IGEM:MIT/2007/Links for Bioremediation Project

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Contents

Protein Surface Display

  1. Wernérus H and Ståhl S. . pmid:15035661. PubMed HubMed [Wernerus04]
  • OmpA, OmpB, OmpC Surface proteins
  1. Koebnik R, Locher KP, and Van Gelder P. . pmid:10931321. PubMed HubMed [koebnik00]

OmpX

  1. Mecsas J, Welch R, Erickson JW, and Gross CA. . pmid:7836315. PubMed 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. . pmid:10543834. PubMed 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. . pmid:7737512. PubMed HubMed [Adey95]
  2. Gebhardt K, Lauvrak V, Babaie E, Eijsink V, and Lindqvist BH. . pmid:9048419. PubMed HubMed [Gebhart96]
  3. Kenan DJ, Walsh EB, Meyers SR, O'Toole GA, Carruthers EG, Lee WK, Zauscher S, Prata CA, and Grinstaff MW. . pmid:16873017. PubMed HubMed [Kenan06]
  4. Menendez A and Scott JK. . pmid:15620878. PubMed HubMed [Menendez05]
All Medline abstracts: PubMed HubMed

Polypyrrole

T59: THRTSTLDYFVI
[11]
  1. Sanghvi AB, Miller KP, Belcher AM, and Schmidt CE. . pmid:15895095. PubMed HubMed [Sanhvi05]

pBAD Promoter Info

  • Arabinose PBAD Promoter[12]
  1. Guzman LM, Belin D, Carson MJ, and Beckwith J. . pmid:7608087. PubMed 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. . pmid:17326661. PubMed HubMed [Dutta07]
  2. Okkeri J and Haltia T. . pmid:16890908. PubMed HubMed [Okkeri06]
  3. Hou Z and Mitra B. . pmid:12746428. PubMed HubMed [Hou03]
  4. Sharma R, Rensing C, Rosen BP, and Mitra B. . pmid:10660539. PubMed 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. . pmid:12829276. PubMed HubMed [Mergeay03]
  2. Mizuno T, Usui K, Nishida S, Unno T, and Obata H. . pmid:17475501. PubMed HubMed [Mizuno07]
  3. Mehta SK and Gaur JP. . pmid:16294830. PubMed HubMed [Mehta05]
  4. Muñoz R, Alvarez MT, Muñoz A, Terrazas E, Guieysse B, and Mattiasson B. . pmid:16307789. PubMed 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. . pmid:16028496. PubMed HubMed [Yang05]
  2. Lefkowitz RJ. . pmid:11. PubMed 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. . pmid:15109722. PubMed HubMed [DeMarco04]
  2. Vivas A, Azcón R, Biró B, Barea JM, and Ruiz-Lozano JM. . pmid:14663492. PubMed HubMed [Vivas03]
  3. Clemens S, Palmgren MG, and Krämer U. . pmid:12119168. PubMed HubMed [Clemes02]
  4. Tripathi RD, Srivastava S, Mishra S, Singh N, Tuli R, Gupta DK, and Maathuis FJ. . pmid:17306392. PubMed HubMed [Tripathi07]
  5. Tripathi RD, Srivastava S, Mishra S, Singh N, Tuli R, Gupta DK, and Maathuis FJ. . pmid:17306392. PubMed HubMed [Tripathi07]
  6. Gutnick DL and Bach H. . pmid:11092618. PubMed HubMed [ick00]
  7. Weinberg ED. . pmid:2530602. PubMed 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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