Membrane-associated transcripts in Arabidopsis; their isolation and characterization by DNA microarray analysis and bioinformatics

The Plant Journal : for Cell and Molecular Biology
Mark de JongGuido Van den Ackerveken

Abstract

Membrane-associated, integral membrane and secreted proteins are of key importance in many cellular processes. For most of the 28,952 predicted proteins in Arabidopsis, the actual subcellular localization has not been demonstrated experimentally. So far, their potential membrane-association has been deduced from algorithms that predict transmembrane domains and signal peptides. However, the comprehensiveness and accuracy of these algorithms is still limited. The majority of membrane-associated and secreted proteins is synthesized on membrane-bound polysomes. Therefore, the isolation and characterization of mRNA associated with membrane-bound polysomes offers an experimental tool for the genome-wide identification of these proteins. Here we describe an efficient method to isolate mRNA from membrane-bound polysomes and report on the validation of the method to enrich for transcripts encoding membrane-associated and secreted proteins. The sensitivity and reproducibility of the isolation method was investigated by DNA microarray analysis. Pearson correlations between transcript levels obtained from three replicate isolations showed that the method is highly reproducible. A significant enrichment for mRNAs encoding proteins containi...Continue Reading

References

Jan 1, 1987·Methods in Enzymology·B M Mechler
Jan 1, 1994·Annual Review of Cell Biology·P Walter, A E Johnson
Oct 1, 1993·The Journal of Cell Biology·J E Wilhelm, R D Vale
Jan 1, 1995·Methods in Cell Biology·E Davies, S Abe
Oct 28, 1998·Trends in Cell Biology·Y Oleynikov, R H Singer
Jul 13, 2000·Journal of Molecular Biology·O EmanuelssonG von Heijne
Dec 20, 2000·FEBS Letters·J NilssonG von Heijne
Apr 11, 2001·Trends in Biochemical Sciences·B Pradet-BaladeJ A Garcia-Sanz
Jul 13, 2001·Bioinformatics·S MöllerR Apweiler
Dec 26, 2001·Nucleic Acids Research·Ron EdgarAlex E Lash
Mar 23, 2002·Cell·Malgorzata KlocLaurence D Etkin
Jan 10, 2003·Nucleic Acids Research·Mark L CroweMartin Trick
Jan 17, 2003·Plant Physiology·Rainer SchwackeReinhard Kunze
Jul 29, 2003·Proceedings of the National Academy of Sciences of the United States of America·John D Storey, Robert Tibshirani
Nov 5, 2003·Methods : a Companion to Methods in Enzymology·Gordon K Smyth, Terry Speed
Mar 19, 2004·Current Biology : CB·Torsten KleffmannSacha Baginsky
Apr 16, 2004·Current Biology : CB·Paul Jarvis
May 18, 2004·The Plant Journal : for Cell and Molecular Biology·Riki KawaguchiJulia Bailey-Serres
Aug 7, 2004·Bioinformatics·James M Wettenhall, Gordon K Smyth
Oct 1, 1993·Current Biology : CB·R H Singer
Oct 6, 2004·Genome Biology·Robert C GentlemanJianhua Zhang
Dec 21, 2004·Nucleic Acids Research·Tanya BarrettRon Edgar
Dec 29, 2004·Current Biology : CB·Paul Jarvis, Colin Robinson
Feb 16, 2005·Plant Physiology·Joke AllemeerschMartin T R Kuiper
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth

❮ Previous
Next ❯

Citations

Nov 29, 2007·Cellular and Molecular Life Sciences : CMLS·R E HalbeisenA P Gerber
Nov 17, 2006·Molecular Biology of the Cell·M GarciaC Jacq
May 27, 2011·Molecular Biology of the Cell·Qiang ChenChristopher V Nicchitta
Jul 17, 2009·Critical Reviews in Biochemistry and Molecular Biology·Katrien Van Der KelenLieven De Veylder
Jul 21, 2009·Trends in Plant Science·J Bailey-SerresPiyada Juntawong
Mar 3, 2009·Current Opinion in Cell Biology·Eric LécuyerHenry M Krause
Feb 20, 2009·Physiologia Plantarum·Won Kyong ChoJae-Yean Kim
Dec 13, 2006·The EMBO Journal·Bert SchepensSigrid Cornelis
Mar 5, 2013·Biochimica Et Biophysica Acta·Benjamin L WeisWilliam Zerges
Aug 7, 2009·Molecular Plant-microbe Interactions : MPMI·Robin P HuibersGuido Van den Ackerveken
Aug 8, 2009·Journal of Proteome Research·Setsuko KomatsuKiyoshi Furukawa

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