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

Polysterene

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]

Bioremediation Papers

Toxicity of Heavy Metals

  1. Silver S and Phung le T. . pmid:16133099. PubMed HubMed [Silver05]


Heavy Metal Resistance Techniques

  1. Bruins MR, Kapil S, and Oehme FW. . pmid:10702338. PubMed HubMed [Bruins00]
  2. Hou YM, Kim R, and Kim SH. . pmid:3056525. PubMed HubMed [Hou88]
All Medline abstracts: PubMed HubMed

Heavy Metal Binding Proteins/Peptides

  1. Samuelson P, Wernérus H, Svedberg M, and Ståhl S. . pmid:10698802. PubMed HubMed [Samuelson00]
  2. Pazirandeh M, Wells BM, and Ryan RL. . pmid:9758845. PubMed HubMed [Biosorbants]
  3. Kotrba P, Dolecková L, de Lorenzo V, and Ruml T. . pmid:10049868. PubMed HubMed [Kotrba99]
  4. Mejáre M and Bülow L. . pmid:11164556. PubMed HubMed [Mejare01]
  5. Lu Y, Berry SM, and Pfister TD. . pmid:11710062. PubMed HubMed [Lu01]
  6. Bae W, Chen W, Mulchandani A, and Mehra RK. . pmid:11042548. PubMed HubMed [Bae00]
All Medline abstracts: PubMed HubMed

Pumps

  • Cadmium(Plasmid pI258 (from S.aureus) cadmium resistance (cadA) gene, complete cds) [21]
  • 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

Sponges

Miscellaneous

  • Arabinose PBAD Promoter[26]
  1. Guzman LM, Belin D, Carson MJ, and Beckwith J. . pmid:7608087. PubMed HubMed [pBAD33]


Heavy Metals

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]
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]

Absorption of Heavy Metals

  1. Tripathi RD, Srivastava S, Mishra S, Singh N, Tuli R, Gupta DK, and Maathuis FJ. . pmid:17306392. PubMed HubMed [Tripathi07]
  2. Weinberg ED. . pmid:2530602. PubMed HubMed [Weinberg89]
All Medline abstracts: PubMed HubMed
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