IGEM:MIT/2007/Links for Bioremediation Project: Difference between revisions

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==Sticky Peptides==
==Sticky Peptides==


===Polysterene===
===Polystyrene===


====Kenan====
====Kenan====
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</biblio>
</biblio>


==Bioremediation Papers==
==pBAD Promoter Info==
 
*Arabinose PBAD Promoter<cite>pBAD33</cite>
 
 
===Heavy Metal Resistance Techniques===
<biblio>
<biblio>
#Bruins00 pmid=10702338
#pBAD33 pmid=7608087
#Hou88 pmid=3056525
</biblio>
</biblio>


 
==Bioremediation Papers==


===Pumps===
===Pumps===
Line 137: Line 133:
#Sharma00 pmid=10660539
#Sharma00 pmid=10660539
</biblio>
</biblio>
===Sponges===
*Mercury [http://www.jstage.jst.go.jp/article/bbb/71/6/1494/_pdf]
==Miscellaneous==
*Arabinose PBAD Promoter<cite>pBAD33</cite>
<biblio>
#pBAD33 pmid=7608087
</biblio>


==Heavy Metals (non e.coli systems)==
==Heavy Metals (non e.coli systems)==

Latest revision as of 14:24, 31 July 2007

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 | PubMed ID:15035661 | HubMed [Wernerus04]
  • OmpA, OmpB, OmpC Surface proteins
  1. 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 | PubMed ID:10931321 | HubMed [koebnik00]

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 | PubMed ID:7836315 | HubMed [Mecsas95]

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

    [OmpX]

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

  1. 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 | PubMed ID:10543834 | HubMed [Xu99]

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

    [OmpC]

Sticky Peptides

Polystyrene

Kenan

  • Strong Binders >150
    • 17 FFPSSWYSHLGVL
    • 18 FFSFFFPASAWGS

Menendez

  • YTGWETWYSFDPFTHYGGPGSRFDFVHDKSEDPIDRSY [7]
  • QDLDHWSYWSMYSTYPTSPGLVPYSWGYGSPNSHTDKL
  • PWWWVSWVDAGGGSLALPTQPSD
  • WGWPTWWGWTGGDARHPSAPEAH
  • WWDPDIWFGWGGAHPPNLIQPIS
  • GWQSGWEWWIGGGNWTSNTTH
  • IYYPFFVWGNYANGGLLSPGHVYSSNFIPLYMQREVSP
  • SSRLAYDHYFPSWRSYIFPGSNSSYYNNSWPTITMETN
  • RPYLYDPNEWHRYYSYLLPGHSYNVQSWPDGLGKSASR
  • LGFSGWYWQGLYGLGSHDPGFIHEQSPAEVAMEDTEQS
  • QTLIDFHDLHYWGAYYGWPGIYDAESGSQAVRHNMTHT
  • DSWPLRIYSGLSNYYHYFPGSLVYNMMYPSLSRLPKGD
  • HHGAMNRYYTWLWDNSRFPGRSYLLSAPATQPEASISQ
  • TYDYTYDWSGLFWSPFTHPGAHMTTHSPWAGHKPHAET
  • EIHGNLYNWSPLLGYSYFPGISPKHISGEVPPRPSTKV
  • PYWMFYGFDWRGGFPPSHQIMDQ
  • WMQSWYYHWGGGETFPIRRDSGG
  • SRTWVLWIRY [8]
  • 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

  1. 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 | PubMed ID:7737512 | HubMed [Adey95]
  2. 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. PubMed ID:9048419 | HubMed [Gebhart96]
  3. 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 | PubMed ID:16873017 | HubMed [Kenan06]
  4. 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 | PubMed ID:15620878 | HubMed [Menendez05]

All Medline abstracts: PubMed | HubMed

Polypyrrole

T59: THRTSTLDYFVI

[11]

  1. 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 | PubMed ID:15895095 | HubMed [Sanhvi05]

pBAD Promoter Info

  • Arabinose PBAD Promoter[12]
  1. 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 | PubMed ID:7608087 | HubMed [pBAD33]

Bioremediation Papers

Pumps

  • Cadmium(Plasmid pI258 (from S.aureus) cadmium resistance (cadA) gene, complete cds) [13]
  • ZntA(Divalent Metal Transporter)
  1. 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 | PubMed ID:17326661 | HubMed [Dutta07]
  2. 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 | PubMed ID:16890908 | HubMed [Okkeri06]
  3. 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 | PubMed ID:12746428 | HubMed [Hou03]
  4. 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 | PubMed ID:10660539 | HubMed [Sharma00]

All Medline abstracts: PubMed | HubMed

Heavy Metals (non e.coli systems)

Other Bacteria

  1. 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 | PubMed ID:12829276 | HubMed [Mergeay03]
  2. 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 | PubMed ID:17475501 | HubMed [Mizuno07]
  3. 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 | PubMed ID:16294830 | HubMed [Mehta05]
  4. 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 | PubMed ID:16307789 | HubMed [Munoz06]

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

    [USGS]

All Medline abstracts: PubMed | HubMed

Phytoremediation

  1. 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 | PubMed ID:16028496 | HubMed [Yang05]
  2. 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 | PubMed ID:11 | HubMed [Kamnev00]

All Medline abstracts: PubMed | HubMed


Heavy Metal Absorption in Plants and Soil

  1. 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 | PubMed ID:15109722 | HubMed [DeMarco04]
  2. 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 | PubMed ID:14663492 | HubMed [Vivas03]
  3. 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 | PubMed ID:12119168 | HubMed [Clemes02]
  4. 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 | PubMed ID:17306392 | HubMed [Tripathi07]
  5. 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 | PubMed ID:17306392 | HubMed [Tripathi07]
  6. 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 | PubMed ID:11092618 | HubMed [ick00]
  7. Weinberg ED. Cellular regulation of iron assimilation. Q Rev Biol. 1989 Sep;64(3):261-90. DOI:10.1086/416359 | PubMed ID:2530602 | HubMed [Weinberg89]

All Medline abstracts: PubMed | HubMed

Biosensors

  1. Paul05 pmid=15734556
  • Using overexpression and purification of proteins for biosensor

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

    [Bontidean98]
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