Transcriptomic Analysis of the Dual Response of Rhodococcus aetherivorans BCP1 to Inorganic Arsenic Oxyanions
Jazyk angličtina Země Spojené státy americké Médium print-electronic
Typ dokumentu časopisecké články, práce podpořená grantem
PubMed
35311511
PubMed Central
PMC9004369
DOI
10.1128/aem.02209-21
Knihovny.cz E-zdroje
- Klíčová slova
- Rhodococcus, arsenic resistance, bacterial stress response, ergothioneine, mycothiol, oxidative phosphorylation, oxidative stress, transcriptomics,
- MeSH
- adenosintrifosfát metabolismus MeSH
- arsen * metabolismus toxicita MeSH
- glukosa metabolismus MeSH
- peroxid vodíku metabolismus MeSH
- Rhodococcus * metabolismus MeSH
- transkriptom MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- adenosintrifosfát MeSH
- arsen * MeSH
- glukosa MeSH
- peroxid vodíku MeSH
Bacterial strains belonging to the genus Rhodococcus are able to degrade various toxic organic compounds and tolerate high concentrations of metal(loid)s. We have previously shown that Rhodococcus aetherivorans BCP1 is resistant to various levels of the two arsenic inorganic species, arsenite [As(III)] and arsenate [As(V)]. However, while arsenite showed toxic effects at concentrations as low as 5 mM, arsenate at 30 mM boosted the growth rate of BCP1 cells and was toxic only at concentrations of >100 mM. Since such behavior could be linked to peculiar aspects of its metabolism, the transcriptomic analysis of BCP1 cells exposed to 5 mM As(III) and 30 mM As(V) was performed in this work. The aim was to clarify the mechanisms underlying the arsenic stress response of the two growth phenotypes in the presence of the two different oxyanions. The results revealed that As(III) induced higher activity of reactive oxygen species (ROS)-scavenging enzymes than As(V) in relation to the expression of enzymes involved in cellular damage recovery and redox buffers/cofactors (ergothioneine, mycofactocin, and mycothiol). Further, As(III) downregulated pathways related to cell division, while both oxyanions downregulated genes involved in glycolysis. Notably, As(V) induced the expression of enzymes participating in the synthesis of metallophores and rearranged the central and energetic metabolism, also inducing alternative pathways for ATP synthesis and glucose consumption. This study, in providing transcriptomic data on R. aetherivorans exposed to arsenic oxyanions, sheds some light on the plasticity of the rhodococcal response to arsenic stress, which may be important for the improvement of biotechnological applications. IMPORTANCE Members of the genus Rhodococcus show high metabolic versatility and the ability to tolerate/resist numerous stress conditions, including toxic metals. R. aetherivorans BCP1 is able to tolerate high concentrations of the two inorganic arsenic oxyanions, arsenite [As(III)] and arsenate [As(V)]. Despite the fact that BCP1 intracellularly converts As(V) into As(III), this strain responds very differently to the presence of these two oxyanions in terms of cell growth and toxic effects. Indeed, while As(III) is highly toxic, exposure to specific concentrations of As(V) seems to boost cell growth. In this work, we investigated the transcriptomic response, ATP synthesis, glucose consumption, and H2O2 degradation in BCP1 cells exposed to As(III) and As(V), inducing two different growth phenotypes. Our results give an overview of the transcriptional rearrangements associated with the dual response of BCP1 to the two oxyanions and provide novel insights into the energetic metabolism of Rhodococcus under arsenic stress.
Center for Biotechnology Bielefeld Germany
Department of Biological Sciences University of Calgarygrid 22072 35 Calgary Canada
Department of Pharmacy and Biotechnology University of Bolognagrid 6292 f Bologna Italy
Institute of Microbiology of the Czech Academy of Sciences Prague Czech Republic
Zobrazit více v PubMed
Coryell M, Roggenbeck BA, Walk ST. 2019. The human gut microbiome’s influence on arsenic toxicity. Curr Pharmacol Rep 5:491–504. 10.1007/s40495-019-00206-4. PubMed DOI PMC
Shen S, Li X-F, Cullen WR, Weinfeld M, Le XC. 2013. Arsenic binding to proteins. Chem Rev 113:7769–7792. 10.1021/cr300015c. PubMed DOI PMC
Ben Fekih I, Zhang C, Li YP, Zhao Y, Alwathnani HA, Saquib Q, Rensing C, Cervantes C. 2018. Distribution of arsenic resistance genes in prokaryotes. Front Microbiol 9:2473. 10.3389/fmicb.2018.02473. PubMed DOI PMC
Garbinski LD, Rosen BP, Chen J. 2019. Pathways of arsenic uptake and efflux. Environ Int 126:585–597. 10.1016/j.envint.2019.02.058. PubMed DOI PMC
Rosen BP. 2002. Biochemistry of arsenic detoxification. FEBS Lett 529:86–92. 10.1016/s0014-5793(02)03186-1. PubMed DOI
Cappelletti M, Presentato A, Piacenza E, Firrincieli A, Turner RJ, Zannoni D. 2020. Biotechnology of Rhodococcus for the production of valuable compounds. Appl Microbiol Biotechnol 104:8567–8594. 10.1007/s00253-020-10861-z. PubMed DOI PMC
Donini E, Firrincieli A, Cappelletti M. 2021. Systems biology and metabolic engineering of Rhodococcus for bioconversion and biosynthesis processes. Folia Microbiol (Praha) 66:701–713. 10.1007/s12223-021-00892-y. PubMed DOI PMC
Cappelletti M, Pinelli D, Fedi S, Zannoni D, Frascari D. 2018. Aerobic co-metabolism of 1,1,2,2-tetrachloroethane by Rhodococcus aetherivorans TPA grown on propane: kinetic study and bioreactor configuration analysis. J Chem Technol Biotechnol 93:155–165. 10.1002/jctb.5335. DOI
Cappelletti M, Fedi S, Zampolli J, Di Canito A, D'Ursi P, Orro A, Viti C, Milanesi L, Zannoni D, Di Gennaro P. 2016. Phenotype microarray analysis may unravel genetic determinants of the stress response by Rhodococcus aetherivorans BCP1 and Rhodococcus opacus R7. Res Microbiol 167:766–773. 10.1016/j.resmic.2016.06.008. PubMed DOI
Pátek M, Grulich M, Nešvera J. 2021. Stress response in Rhodococcus strains. Biotechnol Adv 53:107698. 10.1016/j.biotechadv.2021.107698. PubMed DOI
Alvarez HM, Silva RA, Cesari AC, Zamit AL, Peressutti SR, Reichelt R, Keller U, Malkus U, Rasch C, Maskow T, Mayer F, Steinbüchel A. 2004. Physiological and morphological responses of the soil bacterium Rhodococcus opacus strain PD630 to water stress. FEMS Microbiol Ecol 50:75–86. 10.1016/j.femsec.2004.06.002. PubMed DOI
de Carvalho CCCR, Fischer MA, Kirsten S, Würz B, Wick LY, Heipieper HJ. 2016. Adaptive response of Rhodococcus opacus PWD4 to salt and phenolic stress on the level of mycolic acids. AMB Express 6:66. 10.1186/s13568-016-0241-9. PubMed DOI PMC
Presentato A, Piacenza E, Turner RJ, Zannoni D, Cappelletti M. 2020. Processing of metals and metalloids by Actinobacteria: cell resistance mechanisms and synthesis of metal(loid)-based nanostructures. Microorganisms 8:2027–2037. 10.3390/microorganisms8122027. PubMed DOI PMC
Firrincieli A, Presentato A, Favoino G, Marabottini R, Allevato E, Stazi SR, Scarascia Mugnozza G, Harfouche A, Petruccioli M, Turner RJ, Zannoni D, Cappelletti M. 2019. Identification of resistance genes and response to arsenic in Rhodococcus aetherivorans BCP1. Front Microbiol 10:888. 10.3389/fmicb.2019.00888. PubMed DOI PMC
Presentato A, Piacenza E, Anikovskiy M, Cappelletti M, Zannoni D, Turner RJ. 2018. Biosynthesis of selenium-nanoparticles and -nanorods as a product of selenite bioconversion by the aerobic bacterium Rhodococcus aetherivorans BCP1. N Biotechnol 41:1–8. 10.1016/j.nbt.2017.11.002. PubMed DOI
Presentato A, Piacenza E, Anikovskiy M, Cappelletti M, Zannoni D, Turner RJ. 2016. Rhodococcus aetherivorans BCP1 as cell factory for the production of intracellular tellurium nanorods under aerobic conditions. Microb Cell Fact 15:1–14. 10.1186/s12934-016-0602-8. PubMed DOI PMC
Presentato A, Piacenza E, Darbandi A, Anikovskiy M, Cappelletti M, Zannoni D, Turner RJ. 2018. Assembly, growth and conductive properties of tellurium nanorods produced by Rhodococcus aetherivorans BCP1. Sci Rep 8:3923. 10.1038/s41598-018-22320-x. PubMed DOI PMC
Tucker NP, Hicks MG, Clarke TA, Crack JC, Chandra G, Le Brun NE, Dixon R, Hutchings MI. 2008. The transcriptional repressor protein NsrR senses nitric oxide directly via a [2Fe-2S] cluster. PLoS One 3:e3623. 10.1371/journal.pone.0003623. PubMed DOI PMC
Most P, Papenbrock J. 2015. Possible roles of plant sulfurtransferases in detoxification of cyanide, reactive oxygen species, selected heavy metals and arsenate. Molecules 20:1410–1423. 10.3390/molecules20011410. PubMed DOI PMC
Saini V, Cumming BM, Guidry L, Lamprecht DA, Adamson JH, Reddy VP, Chinta KC, Mazorodze JH, Glasgow JN, Richard-Greenblatt M, Gomez-Velasco A, Bach H, Av-Gay Y, Eoh H, Rhee K, Steyn AJC. 2016. Ergothioneine maintains redox and bioenergetic homeostasis essential for drug susceptibility and virulence of Mycobacterium tuberculosis. Cell Rep 14:572–585. 10.1016/j.celrep.2015.12.056. PubMed DOI PMC
Lupoli TJ, Fay A, Adura C, Glickman MS, Nathan CF. 2016. Reconstitution of a Mycobacterium tuberculosis proteostasis network highlights essential cofactor interactions with chaperone DnaK. Proc Natl Acad Sci USA 113:E7947–E7956. 10.1073/pnas.1617644113. PubMed DOI PMC
Küberl A, Polen T, Bott M. 2016. The pupylation machinery is involved in iron homeostasis by targeting the iron storage protein ferritin. Proc Natl Acad Sci USA 113:4806–4811. 10.1073/pnas.1514529113. PubMed DOI PMC
Sharp JO, Sales CM, LeBlanc JC, Liu J, Wood TK, Eltis LD, Mohn WW, Alvarez-Cohen L. 2007. An inducible propane monooxygenase is responsible for N-nitrosodimethylamine degradation by Rhodococcus sp. strain RHA1. Appl Environ Microbiol 73:6930–6938. 10.1128/AEM.01697-07. PubMed DOI PMC
Cappelletti M, Presentato A, Milazzo G, Turner RJ, Fedi S, Frascari D, Zannoni D. 2015. Growth of Rhodococcus sp. strain BCP1 on gaseous n-alkanes: new metabolic insights and transcriptional analysis of two soluble di-iron monooxygenase genes. Front Microbiol 6:393. 10.3389/fmicb.2015.00393. PubMed DOI PMC
Krishnamoorthy G, Kaiser P, Lozza L, Hahnke K, Mollenkopf H-J, Kaufmann SHE. 2019. Mycofactocin is associated with ethanol metabolism in Mycobacteria. mBio 10:e00190-19. 10.1128/mBio.00190-19. PubMed DOI PMC
Barona-Gómez F, Lautru S, Francois-Xavier F, Leblond P, Pernodet JL, Challis GL. 2006. Multiple biosynthetic and uptake systems mediate siderophore-dependent iron acquisition in Streptomyces coelicolor A3(2) and Stremptomyces ambofaciens ATCC 23877. Microbiology (Reading) 152:3355–3366. 10.1099/mic.0.29161-0. PubMed DOI
Ordóñez E, Thiyagarajan S, Cook JD, Stemmler TL, Gil JA, Mateos LM, Rosen BP. 2008. Evolution of metal(loid) binding sites in transcriptional regulators. J Biol Chem 283:25706–25714. 10.1074/jbc.M803209200. PubMed DOI PMC
Yoshinaga M, Rosen BP. 2014. A C⋅As lyase for degradation of environmental organoarsenical herbicides and animal husbandry growth promoters. Proc Natl Acad Sci USA 111:7701–7706. 10.1073/pnas.1403057111. PubMed DOI PMC
Chen J, Rosen BP. 2020. The arsenic methylation cycle: how microbial communities adapted methylarsenicals for use as weapons in the continuing war for dominance. Front Environ Sci 8:43. 10.3389/fenvs.2020.00043. DOI
Retamal-Morales G, Mehnert M, Schwabe R, Tischler D, Zapata C, Chávez R, Schlömann M, Levicán G. 2018. Detection of arsenic-binding siderophores in arsenic-tolerating Actinobacteria by a modified CAS assay. Ecotoxicol Environ Saf 157:176–181. 10.1016/j.ecoenv.2018.03.087. PubMed DOI
Bosello M, Zeyadi M, Kraas FI, Linne U, Xie X, Marahiel MA. 2013. Structural characterization of the heterobactin siderophores from Rhodococcus erythropolis PR4 and elucidation of their biosynthetic machinery. J Nat Prod 76:2282–2290. 10.1021/np4006579. PubMed DOI
Johnstone TC, Nolan EM. 2015. Beyond iron: non-classical biological functions of bacterial siderophores. Dalton Trans 44:6320–6339. 10.1039/c4dt03559c. PubMed DOI PMC
Retamal-Morales G, Senges CHR, Stapf M, Olguín A, Modak B, Bandow JE, Tischler D, Schlömann M, Levicán G. 2021. Isolation and characterization of arsenic-binding siderophores from Rhodococcus erythropolis S43: role of heterobactin B and other heterobactin variants. Appl Microbiol Biotechnol 105:1731–1744. 10.1007/s00253-021-11123-2. PubMed DOI
Birben E, Sahiner UM, Sackesen C, Erzurum S, Kalayci O. 2012. Oxidative stress and antioxidant defense. World Allergy Organ J 5:9–19. 10.1097/WOX.0b013e3182439613. PubMed DOI PMC
Castro-Severyn J, Pardo-Esté C, Mendez KN, Morales N, Marquez SL, Molina F, Remonsellez F, Castro-Nallar E, Saavedra CP. 2020. Genomic variation and arsenic tolerance emerged as niche specific adaptations by different Exiguobacterium strains isolated from the extreme Salar de Huasco environment in Chilean – Altiplano. Front Microbiol 11:1632. 10.3389/fmicb.2020.01632. PubMed DOI PMC
Sun D, Crowell SA, Harding CM, De Silva PM, Harrison A, Fernando DM, Mason KM, Santana E, Loewen PC, Kumar A, Liu Y. 2016. KatG and KatE confer Acinetobacter resistance to hydrogen peroxide but sensitize bacteria to killing by phagocytic respiratory burst. Life Sci 148:31–40. 10.1016/j.lfs.2016.02.015. PubMed DOI PMC
Carpenter BM, Whitmire JM, Merrell DS. 2009. This is not your mother’s repressor: the complex role of Fur in pathogenesis. Infect Immun 77:2590–2601. 10.1128/IAI.00116-09. PubMed DOI PMC
LeBlanc JC, Gonçalves ER, Mohn WW. 2008. Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 74:2627–2636. 10.1128/AEM.02711-07. PubMed DOI PMC
Fernandez NL, Waters CM. 2019. Cyclic di-GMP increases catalase production and hydrogen peroxide tolerance in vibrio cholerae. Appl Environ Microbiol 85:e01043-19. 10.1128/AEM.01043-19. PubMed DOI PMC
Sardiwal S, Kendall SL, Movahedzadeh F, Rison SCG, Stoker NG, Djordjevic S. 2005. A GAF domain in the hypoxia/NO-inducible Mycobacterium tuberculosis DosS protein binds haem. J Mol Biol 353:929–936. 10.1016/j.jmb.2005.09.011. PubMed DOI
Huang C-J, Wang Z-C, Huang H-Y, Huang H-D, Peng H-L. 2013. YjcC, a c-di-GMP phosphodiesterase protein, regulates the oxidative stress response and virulence of Klebsiella pneumoniae CG43. PLoS One 8:e66740. 10.1371/journal.pone.0066740. PubMed DOI PMC
Ramírez-Díaz MI, Díaz-Pérez C, Vargas E, Riveros-Rosas H, Campos-García J, Cervantes C. 2008. Mechanisms of bacterial resistance to chromium compounds. Biometals 21:321–332. 10.1007/s10534-007-9121-8. PubMed DOI
Crew R, Ramirez MV, England K, Slayden RA. 2015. MadR1, a Mycobacterium tuberculosis cell cycle stress response protein that is a member of a widely conserved protein class of prokaryotic, eukaryotic and archaeal origin. Tuberculosis (Edinb) 95:251–258. 10.1016/j.tube.2015.03.005. PubMed DOI PMC
Lee WL, Gold B, Darby C, Brot N, Jiang X, De Carvalho LPS, Wellner D, St John GWRJ, Jr, Nathan C. 2009. Mycobacterium tuberculosis expresses methionine sulphoxide reductases A and B that protect from killing by nitrite and hypochlorite. Mol Microbiol 71:583–593. 10.1111/j.1365-2958.2008.06548.x. PubMed DOI PMC
Kieser KJ, Rubin EJ. 2014. How sisters grow apart: mycobacterial growth and division. Nat Rev Microbiol 12:550–562. 10.1038/nrmicro3299. PubMed DOI PMC
Striebel F, Imkamp F, Özcelik D, Weber-Ban E. 2014. Pupylation as a signal for proteasomal degradation in bacteria. Biochim Biophys Acta 1843:103–113. 10.1016/j.bbamcr.2013.03.022. PubMed DOI
Fay A, Glickman MS. 2014. An essential nonredundant role for mycobacterial DnaK in native protein folding. PLoS Genet 10:e1004516. 10.1371/journal.pgen.1004516. PubMed DOI PMC
Peña-Ortiz L, Graça AP, Guo H, Braga D, Köllner TG, Regestein L, Beemelmanns C, Lackner G. 2020. Structure elucidation of the redox cofactor mycofactocin reveals oligo-glycosylation by MftF. Chem Sci 11:5182–5190. 10.1039/d0sc01172j. PubMed DOI PMC
Reyes AM, Pedre B, De Armas MI, Tossounian MA, Radi R, Messens J, Trujillo M. 2018. Chemistry and redox biology of mycothiol. Antioxid Redox Signal 28:487–504. 10.1089/ars.2017.7074. PubMed DOI
Dosanjh M, Newton GL, Davies J. 2008. Characterization of a mycothiol ligase mutant of Rhodococcus jostii RHA1. Res Microbiol 159:643–650. 10.1016/j.resmic.2008.08.006. PubMed DOI
Borodina I, Kenny LC, McCarthy CM, Paramasivan K, Pretorius E, Roberts TJ, van der Hoek SA, Kell DB. 2020. The biology of ergothioneine, an antioxidant nutraceutical. Nutr Res Rev 33:190–217. 10.1017/S0954422419000301. PubMed DOI PMC
Rawat M, Av-Gay Y. 2007. Mycothiol-dependent proteins in actinomycetes. FEMS Microbiol Rev 31:278–292. 10.1111/j.1574-6976.2006.00062.x. PubMed DOI
Cumming BM, Chinta KC, Reddy VP, Steyn AJC. 2018. Role of ergothioneine in microbial physiology and pathogenesis. Antioxid Redox Signal 28:431–444. 10.1089/ars.2017.7300. PubMed DOI PMC
Akanmu D, Cecchini R, Aruoma OI, Halliwell B. 1991. The antioxidant action of ergothioneine. Arch Biochem Biophys 288:10–16. 10.1016/0003-9861(91)90158-f. PubMed DOI
Chen J, Yoshinaga M, Garbinski LD, Rosen BP. 2016. Synergistic interaction of glyceraldehydes-3-phosphate dehydrogenase and ArsJ, a novel organoarsenical efflux permease, confers arsenate resistance. Mol Microbiol 100:945–953. 10.1111/mmi.13371. PubMed DOI PMC
Zhang HN, Yang L, Ling JY, Czajkowsky DM, Wang JF, Zhang XW, Zhou YM, Ge F, Yang MK, Xiong Q, Guo SJ, Le HY, Wu SF, Yan W, Liu B, Zhu H, Chen Z, Tao SC. 2015. Systematic identification of arsenic-binding proteins reveals that hexokinase-2 is inhibited by arsenic. Proc Natl Acad Sci USA 112:15084–15089. 10.1073/pnas.1521316112. PubMed DOI PMC
Nakayama T, Yonekura S-I, Yonei S, Zhang-Akiyama Q-M. 2013. Escherichia coli pyruvate:flavodoxin oxidoreductase, YdbK—regulation of expression and biological roles in protection against oxidative stress. Genes Genet Syst 88:175–188. 10.1266/ggs.88.175. PubMed DOI
Li S, Ye Z, Moreb EA, Hennigan JN, Castellanos DB, Yang T, Lynch MD. 2021. Dynamic control over feedback regulatory mechanisms improves NADPH flux and xylitol biosynthesis in engineered E. coli. Metab Eng 64:26–40. 10.1016/j.ymben.2021.01.005. PubMed DOI
Paul BD, Snyder SH. 2010. The unusual amino acid L-ergothioneine is a physiologic cytoprotectant. Cell Death Differ 17:1134–1140. 10.1038/cdd.2009.163. PubMed DOI PMC
Hernández MA, Mohn WW, Martínez E, Rost E, Alvarez AF, Alvarez HM. 2008. Biosynthesis of storage compounds by Rhodococcus jostii RHA1 and global identification of genes involved in their metabolism. BMC Genomics 9:600–614. 10.1186/1471-2164-9-600. PubMed DOI PMC
Maurya RK, Bharti S, Krishnan MY. 2018. Triacylglycerols: fuelling the hibernating Mycobacterium tuberculosis. Front Cell Infect Microbiol 8:450. 10.3389/fcimb.2018.00450. PubMed DOI PMC
Arora N, Gulati K, Patel A, Pruthi PA, Poluri KM, Pruthi V. 2017. A hybrid approach integrating arsenic detoxification with biodiesel production using oleaginous microalgae. Algal Res 24:29–39. 10.1016/j.algal.2017.03.012. DOI
Cook GM, Hards K, Vilchèze C, Hartman T, Berney M. 2014. Energetics of respiration and oxidative phosphorylation in mycobacteria. Microbiol Spectr 2:MGM2-0015-2013. 10.1128/microbiolspec.MGM2-0015-2013. PubMed DOI PMC
Wiseman B, Nitharwal RG, Fedotovskaya O, Schäfer J, Guo H, Kuang Q, Benlekbir S, Sjöstrand D, Ädelroth P, Rubinstein JL, Brzezinski P, Högbom M. 2018. Structure of a functional obligate complex III2IV2 respiratory supercomplex from Mycobacterium smegmatis. Nat Struct Mol Biol 25:1128–1136. 10.1038/s41594-018-0160-3. PubMed DOI
Berney M, Cook GM. 2010. Unique flexibility in energy metabolism allows mycobacteria to combat starvation and hypoxia. PLoS One 5:e8614. 10.1371/journal.pone.0008614. PubMed DOI PMC
Cordero PRF, Bayly K, Leung PM, Huang C, Islam ZF, Schittenhelm RB, King GM, Greening C. 2019. Atmospheric carbon monoxide oxidation is a widespread mechanism supporting microbial survival. ISME J 13:2868–2881. 10.1038/s41396-019-0479-8. PubMed DOI PMC
Berney M, Greening C, Hards K, Collins D, Cook GM. 2014. Three different [NiFe] hydrogenases confer metabolic flexibility in the obligate aerobe Mycobacterium smegmatis. Environ Microbiol 16:318–330. 10.1111/1462-2920.12320. PubMed DOI
Sone N, Fukuda M, Katayama S, Jyoudai A, Syugyou M, Noguchi S, Sakamoto J. 2003. QcrCAB operon of a nocardia-form actinomycete Rhodococcus rhodochrous encodes cytochrome reductase complex with diheme cytochrome cc subunit. Biochim Biophys Acta Bioenerg 1557:125–131. 10.1016/S0005-2728(02)00394-8. PubMed DOI
Kishikawa J, Kabashima Y, Kurokawa T, Sakamoto J. 2010. The cytochrome bcc-aa3-type respiratory chain of Rhodococcus rhodochrous. J Biosci Bioeng 110:42–47. 10.1016/j.jbiosc.2009.12.006. PubMed DOI
Collins MD, Jones D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 45:316–354. 10.1128/mr.45.2.316-354.1981. PubMed DOI PMC
Pecsi I, Hards K, Ekanayaka N, Berney M, Hartman T, Jacobs WR, Cook GM. 2014. Essentiality of succinate dehydrogenase in Mycobacterium smegmatis and its role in the generation of the membrane potential under hypoxia. mBio 5:e01093-14. 10.1128/mBio.01093-14. PubMed DOI PMC
Zhang Y, Chen S, Hao X, Su J-Q, Xue X, Yan Y, Zhu Y-G, Ye J. 2016. Transcriptomic analysis reveals adaptive responses of an enterobacteriaceae strain LSJC7 to arsenic exposure. Front Microbiol 7:636. 10.3389/fmicb.2016.00636. PubMed DOI PMC
Tan MP, Sequeira P, Lin WW, Phong WY, Cliff P, Ng SH, Lee BH, Camacho L, Schnappinger D, Ehrt S, Dick T, Pethe K, Alonso S. 2010. Nitrate respiration protects hypoxic Mycobacterium tuberculosis against acid- and reactive nitrogen species stresses. PLoS One 5:e13356. 10.1371/journal.pone.0013356. PubMed DOI PMC
Sabaty M, Avazeri C, Pignol D, Vermeglio A. 2001. Characterization of the reduction of selenate and tellurite by nitrate reductases. Appl Environ Microbiol 67:5122–5126. 10.1128/AEM.67.11.5122-5126.2001. PubMed DOI PMC
Bailly X, Vanin S, Chabasse C, Mizuguchi K, Vinogradov SN. 2008. A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins. BMC Evol Biol 8:244. 10.1186/1471-2148-8-244. PubMed DOI PMC
French CE, Bell JML, Ward FB. 2008. Diversity and distribution of hemerythrin-like proteins in prokaryotes. FEMS Microbiol Lett 279:131–145. 10.1111/j.1574-6968.2007.01011.x. PubMed DOI
Nocek B, Kochinyan S, Proudfoot M, Brown G, Evdokimova E, Osipiuk J, Edwards AM, Savchenko A, Joachimiak A, Yakunin AF. 2008. Polyphosphate-dependent synthesis of ATP and ADP by the family-2 polyphosphate kinases in bacteria. Proc Natl Acad Sci USA 105:17730–17735. 10.1073/pnas.0807563105. PubMed DOI PMC
Presentato A, Cappelletti M, Sansone A, Ferreri C, Piacenza E, Demeter MA, Crognale S, Petruccioli M, Milazzo G, Fedi S, Steinbüchel A, Turner RJ, Zannoni D. 2018. Aerobic growth of Rhodococcus aetherivorans BCP1 using selected naphthenic acids as the sole carbon and energy sources. Front Microbiol 9:672. 10.3389/fmicb.2018.00672. PubMed DOI PMC
Seufferheld MJ, Alvarez HM, Farias ME. 2008. Role of polyphosphates in microbial adaptation to extreme environments. Appl Environ Microbiol 74:5867–5874. 10.1128/AEM.00501-08. PubMed DOI PMC
Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359. 10.1038/nmeth.1923. PubMed DOI PMC
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, Stoye J, Straube J, Winnebald J, Goesmann A. 2014. ReadXplorer—visualization and analysis of mapped sequences. Bioinformatics 30:2247–2254. 10.1093/bioinformatics/btu205. PubMed DOI PMC
Love MI, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol 15:550–521. 10.1186/s13059-014-0550-8. PubMed DOI PMC
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, Mende DR, Letunic I, Rattei T, Jensen LJ, Von Mering C, Bork P. 2019. EggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 47:D309–D314. 10.1093/nar/gky1085. PubMed DOI PMC
Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP, Medema MH, Weber T. 2021. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 49:W29–W35. 10.1093/nar/gkab335. PubMed DOI PMC