A Substrate-Activated Efflux Pump, DesABC, Confers Zeamine Resistance to Dickeya zeae

Abstract

Zeamines are a family of polyamino phytotoxins produced by Dickeya zeae EC1. These phytotoxins are also potent antibiotics against a range of microorganisms. To understand how D. zeae EC1 can protect itself from the antimicrobial activity of zeamines, we tested whether the ABC transporter genes within the zms (zeamine synthesis) gene cluster were related to zeamine resistance. Our results ruled out the possible involvement of these ABC transporters in zeamine resistance and instead unveiled an RND (resistance-nodulation-cell division) efflux pump, DesABC, which plays an important role in zeamine resistance in D. zeae EC1. The desAB genes are located next to the zms gene cluster, but desC is at a distant location in the bacterial genome. Null mutation of the desABC genes in a zeamine-minus derivative of strain EC1 led to about an 8- to 32-fold decrease in zeamine tolerance level. This efflux pump was zeamine specific and appeared to be conserved only in Dickeya species, which may explain the high potency of zeamines against a wide range of bacterial pathogens. Significantly, expression of the desAB genes was abolished by deletion of zmsA, which encodes zeamine biosynthesis but could be induced by exogenous addition of zeamines. The results suggest that sophisticated and coordinated regulatory mechanisms have evolved to govern zeamine production and tolerance. Taken together, these findings documented a novel signaling role of zeamines and the first resistance mechanism against zeamines, which is a family of potent and promising antibiotics against both Gram-positive and Gram-negative bacterial pathogens. IMPORTANCE Zeamines are a family of newly identified phytotoxins and potent antibiotics produced by D. zeae EC1. Unlike most bacterial organisms, which are highly sensitive, D. zeae EC1 is tolerant to zeamines, but the mechanisms involved are unknown. Our study showed, for the first time, that a new RND efflux pump, DesABC, is indispensable for D. zeae EC1 against zeamines. We found that the DesABC efflux pump was zeamine specific and appeared to be conserved only in the Dickeya species, which may explain the high potency of zeamines against a wide range of bacterial pathogens. We also showed that expression of DesABC efflux system genes was induced by zeamines. These findings not only provide an answer to why D. zeae EC1 is much more tolerant to zeamines than other bacterial pathogens but also document a signaling role of zeamines in modulation of gene expression.

Structure and Function of Rhizosphere Soil and Root Endophytic Microbial Communities Associated With Root Rot of Panax notoginseng

“…The proportion of ABC transporters in the two groups of diseased samples was higher than that in the corresponding two groups of healthy samples, which may be associated with the disease resistance of P. notoginseng . Previous studies have reported that gene modulating resistance helps plants to inhibit pathogenic bacteria and improve plant resistance ( Gong et al, 2020 ; Liang Y. et al, 2020 ; Wang J. et al, 2020 ; Corredor-Moreno et al, 2021 ; Zia et al, 2021 ), while the RND antibiotic efflux mechanism has an efflux effect on various antibiotics; inhibiting these pumps can mitigate antibiotic resistance ( Siriyong et al, 2017 ; Liang et al, 2019 ; Ichinose et al, 2020 ). Our study showed that the RND antibiotic efflux mechanism in diseased samples was greater than that in healthy samples.…”

Resistance-Nodulation-Division Efflux Pump, LexABC, Contributes to Self-Resistance of the Phenazine Di-N-Oxide Natural Product Myxin in Lysobacter antibioticus

“…The RND superfamily is common in Gram-negative bacteria and is a major contributor to multidrug resistance among human pathogens such as Enterococcus faecium , Staphylococcus aureus , Klebsiella pneumoniae , Acinetobacter baumannii , P. aeruginosa , and Enterobacter species ( Li and Nikaido, 2004 , 2009 ). Moreover, RND efflux pumps have also been reported in plant pathogens, for example, Erwinia amylovora ( Pletzer and Weingart, 2014 ), Dickeya species ( Liang et al, 2019 ), and Pseudomonas syringae ( Stoitsova et al, 2008 ). Research into the RND efflux pump in biocontrol bacteria has been limited.…”

A natural single nucleotide mutation in the small regulatory RNA ArcZ ofDickeya solaniswitches off the antimicrobial activities against yeast and bacteria

“…We also observed a slight inhibition exerted by D. solani D s0432-1 against E. coli , but no inhibition towards D. dadantii and P. atrosepticum . Zeamine resistance of D. dadantii could be explained by the presence in its genome of the genes desAB encoding the RDN pump DesAB involved in zeamine efflux (Liang et al ., 2019). In-frame deletion of desA or desB in D. oryzae EC1 leads to a zeamine sensitive phenotype (Liang et al ., 2019).…”

“…Zeamine resistance of D. dadantii could be explained by the presence in its genome of the genes desAB encoding the RDN pump DesAB involved in zeamine efflux (Liang et al ., 2019). In-frame deletion of desA or desB in D. oryzae EC1 leads to a zeamine sensitive phenotype (Liang et al ., 2019). In in planta Tn-seq experiments with D. dadantii 3937 (Royet et al ., 2019), mutants of the genes desA and desB (Dda3937_00787 and Dda3937_00786 respectively) did not display a significant negative or positive variation (Log2 fold-changes −0.09 and +0.44, respectively), suggesting that this RND efflux pump does not play a significant role during D. dadantii plant infection, contrary to the D. dadanti RND efflux pump AcrAB that appeared to be essential for virulence (Royet et al ., 2019).…”