Links for Bioremediation Project

OmpX

1. Mecsas J, Welch R, Erickson JW, and Gross CA. Identification and characterization of an outer membrane protein, OmpX, in Escherichia coli that is homologous to a family of outer membrane proteins including Ail of Yersinia enterocolitica. J Bacteriol. 1995 Feb;177(3):799-804. DOI:10.1128/jb.177.3.799-804.1995 |

[OmpX sequence]

Sequence for CPX

• Total length is 558 bp + length of passenger peptide

1. Native SS - 69 bp

    MKKIACLSALAAVLAFTAGTSVA 

2. Embedded SfiI restriction site - 15 bp

    GQSGQ 

3. Passenger Peptide

    XXXXXXXXXXXXXX 

4. Sequence - 18 bp

    GGQSGQ  

5. S54-F148 - 285 bp

    SGDYNKNQYYGITAGPAYRINDWASIYGVVGVGYGKFQTTEYPTYKHDTSDYGFSYGAGLQFNPMENVALDFSYEQSRIRSVDVGTWIAGVGYRF 

6. Join native C and N - 12 bp

    GGSG 

7. A1-S53 - 159 bp

    ATSTVTGGYAQSDAQGQMNKMGGFNLKYRYEEDNSPLGVIGSFTYTEKSRTAS 

Papers!

2. Samuelson P, Wernérus H, Svedberg M, and Ståhl S. Staphylococcal surface display of metal-binding polyhistidyl peptides. Appl Environ Microbiol. 2000 Mar;66(3):1243-8. DOI:10.1128/AEM.66.3.1243-1248.2000 |
3. Kotrba P, Dolecková L, de Lorenzo V, and Ruml T. Enhanced bioaccumulation of heavy metal ions by bacterial cells due to surface display of short metal binding peptides. Appl Environ Microbiol. 1999 Mar;65(3):1092-8. DOI:10.1128/AEM.65.3.1092-1098.1999 |
4. Pazirandeh M, Wells BM, and Ryan RL. Development of bacterium-based heavy metal biosorbents: enhanced uptake of cadmium and mercury by Escherichia coli expressing a metal binding motif. Appl Environ Microbiol. 1998 Oct;64(10):4068-72. DOI:10.1128/AEM.64.10.4068-4072.1998 |
5. Guzman LM, Belin D, Carson MJ, and Beckwith J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol. 1995 Jul;177(14):4121-30. DOI:10.1128/jb.177.14.4121-4130.1995 |
6. Koebnik R, Locher KP, and Van Gelder P. Structure and function of bacterial outer membrane proteins: barrels in a nutshell. Mol Microbiol. 2000 Jul;37(2):239-53. DOI:10.1046/j.1365-2958.2000.01983.x |

OmpC

[OmpC Sequence]

7. Xu Z and Lee SY. Display of polyhistidine peptides on the Escherichia coli cell surface by using outer membrane protein C as an anchoring motif. Appl Environ Microbiol. 1999 Nov;65(11):5142-7. DOI:10.1128/AEM.65.11.5142-5147.1999 |

Heavy Metals

8. Silver S and Phung le T. A bacterial view of the periodic table: genes and proteins for toxic inorganic ions. J Ind Microbiol Biotechnol. 2005 Dec;32(11-12):587-605. DOI:10.1007/s10295-005-0019-6 |
9. Bruins MR, Kapil S, and Oehme FW. Microbial resistance to metals in the environment. Ecotoxicol Environ Saf. 2000 Mar;45(3):198-207. DOI:10.1006/eesa.1999.1860 |
10. Hou YM, Kim R, and Kim SH. Expression of the mouse metallothionein-I gene in Escherichia coli: increased tolerance to heavy metals. Biochim Biophys Acta. 1988 Nov 10;951(1):230-4. DOI:10.1016/0167-4781(88)90045-0 |
11. De Marco P, Pacheco CC, Figueiredo AR, and Moradas-Ferreira P. Novel pollutant-resistant methylotrophic bacteria for use in bioremediation. FEMS Microbiol Lett. 2004 May 1;234(1):75-80. DOI:10.1016/j.femsle.2004.03.010 |
12. Paul D, Pandey G, Pandey J, and Jain RK. Accessing microbial diversity for bioremediation and environmental restoration. Trends Biotechnol. 2005 Mar;23(3):135-42. DOI:10.1016/j.tibtech.2005.01.001 |
13. Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, Taghavi S, Dunn J, van der Lelie D, and Wattiez R. Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev. 2003 Jun;27(2-3):385-410. DOI:10.1016/S0168-6445(03)00045-7 |
14. Weinberg ED. Cellular regulation of iron assimilation. Q Rev Biol. 1989 Sep;64(3):261-90. DOI:10.1086/416359 |
15. Mizuno T, Usui K, Nishida S, Unno T, and Obata H. Investigation of the basis for Ni tolerance conferred by the expression of TjZnt1 and TjZnt2 in yeast strains. Plant Physiol Biochem. 2007 May;45(5):371-8. DOI:10.1016/j.plaphy.2007.03.019 |
16. Mehta SK and Gaur JP. Use of algae for removing heavy metal ions from wastewater: progress and prospects. Crit Rev Biotechnol. 2005 Jul-Sep;25(3):113-52. DOI:10.1080/07388550500248571 |
17. Muñoz R, Alvarez MT, Muñoz A, Terrazas E, Guieysse B, and Mattiasson B. Sequential removal of heavy metals ions and organic pollutants using an algal-bacterial consortium. Chemosphere. 2006 May;63(6):903-11. DOI:10.1016/j.chemosphere.2005.09.062 |

18. http://water.usgs.gov/wid/html/bioremed.html

19. Yang X, Feng Y, He Z, and Stoffella PJ. Molecular mechanisms of heavy metal hyperaccumulation and phytoremediation. J Trace Elem Med Biol. 2005;18(4):339-53. DOI:10.1016/j.jtemb.2005.02.007 |
20. Clemens S, Palmgren MG, and Krämer U. A long way ahead: understanding and engineering plant metal accumulation. Trends Plant Sci. 2002 Jul;7(7):309-15. DOI:10.1016/s1360-1385(02)02295-1 |
21. Tripathi RD, Srivastava S, Mishra S, Singh N, Tuli R, Gupta DK, and Maathuis FJ. Arsenic hazards: strategies for tolerance and remediation by plants. Trends Biotechnol. 2007 Apr;25(4):158-65. DOI:10.1016/j.tibtech.2007.02.003 |
22. Kamnev AA and van der Lelie D. Chemical and biological parameters as tools to evaluate and improve heavy metal phytoremediation. Biosci Rep. 2000 Aug;20(4):239-58. DOI:10.1023/a:1026436806319 |

Heavy Metals and E. coli

3. Kotrba P, Dolecková L, de Lorenzo V, and Ruml T. Enhanced bioaccumulation of heavy metal ions by bacterial cells due to surface display of short metal binding peptides. Appl Environ Microbiol. 1999 Mar;65(3):1092-8. DOI:10.1128/AEM.65.3.1092-1098.1999 |
23. Nakajima H, Kobayashi K, Kobayashi M, Asako H, and Aono R. Overexpression of the robA gene increases organic solvent tolerance and multiple antibiotic and heavy metal ion resistance in Escherichia coli. Appl Environ Microbiol. 1995 Jun;61(6):2302-7. DOI:10.1128/aem.61.6.2302-2307.1995 |

24. http://pubs.acs.org/cgi-bin/article.cgi/ancham/1998/70/i19/html/ac9803636.html

25. Mejáre M and Bülow L. Metal-binding proteins and peptides in bioremediation and phytoremediation of heavy metals. Trends Biotechnol. 2001 Feb;19(2):67-73. DOI:10.1016/s0167-7799(00)01534-1 |
26. Lu Y, Berry SM, and Pfister TD. Engineering novel metalloproteins: design of metal-binding sites into native protein scaffolds. Chem Rev. 2001 Oct;101(10):3047-80. DOI:10.1021/cr0000574 |
27. Bae W, Chen W, Mulchandani A, and Mehra RK. Enhanced bioaccumulation of heavy metals by bacterial cells displaying synthetic phytochelatins. Biotechnol Bioeng. 2000 Dec 5;70(5):518-24. DOI:10.1002/1097-0290(20001205)70:5<518::aid-bit6>3.0.co;2-5 |
28. Gutnick DL and Bach H. Engineering bacterial biopolymers for the biosorption of heavy metals; new products and novel formulations. Appl Microbiol Biotechnol. 2000 Oct;54(4):451-60. DOI:10.1007/s002530000438 |
29. Valls M and de Lorenzo V. Exploiting the genetic and biochemical capacities of bacteria for the remediation of heavy metal pollution. FEMS Microbiol Rev. 2002 Nov;26(4):327-38. DOI:10.1111/j.1574-6976.2002.tb00618.x |
30. Vivas A, Azcón R, Biró B, Barea JM, and Ruiz-Lozano JM. Influence of bacterial strains isolated from lead-polluted soil and their interactions with arbuscular mycorrhizae on the growth of Trifolium pratense L. under lead toxicity. Can J Microbiol. 2003 Oct;49(10):577-88. DOI:10.1139/w03-073 |
31. Wernérus H and Ståhl S. Biotechnological applications for surface-engineered bacteria. Biotechnol Appl Biochem. 2004 Dec;40(Pt 3):209-28. DOI:10.1042/BA20040014 |