Isolation of Escherichia coli mRNA and comparison of expression using mRNA and total RNA on DNA microarrays

Volker F. Wendisch, Daniel P. Zimmer, Arkady Khodursky, Brian Peter, Nicholas Cozzarelli, Sydney Kustu

Research output: Contribution to journalArticle

51 Scopus citations

Abstract

Bacterial messenger RNA (mRNA) is not coherently polyadenylated, whereas mRNA of Eukarya can be separated from stable RNAs by virtue of polyadenylated 3′-termini. We have developed a method to isolate Escherichia coli mRNA by polyadenylating it in crude cell extracts with E. coli poly(A) polymerase I and purifying it by oligo(dT) chromatography. Differences in lacZRNA levels were similar with purified mRNA and total RNA in dot blot hydridizations for cultures grown with or without gratuitous induction of the lactose operon. More broadly, changes in gene expression upon induction were similar when cDNAs primed from mRNA or total RNA with random hexanucleotides were hydridized to DNA microarrays for the E. coli genome. Comparable signal intensities were obtained with only 1% as much oligo(dT)-purified mRNA as total RNA, and hence in vitro poly(A) tailing appears to be selective for mRNA. These and additional studies of genome-wide expression with DNA microarrays provide evidence that in vitro poly(A) tailing works universally for E. coli mRNAs.

Original languageEnglish (US)
Pages (from-to)205-213
Number of pages9
JournalAnalytical Biochemistry
Volume290
Issue number2
DOIs
StatePublished - Mar 15 2001

Keywords

  • Bacteria
  • DNA microarrays
  • Escherichia coli
  • Messenger RNA
  • Poly(A) polymerase
  • Polyadenylation

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