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

Wei, Hongbin; Dai, Jingcheng; Xia, Ming; Romine, Margaret F.; Shi, Liang; Beliav, Alex; Tiedje, James M.; Nealson, Kenneth H.; Fredrickson, James K.; Zhou, Jizhong; Qiu, Dongru

doi:10.1099/mic.0.000285

Cited by 10 publications

(5 citation statements)

References 49 publications

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“…Two c -type cytochromes, NapB and CymA, are part of periplasmic nitrate reductase Nap in MR-1. Our results are consistent with previous findings that the tetraheme cytochrome CymA is essential for nitrate reduction in both MR-1 and S. putrefaciens W3–18-1 strains [33]. To further explore the biosynthesis of these two c -type cytochromes under supplement of exogenous hemins, we found that there was no significant difference in the transcription levels of cymA and napB genes between the wild-type MR-1 and the MR-1Δ hemH1 Δ hemH2 double mutant (Fig.…”

Section: Resultssupporting

confidence: 94%

Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins

Dai

Liu

et al. 2019

BMC Microbiol

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Background Most species of Shewanella harbor two ferrochelatase paralogues for the biosynthesis of c -type cytochromes, which are crucial for their respiratory versatility . In our previous study of the Shewanella loihica PV-4 strain, we found that the disruption of hemH1 but not hemH2 resulted in a significant accumulation of extracellular protoporphyrin IX (PPIX), but it is different in Shewanella oneidensis MR-1. Hence, the function and transcriptional regulation of two ferrochelatase genes, hemH1 and hemH2 , are investigated in S. oneidensis MR-1. Result In the present study, deletion of either hemH1 or hemH2 in S. oneidensis MR-1 did not lead to overproduction of extracellular protoporphyrin IX (PPIX) as previously described in the hemH1 mutants of S. loihica PV-4. Moreover, supplement of exogenous hemins made it possible to generate the hemH1 and hemH2 double mutant in MR-1, but not in PV-4. Under aerobic condition, exogenous hemins were required for the growth of MR-1Δ hemH1 Δ hemH2 , which also overproduced extracellular PPIX. These results suggest that heme is essential for aerobic growth of Shewanella species and MR-1 could also uptake hemin for biosynthesis of essential cytochrome(s) and respiration. Besides, the exogenous hemin mediated CymA cytochrome maturation and the cellular KatB catalase activity. Both hemH paralogues were transcribed in wild-type MR-1, and the hemH2 transcription was remarkably up-regulated in MR-1Δ hemH1 mutant to compensate for the loss of hemH1 . The periplasmic glutathione peroxidase gene pgpD , located in the same operon with hemH2 , and a large gene cluster coding for iron, heme (hemin) uptake systems are absent in the PV-4 genome. Conclusion Our results indicate that the genetic divergence in gene content and gene expression between these Shewanella species, accounting for the phenotypic difference described here, might be due to their speciation and adaptation to the specific habitats (iron-rich deep-sea vent versus iron-poor freshwater) in which they evolved and the generated mutants could potentially be utilized for commercial production of PPIX. Electronic supplementary material The online version of this article (10.1186/s12866-019-1549-9) contains...

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Section: Resultssupporting

confidence: 94%

Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins

Dai

Liu

et al. 2019

BMC Microbiol

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“…CymA has no known small protein associated and is involved in several respiratory chains in S . oneidensis acting as the quinol oxidase during the reduction of fumarate, DMSO, nitrate and other electron acceptors, except TMAO 38 – 41 . The presence and localization of CymA was tested in cells grown with various substrates showing that it was evenly distributed whatever the nature of the electron acceptor (Fig.…”

Section: Resultsmentioning

confidence: 99%

Small membranous proteins of the TorE/NapE family, crutches for cognate respiratory systems in Proteobacteria

Lemaire

Infossi

Chaouche

et al. 2018

Sci Rep

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In this report, we investigate small proteins involved in bacterial alternative respiratory systems that improve the enzymatic efficiency through better anchorage and multimerization of membrane components. Using the small protein TorE of the respiratory TMAO reductase system as a model, we discovered that TorE is part of a subfamily of small proteins that are present in proteobacteria in which they play a similar role for bacterial respiratory systems. We reveal by microscopy that, in Shewanella oneidensis MR1, alternative respiratory systems are evenly distributed in the membrane contrary to what has been described for Escherichia coli. Thus, the better efficiency of the respiratory systems observed in the presence of the small proteins is not due to a specific localization in the membrane, but rather to the formation of membranous complexes formed by TorE homologs with their c-type cytochrome partner protein. By an in vivo approach combining Clear Native electrophoresis and fluorescent translational fusions, we determined the 4:4 stoichiometry of the complexes. In addition, mild solubilization of the cytochrome indicates that the presence of the small protein reinforces its anchoring to the membrane. Therefore, assembly of the complex induced by this small protein improves the efficiency of the respiratory system.

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“…We were encouraged to find that previously reported ORIs were recapitulated by our assay, including eight functional ORIs in E. coli (RSF1010 17 , p15A 18 , pSa 19 , RK2 14 , pBBR1 20 , pBBR1-UP 21 , pSC101ts 22 , pNG2 3 ), as well as D. zoogloeoides (RK2 23 ), S. putrefaciens (pBBR1 24 ) and Shewanella oneidensis (p15A 25 , pBBR1 25 , pSC101 26 ) (Table 3, Supplementary Table 6).…”

Section: Identification Of Functional Orismentioning

confidence: 89%

A scalable framework for high-throughput identification of functional origins of replication in non-model bacteria

Gilbert¹,

Brumwell²,

Crits-Christoph³

et al. 2023

Preprint

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Microbial genetic manipulation requires access to engineerable plasmids that can be programmed to perturb genes, pathways and genomes. The extensive repertoire of plasmids available for model microbes, such as Escherichia coli, has facilitated fundamental biology studies and synthetic biology applications. However, the scarcity of plasmids for non-model microbes hinders efforts to broaden our biological knowledge and constrains the development of biotechnological solutions. In this study, we introduce a molecular toolkit and multiplexed screen to evaluate functional plasmids in non-model microbes. We constructed a collection of genetic parts consisting of 22 origins of replication (ORIs), 20 antibiotic selectable markers, and 30 molecular barcodes, which can be assembled combinatorially to create a library of plasmids trackable by next-generation DNA sequencing. We demonstrate our approach by delivering a pooled library of 22 ORIs to 12 bacterial species including extremophiles, electroactive bacteria and bioproduction strains. We report, for the first time, DNA delivery by conjugation and functional ORIs for Halomonas alkaliphila, Halomonas neptunia, and Shewanella electrodiphila. Furthermore, we expand the list of functional ORIs for Duganella zoogloeoides, Pseudomonas alcaliphila, Shewanella oneidensis and Shewanella putrefaciens. This screen provides a scalable high-throughput system to rapidly build and identify functional plasmids to establish genetic tractability in non-model microbes.

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

Cited by 10 publications

References 49 publications

Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins

Differential gene content and gene expression for bacterial evolution and speciation of Shewanella in terms of biosynthesis of heme and heme-requiring proteins

Small membranous proteins of the TorE/NapE family, crutches for cognate respiratory systems in Proteobacteria

A scalable framework for high-throughput identification of functional origins of replication in non-model bacteria

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