intramembrane lipid-linked sugar flipping. Reason: GO:0022857 is too general relative to the more informative carbohydrate-derivative transporter rows that ArnE already carries. The experimentally supported activity moves the lipid-linked L-Ara4N donor between the cytoplasmic and periplasmic leaflets of the same membrane, so GO:0140303 'intramembrane lipid transporter activity' is the more accurate existing term for the ArnE/ArnF flippase complex. Proposed replacements: intramembrane lipid transporter activity Supporting Evidence: PMID:17928292 PmrL and PmrM could specifically function to flip undecaprenyl phosphate-alpha-L-Ara4N from the cytosolic to the periplasmic side of the inner membrane, possibly functioning as a heterodimer |
| GO:0046493 lipid A metabolic process | IMP PMID:17928292 An undecaprenyl phosphate-aminoarabinose flippase required f... | ACCEPT | Summary: Chromosomal arnE/pmrL deletion in a pmrAc E. coli background removed more than 95% of L-Ara4N-modified lipid A species without blocking undecaprenyl phosphate-alpha-L-Ara4N synthesis. Reason: This IMP row is a core process annotation for ArnE. The deletion phenotype places ArnE after synthesis of the lipid-linked donor and before ArnT-dependent addition of L-Ara4N to lipid A, directly in lipid A metabolism. Supporting Evidence: PMID:17928292 In the pmrL or pmrM deletion mutants, over 95% of each of the L-Ara4N-modified lipid A species was missing PMID:17928292 undecaprenyl phosphate-alpha-L-Ara4N present in the mutants was less concentrated on the periplasmic surface of the inner membrane |
| GO:0055085 transmembrane transport | IBA GO_REF:0000033 | ACCEPT | Summary: The broad SMR-family IBA captures the transport process inherited by ArnE's transporter family. ArnE's actual substrate is a lipid-linked carbohydrate derivative flipped across the inner-membrane bilayer. Reason: The term is broad but compatible with ArnE biology; the ArnE/ArnF system translocates undecaprenyl phosphate-alpha-L-Ara4N from one side of the inner membrane to the other. The more precise molecular function is intramembrane lipid transporter activity, handled as a new row and as replacements for the generic GO:0022857 activity rows. Supporting Evidence: PMID:17928292 The data imply that both PmrL and PmrM are involved in the translocation of undecaprenyl phosphate-alpha-LAra4N across the inner membrane |
| GO:0055085 transmembrane transport | IEA GO_REF:0000104 | ACCEPT | Summary: The UniRule-based process row is broad but consistent with ArnE's role in translocating undecaprenyl phosphate-alpha-L-Ara4N to the periplasmic face of the inner membrane. Reason: Although ArnE mediates intramembrane flipping rather than release of a water-soluble solute into a different compartment, the substrate does move across the bilayer. This parent process is acceptable beside the more informative carbohydrate-derivative transport annotations. Supporting Evidence: PMID:17928292 The data imply that both PmrL and PmrM are involved in the translocation of undecaprenyl phosphate-alpha-LAra4N across the inner membrane |
| GO:1901264 carbohydrate derivative transport | IBA GO_REF:0000033 | ACCEPT | Summary: The recent PANTHER inference to carbohydrate derivative transport is specific for the ArnE/ArnF subfamily and matches the transport of the L-Ara4N-containing undecaprenyl phosphate donor. Reason: This phylogenetic inference is appropriately narrower than the older broad SMR-family transport IBA. ArnE and ArnF are the experimentally supported E. coli members of this specific family, and the transported undecaprenyl phosphate-alpha-L-Ara4N substrate carries a carbohydrate derivative. Supporting Evidence: PMID:17928292 These results are consistent with the idea that the undecaprenyl phosphate-alpha-L-Ara4N gains access to the periplasmic side of the inner membrane independently of arnT function |
| GO:1901264 carbohydrate derivative transport | IMP PMID:17928292 An undecaprenyl phosphate-aminoarabinose flippase required f... | ACCEPT | Summary: The arnE/pmrL mutant has normal or elevated total undecaprenyl phosphate-alpha-L-Ara4N but much less sulfo-NHS-biotin-accessible donor on the periplasmic surface, supporting a defect in transport of the L-Ara4N-linked carbohydrate derivative. Reason: The membrane-impermeable sulfo-NHS-biotin assay directly tested whether the donor could reach the periplasmic face of the inner membrane. The pmrL/arnE defect therefore supports a core carbohydrate derivative transport process row. Supporting Evidence: PMID:17928292 At the 4-h time point, there was a 4-5-fold reduction in ratio of the monoisotopic peak areas for biotinylated undecaprenyl phosphate-alpha-L-Ara4N compared with unmodified undecaprenyl phosphate-alpha-L-Ara4N PMID:17928292 undecaprenyl phosphate-alpha-L-Ara4N levels were the same or slightly higher in the mutants than in the parent |
| GO:1901505 carbohydrate derivative transmembrane transporter activity | IBA GO_REF:0000033 | ACCEPT | Summary: PANTHER transfers a carbohydrate derivative transporter activity from the ArnE/ArnF node. This is supported for arnE by the pmrL deletion phenotype and by the reduced periplasmic accessibility of the L-Ara4N-linked lipid donor. Reason: The term is not exact about leaflet-to-leaflet lipid flipping, but it correctly captures the carbohydrate-derivative nature of the substrate and is specific enough to keep. A separate NEW row to GO:0140303 captures the intramembrane lipid movement that GO:1901505 lacks. Supporting Evidence: PMID:17928292 The data imply that both PmrL and PmrM are involved in the translocation of undecaprenyl phosphate-alpha-LAra4N across the inner membrane |
| GO:1901505 carbohydrate derivative transmembrane transporter activity | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro transfers an ArnE-family carbohydrate derivative transporter activity that is consistent with the experimentally inferred L-Ara4N donor flippase role. Reason: The InterPro family mapping is biologically appropriate for E. coli ArnE because the ArnE/ArnF system translocates undecaprenyl phosphate-alpha-L-Ara4N. The exact geometry is intramembrane lipid transport, but this term is still a meaningful specific activity rather than a generic transporter parent. Supporting Evidence: PMID:17928292 PmrL and PmrM could specifically function to flip undecaprenyl phosphate-alpha-L-Ara4N from the cytosolic to the periplasmic side of the inner membrane, possibly functioning as a heterodimer |
| GO:1901505 carbohydrate derivative transmembrane transporter activity | IMP PMID:17928292 An undecaprenyl phosphate-aminoarabinose flippase required f... | ACCEPT | Summary: Genetic deletion and sulfo-NHS-biotin labeling place ArnE in the membrane translocation of undecaprenyl phosphate-alpha-L-Ara4N, a lipid-linked carbohydrate derivative. Reason: This IMP activity row is supported by direct arnE mutant data. The donor is still synthesized in the pmrL/arnE mutant but becomes much less accessible to a periplasmic labeling reagent, demonstrating a transporter defect rather than a biosynthetic block. Supporting Evidence: PMID:17928292 The data imply that both PmrL and PmrM are involved in the translocation of undecaprenyl phosphate-alpha-LAra4N across the inner membrane PMID:17928292 Polymyxin resistance was specifically restored to the pmrL deletion mutant AY100 by transformation with pWSK29-PmrL |
| GO:1901760 beta-L-Ara4N-lipid A biosynthetic process | TAS PMID:17928292 An undecaprenyl phosphate-aminoarabinose flippase required f... | ACCEPT | Summary: ArnE acts in the beta-L-Ara4N lipid A modification pathway by flipping the L-Ara4N donor that ArnT uses on the periplasmic side of the inner membrane. Reason: This process term is the specific pathway outcome of the ArnE/ArnF flippase step. The pmrL/arnE mutant directly loses L-Ara4N-modified lipid A, and the biochemical donor-pool and accessibility assays localize the defect to transport of the lipid-linked L-Ara4N donor. Supporting Evidence: PMID:17928292 PmrM and PmrL, now renamed ArnE and ArnF because of their involvement in L-Ara4N modification of lipid A, may be subunits of an undecaprenyl phosphate-alpha-L-Ara4N flippase |
| GO:0140303 intramembrane lipid transporter activity | IMP PMID:17928292 An undecaprenyl phosphate-aminoarabinose flippase required f... | NEW | Summary: ArnE is required for flipping undecaprenyl phosphate-alpha-L-Ara4N from the cytoplasmic to the periplasmic leaflet of the inner membrane. That leaflet-to-leaflet movement of a lipid-linked donor is an intramembrane lipid transporter activity. Reason: Existing rows capture the broad transporter and carbohydrate-derivative aspects of ArnE function but do not assert the exact GO parent for lipid flipping. Yan et al. showed that the arnE/pmrL mutant still synthesized the lipid donor while losing most of its periplasmic accessibility, directly supporting ArnE's role in intramembrane lipid transport. Supporting Evidence: PMID:17928292 PmrL and PmrM could specifically function to flip undecaprenyl phosphate-alpha-L-Ara4N from the cytosolic to the periplasmic side of the inner membrane, possibly functioning as a heterodimer PMID:17928292 At the 4-h time point, there was a 4-5-fold reduction in ratio of the monoisotopic peak areas for biotinylated undecaprenyl phosphate-alpha-L-Ara4N compared with unmodified undecaprenyl phosphate-alpha-L-Ara4N |
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