1887

Studying Gene Expression: Database Searches and Promoter Fusions to Investigate Transcriptional Regulation in Bacteria

    Authors: Betsy M. Martinez-Vaz1,*, Irina Makarevitch1, Shane Stensland1
    VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Department of Biology, Hamline University, Saint Paul, MN 55104
    AUTHOR AND ARTICLE INFORMATION AUTHOR AND ARTICLE INFORMATION
    • Published 20 May 2010
    • Supplemental material available at http://jmbe.asm.org
    • *Corresponding author. Mailing address: Hamline University, Department of Biology, 1536 Hewitt Ave., Saint Paul, MN 55104. Phone: (651) 523-2493. Fax: (651) 523-2620. E-mail: bmartinezvaz01@hamline.edu.
    • Copyright © 2010 American Society for Microbiology
    Source: J. Microbiol. Biol. Educ. May 2010 vol. 11 no. 1 42-49. doi:10.1128/jmbe.v11.i1.101
MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • PDF
    409.44 Kb
  • HTML
    62.11 Kb
  • XML

    Abstract:

    A laboratory project was designed to illustrate how to search biological databases and utilize the information provided by these resources to investigate transcriptional regulation in The students searched several databases (NCBI Genomes, RegulonDB and EcoCyc) to learn about gene function, regulation, and the organization of transcriptional units. A fluorometer and GFP promoter fusions were used to obtain fluorescence data and measure changes in transcriptional activity. The class designed and performed experiments to investigate the regulation of genes necessary for biosynthesis of amino acids and how expression is affected by environmental signals and transcriptional regulators. Assessment data showed that this activity enhanced students’ knowledge of databases, reporter genes and transcriptional regulation.

Key Concept Ranking

Gene Expression and Regulation
0.9304534
Transcription Factor Regulation
0.5406631
Gene Expression
0.4899491
Transcriptional Regulation
0.4609023
Gene Regulation
0.44810122
0.9304534

References & Citations

1. Blauwkamp TA, Ninfa AJ2002Nac-mediated repression of the serA promoter of Escherichia coliMol. Microbiol.4535136310.1046/j.1365-2958.2002.02994.x12123449 http://dx.doi.org/10.1046/j.1365-2958.2002.02994.x
2. Cormack BP, Valdivia R, Falkow S1996FACS-optimized mutants of the green fluorescent protein (GFP)Gene173333810.1016/0378-1119(95)00685-08707053 http://dx.doi.org/10.1016/0378-1119(95)00685-0
3. Datsenko KA, Wanner BL2000One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR productsProc Natl Acad Sci U S A976640664510.1073/pnas.12016329710829079 http://dx.doi.org/10.1073/pnas.120163297
4. Ernsting BR, Denninger JW, Blumenthal RM, Matthews RG1993Regulation of the gltBDF operon of Escherichia coli: how is a leucine-insensitive operon regulated by the leucine-responsive regulatory protein?J. Bacteriol.175716071697901196
5. Keseler IM, Collado-Vides J, Gama-Castro S, et al2005EcoCyc: a comprehensive database resource for Escherichia coliNucleic Acids Res.33Database issueD334D33710.1093/nar/gki108540062 http://dx.doi.org/10.1093/nar/gki108
6. Mosher R2002Using pGLO to demonstrate the effects of catabolite repression on gene expression in Escherichia coli [abstract]Bioscene281723
7. Moss R1997A discovery lab for studying gene regulationThe American Biology Teacher5952252610.2307/4450370 http://dx.doi.org/10.2307/4450370
8. National Research Council2003Bio2010: Transforming Undergraduate Education for Future Research BiologistsNational Academies PressWashington, DC
9. Oliver G, Gosset G, Sanchez-Pescador R, et al1987Determination of the nucleotide sequence for the glutamate synthase structural genes of Escherichia coli K-12Gene6011110.1016/0378-1119(87)90207-13326786 http://dx.doi.org/10.1016/0378-1119(87)90207-1
10. Paul L, Mishra PK, Blumenthal RM, Matthews RG2007Integration of regulatory signals through involvement of multiple global regulators: control of the Escherichia coli gltBDF operon by Lrp, IHF, Crp, and ArgRBMC Microbiol.7210.1186/1471-2180-7-2172338991784095 http://dx.doi.org/10.1186/1471-2180-7-2
11. Salgado H, Gama-Castro S, Peralta-Gil M, et al2006RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditionsNucleic Acids Res.34Database issueD394D39710.1093/nar/gkj1561347518 http://dx.doi.org/10.1093/nar/gkj156
12. Sambrook J, Russell DW2001Molecular Cloning: A Laboratory ManualThird EditionCHSL PressCold Spring Harbor, NY
13. Stambuck B2002Transcriptional and posttranslational regulation of a membrane nutrient transporterBiochemistry and Molecular Biology Education3038839310.1002/bmb.2002.494030060136 http://dx.doi.org/10.1002/bmb.2002.494030060136
14. Tobey KL, Grant GA1986The nucleotide sequence of the serA gene of Escherichia coli and the amino acid sequence of the encoded protein, D-3-phosphoglycerate dehydrogenaseJ. Biol. Chem.26112179121833017965
15. Wu Y, Zhou Y, Song J, Hu X, Ding Y, Zhang Z2008Using green and red fluorescent proteins to teach protein expression, purification, and crystallizationBiochemistry and Molecular Biology Education36435410.1002/bmb.11721591159 http://dx.doi.org/10.1002/bmb.117
16. Zaslaver A, Mayo AE, Rosenberg R, et al2004Just-in-time transcription program in metabolic pathwaysNat Genet3648649110.1038/ng134815107854 http://dx.doi.org/10.1038/ng1348
jmbe.v11.i1.101.citations
jmbe/11/1
content/journal/jmbe/10.1128/jmbe.v11.i1.101
Loading

Citations loading...

Supplemental Material

Loading

Article metrics loading...

/content/journal/jmbe/10.1128/jmbe.v11.i1.101
2010-05-20
2017-09-26

Abstract:

A laboratory project was designed to illustrate how to search biological databases and utilize the information provided by these resources to investigate transcriptional regulation in The students searched several databases (NCBI Genomes, RegulonDB and EcoCyc) to learn about gene function, regulation, and the organization of transcriptional units. A fluorometer and GFP promoter fusions were used to obtain fluorescence data and measure changes in transcriptional activity. The class designed and performed experiments to investigate the regulation of genes necessary for biosynthesis of amino acids and how expression is affected by environmental signals and transcriptional regulators. Assessment data showed that this activity enhanced students’ knowledge of databases, reporter genes and transcriptional regulation.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

/deliver/fulltext/jmbe/11/1/jmbe-11-1-42.xml.a.html?itemId=/content/journal/jmbe/10.1128/jmbe.v11.i1.101&mimeType=html&fmt=ahah

Figures

Image of FIGURE 1

Click to view

FIGURE 1

Experimental data showing the activity of the promoter in cells grown on rich and minimal media. The data shown is an average of six replicas. A paired t-test was performed to evaluate the significance of the results; the data were significant and had a value of less than 0.000002. Fluorescence measurements were obtained after cultures were grown for two hours and had reached an OD600 of 0.4.

Source: J. Microbiol. Biol. Educ. May 2010 vol. 11 no. 1 42-49. doi:10.1128/jmbe.v11.i1.101
Download as Powerpoint
Image of FIGURE 2

Click to view

FIGURE 2

An Example of experimental data obtained by the students. The activity of and promoters was studied in wild type cells and cells lacking L, a transcriptional regulator of both genes. Cells were grown on minimal medium to observe optimal promoter activity for and . The student’s data confirmed that L is a transcriptional activator of and . The data shown is the average of three replicas; error bars indicate the standard error of the mean values.

Source: J. Microbiol. Biol. Educ. May 2010 vol. 11 no. 1 42-49. doi:10.1128/jmbe.v11.i1.101
Download as Powerpoint

This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error