A Crp-Dependent Two-Component System Regulates Nitrate and Nitrite Respiration in Shewanella oneidensis

Dong, Yangyang; Wang, Jixuan; Fu, Huihui; Zhou, Guangqi; Shi, Miaomiao; Gao, Haichun

doi:10.1371/journal.pone.0051643

Cited by 62 publications

(103 citation statements)

References 44 publications

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“…In addition, expression of the nagZ and ampG genes in trans conferred on the corresponding mutants the lowest levels of BlaA activity under all tested conditions. This can be readily explained by overexpression, an intrinsic feature of the multiple-copy vector pHG101 (31,33,34). Based on these results, we conclude that NagZ and AmpG exert a repressive effect on the blaA gene, leading to the elevated resistance to ampicillin at all levels.…”

Section: Resultsmentioning

confidence: 67%

Distinct Roles of Major Peptidoglycan Recycling Enzymes in β-Lactamase Production in Shewanella oneidensis

Yin

Mao

et al. 2014

Antimicrob Agents Chemother

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c ␤-Lactam antibiotics were the earliest discovered and are the most widely used group of antibiotics that work by inactivating penicillin-binding proteins to inhibit peptidoglycan biosynthesis. As one of the most efficient defense strategies, many bacteria produce ␤-lactam-degrading enzymes, ␤-lactamases, whose biochemical functions and regulation have been extensively studied. A signal transduction pathway for ␤-lactamase induction by ␤-lactam antibiotics, consisting of the major peptidoglycan recycling enzymes and the LysR-type transcriptional regulator, AmpR, has been recently unveiled in some bacteria. Because inactivation of some of these proteins, especially the permease AmpG and the ␤-hexosaminidase NagZ, results in substantially elevated susceptibility to the antibiotics, these have been recognized as potential therapeutic targets. Here, we show a contrasting scenario in Shewanella oneidensis, in which the homologue of AmpR is absent. Loss of AmpG or NagZ enhances ␤-lactam resistance drastically, whereas other identified major peptidoglycan recycling enzymes are dispensable. Moreover, our data indicate that there exists a parallel signal transduction pathway for ␤-lactamase induction, which is independent of either AmpG or NagZ.

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Section: Resultsmentioning

confidence: 67%

Distinct Roles of Major Peptidoglycan Recycling Enzymes in β-Lactamase Production in Shewanella oneidensis

Yin

Mao

et al. 2014

Antimicrob Agents Chemother

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“…Comparative genomic analysis reveals that most Shewanella strains contain two types of periplasmic nitrate reductases (Nap), NapC-associated nap-alpha (napE-DABC) and CymA-dependent nap-beta (napDABGH). The well-characterized Shewanella oneidensis MR-1 strain contains only nap-beta (napDABGH) for nitrate ammonification Dong et al, 2012;Simpson et al, 2010) while the Shewanella putrefaciens W3-18-1 strain harbours both CymA-and NapC-dependent nitrate reductases, as well as the NapGH ubiquinol oxidase. These seemingly redundant respiratory chain components may be differentially expressed and functioning under environmental condition gradients such as different oxygen tensions and availability of electron acceptors (Qiu et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1

et al. 2016

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Shewanella putrefaciens W3-18-1 harbours two periplasmic nitrate reductase (Nap) gene clusters, NapC-associated nap-alpha (napEDABC) and CymA-dependent nap-beta (napDAGHB), for dissimilatory nitrate respiration. CymA is a member of the NapC/NirT quinol dehydrogenase family and acts as a hub to support different respiratory pathways, including those on iron [Fe(III)] and manganese [Mn(III, IV)] (hydr)oxide, nitrate, nitrite, fumarate and arsenate in Shewanella strains. However, in our analysis it was shown that another NapC/NirT family protein, NapC, was only involved in nitrate reduction, although both CymA and NapC can transfer quinol-derived electrons to a periplasmic terminal reductase or an electron acceptor. Furthermore, our results showed that NapC could only interact specifically with the Nap-alpha nitrate reductase while CymA could interact promiscuously with Nap-alpha, Nap-beta and the NrfA nitrite reductase for nitrate and nitrite reduction. To further explore the difference in specificity, site-directed mutagenesis on both CymA and NapC was conducted and the phenotypic changes in nitrate and nitrite reduction were tested. Our analyses demonstrated that the Lys-91 residue played a key role in nitrate reduction for quinol oxidation and the Asp-166 residue might influence the maturation of CymA. The Asp-97 residue might be one of the key factors that influence the interaction of CymA with the cytochromes NapB and NrfA.

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“…NarQP-and FNR-dependent regulation of nrfA has been predicted for a number of Gammaproteobacteria (29). Cyclic-AMP receptor protein (Crp)-dependent transcription was also seen in S. oneidensis (27). Regulation by NO-sensitive transcription regulators was seen in E. coli (30) and has been suggested for W. succinogenes (31).…”

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confidence: 98%

“…The induction of nrfA in response to nitrate and nitrite has been documented in E. coli via the two-component systems NarQP and NarXL (26) and in Shewanella oneidensis via NarQP (27). Fumarate and nitrate reductase regulator (FNR)-dependent activation in response to anaerobic conditions was seen in E. coli (26) and Haemophilus influenzae (28).…”

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confidence: 99%

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

et al. 2015

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Sulfate-reducing bacteria (SRB) are sensitive to low concentrations of nitrite, and nitrite has been used to control SRB-related biofouling in oil fields. Desulfovibrio vulgaris Hildenborough, a model SRB, carries a cytochrome c-type nitrite reductase (nrfHA) that confers resistance to low concentrations of nitrite. The regulation of this nitrite reductase has not been directly examined to date. In this study, we show that DVU0621 (NrfR), a sigma54-dependent two-component system response regulator, is the positive regulator for this operon. NrfR activates the expression of the nrfHA operon in response to nitrite stress. We also show that nrfR is needed for fitness at low cell densities in the presence of nitrite because inactivation of nrfR affects the rate of nitrite reduction. We also predict and validate the binding sites for NrfR upstream of the nrfHA operon using purified NrfR in gel shift assays. We discuss possible roles for NrfR in regulating nitrate reductase genes in nitrate-utilizing Desulfovibrio spp. IMPORTANCEThe NrfA nitrite reductase is prevalent across several bacterial phyla and required for dissimilatory nitrite reduction. However, regulation of the nrfA gene has been studied in only a few nitrate-utilizing bacteria. Here, we show that in D. vulgaris, a bacterium that does not respire nitrate, the expression of nrfHA is induced by NrfR upon nitrite stress. This is the first report of regulation of nrfA by a sigma54-dependent two-component system. Our study increases our knowledge of nitrite stress responses and possibly of the regulation of nitrate reduction in SRB. Sulfate-reducing bacteria (SRB) are important members of syntrophic anaerobic microbial communities. While SRB are useful in remediation of contaminated groundwater by reduction of toxic heavy metals (1), they are also a major problem in offshore oil industries, where they cause biofouling due to corrosive sulfide production (2). Additions of nitrate and nitrite have been used to control SRB growth and the resulting biofouling sulfide (3, 4). Nitrite is more effective for inhibition of SRB than nitrate (3), and most SRB are sensitive to low concentrations of nitrite (5, 6). Nitrite is toxic because it inhibits sulfite reduction by competing for the sulfite reductase enzyme (7,8). Also, the reaction of nitrite with sulfide to form polysulfide results in the release of reactive nitrogen species (9).The sensitivity to nitrite varies among SRB. Some SRB, such as Desulfovibrio alaskensis G20, lack any means for reducing the nitrite and are highly sensitive to small amounts of nitrite (10, 11). However, other SRB can reduce nitrite via a cytochrome c-type nitrite reductase, NrfA, and are able to tolerate low millimolar amounts of nitrite (7, 12). NrfA-carrying SRB also can utilize nitrite as the sole terminal electron acceptor (TEA), provided the nitrite is at subinhibitory concentrations (12-14). Some nitritereducing SRB also have the ability to utilize nitrate as the TEA via dissimilatory nitrate/nitrite reduction (15).NrfA is ...

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A Crp-Dependent Two-Component System Regulates Nitrate and Nitrite Respiration in Shewanella oneidensis

Cited by 62 publications

References 44 publications

Distinct Roles of Major Peptidoglycan Recycling Enzymes in β-Lactamase Production in Shewanella oneidensis

Distinct Roles of Major Peptidoglycan Recycling Enzymes in β-Lactamase Production in Shewanella oneidensis

Functional roles of CymA and NapC in reduction of nitrate and nitrite by Shewanella putrefaciens W3-18-1

Regulation of Nitrite Stress Response in Desulfovibrio vulgaris Hildenborough, a Model Sulfate-Reducing Bacterium

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