Identification of the pcaRKF gene cluster from Pseudomonas putida: involvement in chemotaxis, biodegradation, and transport of 4-hydroxybenzoate

Abstract

Aromatic compounds are abundant in the biosphere as components of the complex polymer lignin and as environmental pollutants. The bacterial biodegradation of structurally simple, readily degradable aromatic compounds has been studied with the expectation that this will facilitate work on more recalcitrant members of the group. As a result, much information has been obtained about the enzymology and molecular regulation of aerobic pathways of aromatic compound degradation (6,16,35,53). An aspect of aromatic biology that has received almost no attention, however, is the question of how bacteria sense and respond to the presence of aromatic compounds in their environment. Chemotaxis and transport are two physiological functions that operate in this capacity, and a number of studies have shown that aromatic acids such as benzoate and 4-hydroxybenzoate are strong chemoattractants for Pseudomonas putida, as well as a number of other species of gram-negative bacteria including Agrobacterium spp. and rhizobia (19,20,31,39,40). However, very little is known about the characteristics of the presumed receptor proteins that are responsible for initial attractant recognition. Similarly, although a number of studies have inferred the existence of specific transport systems for aromatic acids and related compounds, only a few detailed studies of aromatic compound permeases have been reported (1, 2, 14, 30), and no molecular analyses of bacterial genes that encode such proteins have been presented.

The LysR-type PcaQ protein regulates expression of a protocatechuate-inducible ABC-type transport system in Sinorhizobium meliloti

“…Protocatechuate catabolic genes are organized into two operons (pcaDCHGB and pcaIJF), whose expression is regulated by the transcriptional regulators PcaQ and PcaR, respectively (MacLean et al, 2006. While systems involved in the active transport of aromatic acids such as protocatechuate have been described in many species, including Pseudomonas putida (Harwood et al, 1994;Nichols & Harwood, 1997), a protocatechuate transport system has yet to be identified in S. meliloti or any other member of the a-proteobacteria. Furthermore, S. meliloti appears to lack protein homologues of the PcaK major facilitator superfamily of aromatic acid transport proteins (Collier et al, 1997;Williams & Shaw 1997;D'Argenio et al, 1999;Ledger et al, 2009).…”

3-Chlorobenzoate is taken up by a chromosomally encoded transport system in Cupriavidus necator JMP134

“…Transporter-mediated uptake of aromatic acids has been reported in several bacteria (Allende et al, 1992(Allende et al, , 1993(Allende et al, , 2000(Allende et al, , 2002Chang & Zylstra, 1999;Collier et al, 1997;Harwood et al, 1994;Higgins & Mandelstam, 1972;Nichols & Harwood, 1997;Prieto & García, 1997;Saint & Romas, 1996;Schleissner et al, 1994;Thayer & Wheelis, Fig. 3.…”

“…A few of these permease-type transport proteins have been biochemically characterized, and the corresponding gene has been described. This category includes benK for benzoate transport, vanK for vanillate, hcaK for hydroxycinnamate, and mucK for muconate, all found in Acinetobacter baylyi ADP-1 (Collier et al, 1997;D'Argenio et al, 1999;Parke & Ornston, 2003;Williams & Shaw, 1997), and pcaK for 4-HB and protocatechuate in P. putida PRS2000 (Harwood et al, 1994).…”

“…Establishment and maintenance of concentration gradients requires the intracellular substrate concentration to be kept low relative to that of the external environment, which may be achieved by rapid transformation of the imported compound to metabolic intermediates (Harwood & Gibson, 1986;Merkel et al, 1989;Wong et al, 1994). In this case, uptake is effectively driven by the activity of catabolic enzymes, and this 'metabolic drag' mechanism (Wong et al, 1994) has been proposed for the uptake of benzoate (Harwood & Gibson, 1986) and 4-hydroxybenzoate (4-HB) (Merkel et al, 1989) in Rhodopseudomonas palustris, and for the uptake of 4-HB by Rhizobium leguminosarum (Wong et al, 1994).Transporter-mediated uptake has been reported for some non-chlorinated aromatic acids, such as benzoate (Collier et al, 1997;Thayer & Wheelis, 1982), 4-HB (Allende et al, 1993;Harwood et al, 1994), protocatechuate (Nichols & Harwood, 1997), mandelate (Higgins & Mandelstam, 1972), phenylacetate (Schleissner et al, 1994), 4-hydroxyphenylacetate (Prieto & García, 1997) and phthalate (Chang & Zylstra, 1999). Only a few of these permease-type transport proteins have been biochemically characterized, and the corresponding genes described.…”

“…Only a few of these permease-type transport proteins have been biochemically characterized, and the corresponding genes described. In most cases, identification of specific genes has been aided by the fact that candidate transport genes are located near to or within a gene cluster encoding the catabolic enzymes responsible for the degradation of aromatic compounds (Harwood et al, 1994;Collier et al, 1997;Chae & Zylstra, 2006).…”