Identification of novel genes that are differentially expressed in human colorectal carcinoma

By using mRNA differential display technology, we have identified three cDNA clones, myl 3, myl 4, and myl 6, to show significant changes in expression between human colorectal tumor and paired normal tissue. Northern blot analysis indicated that clone myl 3 expression was elevated in normal tissue, and clone myl 4 expression was elevated in tumor tissue. Nucleotide sequence analysis revealed that clones myl 3 and myl 4 have not been previously identified. However, clone myl 6 appears to be the human homolog of the 3' end region of tissue inhibitor of metalloproteinase 3 (TIMP-3). Northern blot analysis showed that a 2.5 kb TIMP-3 transcript was expressed at a much higher level in normal tissue than the colorectal tumor.

Helicobacter pylori induces gene expression in human gastric cells identified by mRNA differential display

Changes in gene expression patterns in gastric cells infected with Helicobacter pylori were characterized by means of mRNA differential display. Total RNA preparations were extracted from the H. pylori infected gastric cells and paired non-infected cells, and were probed with candidate clones identified after screening up to 6,000 mRNA species. Among them, four clones, 04G-1, 04G-2, 01G-1, and Cppa-2 show significant expression in the infected cells by Northern blot analysis, and they are 199 bp, 196 bp, 228 bp, and 276 bp in length, respectively. Database search revealed that nucleotide sequences of these clones share very low identity with any known sequence. These results indicate that H. pylori can significantly affect gene expression in gastric cells. Furthermore mRNA differential display can be used in pathogenesis studies to identify new genes in gastric cells in response to insults such as H. pylori.

Identification of sucrose-regulated genes in cultured rice cells using mRNA differential display

In order to get more information about carbon metabolite regulation pathways, cloning and sequence analysis of sucrose-regulated genes from rice-suspension-cultured cells were performed. We used a new method, mRNA differential display, to screen differentially expressed genes under conditions of 3% and no sucrose in the cultured medium. Six candidate clones were identified and sequenced. Clones SI1 and SI2 were repressed by sucrose starvation, while clones SR1, SR2, SR3 and SR4 were induced by sucrose starvation. Nucleotide sequence analysis showed that clone SR2 has 94.8% homology to the salT gene, and clones SI1 and SR3 show 88.3 and 96.9% identity, respectively, to partial cDNA sequences in the GenBank database. The results suggest that mRNA differential display provides an easy and quick way to clone genes involved in the carbon metabolite regulation pathway.

Protein phosphatase inhibitors enhance the expression of an alpha-amylase gene, alpha Amy3, in cultured rice cells

A rice (Oryza sativa L.) gene for alpha-amylase, alpha Amy3, was strongly and rapidly induced by treatment of suspension-cultured cells with okadaic acid (OA), a potent and specific inhibitor of protein serine/threonine phosphatases 1 and 2A. The massive accumulation of alpha Amy3 mRNA in response to OA treatment was due to the stimulation of gene transcription and a partial stabilization of this mRNA. This induction of alpha Amy3 message by OA occurred even though cellular protein synthesis was inhibited. Simultaneous treatment of cultured cells with OA and anisomycin synergistically induced alpha Amy3 expression. In addition, the inhibition of protein synthesis stabilized OA-induced alpha Amy3 mRNA. In the presence of protein kinase inhibitors H7, W7, and H8, alpha Amy3 mRNA accumulation induced by OA was unaffected. These results indicate that OA-dependent alpha Amy3 induction is regulated transcriptionally by a signal transduction pathway involving protein phosphorylation, but independent of both protein kinase C and Ca2+/calmodulin- or Ca(2+)-dependent protein kinases. Furthermore, an AMP-activated protein kinase may be required for this induction of alpha Amy3 expression.

Poly(A) tail shortening of alpha-amylase mRNAs in vegetative tissues of Oryza sativa

The pattern of expression for the entire alpha-amylase gene family in rice vegetative tissues during the developmental growth stages has been studied. We were surprised that the size of rice alpha-amylase mRNAs in the young roots, shoots, and different tissues from adult plant was shorter by approximately 250 bases than that in immature or mature embryos and aleurone layers of seed. Interestingly, the difference in the size of the alpha-amylase mRNAs of rice seed and vegetative tissues is due to the variation in the length of the 3'-poly(A) tracts. In addition, if without glycogen-precipitated treatment for alpha-amylase purification, no alpha-amylases can be detected in vegetative tissues by Western blot analysis. Furthermore, in vitro translation assay revealed that alpha-amylase mRNAs receiving shortened poly(A) tracts in vegetative tissues become translationally repressed. These results indicate that the 3'-poly(A) tract of eukaryotic mRNAs plays an important role in controlling mRNA translatability.