Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source
Status PubMed-not-MEDLINE Jazyk angličtina Země Švýcarsko Médium electronic
Typ dokumentu časopisecké články
Grantová podpora
APVV 19-0519
Slovak Research and Development Agency
No. 17-23794S
Czech Science Foundation
PubMed
38674697
PubMed Central
PMC11052242
DOI
10.3390/microorganisms12040753
PII: microorganisms12040753
Knihovny.cz E-zdroje
- Klíčová slova
- Pseudomonas, biodegradation, genomics, phenanthrene (PHE), polycyclic aromatic hydrocarbons (PAHs), proteomics,
- Publikační typ
- časopisecké články MeSH
In this study, we conducted an extensive investigation of the biodegradation capabilities and stress response of the newly isolated strain Pseudomonas veronii SM-20 in order, to assess its potential for bioremediation of sites contaminated with polycyclic aromatic hydrocarbons (PAHs). Initially, phenotype microarray technology demonstrated the strain's proficiency in utilizing various carbon sources and its resistance to certain stressors. Genomic analysis has identified numerous genes involved in aromatic hydrocarbon metabolism. Biodegradation assay analyzed the depletion of phenanthrene (PHE) when it was added as a sole carbon and energy source. We found that P. veronii strain SM-20 degraded approximately 25% of PHE over a 30-day period, starting with an initial concentration of 600 µg/mL, while being utilized for growth. The degradation process involved PHE oxidation to an unstable arene oxide and 9,10-phenanthrenequinone, followed by ring-cleavage. Comparative proteomics provided a comprehensive understanding of how the entire proteome responded to PHE exposure, revealing the strain's adaptation in terms of aromatic metabolism, surface properties, and defense mechanism. In conclusion, our findings shed light on the promising attributes of P. veronii SM-20 and offer valuable insights for the use of P. veronii species in environmental restoration efforts targeting PAH-impacted sites.
Biomedical Research Center Slovak Academy of Sciences Dubravska c 9 845 05 Bratislava Slovakia
Department of Agriculture Food Environment and Forestry University of Florence 50100 Firenze Italy
Department of Pharmacy and Biotechnology University of Bologna 40126 Bologna Italy
Faculty of Pharmacy Comenius University Odbojarov 10 832 32 Bratislava Slovakia
Faculty of Science Charles University Vinicna 5 12844 Prague Czech Republic
Institute of Microbiology Czech Academy of Sciences Videnska 1083 14220 Prague Czech Republic
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Guarino C., Zuzolo D., Marziano M., Conte B., Baiamonte G., Morra L., Benotti D., Gresia D., Stacul E.R., Cicchella D., et al. Investigation and assessment for an effective approach to the reclamation of polycyclic aromatic hydrocarbon (PAHs) contaminated site: SIN Bagnoli, Italy. Sci. Rep. 2019;9:11522. doi: 10.1038/s41598-019-48005-7. PubMed DOI PMC
Lu C., Hong Y., Liu J., Gao Y., Ma Z., Yang B., Ling W., Waigi M.G. A PAH-degrading bacterial community enriched with contaminated agricultural soil and its utility for microbial bioremediation. Environ. Pollut. 2019;251:773–782. doi: 10.1016/j.envpol.2019.05.044. PubMed DOI
Srivastava S., Kumar M. Biodegradation of polycyclic aromatic hydrocarbons (PAHs): A sustainable approach. In: Shah S., Venkatramanan V.P.R., editors. Sustainable Green Technologies for Environmental Management. Springer; Singapore: 2019. pp. 111–139.
Ghosal D., Ghosh S., Dutta T.K., Ahn Y. Current state of knowledge in microbial degradation of polycyclic aromatic hydrocarbons (PAHs): A review. Front. Microbiol. 2016;7:208111. doi: 10.3389/fmicb.2016.01369. PubMed DOI PMC
Michalska J., Piński A., Zur J., Mrozik A. Analysis of the bioaugmentation potential of Pseudomonas putida OR45a and Pseudomonas putida KB3 in the sequencing batch reactors fed with the phenolic landfill leachate. Water. 2020;12:906. doi: 10.3390/w12030906. DOI
Holmes D.E., Dang Y., Smith J.A. Nitrogen cycling during wastewater treatment. Adv. Appl. Microbiol. 2019;106:113–192. doi: 10.1016/bs.aambs.2018.10.003. PubMed DOI
Jun S.R., Wassenaar T.M., Nookaew I., Hauser L., Wanchai V., Land M., Timm C.M., Lu T.Y.S., Schadt C.W., Doktycz M.J., et al. Diversity of Pseudomonas genomes, including populus-associated isolates, as revealed by comparative genome analysis. Appl. Environ. Microbiol. 2015;82:375–383. doi: 10.1128/AEM.02612-15. PubMed DOI PMC
Zhou Z., Liu Y., Zanaroli G., Wang Z., Xu P., Tang H. Enhancing bioremediation potential of Pseudomonas putida by developing its acid stress tolerance with glutamate decarboxylase dependent system and global regulator of extreme radiation resistance. Front. Microbiol. 2019;10:2033. doi: 10.3389/fmicb.2019.02033. PubMed DOI PMC
Anayo O.F., Scholastica E.C., Peter O.C., Nneji U.G., Obinna A., Mistura L.O. The beneficial roles of Pseudomonas in medicine, industries, and environment: A review. In: Sriramulu D., editor. Pseudomonas aeruginosa—An Armory Within. IntechOpen; London, UK: 2019. pp. 1–13. DOI
Muriel-Millán L.F., Rodríguez-Mejía J.L., Godoy-Lozano E.E., Rivera-Gómez N., Gutierrez-Rios R.-M., Morales-Guzmán D., Trejo-Hernández M.R., Estradas-Romero A., Pardo-López L. Functional and genomic characterization of a Pseudomonas aeruginosa strain isolated from the southwestern gulf of mexico reveals an enhanced adaptation for long-chain alkane degradation. Front. Mar. Sci. 2019;6:572. doi: 10.3389/fmars.2019.00572. DOI
Morales M., Sentchilo V., Bertelli C., Komljenovic A., Kryuchkova-Mostacci N., Bourdilloud A., Linke B., Goesmann A., Harshman K., Segers F., et al. The genome of the toluene-degrading Pseudomonas veronii strain 1YdBTEX2 and its differential gene expression in contaminated sand. PLoS ONE. 2016;11:e0165850. doi: 10.1371/journal.pone.0165850. PubMed DOI PMC
Mullaeva S.A., Delegan Y.A., Streletskii R.A., Sazonova O.I., Petrikov K.V., Ivanova A.A., Dyatlov I.A., Shemyakin I.G., Bogun A.G., Vetrova A.A. Pseudomonas veronii strain 7-41 degrading medium-chain n-alkanes and polycyclic aromatic hydrocarbons. Sci. Rep. 2022;12:20527. doi: 10.1038/s41598-022-25191-5. PubMed DOI PMC
Havryliuk O., Hovorukha V., Patrauchan M., Youssef N.H., Tashyrev O. Draft whole genome sequence for four highly copper resistant soil isolates Pseudomonas lactis strain UKR1, Pseudomonas panacis strain UKR2, and Pseudomonas veronii strains UKR3 and UKR4. Curr. Res. Microb. Sci. 2020;1:44–52. doi: 10.1016/j.crmicr.2020.06.002. PubMed DOI PMC
Brennerova M.V., Zavala-Meneses S.G., Josefiova J., Branny P., Buriankova K., Vetrovsky T., Junca H. A global survey reveals a divergent extradiol dioxygenase clade as a widespread complementary contributor to the biodegradation of mono- and polycyclic aromatic hydrocarbons. Environ. Res. 2022;204:111954. doi: 10.1016/j.envres.2021.111954. PubMed DOI
Lee P.Y., Costumbrado J., Hsu C.Y., Kim Y.H. Agarose gel electrophoresis for the separation of DNA fragments. JoVE. 2012;62:3923. doi: 10.3791/3923. PubMed DOI PMC
Wick R.R., Judd L.M., Gorrie C.L., Holt K.E. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput. Biol. 2017;13:e1005595. doi: 10.1371/journal.pcbi.1005595. PubMed DOI PMC
Aziz R.K., Bartels D., Best A., DeJongh M., Disz T., Edwards R.A., Formsma K., Gerdes S., Glass E.M., Kubal M., et al. The RAST server: Rapid annotations using subsystems technology. BMC Genom. 2008;9:75. doi: 10.1186/1471-2164-9-75. PubMed DOI PMC
Lobb B., Jean-Marie Tremblay B., Moreno-Hagelsieb G., Doxey A.C. An assessment of genome annotation coverage across the bacterial tree of life. Microb. Genom. 2020;6:e000341. doi: 10.1099/mgen.0.000341. PubMed DOI PMC
Meier-Kolthoff J.P., Göker M. TYGS Is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 2019;10:2182. doi: 10.1038/s41467-019-10210-3. PubMed DOI PMC
Checcucci A., Borruso L., Petrocchi D., Perito B. Diversity and metabolic profile of the microbial communities inhabiting the darkened white marble of Florence cathedral. Int. Biodeterior. Biodegrad. 2022;171:105420. doi: 10.1016/j.ibiod.2022.105420. DOI
Galardini M., Mengoni A., Biondi E.G., Semeraro R., Florio A., Bazzicalupo M., Benedetti A., Mocali S. DuctApe: A suite for the analysis and correlation of genomic and OMNILOGTM phenotype microarray data. Genomics. 2014;103:1–10. doi: 10.1016/j.ygeno.2013.11.005. PubMed DOI
Masák J., Čejková A., Jirků V. Isolation of acetone/ethylene glycol utilizing and biofilm forming strains of bacteria. J. Microbiol. Methods. 1997;30:133–139. doi: 10.1016/S0167-7012(97)00055-9. DOI
Yin C., Xiong W., Qiu H., Peng W., Deng Z., Lin S., Liang R. Characterization of the phenanthrene-degrading Sphingobium yanoikuyae SJTF8 in heavy metal co-existing liquid medium and analysis of its metabolic pathway. Microorganisms. 2020;8:946. doi: 10.3390/microorganisms8060946. PubMed DOI PMC
Liu J., Liu S., Sun K., Sheng Y., Gu Y., Gao Y. Colonization on root surface by a phenanthrene-degrading endophytic bacterium and its application for reducing plant phenanthrene contamination. PLoS ONE. 2014;9:e108249. doi: 10.1371/journal.pone.0108249. PubMed DOI PMC
Cajthaml T., Erbanová P., Sasek V., Moeder M. Breakdown products on metabolic pathway of degradation of benz[a]anthracene by a ligninolytic fungus. Chemosphere. 2006;64:560–564. doi: 10.1016/j.chemosphere.2005.11.034. PubMed DOI
Nováková S., Šubr Z., Kováč A., Fialová I., Beke G., Danchenko M. Cucumber mosaic virus resistance: Comparative proteomics of contrasting Cucumis sativus cultivars after long-term infection. J. Proteom. 2020;214:103626. doi: 10.1016/j.jprot.2019.103626. PubMed DOI
Goedhart J., Luijsterburg M.S. VolcaNoseR is a web app for creating, exploring, labeling and sharing volcano plots. Sci. Rep. 2020;10:20560. doi: 10.1038/s41598-020-76603-3. PubMed DOI PMC
Yu N.Y., Wagner J.R., Laird M.R., Melli G., Rey S., Lo R., Dao P., Cenk Sahinalp S., Ester M., Foster L.J., et al. PSORTb 3.0: Improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics. 2010;26:1608. doi: 10.1093/bioinformatics/btq249. PubMed DOI PMC
Imai K., Asakawa N., Tsuji T., Akazawa F., Ino A., Sonoyama M., Mitaku S. SOSUI-GramN: High performance prediction for sub-cellular localization of proteins in gram-negative bacteria. Bioinformation. 2008;2:417. doi: 10.6026/97320630002417. PubMed DOI PMC
Cantalapiedra C.P., Hernández-Plaza A., Letunic I., Bork P., Huerta-Cepas J. EggNOG-Mapper v2: Functional annotation, orthology assignments, and domain prediction at the metagenomic scale. Mol. Biol. Evol. 2021;38:5825–5829. doi: 10.1093/molbev/msab293. PubMed DOI PMC
Imperato V., Portillo-Estrada M., McAmmond B.M., Douwen Y., Van Hamme J.D., Gawronski S.W., Vangronsveld J., Thijs S. Genomic diversity of two hydrocarbon-degrading and plant growth-promoting Pseudomonas species isolated from the oil field of Bóbrka (Poland) Genes. 2019;10:443. doi: 10.3390/genes10060443. PubMed DOI PMC
Montes C., Altimira F., Canchignia H., Castro Á., Sánchez E., Miccono M., Tapia E., Sequeida Á., Valdés J., Tapia P., et al. A draft genome sequence of Pseudomonas veronii R4: A grapevine (Vitis vinifera L.) root-associated strain with high biocontrol potential. Stand. Genom. Sci. 2016;11:1–10. doi: 10.1186/s40793-016-0198-y. PubMed DOI PMC
Valderrama J.A., Durante-Rodríguez G., Blázquez B., García J.L., Carmona M., Díaz E. Bacterial degradation of benzoate: Cross-regulation between aerobic and anaerobic pathways. J. Biol. Chem. 2012;287:10494–10508. doi: 10.1074/jbc.M111.309005. PubMed DOI PMC
Phale P.S., Malhotra H., Shah B.A. Degradation strategies and associated regulatory mechanisms/features for aromatic compound metabolism in bacteria. Adv. Appl. Microbiol. 2020;112:1–65. doi: 10.1016/bs.aambs.2020.02.002. PubMed DOI
Belda E., van Heck R.G.A., José Lopez-Sanchez M., Cruveiller S., Barbe V., Fraser C., Klenk H.P., Petersen J., Morgat A., Nikel P.I., et al. The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis. Environ. Microbiol. 2016;18:3403–3424. doi: 10.1111/1462-2920.13230. PubMed DOI
Elomari M., Coroler L., Hoste B., Gillis M., Izard D., Leclerc H. DNA relatedness among Pseudomonas strains isolated from natural mineral waters and proposal of Pseudomonas veronii sp. nov. Int. J. Syst. Bacteriol. 1996;46:1138–1144. doi: 10.1099/00207713-46-4-1138. PubMed DOI
Li G., Lu C.D. The cryptic dsda gene encodes a functional D-serine dehydratase in Pseudomonas aeruginosa PAO1. Curr. Microbiol. 2016;72:788–794. doi: 10.1007/s00284-016-1021-0. PubMed DOI
Remus-Emsermann M.N.P., Schmid M., Gekenidis M.T., Pelludat C., Frey J.E., Ahrens C.H., Drissner D. Complete genome sequence of Pseudomonas citronellolis P3B5, a candidate for microbial phyllo-remediation of hydrocarbon-contaminated sites. Stand. Genom. Sci. 2016;11:75. doi: 10.1186/s40793-016-0190-6. PubMed DOI PMC
Saati-Santamaría Z., Baroncelli R., Rivas R., García-Fraile P. Comparative genomics of the genus Pseudomonas reveals host- and environment-specific evolution. Microbiol. Spectr. 2022;10:e0237022. doi: 10.1128/spectrum.02370-22. PubMed DOI PMC
Ramsey C., MacGowan A.P. A review of the pharmacokinetics and pharmacodynamics of aztreonam. J. Antimicrob. Chemother. 2016;71:2704–2712. doi: 10.1093/jac/dkw231. PubMed DOI
Alav I., Kobylka J., Kuth M.S., Pos K.M., Picard M., Blair J.M.A., Bavro V.N. Structure, assembly, and function of tripartite efflux and type 1 secretion systems in gram-negative bacteria. Chem. Rev. 2021;121:5479–5596. doi: 10.1021/acs.chemrev.1c00055. PubMed DOI PMC
Nag A., Mehra S. A major facilitator superfamily (MFS) efflux pump, SCO4121, from Streptomyces coelicolor with roles in multidrug resistance and oxidative stress tolerance and its regulation by a MARR regulator. Appl. Environ. Microbiol. 2021;87:e02238-20. doi: 10.1128/AEM.02238-20. PubMed DOI PMC
Pasqua M., Grossi M., Scinicariello S., Aussel L., Barras F., Colonna B., Prosseda G. The MFS efflux pump EmrKY contributes to the survival of Shigella within macrophages. Sci. Rep. 2019;9:2906. doi: 10.1038/s41598-019-39749-3. PubMed DOI PMC
Jiang Y., Huang H., Wu M., Yu X., Chen Y., Liu P., Li X. Pseudomonas sp. LZ-Q continuously degrades phenanthrene under hypersaline and hyperalkaline condition in a membrane bioreactor system. Biophys. Rep. 2015;1:156–167. doi: 10.1007/s41048-016-0018-3. PubMed DOI PMC
Bisht S., Pandey P., Bhargava B., Sharma S., Kumar V., Sharma K.D. Bioremediation of polyaromatic hydrocarbons (PAHs) using rhizosphere technology. Braz. J. Microbiol. 2015;46:7. doi: 10.1590/S1517-838246120131354. PubMed DOI PMC
Puntus I.F., Filonov A.E., Akhmetov L.I., Karpov A.V., Boronin A.M. Phenanthrene degradation by bacteria of the genera Pseudomonas and Burkholderia in model soil systems. Mikrobiologiia. 2008;77:11–20. doi: 10.1134/S0026261708010025. PubMed DOI
Isaac P., Martínez F.L., Bourguignon N., Sánchez L.A., Ferrero M.A. Improved PAHs removal performance by a defined bacterial consortium of indigenous Pseudomonas and Actinobacteria from Patagonia, Argentina. Int. Biodeterior. Biodegrad. 2015;101:23–31. doi: 10.1016/j.ibiod.2015.03.014. DOI
Zhao H.P., Wu Q.S., Wang L., Zhao X.T., Gao H.W. Degradation of phenanthrene by bacterial strain isolated from soil in oil refinery fields in Shanghai China. J. Hazard. Mater. 2009;164:863–869. doi: 10.1016/j.jhazmat.2008.08.098. PubMed DOI
Mawad A., Albasri H., Shalkami A.G., Alamri S., Hashem M. Synergistic degradation of phenanthrene by constructed Pseudomonas spp. consortium compared with pure strains. Environ. Technol. Innov. 2021;24:101942. doi: 10.1016/j.eti.2021.101942. DOI
Nwinyi O.C., Ajayi O.O., Amund O.O. Degradation of polynuclear aromatic hydrocarbons by two strains of Pseudomonas. Braz. J. Microbiol. 2016;47:551. doi: 10.1016/j.bjm.2016.04.026. PubMed DOI PMC
Volkering F., Breure A.M., Sterkenburg A., van Andel J.G. Microbial degradation of polycyclic aromatic hydrocarbons: Effect of substrate availability on bacterial growth kinetics. Appl. Microbiol. Biotechnol. 1992;36:548–552. doi: 10.1007/BF00170201. DOI
Hua F., Wang H.Q. Uptake and trans-membrane transport of petroleum hydrocarbons by microorganisms. Biotechnol. Biotechnol. Equip. 2014;28:165–175. doi: 10.1080/13102818.2014.906136. PubMed DOI PMC
Pozdnyakova N., Muratova A., Turkovskaya O. Degradation of polycyclic aromatic hydrocarbons by co-culture of Pleurotus ostreatus Florida and Azospirillum brasilense. Appl. Microbiol. 2022;2:735–748. doi: 10.3390/applmicrobiol2040056. DOI
Hadibarata T., Tachibana S., Askari M. Identification of metabolites from phenanthrene oxidation by phenoloxidases and dioxygenases of Polyporus sp. S133. J. Microbiol. Biotechnol. 2011;21:299–304. doi: 10.4014/jmb.1011.11009. PubMed DOI
Hidayat A., Yanto D.H.Y. Biodegradation and metabolic pathway of phenanthrene by a new tropical fungus, Trametes hirsuta D7. J. Environ. Chem. Eng. 2018;6:2454–2460. doi: 10.1016/j.jece.2018.03.051. DOI
Hammel K., Gai W., Green B., Moen M. Oxidative degradation of phenanthrene by the ligninolytic fungus Phanerochaete chrysosporium. Appl. Environ. Microbiol. 1992;58:1832–1838. doi: 10.1128/aem.58.6.1832-1838.1992. PubMed DOI PMC
Teng C., Wu S., Gong G. Bio-removal of phenanthrene, 9-fluorenone and anthracene-9,10-dione by laccase from Aspergillus niger in waste cooking oils. Food Control. 2019;105:219–225. doi: 10.1016/j.foodcont.2019.06.015. DOI
Muratova A., Pozdnyakova N., Makarov O., Baboshin M., Baskunov B., Myasoedova N., Golovleva L., Turkovskaya O. Degradation of phenanthrene by the rhizobacterium Ensifer meliloti. Biodegradation. 2014;25:787–795. doi: 10.1007/s10532-014-9699-9. PubMed DOI
Kim Y.H., Freeman J.P., Moody J.D., Engesser K.H., Cerniglia C.E. Effects of pH on the degradation of phenanthrene and pyrene by Mycobacterium vanbaalenii PYR-1. Appl. Microbiol. Biotechnol. 2005;67:275–285. doi: 10.1007/s00253-004-1796-y. PubMed DOI
Seo J.-S., Keum Y.-S., Li Q.X. Mycobacterium aromativorans JS19b1T degrades phenanthrene through C-1,2, C-3,4 and C-9,10 dioxygenation pathways. Int. Biodeterior. Biodegrad. 2012;70:96. doi: 10.1016/j.ibiod.2012.02.005. PubMed DOI PMC
Barone R., Nastro R.A., Gambino E., Toscanesi M., Picciall G., Napoli L.D., Trifuoggi M., Piccialli V., Guida M. Pseudomonas anguilliseptica strain-A1 degradation of polycyclic aromatic hydrocarbons in soil microcosms: Focus on detoxification activity and free water-soluble protein extracts kinetics and efficiency. J. Bioremediat. Biodegrad. 2017;8:1–7. doi: 10.4172/2155-6199.1000418. DOI
Guzik U., Greń I., Hupert-Kocurek K., Wojcieszyńska D. Catechol 1,2-dioxygenase from the new aromatic compounds–degrading Pseudomonas putida strain n6. Int. Biodeterior. Biodegrad. 2011;65:504–512. doi: 10.1016/j.ibiod.2011.02.001. DOI
Borowski T., Georgiev V., Siegbahn P.E.M. Catalytic reaction mechanism of homogentisate dioxygenase: A hybrid DFT study. J. Am. Chem. Soc. 2005;127:17303–17314. doi: 10.1021/ja054433j. PubMed DOI
Setlhare B., Kumar A., Mokoena M.P., Olaniran A.O. Catechol 1,2-dioxygenase is an analogue of homogentisate 1,2-dioxygenase in Pseudomonas chlororaphis Strain UFB2. Int. J. Mol. Sci. 2019;20:61. doi: 10.3390/ijms20010061. PubMed DOI PMC
Kamimura N., Masai E. The protocatechuate 4,5-cleavage pathway: Overview and new findings. In: Nojiri H., Tsuda M., Fukuda M., Kamagata Y., editors. Biodegradative Bacteria. Springer; Tokyo, Japan: 2013. pp. 207–226. DOI
Guzik U., Hupert-Kocurek K., Wojcieszysk D. Intradiol dioxygenases—The key enzymes in xenobiotics degradation. In: Chamy R., Rosenkranz F., editors. Biodegradation of Hazardous and Special Products. IntechOpen; London, UK: 2013. DOI
Ladino-Orjuela G., Gomes E., da Silva R., Salt C., Parsons J.R. Metabolic pathways for degradation of aromatic hydrocarbons by bacteria. Rev. Environ. Contam. Toxicol. 2016;237:105–121. doi: 10.1007/978-3-319-23573-8_5. PubMed DOI
Cafaro V., Izzo V., Scognamiglio R., Notomista E., Capasso P., Casbarra A., Pucci P., Di Donato A. Phenol hydroxylase and toluene/o-xylene monooxygenase from Pseudomonas stutzeri OX1: Interplay between two enzymes. Appl. Environ. Microbiol. 2004;70:2211–2219. doi: 10.1128/AEM.70.4.2211-2219.2004. PubMed DOI PMC
Robrock K.R., Mohn W.W., Eltis L.D., Alvarez-Cohen L. Biphenyl and ethylbenzene dioxygenases of Rhodococcus jostii RHA1 transform PBDEs. Biotechnol. Bioeng. 2011;108:313–321. doi: 10.1002/bit.22952. PubMed DOI
Yang X., Xie F., Zhang G., Shi Y., Qian S. Purification, characterization, and substrate specificity of two 2,3-dihydroxybiphenyl 1,2-dioxygenase from Rhodococcus sp. R04, showing their distinct stability at various temperature. Biochimie. 2008;90:1530–1538. doi: 10.1016/j.biochi.2008.05.020. PubMed DOI
Perez-Dominguez F., Carrillo-Beltrán D., Blanco R., Muñoz J.P., León-Cruz G., Corvalan A.H., Urzúa U., Calaf G.M., Aguayo F. Role of pirin, an oxidative stress sensor protein, in epithelial carcinogenesis. Biology. 2021;10:116. doi: 10.3390/biology10020116. PubMed DOI PMC
Widiatningrum T., Maeda S., Kataoka K., Sakurai T. A pirin-like protein from Pseudomonas stutzeri and its quercetinase activity. Biochem. Biophys. Rep. 2015;3:144. doi: 10.1016/j.bbrep.2015.08.001. PubMed DOI PMC
Soo P.C., Horng Y.T., Lai M.J., Wei J.R., Hsieh S.C., Chang Y.L., Tsai Y.H., Lai H.C. Pirin regulates pyruvate catabolism by interacting with the pyruvate dehydrogenase E1 subunit and modulating pyruvate dehydrogenase activity. J. Bacteriol. 2007;189:109–118. doi: 10.1128/JB.00710-06. PubMed DOI PMC
Hickman S.J., Cooper R.E.M., Bellucci L., Paci E., Brockwell D.J. Gating of TonB-dependent transporters by substrate-specific forced remodelling. Nat. Commun. 2017;8:14804. doi: 10.1038/ncomms14804. PubMed DOI PMC
Akhtar A.A., Turner D.P.J. The role of bacterial ATP-binding cassette (ABC) transporters in pathogenesis and virulence: Therapeutic and vaccine potential. Microb. Pathog. 2022;171:105734. doi: 10.1016/j.micpath.2022.105734. PubMed DOI
Fujita M., Mori K., Hara H., Hishiyama S., Kamimura N., Masai E. A TonB-dependent receptor constitutes the outer membrane transport system for a lignin-derived aromatic compound. Commun. Biol. 2019;2:432. doi: 10.1038/s42003-019-0676-z. PubMed DOI PMC
Samantarrai D., Sagar A.L., Gudla R., Siddavattam D. TonB-dependent transporters in Sphingomonads: Unraveling their distribution and function in environmental adaptation. Microorganisms. 2020;8:359. doi: 10.3390/microorganisms8030359. PubMed DOI PMC
Tang K., Jiao N., Liu K., Zhang Y., Li S. Distribution and functions of TonB-dependent transporters in marine bacteria and environments: Implications for dissolved organic matter utilization. PLoS ONE. 2012;7:e41204. doi: 10.1371/journal.pone.0041204. PubMed DOI PMC
Michalska K., Chang C., Mack J.C., Zerbs S., Joachimiak A., Collart F.R. characterization of transport proteins for aromatic compounds derived from lignin: Benzoate derivative binding proteins. J. Mol. Biol. 2012;423:555–575. doi: 10.1016/j.jmb.2012.08.017. PubMed DOI PMC
Jerina D.M. The 1982 Bernard B. Brodie award lecture. Metabolism of aromatic hydrocarbons by the cytochrome P-450 system and epoxide hydrolase. Drug Metab. Dispos. 1983;11:1–4. PubMed
Zeinali M., Vossoughi M., Ardestani S.K. Degradation of phenanthrene and anthracene by Nocardia otitidiscaviarum strain TSH1, a moderately thermophilic bacterium. J. Appl. Microbiol. 2008;105:398–406. doi: 10.1111/j.1365-2672.2008.03753.x. PubMed DOI
Haroune N., Combourieu B., Besse P., Sancelme M., Reemtsma T., Kloepfer A., Diab A., Knapp J.S., Baumberg S., Delort A.M. Benzothiazole degradation by Rhodococcus pyridinovorans strain PA: Evidence of a catechol 1,2-dioxygenase activity. Appl. Environ. Microbiol. 2002;68:6114–6120. doi: 10.1128/AEM.68.12.6114-6120.2002. PubMed DOI PMC
Meulenberg R., Rijnaarts H.H.M., Doddema H.J., Field J.A. Partially oxidized polycyclic aromatic hydrocarbons show an increased bioavailability and biodegradability. FEMS Microbiol. Lett. 1997;152:45–49. doi: 10.1111/j.1574-6968.1997.tb10407.x. PubMed DOI
Suman J., Sredlova K., Fraraccio S., Jerabkova M., Strejcek M., Kabickova H., Cajthaml T., Uhlik O. Transformation of hydroxylated polychlorinated biphenyls by bacterial 2-hydroxybiphenyl 3-monooxygenase. Chemosphere. 2024;349:140909. doi: 10.1016/j.chemosphere.2023.140909. PubMed DOI
Setlhare B., Kumar A., Mokoena M.P., Pillay B., Olaniran A.O. Phenol hydroxylase from Pseudomonas sp. KZNSA: Purification, characterization and prediction of three-dimensional structure. Int. J. Biol. Macromol. 2020;146:1000–1008. doi: 10.1016/j.ijbiomac.2019.09.224. PubMed DOI
Marx D.C., Plummer A.M., Faustino A.M., Devlin T., Roskopf M.A., Leblanc M.J., Lessen H.J., Amann B.T., Fleming P.J., Krueger S., et al. SurA is a cryptically grooved chaperone that expands unfolded outer membrane proteins. Proc. Natl. Acad. Sci. USA. 2020;117:28026–28035. doi: 10.1073/pnas.2008175117. PubMed DOI PMC
Bugg T., Foght J.M., Pickard M.A., Gray M.R. Uptake and active efflux of polycyclic aromatic hydrocarbons by Pseudomonas fluorescens LP6a. Appl. Environ. Microbiol. 2000;66:5387. doi: 10.1128/AEM.66.12.5387-5392.2000. PubMed DOI PMC
Broniatowski M., Binczycka M., Wójcik A., Flasiński M., Wydro P. Polycyclic aromatic hydrocarbons in model bacterial membranes–Langmuir monolayer studies. Biochim. Biophys. Acta-Biomembr. 2017;1859:2402–2412. doi: 10.1016/j.bbamem.2017.09.017. PubMed DOI
Scott C.C., Finnerty W.R. Characterization of intracytoplasmic hydrocarbon inclusions from the hydrocarbon-oxidizing Acinetobacter species HO1-N. J. Bacteriol. 1976;127:481. doi: 10.1128/jb.127.1.481-489.1976. PubMed DOI PMC
Wang H., Jiang R., Kong D., Liu Z., Wu X., Xu J., Li Y. Transmembrane transport of polycyclic aromatic hydrocarbons by bacteria and functional regulation of membrane proteins. Front. Environ. Sci. Eng. 2020;14:9. doi: 10.1007/s11783-019-1188-2. DOI
Misra H.S., Rajpurohit Y.S., Khairnar N.P. Pyrroloquinoline-quinone and its versatile roles in biological processes. J. Biosci. 2012;37:313–325. doi: 10.1007/s12038-012-9195-5. PubMed DOI
Poole K., Neshat S., Krebes K., Heinrichs D.E. Cloning and nucleotide sequence analysis of the ferripyoverdine receptor gene FpvA of Pseudomonas aeruginosa. J. Bacteriol. 1993;175:4597. doi: 10.1128/jb.175.15.4597-4604.1993. PubMed DOI PMC
Ghysels B., Dieu B.T.M., Beatson S.A., Pirnay J.P., Ochsner U.A., Vasil M.L., Cornelis P. FpvB, an alternative type i ferripyoverdine receptor of Pseudomonas aeruginosa. Microbiology. 2004;150:1671–1680. doi: 10.1099/mic.0.27035-0. PubMed DOI
Holden V.I., Breen P., Houle S., Dozois C.M., Bachman M.A. Klebsiella pneumoniae siderophores induce inflammation, bacterial dissemination, and HIF-1ɑ stabilization during pneumonia. mBio. 2016;7:e01397-16. doi: 10.1128/mBio.01397-16. PubMed DOI PMC