IGEM:MIT/2007/Links for Bioremediation Project

Protein Surface Display

1. 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 |

OmpX

2. 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 |

3. http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=559693

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 

OmpC

4. 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 |

5. http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=15832358 OmpC Sequence

Sticky Peptides

Polysterene

Kenan

• Strong Binders >150
  • 17 FFPSSWYSHLGVL
  • 18 FFSFFFPASAWGS

Menendez

• YTGWETWYSFDPFTHYGGPGSRFDFVHDKSEDPIDRSY [6]
• QDLDHWSYWSMYSTYPTSPGLVPYSWGYGSPNSHTDKL
• PWWWVSWVDAGGGSLALPTQPSD
• WGWPTWWGWTGGDARHPSAPEAH
• WWDPDIWFGWGGAHPPNLIQPIS
• GWQSGWEWWIGGGNWTSNTTH
• IYYPFFVWGNYANGGLLSPGHVYSSNFIPLYMQREVSP
• SSRLAYDHYFPSWRSYIFPGSNSSYYNNSWPTITMETN
• RPYLYDPNEWHRYYSYLLPGHSYNVQSWPDGLGKSASR
• LGFSGWYWQGLYGLGSHDPGFIHEQSPAEVAMEDTEQS
• QTLIDFHDLHYWGAYYGWPGIYDAESGSQAVRHNMTHT
• DSWPLRIYSGLSNYYHYFPGSLVYNMMYPSLSRLPKGD
• HHGAMNRYYTWLWDNSRFPGRSYLLSAPATQPEASISQ
• TYDYTYDWSGLFWSPFTHPGAHMTTHSPWAGHKPHAET
• EIHGNLYNWSPLLGYSYFPGISPKHISGEVPPRPSTKV
• PYWMFYGFDWRGGFPPSHQIMDQ
• WMQSWYYHWGGGETFPIRRDSGG

---

• SRTWVLWIRY [7]
• LSAWARWGSS
• SRGFWLVWEQ
• TWTLWFASMS
• VDWVGWGASW
• WVEWRRGWLS
• PWNAWGRTWV
• GGWAMWGRVW
• WMRWGRSWGR
• GSWKEWGGAW
• SAWVRWGRVW
• WSAWVGDWAL
• GVIHWRAWGGDW
• LNWRGGWNWF
• WRLGFARWIG
• WGYVFHGWNL
• CCWGYGGSLV
• VYRVIWFVGR
• FHAFHAWSAA
• GSVWWQAHVDR
• LWGGLYGIWM
• MWGMHWAEGW
• FLPYARWFSR
• VIYYFLVMFM
• VCFVMFSMCR
• RPVAGDHPGS

---

• FHENWPS

---

• FHWTWYW

---

• WHRWPWLVSG
• WHWWYWALDR

---

• APFYYSWFPSYMAEGLPSPSPLDPVQDNLY

• Notes:
  • Fixed residues at the N and C terminus of the peptides are not shown, fixed amino acids within the sequences are double-underlined.
  • Unpublished results, plate binding confirmed by ELISA.

Bibliography

6. Adey NB, Mataragnon AH, Rider JE, Carter JM, and Kay BK. Characterization of phage that bind plastic from phage-displayed random peptide libraries. Gene. 1995 Apr 14;156(1):27-31. DOI:10.1016/0378-1119(95)00058-e |
7. Gebhardt K, Lauvrak V, Babaie E, Eijsink V, and Lindqvist BH. Adhesive peptides selected by phage display: characterization, applications and similarities with fibrinogen. Pept Res. 1996 Nov-Dec;9(6):269-78.
8. Kenan DJ, Walsh EB, Meyers SR, O'Toole GA, Carruthers EG, Lee WK, Zauscher S, Prata CA, and Grinstaff MW. Peptide-PEG amphiphiles as cytophobic coatings for mammalian and bacterial cells. Chem Biol. 2006 Jul;13(7):695-700. DOI:10.1016/j.chembiol.2006.06.013 |
9. Menendez A and Scott JK. The nature of target-unrelated peptides recovered in the screening of phage-displayed random peptide libraries with antibodies. Anal Biochem. 2005 Jan 15;336(2):145-57. DOI:10.1016/j.ab.2004.09.048 |

Polypyrrole

T59: THRTSTLDYFVI

[10]

10. Sanghvi AB, Miller KP, Belcher AM, and Schmidt CE. Biomaterials functionalization using a novel peptide that selectively binds to a conducting polymer. Nat Mater. 2005 Jun;4(6):496-502. DOI:10.1038/nmat1397 |

Bioremediation Papers

Toxicity of Heavy Metals

11. 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 |

Cadmium

• Summary: Cd causes damage to cells primarily by the generation of reactive oxygen species (ROS), which causes single-strand DNA damage and disrupts the synthesis of nucleic acids and proteins. Cd is also an inhibitor of the DNA mismatch repair system…Results of this study confirmed that Cd toxicity caused profound changes in gene expression in which several stress response systems were induced simultaneously.

12. Wang PZ and Novick RP. Nucleotide sequence and expression of the beta-lactamase gene from Staphylococcus aureus plasmid pI258 in Escherichia coli, Bacillus subtilis, and Staphylococcus aureus. J Bacteriol. 1987 Apr;169(4):1763-6. DOI:10.1128/jb.169.4.1763-1766.1987 |

[1]

Heavy Metal Resistance Techniques

13. 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 |
14. 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 |

Heavy Metal Binding Proteins/Peptides

15. 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 |
16. 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 |
17. 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 |
18. 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 |
19. 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 |
20. 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 |

Pumps

• Cadmium(Plasmid pI258 (from S.aureus) cadmium resistance (cadA) gene, complete cds) [12]
• ZntA(Divalent Metal Transporter)

21. Dutta SJ, Liu J, Stemmler AJ, and Mitra B. Conservative and nonconservative mutations of the transmembrane CPC motif in ZntA: effect on metal selectivity and activity. Biochemistry. 2007 Mar 27;46(12):3692-703. DOI:10.1021/bi0616394 |
22. Okkeri J and Haltia T. The metal-binding sites of the zinc-transporting P-type ATPase of Escherichia coli. Lys693 and Asp714 in the seventh and eighth transmembrane segments of ZntA contribute to the coupling of metal binding and ATPase activity. Biochim Biophys Acta. 2006 Nov;1757(11):1485-95. DOI:10.1016/j.bbabio.2006.06.008 |
23. Hou Z and Mitra B. The metal specificity and selectivity of ZntA from Escherichia coli using the acylphosphate intermediate. J Biol Chem. 2003 Aug 1;278(31):28455-61. DOI:10.1074/jbc.M301415200 |
24. Sharma R, Rensing C, Rosen BP, and Mitra B. The ATP hydrolytic activity of purified ZntA, a Pb(II)/Cd(II)/Zn(II)-translocating ATPase from Escherichia coli. J Biol Chem. 2000 Feb 11;275(6):3873-8. DOI:10.1074/jbc.275.6.3873 |

Promoters

• Cadmium(pCN39, a derivative of pCN37 with a temperature-sensitive replicon)

[25]

1. [Two Good Cadmium Promoters]

• Mercury (Pmer)

26. =

    • Mercury [1]

    Miscellaneous

    • Arabinose PBAD Promoter[1]

    <biblio>

27. 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 |

Outer Membrane Proteins

• OmpA, OmpB, OmpC Surface proteins[28]

28. 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 |

Heavy Metals

Review articles

29. 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 |
30. 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 |

Other Bacteria

31. 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 |
32. 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 |
33. 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 |
34. 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 |

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

Phytoremediation

36. 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 |
37. Lefkowitz RJ. Identification of adenylate cyclase-coupled beta-adrenergic receptors with radiolabeled beta-adrenergic antagonists. Biochem Pharmacol. 1975 Sep 15;24(18):1651-8. DOI:10.1016/0006-2952(75)90001-5 |

Heavy Metal Absorption in Plants and Soil

38. 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 |
39. 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 |
40. 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 |
41. 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 |

Heavy Metals and E. coli

Heavy Metal Resistance

42. 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 |

Biosensors

1. Paul05 pmid=15734556

• Using overexpression and purification of proteins for biosensor

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

Absorption of Heavy Metals

41. 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 |
45. Weinberg ED. Cellular regulation of iron assimilation. Q Rev Biol. 1989 Sep;64(3):261-90. DOI:10.1086/416359 |