Skip to main content
SpringerLink
Log in

Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46

  • Genomics, transcriptomics, proteomics
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

Biodiesel production-derived waste glycerol (WG) was previously investigated as potential carbon source for medium chain length polyhydroxyalkanoate (mcl-PHA) production by Pseudomonas putida LS46. In this study, we evaluated the effect of impurities in the WG on P. putida LS46 physiology during exponential growth and corresponding changes in transcription and protein expression profiles compared with cells grown on pure, reagent grade glycerol. High concentration of metal ions, such as Na+, and numbers of heavy metals ion, such as copper, ion, zinc, were detected in biodiesel-derived WG. Omics analysis from the corresponding cultures suggested altered expression of genes involved in transport and metabolism of ammonia and heavy metal ions. Expression of three groups of heavy metal homeostasis genes was significantly changed (mostly upregulated) in WG cultures and included the following: copper-responded cluster 1 and 2 genes, primarily containing cusABC; two copies of copAB and heavy metal translocating P-type ATPase; Fur-regulated, TonB-dependent siderophore receptor; and several cobalt/zinc/cadmium transporters. Expression of these genes suggests regulation of intracellular concentrations of heavy metals during growth on biodiesel-derived glycerol. Finally, a number of genes involved in adapting to, or metabolizing free fatty acids and other nonheavy metal contaminants, such as Na+, were also upregulated in P. putida LS46 grown on biodiesel-derived glycerol.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bender C, Cooksey D (1987) Molecular cloning of copper resistance genes from Pseudomonas syringae pv. tomato. J Bacteriol 169:470–474

    CAS  PubMed Central  PubMed  Google Scholar 

  • Brown NL, Ford SJ, Pridmore RD, Fritzinger DC (1983) Deoxyribonucleic acid sequence of a gene from the Pseudomonas transposon TN501 encoding mercuric reductase. Biochemistry 22:4089–4095. doi:10.1021/bi00286a015

    Article  CAS  PubMed  Google Scholar 

  • Brown NL, Stoyanov JV, Kidd SP, Hobman JL (2003) The MerR family of transcriptional regulators. FEMS Microbiol Rev 27:145–163. doi:10.1016/S0168-6445(03)00051-2

    Article  CAS  PubMed  Google Scholar 

  • Cánovas D, Cases I, De Lorenzo V (2003) Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis. Environ Microbiol 5:1242–1256. doi:10.1111/j.1462-2920.2003.00463.x

    Article  PubMed  Google Scholar 

  • Cha JS, Cooksey DA (1991) Copper resistance in Pseudomonas syringae mediated by periplasmic and outer membrane proteins. Proc Natl Acad Sci 88:8915–8919. doi:10.1073/pnas.88.20.8915

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Chatzifragkou A, Papanikolaou S (2012) Effect of impurities in biodiesel-derived waste glycerol on the performance and feasibility of biotechnological processes. Appl Microbiol Biotechnol 95:13 27. doi:10.1007/s00253-012-4111-3

  • Escapa I, Del Cerro C, García J, Prieto M (2013) The role of GlpR repressor in Pseudomonas putida KT2440 growth and PHA production from glycerol. Environ Microbiol 15:93–110. doi:10.1111/j.1462-2920.2012.02790.x

    Article  CAS  PubMed  Google Scholar 

  • Fan F, Ghanem M, Gadda G (2004) Cloning, sequence analysis, and purification of choline oxidase from < i > Arthrobacter globiformis</i>: a bacterial enzyme involved in osmotic stress tolerance. Arch Biochem Biophys 421:149–158. doi:10.1016/j.abb.2003.10.003

    Article  CAS  PubMed  Google Scholar 

  • Fu J, Sharma U, Sparling R, Cicek N, Levin DB (2014) Evaluation of medium-chain length Polyhydroxyalkanoate production by Pseudomonas putida LS46 using biodiesel by-product streams. Can J Microbiol 60:461–468. doi:10.1139/cjm-2014-0108

    Article  CAS  PubMed  Google Scholar 

  • González-Guerrero M, Raimunda D, Cheng X, Argüello JM (2010) Distinct functional roles of homologous Cu + efflux ATPases in Pseudomonas aeruginosa. Mol Microbiol 78:1246–1258. doi:10.1111/j.1365-2958.2010.07402.x

    Article  PubMed  Google Scholar 

  • Gungormusler-Yilmaz M, Shamshurin D, Grigoryan M, Taillefer M, Spicer V, Krokhin OV, Sparling R, Levin DB (2014) Reduced catabolic protein expression in Clostridium butyricum DSM 10702 correlate with reduced 1, 3-propanediol synthesis at high glycerol loading. AMB Express 4:63–77. doi:10.1186/s13568-014-0063-6

    Article  PubMed Central  PubMed  Google Scholar 

  • Gutiérrez-Barranquero JA, de Vicente A, Carrión VJ, Sundin GW, Cazorla FM (2013) Recruitment and rearrangement of three different genetic determinants into a conjugative plasmid increase copper resistance in Pseudomonas syringae. Appl Environ Microbiol 79:1028–1033. doi:10.1128/AEM.02644-12

    Article  PubMed Central  PubMed  Google Scholar 

  • Haney CJ, Grass G, Franke S, Rensing C (2005) New developments in the understanding of the cation diffusion facilitator family. J Ind Microbiol Biotechnol 32:215–226. doi:10.1007/s10295-005-0224-3

    Article  CAS  PubMed  Google Scholar 

  • Hantke K (2001) Bacterial zinc transporters and regulators. In: Mark W (ed) Zinc Biochemistry, Physiology, and Homeostasis. Springer, Berlin, pp 53–63

    Chapter  Google Scholar 

  • Hassett DJ, Sokol PA, Howell ML, Ma JF, Schweizer HT, Ochsner U, Vasil ML (1996) Ferric uptake regulator (Fur) mutants of Pseudomonas aeruginosa demonstrate defective siderophore-mediated iron uptake, altered aerobic growth, and decreased superoxide dismutase and catalase activities. J Bacteriol 178:3996–4003

    CAS  PubMed Central  PubMed  Google Scholar 

  • Hu RM, Liao ST, Huang CC, Huang YW, Yang TC (2012) An inducible fusaric acid tripartite efflux pump contributes to the fusaric acid resistance in Stenotrophomonas maltophilia. PLoS ONE 7:e51053. doi:10.1371/journal.pone.0051053

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kenny ST, Runic JN, Kaminsky W, Woods T, Babu RP, O’Connor KE (2012) Development of a bioprocess to convert PET derived terephthalic acid and biodiesel derived glycerol to medium chain length polyhydroxyalkanoate. Appl Microbiol Biotechnol 95:623–633. doi:10.1007/s00253-012-4058-4

    Article  CAS  PubMed  Google Scholar 

  • Kosono S, Haga K, Tomizawa R, Kajiyama Y, Hatano K, Takeda S, Wakai Y, Hino M, Kudo T (2005) Characterization of a multigene-encoded sodium/hydrogen antiporter (Sha) from Pseudomonas aeruginosa: its involvement in pathogenesis. J Bacteriol 187:5242–5248. doi:10.1128/JB.187.15.5242-5248.2005

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Leedjärv A, Ivask A, Virta M (2008) Interplay of different transporters in the mediation of divalent heavy metal resistance in Pseudomonas putida KT2440. J Bacteriol 190:2680–2689. doi:10.1128/JB.01494-07

    Article  PubMed Central  PubMed  Google Scholar 

  • Li XZ, Barré N, Poole K (2000) Influence of the MexA-MexB-OprM multidrug efflux system on expression of the MexC-MexD-OprJ and MexE-MexF-OprN multidrug efflux systems in Pseudomonas aeruginosa. J Antimicrob Chemother 46:885–893. doi:10.1093/jac/46.6.885

    Article  CAS  PubMed  Google Scholar 

  • Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Pillay M, Ratner A, Huang J, Woyke T, Huntemann M (2013) IMG 4 version of the integrated microbial genomes comparative analysis system. Nucleic Acids Res 42:D560–D567. doi:10.1093/nar/gkt963

    Article  PubMed Central  PubMed  Google Scholar 

  • Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, Taghavi S, Dunn J, Lelie D, Wattiez R (2003) Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal‐responsive genes. FEMS Microbiol Rev 27:385–410. doi:10.1016/S0168-6445(03)00045-7

    Article  CAS  PubMed  Google Scholar 

  • Michéa H, Mehri HU, Gotoh N, Kocjancic Curty L, Pechère JC (1997) Characterization of MexE–MexF–OprN, a positively regulated multidrug efflux system of Pseudomonas aeruginosa. Mol Microbiol 23:345–354. doi:10.1046/j.1365-2958.1997.2281594.x

    Article  Google Scholar 

  • Miller C, Pettee B, Zhang C, Pabst M, McLean J, Anderson A (2009) Copper and cadmium: responses in Pseudomonas putida KT2440. Lett Appl Microbiol 49:775–783. doi:10.1111/j.1472-765X.2009.02741.x

    Article  CAS  PubMed  Google Scholar 

  • Nies DH (1999) Microbial heavy-metal resistance. Appl Microbiol Biotechnol 51:730–750

    Article  CAS  PubMed  Google Scholar 

  • Pabst MW, Miller CD, Dimkpa CO, Anderson AJ, McLean JE (2010) Defining the surface adsorption and internalization of copper and cadmium in a soil bacterium Pseudomonas putida. Chemosphere 81:904–910. doi:10.1016/j.chemosphere.2010.07.069

    Article  CAS  PubMed  Google Scholar 

  • Pan JH, Chen Y, Huang YH, Tao YW, Wang J, Li Y, Peng Y, Dong T, Lai XM, Lin YC (2011) Antimycobacterial activity of fusaric acid from a mangrove endophyte and its metal complexes. Arch Pharm Res 34:1177–1181. doi:10.1007/s12272-011-0716-9

    Article  CAS  PubMed  Google Scholar 

  • Posada JA, Naranjo JM, López JA, Higuita JC, Cardona CA (2011) Design and analysis of poly-3-hydroxybutyrate production processes from crude glycerol. Process Biochem 46:310–317. doi:10.1016/j.procbio.2010.09.003

    Article  CAS  Google Scholar 

  • Pyle DJ, Garcia RA, Wen Z (2008) Producing docosahexaenoic acid (DHA)-rich algae from biodiesel-derived crude glycerol: effects of impurities on DHA production and algal biomass composition. J Agric Food Chem 56:3933–3939. doi:10.1021/jf800602s

    Article  CAS  PubMed  Google Scholar 

  • Saier MH, Reddy VS, Tamang DG, Västermark Å (2014) The transporter classification database. Nucleic Acids Res 34:D181–D186. doi:10.1093/nar/gkt1097

    Article  Google Scholar 

  • Sharma PK, Fu J, Cicek N, Sparling R, Levin DB (2012) Kinetics of medium-chain-length polyhydroxyalkanoate production by a novel isolate of Pseudomonas putida LS46. Can J Microbiol 58:982–989. doi:10.1139/w2012-074

    Article  CAS  PubMed  Google Scholar 

  • Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36. doi:10.1093/nar/28.1.33

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Teitzel GM, Geddie A, Susan K, Kirisits MJ, Whiteley M, Parsek MR (2006) Survival and growth in the presence of elevated copper: transcriptional profiling of copper-stressed Pseudomonas aeruginosa. J Bacteriol 188:7242–7256. doi:10.1128/JB.00837-06

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Thompson J, He B (2006) Characterization of crude glycerol from biodiesel production from multiple feedstocks. Appl Eng Agric 22:261–267

    Article  Google Scholar 

  • Tortajada M, Ferreira da Silva L, Prieto MA (2013) Second-generation functionalized mediumchain-length polyhydroxyalkanoates: the gateway to high-value bioplastic applications. Int Microbiol 16:1–15

    CAS  PubMed  Google Scholar 

  • Utsumi R, Yagi T, Katayama S, Katsuragi K, Tachibana K, Toyoda H, Ouchi S, Obata K, Shibana Y, Noda M (1991) Molecular cloning and characterization of the fusaric acid-resistance gene from Pseudomonas cepacia. Agric Biol Chem 55:1913–1918

    Article  CAS  PubMed  Google Scholar 

  • Verbeke TJ, Spicer V, Krokhin OV, Zhang X, Schellenberg JJ, Fristensky B, Wilkins JA, Levin DB, Sparling R (2013) Thermoanaerobacter thermohydrosulfuricus WC1 shows protein complement stability during the fermentation of key lignocellulose-derived substrates. Appl Environ Microbiol 80:1602–1625. doi:10.1128/AEM.03555-13

    Article  PubMed  Google Scholar 

  • Verhoef S, Gao N, Ruijssenaars HJ, de Winde JH (2014) Crude glycerol as feedstock for the sustainable production of p-hydroxybenzoate by Pseudomonas putida S12. New Biotechnol 31:114–119. doi:10.1016/j.nbt.2013.08.006

    Article  CAS  Google Scholar 

  • Wargo MJ, Szwergold BS, Hogan DA (2008) Identification of two gene clusters and a transcriptional regulator required for Pseudomonas aeruginosa glycine betaine catabolism. J Bacteriol 190:2690–2699. doi:10.1128/JB.01393-07

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Wu X, Monchy S, Taghavi S, Zhu W, Ramos J, van der Lelie D (2011) Comparative genomics and functional analysis of niche - specific adaptation in Pseudomonas putida. FEMS Microbiol Rev 35:299–323. doi:10.1111/j.1574-6976.2010.00249.x

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zhang W, Chen L, Liu D (2012) Characterization of a marine-isolated mercury-resistant Pseudomonas putida strain SP1 and its potential application in marine mercury reduction. Appl Microbiol Biotechnol 93:1305–1314. doi:10.1007/s00253-011-3454-5

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This work was funded by Genome Canada, through the Applied Genomics Research in Bioproducts or Crops (ABC) program for the grant titled, “Microbial Genomics for Biofuels and Co-Products from Biorefining Processes,” and by the government of the Province of Manitoba through the Manitoba Research Innovation Fund (MRIF) and the Manitoba Rural Adaptation Council (MRAC).

Author information

Authors and Affiliations

  1. Department of Biosystems Engineering, University of Manitoba, Winnipeg, MB, Canada

    Jilagamazhi Fu, Parveen Sharma, Nazim Cicek & David. B. Levin

  2. Department of Internal Medicine and Manitoba Centre for Proteomics and Systems Biology, University of Manitoba, Winnipeg, MB, Canada

    Vic Spicer, Oleg V. Krokhin & John A. Wilkins

  3. Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada

    Xiangli Zhang & Brian Fristensky

  4. Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada

    Richard Sparling

Authors
  1. Jilagamazhi Fu
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Parveen Sharma
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vic Spicer
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Oleg V. Krokhin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiangli Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Brian Fristensky
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. John A. Wilkins
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Nazim Cicek
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Richard Sparling
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. David. B. Levin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to David. B. Levin.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

(PDF 1059 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fu, J., Sharma, P., Spicer, V. et al. Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46. Appl Microbiol Biotechnol 99, 5583–5592 (2015). https://doi.org/10.1007/s00253-015-6685-z

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-015-6685-z

Keywords

Search

Navigation