Abstract
Nickel (Ni(II)) toxicity is addressed by many different bacteria, but bacterial responses to nickel stress are still unclear. Therefore, we studied the effect of Ni(II) toxicity on cell proliferation of α-proteobacterium Caulobacter crescentus. Next, we showed the mechanism that allows C. crescentus to survive in Ni(II) stress condition. Our results revealed that the growth of C. crescentus is severely affected when the bacterium was exposed to different Ni(II) concentrations, 0.003 mM slightly affected the growth, 0.008 mM reduced the growth by 50%, and growth was completely inhibited at 0.015 mM. It was further shown that Ni(II) toxicity induced mislocalization of major regulatory proteins such as MipZ, FtsZ, ParB, and MreB, resulting in dysregulation of the cell cycle. GC-MS metabolomics analysis of Ni(II) stressed C. crescentus showed an increased level of nine important metabolites including TCA cycle intermediates and amino acids. This indicates that changes in central carbon metabolism and nitrogen metabolism are linked with the disruption of cell division process. Addition of malic acid, citric acid, alanine, proline, and glutamine to 0.015 mM Ni(II)-treated C. crescentus restored its growth. Thus, the present work shows a protective effect of these organic acids and amino acids on Ni(II) toxicity. Metabolic stimulation through the PutA/GlnA pathway, accelerated degradation of CtrA, and Ni-chelation by organic acids or amino acids are some of the possible mechanisms suggested to be involved in enhancing C. crescentus’s tolerance. Our results shed light on the mechanism of increased Ni(II) tolerance in C. crescentus which may be useful in bioremediation strategies and synthetic biology applications such as the development of whole cell biosensor.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Beaufay F, Coppine J, Mayard A, Laloux G, De Bolle X, Hallez R (2015) A NAD-dependent glutamate dehydrogenase coordinates metabolism with cell division in Caulobacter crescentus. EMBO J 34(13):1786–1800. https://doi.org/10.15252/embj.201490730
Bhatia NP, Walsh KB, Baker AJ (2005) Detection and quantification of ligands involved in nickel detoxificationn in a herbaceous Ni hyperaccumulator Stackhousia tryonii Bailey. J Exp Bot 56(415):1343–1349
Bongaerts G, Uitzetter J, Brouns R, Vogels G (1978) Uricase of Bacillus fastidiosus properties and regulation of synthesis. Biochim Biophys Acta 527(2):348–358
Booth SC, Weljie AM, Turner RJ (2015) Metabolomics reveals differences of metal toxicity in cultures of Pseudomonas pseudoalcaligenes KF707 grown on different carbon sources. Front Microbiol 6(827). https://doi.org/10.3389/fmicb.2015.00827
Boutte CC, Henry JT, Crosson S (2012) ppGpp and polyphosphate modulate cell cycle progression in Caulobacter crescentus. J Bacteriol 194(1):28–35. https://doi.org/10.1128/JB.05932-11
Britos L, Abeliuk E, Taverner T, Lipton M, McAdams H, Shapiro L (2011) Regulatory response to carbon starvation in Caulobacter crescentus. PLoS One 6(4):e18179. https://doi.org/10.1371/journal.pone.0018179
Carballido-López R (2006) The bacterial actin-like cytoskeleton. Microbiol Mol Biol Rev 70(4):888–909. https://doi.org/10.1128/MMBR.00014-06
Cheng Z, Lin M, Rikihisa Y (2014) Ehrlichia chaffeensis proliferation begins with NtrY/NtrX and PutA/GlnA upregulation and CtrA degradation induced by proline and glutamine uptake. mBio 5(6):e02141-14. https://doi.org/10.1128/mBio.02141-14
Copley SD, Frank E, Kirsch WM, Koch TH (1992) Detection and possible origins of aminomalonic acid in protein hydrolysates. Anal Biochem 201(1):152–157. https://doi.org/10.1016/0003-2697(92)90188-D
Csonka LN (1989) Physiological and genetic responses of bacteria to osmotic stress. Microbiol Rev 53(1):121–147
Curtis PD, Brun YV (2010) Getting in the loop: regulation of development in Caulobacter crescentus. Microbiol Mol Biol Rev 74(1):13–41. https://doi.org/10.1128/MMBR.00040-09
Das KK, Das SN, Dhundasi SA (2008) Nickel, its adverse health effects & oxidative stress. Indian J Med Res 128(4):412–425
Debussche L, Couder M, Thibaut D, Cameron B, Crouzet J, Blanche F (1992) Assay, purification, and characterization of cobaltochelatase, a unique complex enzyme catalyzing cobalt insertion in hydrogenobyrinic acid a,c-diamide during coenzyme B12 biosynthesis in Pseudomonas denitrificans. J Bacteriol 174(22):7445–7451
Denkhaus E, Salnikow K (2002) Nickel essentiality, toxicity, and carcinogenicity. Crit Rev Oncol Hematol 42(1):35–56
Figge RM, Easter J, Gober JW (2003) Productive interaction between the chromosome partitioning proteins, ParA and ParB, is required for the progression of the cell cycle in Caulobacter crescentus. Mol Microbiol 47(5):1225–1237. https://doi.org/10.1046/j.1365-2958.2003.03367.x
Figge RM, Divakaruni AV, Gober JW (2004) MreB, the cell shape-determining bacterial actin homologue, co-ordinates cell wall morphogenesis in Caulobacter crescentus. Mol Microbiol 51(5):1321–1332. https://doi.org/10.1111/j.1365-2958.2003.03936.x
Freeman JL, Persans MW, Nieman K, Albrecht C, Peer W, Pickering IJ, Salt DE (2004) Increased glutathione biosynthesis plays a role in nickel tolerance in Thlaspi nickel hyperaccumulators. Plant Cell 16(8):2176–2191. https://doi.org/10.1105/tpc.104.023036
Gitai Z, Dye N, Shapiro L (2004) An actin-like gene can determine cell polarity in bacteria. Proc Natl Acad Sci U S A 101(23):8643–8648. https://doi.org/10.1073/pnas.0402638101
Goley ED, Yeh YC, Hong SH, Fero MJ, Abeliuk E, McAdams HH, Shapiro L (2011) Assembly of the Caulobacter cell division machine. Mol Microbiol 80(6):1680–1698. https://doi.org/10.1111/j.1365-2958.2011.07677.x
Harth G, Maslesa-Galic S, Tullius MV, Horwitz MA (2005) All four Mycobacterium tuberculosis glnA genes encode glutamine synthetase activities but only GlnA1 is abundantly expressed and essential for bacterial homeostasis. Mol Microbiol 58(4):1157–1172. https://doi.org/10.1111/j.1365-2958.2005.04899.x
He ZL, Yang XE, Stoffella PJ (2005) Trace elements in agroecosystems and impacts on the environment. J Trace Elem Med Biol 19(2–3):125–140. https://doi.org/10.1016/j.jtemb.2005.02.010
Heinrich K, Sobetzko P, Jonas K (2016) A kinase-phosphatase switch transduces environmental information into a bacterial cell cycle circuit. PLoS Genet 12(12):e1006522. https://doi.org/10.1371/journal.pgen.1006522
Herawati N, Suzuki S, Hayashi K, Rivai IF, Koyama H (2000) Cadmium, copper and zinc levels in rice and soil of Japan, Indonesia and China by soil type. Bull Environ Contam Toxicol 64(1):33–39. https://doi.org/10.1007/s001289910006
Hillson NJ, Hu P, Andersen GL, Shapiro L (2007) Caulobacter crescentus as a whole-cell uranium biosensor. Appl Environ Microbiol 73(23):7615–7621. https://doi.org/10.1128/AEM.01566-07
Homer FA, Reeves R, Brooks RR (1995) The possible involvement of amino acids in nickel chelation in some nickel accumulating plants. Curr Top Phytochem 14:31–33
Hoque MA, Banu MN, Nakamura Y, Shimoishi Y, Murata Y (2008) Proline and glycinebetaine enhance antioxidant defense and methylglyoxal detoxification systems and reduce NaCl-induced damage in cultured tobacco cells. J Plant Physiol 165(8):813–824. https://doi.org/10.1016/j.jplph.2007.07.013
Hu P, Brodie EL, Suzuki Y, McAdams HH, Andersen GL (2005) Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus. J Bacteriol 187(24):8437–8449. https://doi.org/10.1128/JB.187.24.8437-8449.2005
Hughes V, Jiang C, Brun Y (2012) Caulobacter crescentus. Curr Biol 22(13):507–509
Jensen RB, Wang SC, Shapiro L (2002) Dynamic localization of proteins and DNA during a bacterial cell cycle. Nat Rev Mol Cell Biol 3(3):167–176. https://doi.org/10.1038/nrm758
Jespersen D, Yu J, Huang B (2017) Metabolic effects of acibenzolar-S-methyl for improving heat or drought stress in creeping bentgrass. Front Plant Sci 8(1224). https://doi.org/10.3389/fpls.2017.01224
Jonas K, Liu J, Chien P, Laub MT (2013) Proteotoxic stress induces a cell cycle arrest by stimulating Lon to degrade the replication initiator DnaA. Cell 154(3):623–636. https://doi.org/10.1016/j.cell.2013.06.034
Kalliri E, Grzyska PK, Hausinger RP (2005) Kinetic and spectroscopic investigation of CoII, NiII, and N-oxalylglycine inhibition of the FeII/alpha-ketoglutarate dioxygenase, TauD. Biochem Biophys Res Commun 338(1):191–197. https://doi.org/10.1016/j.bbrc.2005.08.223
Kawahara Y, Ohsumi T, Yoshihara Y, Ikeda S (1989) Proline in the osmoregulation of Brevibacterium lactofermentum. Agric Biol Chem 53(9):2475–2479
Kersten WJ, Brooks RR, Reeves RD, Jaffré A (1980) Nature of nickel complexes in Psychotria douarrei and other nickel-accumulating plants. Phytochemistry 19(9):1963–1965. https://doi.org/10.1016/0031-9422(80)83013-5
Kroeger KM, Hashimoto M, Kow YW, Greenberg MM (2003) Cross-linking of 2-deoxyribonolactone and its beta-elimination product by base excision repair enzymes. Biochemistry 42(8):2449–2455. https://doi.org/10.1021/bi027168c
Lam H, Schofield WB, Jacobs-Wagner C (2005) A landmark protein essential for establishing and perpetuating the polarity of a bacterial cell. Cell 124(5):1011–1023. https://doi.org/10.1016/j.cell.2005.12.040
Lee J, Reeves RD, Brooks RR, Jaffré T (1978) The relation between nickel and citric acid in some nickel-accumulating plants. Phytochemistry 17(6):1033–1035. https://doi.org/10.1016/S0031-9422(00)94274-2
Leslie DJ, Heinen C, Schramm FD, Thüring M, Aakre CD, Murray SM, Laub MT, Jonas K (2015) Nutritional control of DNA replication initiation through the proteolysis and regulated translation of DnaA. PLoS Genet 11(7):e1005342. https://doi.org/10.1371/journal.pgen.100534
Liang X, Zhang L, Natarajan SK, Becker DF (2013) Proline mechanisms of stress survival. Antioxid Redox Signal 19(9):998–1011. https://doi.org/10.1089/ars.2012.5074
Louwrier A, Knowles CJ (1996) The purification and characterization of a novel D-specific carbamoylase enzyme from an Agrobacterium sp. Enzym Microb Technol 19(8):562–571. https://doi.org/10.1016/0141-0229(95)00044-5
Macomber L, Hausinger RP (2011) Mechanisms of nickel toxicity in microorganisms. Metallomics 3(11):1153–1162. https://doi.org/10.1039/c1mt00063b
Mohapatra SS, Fioravanti A, Biondi EG (2014) DNA methylation in Caulobacter and other Alphaproteobacteria during cell cycle progression. Trends Microbiol 22(9):528–535. https://doi.org/10.1016/j.tim.2014.05.003
Mohl DA, Easter J, Gober JW (2001) The chromosome partitioning protein, ParB, is required for cytokinesis in Caulobacter crescentus. Mol Microbiol 42(3):741–755. https://doi.org/10.1046/j.1365-2958.2001.02643.x
Monahan LG, Hajduk IV, Blaber SP, Charles IG, Harry EJ (2014) Coordinating bacterial cell division with nutrient availability: a role for glycolysis. mBio 5(3):e00935-14. https://doi.org/10.1128/mBio.00935-14
Montargès-Pelletier E, Chardot V, Echevarria G, Michot LJ, Bauer A, Morel JL (2008) Identification of nickel chelators in three hyperaccumulating plants: an X-ray spectroscopic study. Phytochemistry 69(8):1695–1709. https://doi.org/10.1016/j.phytochem.2008.02.009
Mulrooney SB, Hausinger RP (2003) Nickel uptake and utilization by microorganisms. FEMS Microbiol Rev 27(2–3):239–261. https://doi.org/10.1016/S0168-6445(03)00042-1
Navarro C, Wu LF, Mandrand-Berthelot MA (1993) The nik operon of Escherichia coli encodes a periplasmic binding-protein-dependent transport system for nickel. Mol Microbiol 9(6):1181–1191. https://doi.org/10.1111/j.1365-2958.1993.tb01247.x
Niemirowicz G, Parussini F, Agüero F, Cazzulo JJ (2007) Two metallocarboxypeptidases from the protozoan Trypanosoma cruzi belong to the M32 family, found so far only in prokaryotes. Biochem J 401(2):399–410. https://doi.org/10.1042/BJ20060973
Patel J, Zhang Q, McKay RM, Vincent R, Xu Z (2010) Genetic engineering of Caulobacter crescentus for removal of cadmium from water. Appl Biochem Biotechnol 160(1):232–243. https://doi.org/10.1007/s12010-009-8540
Reisenauer A, Shapiro L (2002) DNA methylation affects the cell cycle transcription of the CtrA global regulator in Caulobacter. EMBO J 21(18):4969–4977. https://doi.org/10.1093/emboj/cdf490
Rodrigue A, Effantin G, Mandrand-Berthelot MA (2005) Identification of rcnA (yohM), a nickel and cobalt resistance gene in Escherichia coli. J Bacteriol 187(8):2912–2916. https://doi.org/10.1128/JB.187.8.2912-2916.2005
Ron E, Grossman N, Helmstetter CE (1977) Control of cell division in Escherichia coli: effect of amino acid starvation. J Bacteriol 129(2):569–573
Sato K, Okubo A, Yamazaki S (1998) Characterization of a multi-copper enzyme, nitrous oxide reductase, from Rhodobacter sphaeroides f. sp. denitrificans. J Biochem 124(1):51–54. https://doi.org/10.1093/oxfordjournals.jbchem.a022096
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9(7):676–682. https://doi.org/10.1038/nmeth.2019
Sharma SS, Dietz KJ (2005) The significance of amino acids and amino acid-derived molecules in plant responses and adaptation to heavy metal stress. J Exp Bot 57(4):711–726. https://doi.org/10.1093/jxb/erj073
Sharma SS, Dietz KJ (2009) The relationship between metal toxicity and cellular redox imbalance. Trends Plant Sci 14(1):43–50. https://doi.org/10.1016/j.tplants.2008.10.007
Singh S, Parihar P, Singh R, Singh VP, Prasad SM (2016) Heavy metal tolerance in plants: role of transcriptomics, proteomics, metabolomics, and ionomics. Front Plant Sci 6(1143). https://doi.org/10.3389/fpls.2015.01143
Siripornadulsil S, Traina S, Verma DP, Sayre RT (2002) Molecular mechanisms of proline-mediated tolerance to toxic heavy metals in transgenic microalgae. Plant Cell 14(11):2837–2847. https://doi.org/10.1105/tpc.004853
Stähler FN, Odenbreit S, Haas R, Wilrich J, Van Vliet AH, Kusters JG, Kist M, Bereswill S (2006) The novel Helicobacter pylori CznABC metal efflux pump is required for cadmium, zinc, and nickel resistance, urease modulation, and gastric colonization. Infect Immun 74(7):3845–3852. https://doi.org/10.1128/IAI.02025-05
Talanova V, Titov A, Boeva N (2000) Effect of increasing concentration of lead and cadmium on cucumber seedlings. Biol Plant 43(3):441–444. https://doi.org/10.1023/A:1026735603890
Tchounwou PB, Yedjou CG, Patlolla AK, Sutton DJ (2012) Heavy metals toxicity and the environment. EXS 101:133–164. https://doi.org/10.1007/978-3-7643-8340-4_6
Thanbichler M, Shapiro L (2006) MipZ, a spatial regulator coordinating chromosome segregation with cell division in Caulobacter. Cell 126(1):147–162. https://doi.org/10.1016/j.cell.2006.05.038
US EPA (2014) Priority Pollutant List. https://www.epa.gov/sites/production/files/2015-09/documents/priority-pollutant-list-epa.pdf
Viollier PH, Thanbichler M, McGrath PT, West L, Meewan M, McAdams HH, Shapiro L (2004) Rapid and sequential movement of individual chromosomal loci to specific subcellular locations during bacterial DNA replication. Proc Natl Acad Sci U S A 101(25):9257–9262
Wang M, Bai J, Chen WN, Ching CB (2010) Metabolomic profiling of cellular responses to carvedilol enantiomers in vascular smooth muscle cells. PLoS One 5(11):e15441. https://doi.org/10.1371/journal.pone.0015441
Xia J, Sinelnikov IV, Han B, Wishart DS (2015) MetaboAnalyst 3.0—making metabolomics more meaningful. Nucleic Acids Res 43(W1):W251–W257. https://doi.org/10.1093/nar/gkv380
Yusuf M, Fariduddin Q, Ahmad A (2002) 24-Epibrassinolide modulates growth, nodulation, antioxidant system, and osmolyte in tolerant and sensitive varieties of Vigna radiata under different levels of nickel: a shotgun approach. Plant Physiol Biochem 57:143–153. https://doi.org/10.1016/j.plaphy.2012.05.004
Yusuf M, Fariduddun Q, Hayat S, Ahmad A (2011) Nickel: an overview of uptake, essentiality and toxicity in plants. Bull Environ Contam Toxicol 86(1):1–17. https://doi.org/10.1007/s00128-010-0171-1
Zhou Y, Larson JD, Bottoms CA, Arturo EC, Henzl MT, Jenkins JL, Nix JC, Becker DF, Tanner JJ (2008) Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA. J Mol Biol 381(1):174–188. https://doi.org/10.1016/j.jmb.2008.05.084
Acknowledgements
The authors would like to thank the Nanyang Environment and Water Research Institute (NEWRI), Singapore, and the Interdisciplinary Graduate School (IGS), Nanyang Technological University, Singapore, for the award of research scholarship to Abhishek Jain and the support for this research. We would also like to thank Asst. Prof. M.H. Tan (Nanyang Technological University) for supplying us strains.
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare that they have no conflicts of interest.
Ethical approval
This article does not contain any studies with human participants or animals performed by any of the authors.
Electronic supplementary materials
ESM 1
(PDF 610 kb)
Rights and permissions
About this article
Cite this article
Jain, A., Chen, W.N. Involvement of organic acids and amino acids in ameliorating Ni(II) toxicity induced cell cycle dysregulation in Caulobacter crescentus: a metabolomics analysis. Appl Microbiol Biotechnol 102, 4563–4575 (2018). https://doi.org/10.1007/s00253-018-8938-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-018-8938-0