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Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups.

Godoy P, Molina-Henares AJ, de la Torre J, Duque E, Ramos JL - Microb Biotechnol (2010)

Bottom Line: We validated in silico data regarding efflux pumps in groups 1 and 3 using 9 different mutants.Four mutants belonging to group 2 were found to be more sensitive than the wild-type to oxidative stress-inducing agents such as bipyridyl and methyl viologen.The two remaining mutants belonging to group 4 were found to be more sensitive than the parental to tetracycline and one of them was particularly sensitive to rubidium and chromate.

View Article: PubMed Central - PubMed

Affiliation: Consejo Superior de Investigaciones Científicas, Department of Environmental Protection, E-18008 Granada, Spain.

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Phylogenetic tree of efflux pumps and assigned function. The phylogenetic tree was constructed using the tree program. The function of the characterized pumps in each of the four groups is indicated to the right of the cluster.
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f2: Phylogenetic tree of efflux pumps and assigned function. The phylogenetic tree was constructed using the tree program. The function of the characterized pumps in each of the four groups is indicated to the right of the cluster.

Mentions: The generalized profile for RND efflux pumps, generated automatically using the 16 seed sequences (shown in Table S1), was run, by Provalidator, against all entries in the SwissProt and TrEMBL databases (Siezen and Wilson, 2008). Around 2000 proteins ranging in length from 950 to 1200 amino acids were identified as members of the RND efflux pump family (Table S2). The profile yielded a Z‐score of > 50 for all of these proteins, a value well above the empirically determined value of 8.5 that guarantees biological relevance for family member identification. Z‐scores were used to classify the proteins into four well‐defined groups based on intervals of about 50 arbitrary units on the Z‐score scale (Fig. 1). A phylogenetic tree was also constructed, and the sequences of each Z‐score group tended to cluster together (Fig. 2), suggesting that protein function within these groups may be related. When proteins in these clusters were analysed with regard to their function, we found that those in group 1 were antibiotic/drug efflux pumps such as the Mex/Ttg pumps of Pseudomonas (Li et al., 1995; 1998; Köhler et al., 1997; Ramos et al., 1998; Rojas et al., 2001; Poole, 2004; Jeannot et al., 2008; Fernández et al., 2009), the Acr pumps of enteric bacteria (Ma et al., 1993; Zgurskaya and Nikaido, 1999; Kobayashi et al., 2001) and the Cme pump of Acinetobacter spp. (Magnet et al., 2001; Chau et al., 2004). Group 3 included metal resistance efflux pumps such as Czc/Cnr from Ralstonia (Stähler et al., 2006), and Sil from Salmonella (McHugh et al., 1975; Gupta et al., 1999; Silver, 2003), among others. No known function was found to be previously assigned to members of the proteins in groups 2 and 4.


Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups.

Godoy P, Molina-Henares AJ, de la Torre J, Duque E, Ramos JL - Microb Biotechnol (2010)

Phylogenetic tree of efflux pumps and assigned function. The phylogenetic tree was constructed using the tree program. The function of the characterized pumps in each of the four groups is indicated to the right of the cluster.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3815342&req=5

f2: Phylogenetic tree of efflux pumps and assigned function. The phylogenetic tree was constructed using the tree program. The function of the characterized pumps in each of the four groups is indicated to the right of the cluster.
Mentions: The generalized profile for RND efflux pumps, generated automatically using the 16 seed sequences (shown in Table S1), was run, by Provalidator, against all entries in the SwissProt and TrEMBL databases (Siezen and Wilson, 2008). Around 2000 proteins ranging in length from 950 to 1200 amino acids were identified as members of the RND efflux pump family (Table S2). The profile yielded a Z‐score of > 50 for all of these proteins, a value well above the empirically determined value of 8.5 that guarantees biological relevance for family member identification. Z‐scores were used to classify the proteins into four well‐defined groups based on intervals of about 50 arbitrary units on the Z‐score scale (Fig. 1). A phylogenetic tree was also constructed, and the sequences of each Z‐score group tended to cluster together (Fig. 2), suggesting that protein function within these groups may be related. When proteins in these clusters were analysed with regard to their function, we found that those in group 1 were antibiotic/drug efflux pumps such as the Mex/Ttg pumps of Pseudomonas (Li et al., 1995; 1998; Köhler et al., 1997; Ramos et al., 1998; Rojas et al., 2001; Poole, 2004; Jeannot et al., 2008; Fernández et al., 2009), the Acr pumps of enteric bacteria (Ma et al., 1993; Zgurskaya and Nikaido, 1999; Kobayashi et al., 2001) and the Cme pump of Acinetobacter spp. (Magnet et al., 2001; Chau et al., 2004). Group 3 included metal resistance efflux pumps such as Czc/Cnr from Ralstonia (Stähler et al., 2006), and Sil from Salmonella (McHugh et al., 1975; Gupta et al., 1999; Silver, 2003), among others. No known function was found to be previously assigned to members of the proteins in groups 2 and 4.

Bottom Line: We validated in silico data regarding efflux pumps in groups 1 and 3 using 9 different mutants.Four mutants belonging to group 2 were found to be more sensitive than the wild-type to oxidative stress-inducing agents such as bipyridyl and methyl viologen.The two remaining mutants belonging to group 4 were found to be more sensitive than the parental to tetracycline and one of them was particularly sensitive to rubidium and chromate.

View Article: PubMed Central - PubMed

Affiliation: Consejo Superior de Investigaciones Científicas, Department of Environmental Protection, E-18008 Granada, Spain.

Show MeSH
Related in: MedlinePlus