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]

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.
  1. Wang PZ and Novick RP. . pmid:3104315. PubMed HubMed [Wang95]

[1]

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) [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

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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