5-Fluorouracil (5-FU) is a classic chemotherapeutic drug that has been widely used for breast cancer treatment. Although aberrant expression of protein-coding genes was observed after 5-FU treatment, the regulatory mechanism remains poorly understood. MicroRNAs (miRNAs) are a newly identified class of small regulatory RNAs which play an important role in gene regulation at the post-transcriptional levels. Recent evidence suggests an important role of miRNAs in initiation, progression, and metastasis of human cancers. In this study, using a combined advanced microarray and quantitative real-time PCR (qRT-PCR) technology, we show that 5-FU significantly alters the global expression profile of miRNAs in vitro. After 48 h of treatment with a low dose (0.01 µM), 42 miRNAs were differentially expressed in MCF-7 breast cancer cell line. Of these, 23 miRNAs were up-regulated with up to 4.59-fold changes, while 19 were down-regulated with up to 1.89-fold changes. A majority of these miRNAs are associated with cancer development, progression, and metastasis. Target prediction and GO analysis suggest that these differentially expressed miRNAs potentially target many oncogenes, tumor suppressor genes and genes related to programmed cell death, activation of immune response, and cellular catabolic processes.
ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAssessment of Molecular Construction in Undergraduate BiochemistryDavid C. Richardson , Jane S. Richardson , Rudy Sirochman , Steven W. Weiner , Mary Farwell , Cindy Putnam-Evans , Deborah Booth , and Robert C. Bateman Jr.View Author Information Department of Biochemistry, Duke University Medical Center, Durham, NC 27710 Science Education, Georgia State University, Atlanta, GA 30303 Department of Chemistry, Muhlenberg College, Allentown, PA 18104 Department of Biology, East Carolina University, Greenville, NC 27858 Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, MS 39406Cite this: J. Chem. Educ. 2005, 82, 12, 1854Publication Date (Web):December 1, 2005Publication History Received3 August 2009Published online1 December 2005Published inissue 1 December 2005https://pubs.acs.org/doi/10.1021/ed082p1854https://doi.org/10.1021/ed082p1854research-articleACS PublicationsRequest reuse permissionsArticle Views233Altmetric-Citations12LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Biochemistry,Software,Students,Testing and assessment,Undergraduates Get e-Alerts
Summary We have designed a set of nine plasmids containing the Bacillus pumilis cat gene with one of three Shine‐Dalgarno (SD) sequences ( weak, strong or stronger ) and one of three initiation codons (AUG, GUG or UUG). These constructions have been used to determine the effect of ribosomal protein S1, SD and initiation codon sequences and Escherichia coli ribosomal protein S1 on translation in vitro by E. coli and B. subtilis ribosomes. Translation of these nine constructions was determined with three types of ribosomes: E. coli containing ribosomal protein S1, E. coli depleted of S1, and B. subtilis which is naturally free of S1. E. coli ribosomes were able to translate all nine transcripts with variable efficiencies. B. subtilis and S1 ‐depleted E. coli ribosomes were similar to each other and differed from non‐depleted E. coli ribosomes in that they required strong or stronger SD sequences and were unable to translate any of the weak transcripts. Addition of S1 from either E. coli or Micrococcus luteus , a Gram‐positive bacterium, enabled S1‐depleted E. coli ribosomes to translate mRNAs with weak SD sequences but had no effect on B. subtilis ribosomes. AUG was the preferred initiation codon for all ribosome types; however, B. subtilis ribosomes showed greater tolerance for the non‐AUG codons than either type of E. coli ribosome. The presence of a strong or stronger SD sequence increased the efficiency by which E. coli ribosomes could utilize non‐AUG codons. The effect of non‐AUG initiation codons was dependent on the SD with which they were associated, but the effect of the SD sequence was independent of the initiation codon. We conclude that the presence of a strong SD sequence alone is able to substitute for at least part of the activities of ribosomal protein S1, and that ribosomes that exhibit S1 ‐independent translation on such messages also show less reliance on AUG as an initiation codon.
Bcl-2 is an anti-apoptotic protein that is frequently over-expressed in cancer cells but its role in carcinogenesis is not clear. We are interested in how Bcl-2 expression affects non-cancerous breast cells and its role in the cell cycle. We prepared an MCF10A breast epithelial cell line that stably over-expressed Bcl-2. We analyzed the cells by flow cytometry after synchronization, and used cDNA microarrays with quantitative reverse-transcription PCR (qRT-PCR) to determine differences in gene expression. The microarray data was subjected to two pathway analysis tools, parametric analysis of gene set enrichment (PAGE) and ingenuity pathway analysis (IPA), and western analysis was carried out to determine the correlation between mRNA and protein levels. The MCF10A/Bcl-2 cells exhibited a slow-growth phenotype compared to control MCF10A/Neo cells that we attributed to a slowing of the G1-S cell cycle transition. A total of 363 genes were differentially expressed by at least two-fold, 307 up-regulated and 56 down-regulated. PAGE identified 22 significantly changed gene sets. The highest ranked network of genes identified by IPA contained 24 genes. Genes that were chosen for further analysis were confirmed by qRT-PCR, however, the western analysis did not always confirm differential expression of the proteins. Down-regulation of the phosphatase CDC25A could solely be responsible for the slow growth phenotype in MCF10A/Bcl-2 cells. Increased levels of GTPase Cdc42 could be adding to this effect. PAGE and IPA are valuable tools for microarray analysis, but protein expression results do not always follow mRNA expression results.
Bacillus subtilis and related gram-positive bacteria which have low to moderate genomic G + C contents are unable to efficiently translate mRNA derived from gram-negative bacteria, whereas Escherichia coli and other gram-negative bacteria are able to translate mRNA from both types of organisms. This phenomenon has been termed translational species specificity. Ribosomes from the low-G + C-content group (low-G + C group) of gram-positive organisms (B. subtilis and relatives) lack an equivalent to Escherichia ribosomal protein S1. The requirement for S1 for translation in E. coli (G. van Dieijen, P. H. van Knippenberg, J. van Duin, B. Koekman, and P. H. Pouwels, Mol. Gen. Genet. 153:75-80, 1977) and its specific role (A.R. Subramanian, Trends Biochem. Sci. 9:491-494, 1984) have been proposed. The group of gram-positive bacteria characterized by high genomic G + C content (formerly Actinomyces species and relatives) contain S1, in contrast to the low-G + C group (K. Mikulik, J. Smardova, A. Jiranova, and P. Branny, Eur. J. Biochem. 155:557-563, 1986). It is not known whether members of the high-G + C group are translationally specific, although there is evidence that one genus, Streptomyces, can express Escherichia genes in vivo (M. J. Bibb and S. N. Cohen, Mol. Gen. Genet. 187:265-277, 1985; J. L. Schottel, M. J. Bibb, and S. N. Cohen, J. Bacteriol. 146:360-368, 1981). In order to determine whether the organisms of this group are translationally specific, we examined the in vitro translational characteristics of a member of the high-G + C group, Micrococcus luteus, whose genomic G + C content is 73%. A semipurified coupled transcription-translation system of M. luteus translates Escherichia mRNA as well as Bacillus and Micrococcus mRNA. Therefore, M. luteus is translationally nonspecific and resembles E. coli rather than B. subtilis in its translational characteristics.
