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The On’s and Off’s of Gene Expression Gene expression is regulated • The fact: – Virtually every cell in an organism contains the same DNA and the same genes. • The big questions: – Why are liver cells liver and not brain? – Why are leaf cells leaf and not root? • The answer: – Not all genes are expressed in all cells. Why regulate gene expression? • To conserve energy • To respond to intracelluar signals • To respond to environmental conditions Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. How does gene regulation occur? Genes can be regulated anywhere in the process of information transfer. DNA mRNA protein protein function • Promoter: site for RNA polymerase binding • RNA coding region • Transcription termination signals Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. Organization of a transcription unit In prokaryotes, DNA sequences--located about 10 and about 35 bases upstream of the transcription start site-serve as binding sites for RNA polymerase. Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. What makes a promoter? In prokaryotes, regulation is pretty simple • Prokaryotic transcription is controlled by binding of RNA polymerase to the promoter. • Two options – If RNA polymerase is bound, gene is transcribed. • The gene is “on”. • The gene is “expressed”. – If RNA polymerase does not bind, gene is not transcribed. • The gene is “off”. • The gene is “not expressed”, How is RNA polymerase binding controlled? • Negative regulation – Interferes with RNA polymerase binding – Binding of repressor proteins • Positive regulation – Promotes RNA polymerase binding – Binding of activator proteins. Negative regulation example: lac genes • In Escherichia coli, the lac genes are needed to use the sugar lactose as a carbon source. • Expression of the lac genes is regulated. – The genes are expressed only if lactose is in the growth medium. – The genes are not expressed if glucose is present instead. • When glucose is present, the lac genes are turned off by a repressor protein. The lac repressor binds DNA • lac repressor binds to a DNA sequence called the operator. • The operator sequence overlaps the promoter. • When repressor binds to the operator, it interferes with RNA polymerase binding to the promoter. Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. Eukaryotic gene regulation is complex • Three types of RNA polymerase. – RNA polymerase I transcribes the large ribosomal RNAs. – RNA polymerase II transcribes mRNAs. – RNA polymerase III transcribes tRNAs and small ribosomal RNAs. • Each polymerase recognizes its own promoter. • Core of the promoter contains binding sites for basal transcription machinery • Regulatory part of the promoter contains binding sites for regulatory proteins Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. RNA polymerase II promoters Transcription Factors • Positive activators of transcription • Basal transcription factors bind to core promoter or to each other to facilitate binding RNA polymerase II. This positions RNA polymerase II for transcription. • Regulatory transcription factors bind to regulatory promoter elements. Their binding permits transcription by RNA polymerase II. Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. Assembly of basal transcription machinery Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. Initiation of transcription Different sequence motifs can be “mixed and matched” to recruit binding by various transcription factors. Pierce, B. 2005. Genetics, a conceptal approach. 2nd Ed. WH Freeman. Modular nature of regulatory promoters Expression of transcription factors • Constitutive – Expressed all the time, in many cell types – Examples include factors for: glucose metabolism; RNA and protein synthesis; ATP synthesis • Regulated – Expressed at specific times, in specific places – Examples include factors that respond to various signals (internal or external) • Synthesis of purple anthocyanin pigments in corn can occur in the kernel or in the plant. • The tissue-specificity is due to expression of different regulatory transcription factors. Karen Cone Anthocyanin pigment synthesis in corn Tissue-specificity of anthocyanin synthesis • Kernel-specific – Genes in the pigment pathway are turned on by the colored kernel (C1) transcription factor. – C1 is only expressed in the kernel, not in the plant. • Plant-specific – Genes in the pigment pathway are turned on by the purple plant (PL1) transcription factor. – PL1 is expressed only in plant organs, not in the kernel. Environmental regulation of anthocyanin synthesis MaizeGDB.org Light-dependent (“sun-red”) pigmentation What causes the “sun-red” pigmentation? QuickTime™ and a TIFF (Uncomp resse d) d eco mpres sor are nee ded to s ee this picture . Light turns on expression Light-dependent Transcription Factor pl1 gene LRE* promoter * Light-responsive element TATA Transcription • Water – Too much (flooding): wilting, yellowing, death – Too little (drought): wilting, yellowing, death – Wilt in motion http://plantsinmotion.bio.indiana.edu/pla ntmotion/vegetative/veg.html QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Coffee plant under drought stress http://www2.hawaii.edu/~coffee/drought2.jpg Other environmental cues and effects Other environmental cues and effects • Nitrogen deficiency QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Coffee plants: Normal on left, nitrogen-deprived on right http://www2.hawaii.edu/~coffee/y-nitrogen1.jpg Other environmental effects on gene expression Light effects on development of bean plants http://facstaff.bloomu.edu/chamuris/concepts2/pics/bean_etiol1.jpg Pathogen-induced changes in gene expression http://www.apsnet.org/education/LessonsPlantPath/BacterialSpot Susceptible pepper plant infected with bacterial pathogen Disease resistant pepper plant inoculated with bacterial pathogen QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Disease spreads through leaf. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Expression of plant resistance gene limits spread of bacteria. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Examples of intracellular modulators of gene expression • Hormones – Auxin in plants regulates phototropism (growth towards light) – Sex hormones in animals control sexual development • Growth factors • Small molecules – cyclic AMP – Ca++ – Lipids Summary • All cells of an organism contain the same DNA and thus the same genes • Not all of the genes are expressed in every cell. • Some genes (housekeeping) are expressed in many cell types. • Expression of most genes is regulated in response to environmental or cellular signals.