autoinducer-binding domain” at theN-terminal end. Examine
protein sequences positive for IPR005143 for the presence of
any of the three signatures namely IPR000792 (transcription
regulator LuxR,C-terminal), IPR016032 (signal transduction
response regulator, C-terminal effector), or IPR011991
(winged HTH DNA-binding domain). A typical QS LuxR
protein can be identified by the presence of one of the three
combinations of different domain architectures in the InterPro
collection: IPR005143 (ABD)-IPR000792, IPR005143-
IPR016032, and IPR005143-IPR011991.- Determining QS-related characteristics of the QS LuxR-coding
region/genome: If the protein sequence of interest has been
identified as a QS LuxR protein by in silico analyses, the next
step is to analyze the remainder of the genome for the presence
of genes that could code for other LuxI or LuxR homologs.
Carry out a BLASTP or a PFAM search using the predicted
protein sequences of the genome of interest to identify any
proteins that might code for LuxI homolog. Take the putative
LuxI homolog protein and carry out InterProScan of the iden-
tified sequence to verify the presence of IPR001690 (autoindu-
cer synthesis protein) and IPR018311 (autoinducer synthesis,
conserved site) domain, the protein signatures of the LuxI
homolog. To analyze the neighboring regions for a LuxR homo-
log, retrieve flanking sequences and analyze using SynTax [29]
or annotate using tools available at FGENESB [30]. - Interpretation of results of the InterProScan search and the
context search in the genomes/sequences of interest: If no
gene coding for a LuxI homolog was found in the genome or
in the genomic locus near the gene coding for QS domain
LuxR protein and if no unpaired or extra genes coding for
LuxI homologs were present in the remainder of the genome,
the QS LuxR protein of interest may be classified as a LuxR solo
or orphan.
3.1.2 Classification of
LuxR Solo Types
AHL-binding QS LuxR proteins are characterized by the presence
of all nine key residues which have been reported to be invariant
previously, six of which are in the AHL-binding domain and three
in the DNA-binding region (W57, Y61, D70, P71, W85, G113,
E178, L182, G188) with respect to TraR (see Note 7)ofA.
tumefaciens[3, 19]. In contrast, non-AHL-binding LuxR solos
are characterized by variation in at least one of the six key residues
in the autoinducer-binding domain. Although it is not clear if these
differences alone are sufficient to determine altered ligand specific-
ity, the changes in the key amino acid residues could be a way to
distinguish types of LuxR solos. Therefore, by analyzing the pro-
tein sequence of a newly identified LuxR solo, it is possible to
classify it putatively into AHL-binding or non-AHL-binding150 Vittorio Venturi et al.