The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB

Simpson, P.; Richardson, David J.; Codd, Rachel

doi:10.1099/mic.0.034421-0

Cited by 70 publications

(58 citation statements)

References 99 publications

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“…On the basis of the phylogenetic analysis, the NapA orthologous in the genus Shewanella could be divided into NAP-b and NAP-a as suggested previously (Simpson et al, 2010). The NAP-a cluster could be further divided into two subclusters: Nap-a-1 and Nap-a-2.…”

Section: Evolutionary Relationships Of Napsmentioning

confidence: 87%

“…The phylogenetic tree in Figure 2 contains 183 NapA sequences, which are mainly from those previously described (Simpson et al, 2010), in addition we added the NapA of S. violacea DSS12, S. benthica KT99, and monomeric NAS of Bacillus subtilis, Klebsiella oxytoca, Rhodobacter capsulatus and Synechococcus elongatus. We used formate dehydrogenase protein of Bacillus cereus as the out-group, as formate dehydrogenase also belongs to DMSO (dimethyl sulfoxide) reductase family protein.…”

Section: Constructing the Phylogenetic Treementioning

confidence: 99%

“…A recent review of the genomes of 19 Shewanella strains shows that most of the Shewanella contain two types of NAP: NAP-a and NAP-b (Simpson et al, 2010). Considering the unparalleled capability of Shewanella to utilize a variety of substrates, the presence of two NAPs may reflect an adaptation of Shewanella to cope with the various environmental conditions.…”

Section: Introductionmentioning

confidence: 99%

“…Considering the unparalleled capability of Shewanella to utilize a variety of substrates, the presence of two NAPs may reflect an adaptation of Shewanella to cope with the various environmental conditions. There are several implications for this special feature of Shewanella genus: (1) The excess nap gene cluster may not be expressed, similarly as the two dimethylsulfoxide reductase gene clusters in S. oneidensis MR-1 (Gralnick et al, 2006); (2) The two NAP systems may have distinct physiological functions such as NAP-a may serve in denitrification or redox balancing (Simpson et al, 2010); (3) The double copy of nap gene are functionally redundant. Besides all these possibilities, it is still an open question that what is the evolutionary relationship of the two NAPs?…”

Section: Introductionmentioning

confidence: 99%

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Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3

Chen

Wang

et al. 2010

The ISME Journal

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Most of the Shewanella species contain two periplasmic nitrate reductases (NAP-a and NAP-b), which is a unique feature of this genus. In the present study, the physiological function and evolutionary relationship of the two NAP systems were studied in the deep-sea bacterium Shewanella piezotolerans WP3. Both of the WP3 nap gene clusters: nap-a (napD1A1B1C) and nap-b (napD2A2B2) were shown to be involved in nitrate respiration. Phylogenetic analyses suggest that NAP-b originated earlier than NAP-a. Tetraheme cytochromes NapC and CymA were found to be the major electron deliver proteins, and CymA also served as a sole electron transporter towards nitrite reductase. Interestingly, a DnapA2 mutant with the single functional NAP-a system showed better growth than the wild-type strain, when grown in nitrate medium, and it had a selective advantage to the wild-type strain. On the basis of these results, we proposed the evolution direction of nitrate respiration system in Shewanella: from a single NAP-b to NAP-b and NAP-a both, followed by the evolution to a single NAP-a. Moreover, the data presented here will be very useful for the designed engineering of Shewanella for more efficient respiring capabilities for environmental bioremediation.

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Section: Evolutionary Relationships Of Napsmentioning

confidence: 87%

Section: Constructing the Phylogenetic Treementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3

Chen

Wang

et al. 2010

The ISME Journal

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“…This "overflow" of excess electrons is frequently dissipated via enzymes that, like Nap, are directly uncoupled from energy conservation. The Rhodobacter sphaeroides 2.4.3 genome has two related but nonidentical Nap-encoding gene clusters (40,43). While many denitrifiers have multiple nitrate reductases, it is rare for one bacterium to have two versions of the same type.…”

mentioning

confidence: 99%

Physiological Roles for Two Periplasmic Nitrate Reductases in Rhodobacter sphaeroides 2.4.3 (ATCC 17025)

Hartsock

Shapleigh

2011

Journal of Bacteriology

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The metabolically versatile purple bacterium Rhodobacter sphaeroides 2.4.3 is a denitrifier whose genome contains two periplasmic nitrate reductase-encoding gene clusters. This work demonstrates nonredundant physiological roles for these two enzymes. One cluster is expressed aerobically and repressed under low oxygen while the second is maximally expressed under low oxygen. Insertional inactivation of the aerobically expressed nitrate reductase eliminated aerobic nitrate reduction, but cells of this strain could still respire nitrate anaerobically. In contrast, when the anaerobic nitrate reductase was absent, aerobic nitrate reduction was detectable, but anaerobic nitrate reduction was impaired. The aerobic nitrate reductase was expressed but not utilized in liquid culture but was utilized during growth on solid medium. Growth on a variety of carbon sources, with the exception of malate, the most oxidized substrate used, resulted in nitrite production on solid medium. This is consistent with a role for the aerobic nitrate reductase in redox homeostasis. These results show that one of the nitrate reductases is specific for respiration and denitrification while the other likely plays a role in redox homeostasis during aerobic growth.Nitrate reduction is widespread among bacteria, where it is used for both assimilatory and dissimilatory processes (14, 37). Assimilatory nitrate reduction produces nitrite, which is further reduced to ammonia and incorporated into cell biomass. Dissimilatory processes include denitrification, the respiration of nitrate to nitrogen gas, and ammonification, i.e., the respiration of nitrate to ammonia. These varied uses for nitrate make its reduction an important reaction in the global nitrogen cycle (5). The use of chemically fixed sources of nitrogen as fertilizer has led to nitrate being a common cause of eutrophication, increasing the significance of nitrate reduction in global biogeochemical cycles (5). Understanding the regulation and physiological roles of nitrate reductases in diverse organisms will allow more accurate modeling and predictions of nitrate fate in the environment.There is one type of assimilatory nitrate reductase, known as Nas, but there are two dissimilatory types, referred to as Nar and Nap. Nas is cytoplasmic, Nar is membrane bound, and Nap is localized to the periplasm (37). Environmental surveys for the dissimilatory Nap-and Nar-type genes demonstrate an almost equal representation of both groups (4). Many bacteria with Nap have NapABC as the functional core, where NapA is the catalytic subunit and NapB and NapC are heme-containing subunits involved in electron transfer (14). NapA has a molybdenum cofactor as the site of nitrate reduction. NapA and NapB form a periplasmic complex while NapC is membrane associated to mediate electron transfer from quinol to NapAB. While Nap turnover is not directly associated with generation of a proton motive force (PMF), electron flow through NADH dehydrogenase along with the further reduction steps, as in denitrification, w...

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Directing the Biosynthesis of Putrebactin or Desferrioxamine B in Shewanella putrefaciens through the Upstream Inhibition of Ornithine Decarboxylase

Soe

Pakchung

Codd

2012

Chemistry & Biodiversity

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To manage iron acquisition in an oxic environment, Shewanella putrefaciens produces the macrocyclic dihydroxamic acid putrebactin (PB) as its native siderophore. In this work, we have established the siderophore profile of S. putrefaciens in cultures augmented with the native PB precursor putrescine and in putrescine-depleted cultures. Compared to base medium, PB increased by two-fold in cultures of S. putrefaciens with 10 mM NaCl and 20 mM exogenous putrescine. In cultures augmented with 1,4-diaminobutan-2-one (DAB), PB decreased with only 0.02-fold PB detectable at 10 mM DAB. As an ornithine decarboxylase (ODC) inhibitor, DAB depleted levels of endogenous putrescine which attenuated downstream PB assembly. Under putrescine-depleted conditions, S. putrefaciens produced as its replacement siderophore the cadaverine-based desferrioxamine B (DFO-B), as characterised by ESI-MS of the Fe(III)-loaded form (m/z(obs) 614.13; m/z(calc) 614.27). A third siderophore, independent of DAB, was observed in low levels. LC/MS Analysis of the Fe(III)-loaded extract gave m/z(obs) 440.93, which, formulated as a 1:1 Fe(III) complex with a macrocyclic dihydroxamic acid, comprising one putrescine- and one cadaverine-based precursor (m/z(calc) 440.14). These results show that the production of native PB or non-native DFO-B by S. putrefaciens can be directed though upstream inhibition of ODC. This approach could be used to increase the molecular diversity of siderophores produced by S. putrefaciens and to map alternative diamine-dependent metabolites.

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The periplasmic nitrate reductase in Shewanella: the resolution, distribution and functional implications of two NAP isoforms, NapEDABC and NapDAGHB

Cited by 70 publications

References 99 publications

Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3

Physiological and evolutionary studies of NAP systems in Shewanella piezotolerans WP3

Physiological Roles for Two Periplasmic Nitrate Reductases in Rhodobacter sphaeroides 2.4.3 (ATCC 17025)

Directing the Biosynthesis of Putrebactin or Desferrioxamine B in Shewanella putrefaciens through the Upstream Inhibition of Ornithine Decarboxylase

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