DOI: 10.5061/dryad.866t1g21s
title: RefAHL: A curated quorum sensing reference linking diverse LuxI-type signal synthases with their acyl-homoserine lactone products

description: Some bacteria use acyl-homoserine lactone (AHL) signals in quorum sensing,
 a type of cell-cell communication. Here we present “RefAHL”, a curated
 collection of LuxI-type AHL synthases with their AHL structures and
 associated metadata. RefAHL is publicly available as a community resource
 to help catalog LuxI-type diversity encoded in (meta)genomic data.
description: The RefAHL dataset was collected, assembled and curated by humans
 from the public scientific literature.
description: # RefAHL: A curated quorum sensing reference linking diverse LuxI-type
 signal synthases with their acyl-homoserine lactone products Dataset DOI:
 [10.5061/dryad.866t1g21s](10.5061/dryad.866t1g21s) ## Description of the
 data and file structure Here we curate a list of previously published LuxI
 homologs, which have been experimentally demonstrated to synthesize an
 acyl homoserine lactone (AHL) signal of well-supported structure. We refer
 to this collection as “RefAHL” and will update the collection when new
 LuxI-AHL signals are defined. Contact Amy Schaefer
 ([amyschae@uw.edu](mailto:amyschae@uw.edu)) or Aaron Puri
 ([a.puri@utah.edu](mailto:a.puri@utah.edu)) with any questions or to
 submit newly defined LuxI-AHL signal pairs. There are two associated files
 (note that date suffixes in YYYYMMDD format will change in future
 versions). ### Files and variables #### File:
 RefAHL\_complete\_revYYYYMMDD.xlsx **Description:** The
 RefAHL_complete_revYYYYMMDD.xlsx file has Tab 1 ("RefAHL
 LuxI-AHL"), Tab 2 (“AHL compounds”), and Tab 3 ("RefAHL
 confidence ranking"), which contain the following variables (columns)
 and their descriptions: ##### Variables * (1) RefAHL identifier: Unique
 RefAHL name, comprised from the beginning of the genera/clone name
 (letters) and a number; if a LuxI homolog has &gt;65% amino acid identity
 and synthesizes the same AHL product with an existing RefAHL LuxI, they
 are given the same RefAHL ID with a subcategory letter (e.g. Mes_001a,
 Mes_001b) (1) Taxonomy or clone: Indicates either bacterial Class taxonomy
 or clone if derived from metagenomic sequence (1) Published LuxI homolog
 name: Most, but not all, LuxI homologs have an associated gene/protein
 name; for those homologs in the same RefAHL identifier grouping the shared
 percent amino acid identity is indicated in parentheses (1) Major AHL
 (defined in Tab 2): The abbreviation of the major AHL signal synthesized
 by the LuxI homolog; in cases where cognate LuxR activity data is not
 available, the major AHL is defined as the most abundant AHL produced; see
 Tab 2 for full compound names and additional chemical information; in
 cases where the major AHL depends on the growth condition or strain
 background, this is listed in parentheses [e.g. in minimal medium (M9) vs.
 rich medium (K9) for Burk_007] (1) AHL confidence category (defined in Tab
 3):  Confidence category ranking for the AHL product synthesized by the
 LuxI homolog depending upon its associated data; see Tab 3 for specific
 criteria (1) Strain or metagenome:  Name of the bacterial strain or
 metagenomic library clone encoding the LuxI homolog gene (1) Reference(s)
 (PMID): Reference(s) for the data summarized in RefAHL; in most cases this
 is the PubMed identifier (PMID) number for published manuscript(s); one
 entry references unpublished 14C-methionine feeding data, which supports
 the published relaxed-specificity bioassay data (1) LuxI-homolog protein
 sequence: Amino acid sequence of the LuxI homolog (1) IMG gene
 identifier: Unique object identifier of the LuxI homolog gene in the
 JGI-IMG database; ‘none’ indicates the genome sequence is not hosted by
 IMG  (1) GenBank identifier: Unique object identifier of the LuxI homolog
 gene in the GenBank database; only used when there was no IMG identifier
 available * (2) AHL abbreviation: Abbreviation of the acyl homoserine
 lactone (AHL) structure used in Tab 1 (2) AHL common name: Common chemical
 name of the AHL structure (2) PubChem compound: Unique object identifier
 of the AHL structure in the NIH PubChem database; ‘not available’
 indicates the AHL has an undefined double bond so a PubChem number cannot
 be assigned; 'none' indicates the compound has not been
 deposited in PubChem (2) AHL isomeric SMILES: The isomeric Simplified
 Molecular Input Line Entry System sstructure line notation, which
 describes the AHL structures; we assume a stereochemistry of L for the
 homoserine lactone and R for any 3-hydroxy acyl groups; ‘not available’
 indicates the AHL has an undefined double bond so an isomeric SMILES
 cannot be assigned (2) AHL formula: Chemical formula for the AHL structure
 (2) AHL monoisotopic mass: Monoisotopic mass for the AHL structure * (3)
 Category: Confidence ranking of data used to assign the AHL structure;
 lower values denote better confidence (3) Criteria: Criteria used to
 assign the category confidence rank; the rationale for omitting data
 (superscript note a) that utilize only relaxed-specificity bioassays is
 discussed in the manuscript text #### File: RefAHL\_rev20250421.fasta
 **Description:** The RefAHL_revYYYYMMDD.fasta file contains the following:
 Header: Contains the RefAHL identifier and Major AHL separated by an
 underscore for each LuxI homolog entry listed in .xls spreadsheet in fasta
 format; the text ‘RefAHL’ is included for each header for easy filtering
 Sequence: One letter coded amino acid sequence for the LuxI homolog ##
 Code/software .xlsx files can be opened with any version of Microsoft
 Excel, as well as Google Sheets, WPS Office or OpenOffice Calc .fasta
 files can be opened with any text editor  ## Access information Other
 publicly accessible locations of the data: * none Data was derived from
 the following sources: * data was assembled from the original references
 as cited in RefAHL.