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3 Biotech

, 9:120 | Cite as

Complete genome sequence of Raoultella sp. strain X13, a promising cell factory for the synthesis of CdS quantum dots

  • Shaozu Xu
  • Xuesong Luo
  • Yonghui Xing
  • Song Liu
  • Qiaoyun Huang
  • Wenli ChenEmail author
Genome Reports
  • 106 Downloads

Abstract

A novel cadmium-resistant bacterium, Raoultella sp. strain X13, recently isolated from heavy metal-contaminated soil, and this strain can synthesize CdS quantum dots using cadmium nitrate [Cd(NO4)2] and l-cysteine. Biomineralization of CdS by strain X13 can efficiently remove cadmium from aqueous solution. To illuminate the molecular mechanisms for the biosynthesis of CdS nanoparticle, the complete genome of Raoultella sp. strain X13 was sequenced. The whole genome sequence comprises a circular chromosome and a circular plasmid. Cysteine desulfhydrase smCSE has been previously found to be associated with the synthesis of CdS quantum dots. Bioinformatics analysis indicated that the genome of Raoultella sp. strain X13 encodes five putative cysteine desulfhydrases and all of them are located in the chromosome. The genome information may help us to determine the molecular mechanisms of the synthesis of CdS quantum dots and potentially enable us to engineer this microorganism for applications in biotechnology.

Keywords

Raoultella sp. strain X13 Genome sequence CdS Cysteine desulfhydrase 

Notes

Acknowledgements

The research was financially supported by The National Key Research and Development Program of China (2017YFA0605001 and 2016YFD0800206) and The Technical Innovation Major Projects of Hubei Province (2018ABA092).

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Supplementary material

13205_2019_1649_MOESM1_ESM.doc (442 kb)
Supplementary material 1 (DOC 442 KB)

References

  1. Alivisatos AP, Gu W, Larabell C (2005) Quantum dots as cellular probes. Ann Rev Biomed Eng 7:55–76CrossRefGoogle Scholar
  2. Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29:2607–2618CrossRefGoogle Scholar
  3. Chu L, Ebersole JL, Kurzban GP, Holt SC (1997) Cystalysin, a 46-kilodalton cysteine desulfhydrase from Treponema denticola, with hemolytic and hemoxidative activities. Infect Immun 65:3231–3238PubMedPubMedCentralGoogle Scholar
  4. Crouse D, Crouse M (2006) Design and numerical modeling of normal-oriented quantum wire infrared photodetector array. Infrared Phys Technol 48:227–234CrossRefGoogle Scholar
  5. Cunningham DP, Lundie LL (1993) Precipitation of cadmium by Clostridium thermoaceticum. Appl Environ Microbiol 59:7–14PubMedPubMedCentralGoogle Scholar
  6. Drancourt M, Bollet C, Carta A, Roussselier P (2001) Phylogenetic analyses of Klebsiella species delineate Klebsiella and Raoultella gen. nov., with description of Raoultella ornithinolytica comb. nov., Raoultella terrigena comb. nov. and Raoultella planticola comb. nov. Int J Syst Evol Microbiol 51:925–932CrossRefGoogle Scholar
  7. Dunleavy R, Lu L, Kiely CJ, Mcintosh S, Berger BW (2016) Single-enzyme biomineralization of cadmium sulfide nanocrystals with controlled optical properties. Proc Natl Acad Sci USA 113:5275–5280CrossRefGoogle Scholar
  8. Edwards CD, Beatty JC, Loiselle JB, Vlassov KA, Lefebvre DD (2013) Aerobic transformation of cadmium through metal sulfide biosynthesis in photosynthetic microorganisms. BMC Microbiol 13:1–11CrossRefGoogle Scholar
  9. Fukamachi H, Nakano Y, Yoshimura M, Koga T (2002) Cloning and characterization of the l -cysteine desulfhydrase gene of Fusobacterium nucleatum. FEMS Microbiol Lett 215:75–80PubMedGoogle Scholar
  10. Gallardo C, Monras JP, Plaza DO, Collao B, Saona LA, Duran-Toro V, Venegas FA, Soto C, Ulloa G, Vasquez CC (2014) Low-temperature biosynthesis of fluorescent semiconductor nanoparticles (CdS) by oxidative stress resistant Antarctic bacteria. J Biotechnol 187:108–115CrossRefGoogle Scholar
  11. Ionov L, Sapra S, Synytska A, Rogach AL, Stamm M, Diez S (2010) Fast and spatially resolved environmental probing using stimuli-responsive polymer layers and fluorescent nanocrystals. Adv Mater 18:1453–1457CrossRefGoogle Scholar
  12. Kim T, Cho S, Han M, Lee WS, Lee M, Um J, Seo Y JH (2017) High production of 2,3-butanediol from glycerol without 1,3-propanediol formation by Raoultella ornithinolytica B6. Appl Microbiol Biotechnol 101:2821–2830CrossRefGoogle Scholar
  13. Klein DL, Roth RA, Lim KL, Alivisatos AP, Mceuen PL (1997) A single-electron transistor made from a cadmium selenide nanocrystal. Nature 389:699–701CrossRefGoogle Scholar
  14. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones SJ, Marra MA (2009) Circos: an information aesthetic for comparative genomics. Genome Res 19:1639–1645CrossRefGoogle Scholar
  15. Lagesen K, Hallin Rodland PE, Staerfeldt H, Rognes T, Ussery D (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108CrossRefGoogle Scholar
  16. Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, Li Y, Li S, Shan G, Kristiansen K (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20:265–272CrossRefGoogle Scholar
  17. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964CrossRefGoogle Scholar
  18. Mandal S, Rautaray D, Sanyal A, Sastry M (2004) Synthesis and assembly of CdS nanoparticles in Keggin ion colloidal particles as templates. J Phys Chem B 108:7126–7131CrossRefGoogle Scholar
  19. Medintz IL, Uyeda HT, Goldman ER, Mattoussi H (2005) Quantum dot bioconjugates for imaging, labelling and sensing. Nat Mater 4:435–446CrossRefGoogle Scholar
  20. Nag A, Sapra S, Gupta SS, Prakash A, Ghangrekar A, Periasamy N, Sarma DD (2008) Luminescence in Mn-doped CdS nanocrystals. Bull Mater Sci 31:561–568CrossRefGoogle Scholar
  21. Nozik AJ, Beard MC, Luther JM, Law M, Ellingson RJ, Johnson JC (2010) Semiconductor quantum dots and quantum dot arrays and applications of multiple exciton generation to third-generation photovoltaic solar cells. Chem Rev 110:6873–6890CrossRefGoogle Scholar
  22. Ping L, Guo Q, Chen X, Yuan X, Zhang C, Zhao H (2017) Biodegradation of pyrene and benzo[a]pyrene in the liquid matrix and soil by a newly identified Raoultella planticola strain. 3 Biotech 7: 56CrossRefGoogle Scholar
  23. Sklodowska A, Mielnicki S, Drewniak L (2018) Raoultella sp. SM1, a novel iron-reducing and uranium-precipitating strain. Chemosphere 195:722–726CrossRefGoogle Scholar
  24. Wang CL, Lum AM, Ozuna SC, Clark DS, Keasling JD (2001) Aerobic sulfide production and cadmium precipitation by escherichia coli expressing the treponema denticola cysteine desulfhydrase gene. Appl Microbiol Biotechnol 56:425–430CrossRefGoogle Scholar
  25. Yang C, Zhou X, Wang L, Tian X, Wang Y, Pi Z (2009) Preparation and tunable photoluminescence of alloyed CdS × Se 1 − × nanorods. J Mater Sci 44:3015–3019CrossRefGoogle Scholar
  26. Yang Z, Lu L, Berard VF, He Q, Kiely C, Berger BW, Mcintosh S (2015) Biomanufacturing of CdS quantum dots. Green Chem 17:3775–3782CrossRefGoogle Scholar
  27. Yano T, Fukamachi H, Yamamoto M, Igarashi T (2009) Characterization of l-cysteine desulfhydrase from Prevotella intermedia. Oral Microbiol Immunol 24:485–492CrossRefGoogle Scholar
  28. Yoshida Y, Nakano Y, Amano A, Yoshimura M, Fukamachi H, Oho T, Koga T (2002) Icd from Streptococcus anginosus encodes a C–S lyase with alpha, beta-elimination activity that degrades l-cysteine. Microbiology 148:3961–3970CrossRefGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanChina
  2. 2.Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and EnvironmentHuazhong Agricultural UniversityWuhanChina

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