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Plant and Soil

, Volume 426, Issue 1–2, pp 365–381 | Cite as

Genome-wide analysis and expression profiling of the HMA gene family in Brassica napus under cd stress

  • Nannan Li
  • Hua Xiao
  • Juanjuan Sun
  • Shufeng Wang
  • Jingchao Wang
  • Peng Chang
  • Xinbin Zhou
  • Bo Lei
  • Kun Lu
  • Feng Luo
  • Xiaojun Shi
  • Jiana Li
Regular Article
  • 408 Downloads

Abstract

Background and aims

Brassica napus (B. napus), one of the most important oil crop species, is highly tolerant to and accumulates high amounts of cadmium (Cd). Many iron transporters in plants have been identified to be Cd transporters. For example, some members of the heavy metal P1B-ATPase transporter family are responsible for Cd translocation in various plant species and play a vital role in Cd detoxification. However, the Cd translocation mechanism in B. napus and the characterization of the heavy metal ATPase (HMA) in B. napus remain unknown.

Methods

B. napus plants were treated with 50 μM or 200 μM Cd in soil for 30 days during the initial flowering stage. The dry weight of the plants and the Cd contents within their various tissues were then measured, after which the RNA in the leaves was extracted for transcriptomic analysis and subsequent quantitative real-time PCR (qRT-PCR) assays. After all the significantly regulated iron transporters were screened in response to Cd stress, the BnHMA gene family was identified and shown to link BnHMA genes with Cd translocation in the leaves of B. napus.

Results

The transcriptomic analysis of B. napus leaves in response to Cd treatment revealed that several HMA genes (BnHMA2;2, BnHMA2;3 and BnHMA2;5) respond to Cd stress. We further examined the whole HMA family in B. napus; 31 BnHMA genes were subsequently identified. Their expression levels in different tissues and stages as well as their phylogenetic tree, gene structure, chromosomal location, conserved motifs, 3D models and subcellular localization were analyzed. The results showed that these HMA genes exhibit typical characteristics of HMA genes. In addition, the qRT-PCR results showed that the BnHMA2;3 expression levels in the B. napus plants treated with 50 μM or 200 μM Cd were seven- and ninefold greater than those under Cd-free conditions, respectively. Additional yeast experiment assays verified that BnHMA2;3 can transport Cd.

Conclusion

BnHMA2;3 may play an important role in Cd translocation in the leaves of B. napus. The results of this study may provide direction and useful information for increased understanding of the Cd stress-response mechanism.

Keywords

Cadmium Heavy metal ATPase Metal transporter Brassica napus 

Abbreviations

HMA

P1B-ATPase

B. napus

Brassica napus

ZS11

Zhongshuang

Cd

Cadmium

Zn

Zinc

Cu

Copper

Fe

Iron

NJ

Neighbor-joining

DEGs

Differentially expressed genes

GO

Gene Ontology

Notes

Funding information

This work was supported by National Key R & D Program of China (2017YFD0200200- 2017YFD0200208),the National Natural Foundation of China (31,400,063; C150705) and Fundamental Research Funds for the Central Universities (XDJK2017B030; SWU116021)., Research Funds of Scientific Platform and Base Construction (cstc2014pt-sy0017), the Key Special Program of China National Tobacco Corporation (TS-02–20,110,014), the Key Laboratory Program of China National Tobacco Corporation (110201603009) and The Recruitment Program for Foreign Experts (No. WQ20125500073).

Compliance with ethical standards

Competing financial interests

The authors declare no competing financial interests.

Supplementary material

11104_2018_3637_MOESM1_ESM.docx (2.2 mb)
ESM 1 (DOCX 2228 kb)

References

  1. Argüello JM (2003) Identification of ion-selectivity determinants in heavy-metal transport P 1B -type ATPases. J Membr Biol 195:93–108.  https://doi.org/10.1007/s00232-003-2048-2 CrossRefPubMedGoogle Scholar
  2. Argüello JM, Eren E, Gonzálezguerrero M (2007) The structure and function of heavy metal transport P1B-ATPases. Biometals 20:233–248CrossRefPubMedGoogle Scholar
  3. Axelsen KB, Palmgren MG (2001) Inventory of the superfamily of P-type ion pumps in Arabidopsis. Plant Physiol 126:696–706CrossRefPubMedPubMedCentralGoogle Scholar
  4. Bailey TL, Williams N, Misleh C, Li WW (2006) MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 34:W369–W373CrossRefPubMedPubMedCentralGoogle Scholar
  5. Briesemeister S, Rahnenführer J, Kohlbacher O (2010a) Going from where to why—interpretable prediction of protein subcellular localization. Bioinformatics 26:1232–1238CrossRefPubMedPubMedCentralGoogle Scholar
  6. Briesemeister S, Rahnenführer J, Kohlbacher O (2010b) YLoc—an interpretable web server for predicting subcellular localization. Nucleic Acids Res 38:W497–W502.  https://doi.org/10.1093/nar/gkq477 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Chalhoub B, Denoeud F, Liu S, Parkin IA, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Correa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VH, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CH, Wang X, Canaguier A, Chauveau A, Berard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang X, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P (2014) Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome Science 345: 950–953.  https://doi.org/10.1126/science.1253435.
  8. Cheng F, Mandakova T, Wu J, Xie Q, Lysak MA, Wang X (2013) Deciphering the diploid ancestral genome of the Mesohexaploid Brassica rapa. Plant Cell 25:1541–1554.  https://doi.org/10.1105/tpc.113.110486 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Chiang HC, Jingchi Lo A, Yeh KC (2006) Genes associated with heavy metal tolerance and accumulation in Zn/cd Hyperaccumulator Arabidopsis halleri: a genomic survey with cDNA microarray. Environ Sci Technol 40:6792–6798CrossRefPubMedGoogle Scholar
  10. Choppala G, Saifullah, Bolan N, Bibi S, Iqbal M, Rengel Z, Kunhikrishnan A, Ashwath N, Ok YS (2014) Cellular mechanisms in higher plants governing tolerance to cadmium toxicity. Crit Rev Plant Sci 33:374–391.  https://doi.org/10.1080/07352689.2014.903747 CrossRefGoogle Scholar
  11. Cohen CK, Garvin DF, Kochian LV (2004) Kinetic properties of a micronutrient transporter from Pisum sativum indicate a primary function in Fe uptake from the soil. Planta 218:784–792.  https://doi.org/10.1007/s00425-003-1156-7 CrossRefPubMedGoogle Scholar
  12. Connolly EL (2002) Expression of the IRT1 metal transporter is controlled by metals at the levels of transcript and protein accumulation. The Plant Cell Online 14:1347–1357.  https://doi.org/10.1105/tpc.001263 CrossRefGoogle Scholar
  13. Deng F, Yamaji N, Xia J, Ma JF (2013) A member of the heavy metal P-type ATPase OsHMA5 is involved in xylem loading of copper in rice. Plant Physiol 163:1353–1362.  https://doi.org/10.1104/pp.113.226225 CrossRefPubMedPubMedCentralGoogle Scholar
  14. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P (2002) Systematic identification of novel protein domain families associated with nuclear functions. Genome Res 12:47–56CrossRefPubMedPubMedCentralGoogle Scholar
  15. Eckhardt U, Mas MA, Buckhout TJ (2001) Two iron-regulated cation transporters from tomato complement metal uptake-deficient yeast mutants. Plant Mol Biol 45:437–448CrossRefPubMedGoogle Scholar
  16. Ferreyroa GV, Lagorio MG, Trinelli MA, Lavado RS, Molina FV (2017) Lead effects on Brassica napus photosynthetic organs. Ecotoxicol Environ Saf 140:123–130.  https://doi.org/10.1016/j.ecoenv.2017.02.031 CrossRefPubMedGoogle Scholar
  17. Gallego SM, Pena LB, Barcia RA, Azpilicueta CE, Iannone MF, Rosales EP, Zawoznik MS, Groppa MD, Benavides MP (2012) Unravelling cadmium toxicity and tolerance in plants: insight into regulatory mechanisms. Environ Exp Bot 83:33–46.  https://doi.org/10.1016/j.envexpbot.2012.04.006 CrossRefGoogle Scholar
  18. Hanikenne M, Talke IN, Haydon MJ, Lanz C, Nolte A, Motte P, Kroymann J, Weigel D, Krämer U (2008) Evolution of metal hyperaccumulation required cis-regulatory changes and triplication of HMA4. Nature 453:391–395.  https://doi.org/10.1038/nature06877 CrossRefPubMedGoogle Scholar
  19. Hermand V, Julio E, Dorlhac de Borne F, Punshon T, Ricachenevsky FK, Bellec A, Gosti F, Berthomieu P (2014) Inactivation of two newly identified tobacco heavy metal ATPases leads to reduced Zn and cd accumulation in shoots and reduced pollen germination. Metallomics : integrated biometal science 6:1427–1440.  https://doi.org/10.1039/c4mt00071d. CrossRefGoogle Scholar
  20. Hoglund A, Donnes P, Blum T, Adolph HW, Kohlbacher O (2006) MultiLoc: prediction of protein subcellular localization using N-terminal targeting sequences, sequence motifs and amino acid composition. Bioinformatics 22:1158–1165.  https://doi.org/10.1093/bioinformatics/btl002 CrossRefPubMedGoogle Scholar
  21. Horton P, Park K, Obayashi T, Nakai K (2006) Protein subcellular localization prediction with wolf PSORT. Asia-Pacific bioinformatics conference 13–16 February. Taipei, Taiwan, p 2006Google Scholar
  22. Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G (2015) GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics 31:1296–1297.  https://doi.org/10.1093/bioinformatics/btu817 CrossRefPubMedGoogle Scholar
  23. Ishimaru Y, Takahashi R, Bashir K, Shimo H, Senoura T, Sugimoto K, Ono K, Yano M, Ishikawa S, Arao T, Nakanishi H, Nishizawa NK (2012) Characterizing the role of rice NRAMP5 in manganese, Iron and cadmium transport. Sci Rep 2:286.  https://doi.org/10.1038/srep00286 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Jian H, Lu K, Yang B, Wang T, Zhang L, Zhang A, Wang J, Liu L, Qu C, Li J (2016) Genome-wide analysis and expression profiling of the SUC and SWEET gene families of sucrose transporters in oilseed rape (Brassica napus L.) Front Plant Sci 7.  https://doi.org/10.3389/fpls.2016.01464
  25. Jones P, Binns D, Chang HY, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong SY, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30:1236–1240.  https://doi.org/10.1093/bioinformatics/btu031 CrossRefPubMedPubMedCentralGoogle Scholar
  26. Kaundal R, Saini R, Zhao PX (2010) Combining machine learning and homology-based approaches to accurately predict subcellular localization in Arabidopsis. Plant Physiol 154:36–54.  https://doi.org/10.1104/pp.110.156851 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Korenkov V, King B, Hirschi K, Wagner GJ (2009) Root-selective expression of AtCAX4 and AtCAX2 results in reduced lamina cadmium in field-grown Nicotiana tabacum L. Plant Biotechnol J 7:219–226.  https://doi.org/10.1111/j.1467-7652.2008.00390.x CrossRefPubMedGoogle Scholar
  28. Lamesch P, Berardini TZ, Li D, Swarbreck D, Wilks C, Sasidharan R, Muller R, Dreher K, Alexander DL, Garcia-Hernandez M, Karthikeyan AS, Lee CH, Nelson WD, Ploetz L, Singh S, Wensel A, Huala E (2012) The Arabidopsis information resource (TAIR): improved gene annotation and new tools. Nucleic Acids Res 40:D1202–D1210.  https://doi.org/10.1093/nar/gkr1090 CrossRefPubMedGoogle Scholar
  29. Lee S, Kim YY, Lee Y, An G (2007) Rice P1B-type heavy-metal ATPase, OsHMA9, is a metal efflux protein. Plant Physiol 145:831–842.  https://doi.org/10.1104/pp.107.102236 CrossRefPubMedPubMedCentralGoogle Scholar
  30. Li D, Xu X, Hu X, Liu Q, Wang Z, Zhang H, Wang H, Wei M, Wang H, Liu H, Li C (2015) Genome-wide analysis and heavy metal-induced expression profiling of the HMA gene family in Populus trichocarpa. Front Plant Sci 6:1149.  https://doi.org/10.3389/fpls.2015.01149 PubMedPubMedCentralGoogle Scholar
  31. Ma JF, Ueno D, Zhao FJ, McGrath SP (2005) Subcellular localisation of cd and Zn in the leaves of a cd-hyperaccumulating ecotype of Thlaspi caerulescens. Planta 220:731–736.  https://doi.org/10.1007/s00425-004-1392-5 CrossRefPubMedGoogle Scholar
  32. Morel M, Crouzet J, Gravot A, Auroy P, Leonhard N, Vavasseur A, Richaud P (2009) AtHMA3, a P1B-ATPase allowing cd/Zn/co/Pb vacuolar storage in Arabidopsis. Plant Physiol 149:894–904CrossRefPubMedPubMedCentralGoogle Scholar
  33. Mwamba TM, Li L, Gill RA, Islam F, Nawaz A, Ali B, Farooq MA, Lwalaba JL, Zhou W (2016) Differential subcellular distribution and chemical forms of cadmium and copper in Brassica napus. Ecotoxicol Environ Saf 134P1:239–249.  https://doi.org/10.1016/j.ecoenv.2016.08.021 CrossRefPubMedGoogle Scholar
  34. Palmgren M (1999) Pumping with plant P-type ATPases. J Exp Bot 50:883–893.  https://doi.org/10.1093/jexbot/50.suppl_1.883 CrossRefGoogle Scholar
  35. Pierleoni A, Martelli PL, Fariselli P, Casadio R (2006) BaCelLo: a balanced subcellular localization predictor. Bioinformatics 22:e408–e416.  https://doi.org/10.1093/bioinformatics/btl222 CrossRefPubMedGoogle Scholar
  36. Qiu RL, Tang YT, Fang XH, Chaney RL, Yin-Ming LI, Scott AJ, Liu W, Zeng XW (2004) Phytoremediation of heavy metal contaminated soil and its mechanism. Acta Scientiarum Naturalium Universitatis SunyatseniGoogle Scholar
  37. Rascio N, Navari-Izzo F (2011) Heavy metal hyperaccumulating plants: how and why do they do it? And what makes them so interesting? Plant science : an international journal of experimental plant biology 180:169–181.  https://doi.org/10.1016/j.plantsci.2010.08.016. CrossRefGoogle Scholar
  38. Sasaki A, Yamaji N, Yokosho K, Ma JF (2012) Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice. Plant Cell 24:2155–2167.  https://doi.org/10.1105/tpc.112.096925 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Selvam A, Wong JW-C (2009) Cadmium uptake potential of Brassica napus cocropped with Brassica parachinensis and Zea mays. J Hazard Mater 167:170–178.  https://doi.org/10.1016/j.jhazmat.2008.12.103 CrossRefPubMedGoogle Scholar
  40. Siemianowski O, Barabasz A, Kendziorek M, Ruszczynska A, Bulska E, Williams LE, Antosiewicz DM (2014) HMA4 expression in tobacco reduces cd accumulation due to the induction of the apoplastic barrier. J Exp Bot 65:1125–1139.  https://doi.org/10.1093/jxb/ert471 CrossRefPubMedPubMedCentralGoogle Scholar
  41. Smith AT, Smith KP, Rosenzweig AC (2014) Diversity of the metal-transporting P1B-type ATPases. JBIC Journal of Biological Inorganic Chemistry 19:947–960.  https://doi.org/10.1007/s00775-014-1129-2 CrossRefPubMedGoogle Scholar
  42. Takahashi R, Ishimaru Y, Shimo H, Ogo Y, Senoura T, Nishizawa NK, Nakanishi H (2012) The OsHMA2 transporter is involved in root-to-shoot translocation of Zn and cd in rice. Plant Cell Environ 35:1948–1957.  https://doi.org/10.1111/j.1365-3040.2012.02527.x CrossRefPubMedGoogle Scholar
  43. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599.  https://doi.org/10.1093/molbev/msm092 CrossRefPubMedGoogle Scholar
  44. Thomine S, Wang R, Ward JM, Crawford NM, Schroeder JI (2000) Cadmium and iron transport by members of a plant metal transporter family in Arabidopsis with homology to Nramp genes. Proc Natl Acad Sci U S A 97:4991–4996CrossRefPubMedPubMedCentralGoogle Scholar
  45. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515.  https://doi.org/10.1038/nbt.1621 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Waalkes MP (2000) Cadmium carcinogenesis in review. J Inorg Biochem 79:241–244CrossRefPubMedGoogle Scholar
  47. Wang L, Feng Z, Wang X, Wang X, Zhang X (2010) DEGseq: an R package for identifying differentially expressed genes from RNA-seq data. Bioinformatics 26:136–138.  https://doi.org/10.1093/bioinformatics/btp612 CrossRefPubMedGoogle Scholar
  48. Williams LE, Mills RF (2005) P(1B)-ATPases--an ancient family of transition metal pumps with diverse functions in plants. Trends Plant Sci 10:491–502.  https://doi.org/10.1016/j.tplants.2005.08.008 CrossRefPubMedGoogle Scholar
  49. Wong CK, Cobbett CS (2009) HMA P-type ATPases are the major mechanism for root-to-shoot cd translocation in Arabidopsis thaliana. The New Phytologist 181:71–78.  https://doi.org/10.1111/j.1469-8137.2008.02638.x. CrossRefPubMedGoogle Scholar
  50. Wong CK, Jarvis RS, Sherson SM, Cobbett CS (2009) Functional analysis of the heavy metal binding domains of the Zn/cd-transporting ATPase, HMA2, in Arabidopsis thaliana. The New phytologist 181:79–88.  https://doi.org/10.1111/j.1469-8137.2008.02637.x CrossRefPubMedGoogle Scholar
  51. Xu G, Guo C, Shan H, Kong H (2012) Divergence of duplicate genes in exon-intron structure. Proc Natl Acad Sci U S A 109:1187–1192.  https://doi.org/10.1073/pnas.1109047109 CrossRefPubMedPubMedCentralGoogle Scholar
  52. Yamaji N, Xia J, Mitani-Ueno N, Yokosho K, Feng Ma J (2013) Preferential delivery of zinc to developing tissues in rice is mediated by P-type heavy metal ATPase OsHMA2. Plant Physiol 162:927–939.  https://doi.org/10.1104/pp.113.216564 CrossRefPubMedPubMedCentralGoogle Scholar
  53. Yang XE, Long XX, Ye HB, He ZL, Calvert DV, Stoffella PJ (2004) Cadmium tolerance and hyperaccumulation in a new Zn-hyperaccumulating plant species ( Sedum alfredii Hance). Plant Soil 259:181–189CrossRefGoogle Scholar
  54. Yu CS, Lin CJ, Hwang JK (2004) Predicting subcellular localization of proteins for gram-negative bacteria by support vector machines based on n-peptide compositions. Protein science : a publication of the Protein Society 13:1402–1406.  https://doi.org/10.1110/ps.03479604 CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Nannan Li
    • 1
    • 2
  • Hua Xiao
    • 1
  • Juanjuan Sun
    • 1
  • Shufeng Wang
    • 1
  • Jingchao Wang
    • 1
  • Peng Chang
    • 1
  • Xinbin Zhou
    • 1
  • Bo Lei
    • 3
  • Kun Lu
    • 2
    • 4
  • Feng Luo
    • 1
  • Xiaojun Shi
    • 1
  • Jiana Li
    • 2
    • 3
  1. 1.College of Resources and EnvironmentSouthwest UniversityChongqingPeople’s Republic of China
  2. 2.Southwest UniversityAcademy of Agricultural ScienceChongqingPeople’s Republic of China
  3. 3.Upland Flue-Cured Tobacco Quality and Ecology Key Laboratory of China TobaccoGuizhou Academy of Tobacco ScienceGuiyangChina
  4. 4.College of Agronomy and BiotechnologySouthwest UniversityChongqingPeople’s Republic of China

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