Lecture 4 - Transcription Regulation in Prokaryotes | Molecular Biology (DNA) by ILLL, DU - Biotechnology Engineering (BT) PDF Download

 Page 1


 
 
1 | P a g e 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: TRANSCRIPTION REGULATION IN PROKARYOTES 
LESSON DEVELOPER: Dr. CHARU DOGRA RAWAT 
COLLEGE/DEPT: RAMJAS COLLEGE 
UNIVERSITY OF DELHI 
 
 
  
Page 2


 
 
1 | P a g e 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: TRANSCRIPTION REGULATION IN PROKARYOTES 
LESSON DEVELOPER: Dr. CHARU DOGRA RAWAT 
COLLEGE/DEPT: RAMJAS COLLEGE 
UNIVERSITY OF DELHI 
 
 
  
 
 
2 | P a g e 
Institute of Lifelong Learning, University of Delhi 
Table of Contents  
Chapter: Transcription Regulation in Prokaryotes 
• Introduction 
? Learning objectives 
• Genetic organization in bacteria – concept of an operon 
• Components of an operon 
• Principles of Transcriptional Regulation 
• Gene Regulation is brought about by Regulatory Proteins 
• Regulatory proteins may be assisted by coregulators 
• Regulatory proteins often control their own synthesis: 
autoregulation 
• Regulatory proteins regulate gene expression by ordering 
recruitment of RNA polymerase or by obstructing its binding 
• Regulatory proteins can regulate gene expression after RNA 
polymerase binding 
• Regulatory proteins often have a dual role 
• Regulatory proteins can bind at a distance: DNA looping 
• Regulatory proteins interplay: antiactivation and antirepression 
• Regulatory proteins may exert a combinatorial control 
• Regulation can occur at levels beyond transcription initiation 
• Regulation of Transcription Initiation: the lac operon 
• Structure of the lac operon 
• Regulatory proteins of the lac operon 
• Discovery of the lac operon – role of mutants 
• Regulation of the lac operon 
? Negative Regulation 
? The lac operon is “leaky” 
? Feedback control 
? Positive regulation 
? Catabolite control 
• Regulation at steps after Transcription Initiation: the trp operon 
• Structure of the trp operon 
• Regulatory protein of the trp operon 
• Regulation of the trp operon 
Page 3


 
 
1 | P a g e 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: TRANSCRIPTION REGULATION IN PROKARYOTES 
LESSON DEVELOPER: Dr. CHARU DOGRA RAWAT 
COLLEGE/DEPT: RAMJAS COLLEGE 
UNIVERSITY OF DELHI 
 
 
  
 
 
2 | P a g e 
Institute of Lifelong Learning, University of Delhi 
Table of Contents  
Chapter: Transcription Regulation in Prokaryotes 
• Introduction 
? Learning objectives 
• Genetic organization in bacteria – concept of an operon 
• Components of an operon 
• Principles of Transcriptional Regulation 
• Gene Regulation is brought about by Regulatory Proteins 
• Regulatory proteins may be assisted by coregulators 
• Regulatory proteins often control their own synthesis: 
autoregulation 
• Regulatory proteins regulate gene expression by ordering 
recruitment of RNA polymerase or by obstructing its binding 
• Regulatory proteins can regulate gene expression after RNA 
polymerase binding 
• Regulatory proteins often have a dual role 
• Regulatory proteins can bind at a distance: DNA looping 
• Regulatory proteins interplay: antiactivation and antirepression 
• Regulatory proteins may exert a combinatorial control 
• Regulation can occur at levels beyond transcription initiation 
• Regulation of Transcription Initiation: the lac operon 
• Structure of the lac operon 
• Regulatory proteins of the lac operon 
• Discovery of the lac operon – role of mutants 
• Regulation of the lac operon 
? Negative Regulation 
? The lac operon is “leaky” 
? Feedback control 
? Positive regulation 
? Catabolite control 
• Regulation at steps after Transcription Initiation: the trp operon 
• Structure of the trp operon 
• Regulatory protein of the trp operon 
• Regulation of the trp operon 
 
 
3 | P a g e 
Institute of Lifelong Learning, University of Delhi 
? Negative Regulation 
? Attenuation 
• Summary 
• Exercise 
• Glossary 
• References/Weblinks
  
Page 4


 
 
1 | P a g e 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: TRANSCRIPTION REGULATION IN PROKARYOTES 
LESSON DEVELOPER: Dr. CHARU DOGRA RAWAT 
COLLEGE/DEPT: RAMJAS COLLEGE 
UNIVERSITY OF DELHI 
 
 
  
 
 
2 | P a g e 
Institute of Lifelong Learning, University of Delhi 
Table of Contents  
Chapter: Transcription Regulation in Prokaryotes 
• Introduction 
? Learning objectives 
• Genetic organization in bacteria – concept of an operon 
• Components of an operon 
• Principles of Transcriptional Regulation 
• Gene Regulation is brought about by Regulatory Proteins 
• Regulatory proteins may be assisted by coregulators 
• Regulatory proteins often control their own synthesis: 
autoregulation 
• Regulatory proteins regulate gene expression by ordering 
recruitment of RNA polymerase or by obstructing its binding 
• Regulatory proteins can regulate gene expression after RNA 
polymerase binding 
• Regulatory proteins often have a dual role 
• Regulatory proteins can bind at a distance: DNA looping 
• Regulatory proteins interplay: antiactivation and antirepression 
• Regulatory proteins may exert a combinatorial control 
• Regulation can occur at levels beyond transcription initiation 
• Regulation of Transcription Initiation: the lac operon 
• Structure of the lac operon 
• Regulatory proteins of the lac operon 
• Discovery of the lac operon – role of mutants 
• Regulation of the lac operon 
? Negative Regulation 
? The lac operon is “leaky” 
? Feedback control 
? Positive regulation 
? Catabolite control 
• Regulation at steps after Transcription Initiation: the trp operon 
• Structure of the trp operon 
• Regulatory protein of the trp operon 
• Regulation of the trp operon 
 
 
3 | P a g e 
Institute of Lifelong Learning, University of Delhi 
? Negative Regulation 
? Attenuation 
• Summary 
• Exercise 
• Glossary 
• References/Weblinks
  
Transcription Regulation In Prokaryotes 
                                               
                                  Institute of Lifelong Learning, University of Delhi     4 
  
Introduction 
All cells contain the same genetic material yet they get differentiated (structurally and 
functionally) from one another. These differences are attributed to the different set of 
proteins present in them and/or differences in the quantity of proteins they produce (it 
should be noted here that most of the proteins are same in all the cells, it is the difference 
in relatively few types of proteins that lead to differentiation). These differences in the 
quality or quantity of proteins present in cells are achieved by regulation of gene 
expression, a process commonly called as gene regulation. Thus, cells differ from one 
another not due to differences at the genetic level but instead due to the differences in the 
expression of some genes in different cells. Even in a particular cell such differences can 
arise over a period of time or as a response to external conditions.     
In a cell, DNA is transcribed into RNA that is then translated into a protein product (which 
can be structural, enzymatic, or other function). To alter the expression of a gene, 
regulation can principally occur at any stage of this course. In prokaryotes, the most 
common way of regulating gene expression is by influencing the rate at which transcription 
(DNA to RNA) is initiated. This rate of transcription ranges from =zero‘ where the gene is not 
transcribed at all and thus, there is no gene expression (gene is turned =off‘) to =maximum‘ 
where the gene is continuously transcribed (gene is turned =on‘), at least for some time. 
Many common processes in a cell such as, metabolism, cell division, response to 
environmental conditions etc. are regulated in this manner.   
In this chapter, we will study the regulation of transcription in prokaryotes in general by 
studying regulation of two sets of proteins (enzymes) needed to carry out certain metabolic 
processes in bacteria. This regulation is a consequence of prevalent external conditions to 
which the bacteria respond by one way or the other. One set of enzymes is involved in 
obtaining and metabolizing a disaccharide called lactose (a common milk sugar composed of 
glucose and galactose). The other set of enzymes catalyzes the synthesis of a non-essential 
amino acid, tryptophan.   
Learning objectives 
After studying this chapter, you should have an understanding of  
? the operon model of gene regulation in prokaryotes 
? the role of regulatory proteins (protein : DNA interactions) in regulating transcription 
initiation in prokaryotes 
? mechanisms of transcriptional regulation 
? positive and negative regulation; inducible and repressible systems 
? regulation of E. coli lac and trp operons 
Genetic organization in bacteria – concept of an operon 
In prokaryotes, genes are often clustered together (separated only by a few base pairs) and 
put under the control of a single promoter (and other regulatory elements). Such a set of 
genes that are co-regulated with its regulatory machinery forms an operon (Figure 1). The 
genes are co-transcribed into a polycistronic mRNA which refers to a messenger RNA 
containing transcripts of two or more neighboring cistrons (segments of DNA that code for a 
polypeptide chain). In other words, polycistronic mRNA is an mRNA that code for more than 
one polypeptide chain (as against monocistronic mRNA that contains transcript of a single 
coding region and codes for a single polypeptide). Often the genes clustered in an operon 
are related structurally or functionally. For instance, enzymes that are part of the same 
Page 5


 
 
1 | P a g e 
Institute of Lifelong Learning, University of Delhi 
 
 
 
 
 
 
 
 
 
MOLECULAR BIOLOGY 
LESSON NAME: TRANSCRIPTION REGULATION IN PROKARYOTES 
LESSON DEVELOPER: Dr. CHARU DOGRA RAWAT 
COLLEGE/DEPT: RAMJAS COLLEGE 
UNIVERSITY OF DELHI 
 
 
  
 
 
2 | P a g e 
Institute of Lifelong Learning, University of Delhi 
Table of Contents  
Chapter: Transcription Regulation in Prokaryotes 
• Introduction 
? Learning objectives 
• Genetic organization in bacteria – concept of an operon 
• Components of an operon 
• Principles of Transcriptional Regulation 
• Gene Regulation is brought about by Regulatory Proteins 
• Regulatory proteins may be assisted by coregulators 
• Regulatory proteins often control their own synthesis: 
autoregulation 
• Regulatory proteins regulate gene expression by ordering 
recruitment of RNA polymerase or by obstructing its binding 
• Regulatory proteins can regulate gene expression after RNA 
polymerase binding 
• Regulatory proteins often have a dual role 
• Regulatory proteins can bind at a distance: DNA looping 
• Regulatory proteins interplay: antiactivation and antirepression 
• Regulatory proteins may exert a combinatorial control 
• Regulation can occur at levels beyond transcription initiation 
• Regulation of Transcription Initiation: the lac operon 
• Structure of the lac operon 
• Regulatory proteins of the lac operon 
• Discovery of the lac operon – role of mutants 
• Regulation of the lac operon 
? Negative Regulation 
? The lac operon is “leaky” 
? Feedback control 
? Positive regulation 
? Catabolite control 
• Regulation at steps after Transcription Initiation: the trp operon 
• Structure of the trp operon 
• Regulatory protein of the trp operon 
• Regulation of the trp operon 
 
 
3 | P a g e 
Institute of Lifelong Learning, University of Delhi 
? Negative Regulation 
? Attenuation 
• Summary 
• Exercise 
• Glossary 
• References/Weblinks
  
Transcription Regulation In Prokaryotes 
                                               
                                  Institute of Lifelong Learning, University of Delhi     4 
  
Introduction 
All cells contain the same genetic material yet they get differentiated (structurally and 
functionally) from one another. These differences are attributed to the different set of 
proteins present in them and/or differences in the quantity of proteins they produce (it 
should be noted here that most of the proteins are same in all the cells, it is the difference 
in relatively few types of proteins that lead to differentiation). These differences in the 
quality or quantity of proteins present in cells are achieved by regulation of gene 
expression, a process commonly called as gene regulation. Thus, cells differ from one 
another not due to differences at the genetic level but instead due to the differences in the 
expression of some genes in different cells. Even in a particular cell such differences can 
arise over a period of time or as a response to external conditions.     
In a cell, DNA is transcribed into RNA that is then translated into a protein product (which 
can be structural, enzymatic, or other function). To alter the expression of a gene, 
regulation can principally occur at any stage of this course. In prokaryotes, the most 
common way of regulating gene expression is by influencing the rate at which transcription 
(DNA to RNA) is initiated. This rate of transcription ranges from =zero‘ where the gene is not 
transcribed at all and thus, there is no gene expression (gene is turned =off‘) to =maximum‘ 
where the gene is continuously transcribed (gene is turned =on‘), at least for some time. 
Many common processes in a cell such as, metabolism, cell division, response to 
environmental conditions etc. are regulated in this manner.   
In this chapter, we will study the regulation of transcription in prokaryotes in general by 
studying regulation of two sets of proteins (enzymes) needed to carry out certain metabolic 
processes in bacteria. This regulation is a consequence of prevalent external conditions to 
which the bacteria respond by one way or the other. One set of enzymes is involved in 
obtaining and metabolizing a disaccharide called lactose (a common milk sugar composed of 
glucose and galactose). The other set of enzymes catalyzes the synthesis of a non-essential 
amino acid, tryptophan.   
Learning objectives 
After studying this chapter, you should have an understanding of  
? the operon model of gene regulation in prokaryotes 
? the role of regulatory proteins (protein : DNA interactions) in regulating transcription 
initiation in prokaryotes 
? mechanisms of transcriptional regulation 
? positive and negative regulation; inducible and repressible systems 
? regulation of E. coli lac and trp operons 
Genetic organization in bacteria – concept of an operon 
In prokaryotes, genes are often clustered together (separated only by a few base pairs) and 
put under the control of a single promoter (and other regulatory elements). Such a set of 
genes that are co-regulated with its regulatory machinery forms an operon (Figure 1). The 
genes are co-transcribed into a polycistronic mRNA which refers to a messenger RNA 
containing transcripts of two or more neighboring cistrons (segments of DNA that code for a 
polypeptide chain). In other words, polycistronic mRNA is an mRNA that code for more than 
one polypeptide chain (as against monocistronic mRNA that contains transcript of a single 
coding region and codes for a single polypeptide). Often the genes clustered in an operon 
are related structurally or functionally. For instance, enzymes that are part of the same 
Transcription Regulation In Prokaryotes 
                                               
                                  Institute of Lifelong Learning, University of Delhi     5 
  
metabolic pathway (however different in their molecular functions) form an operon.  
Coordinated regulation ensures a single signal to direct the synthesis of several related 
proteins in similar amounts and at the same time.  
Figure 1. Schematic representation of an operon. Operon consists of a set 
of structural genes co-regulated by the regulatory elements (promoter, operator). These 
elements along with the regulatory genes respond to the environmental cues. Genes are co-
transcribed into a polycistronic mRNA that code for more than one protein. 
Source: Author 
 
Value addition: Fact-file 
Heading Text: Eukaryotic operons 
Body Text:  
The genes of eukaryotes are generally considered to be monocistronic, each with its own 
promoter at the 5‘ end and a transcription terminator at the 3‘ end. The genomes of 
nematodes, ascidians, and trypanosomes are unusual among most eukaryotes in that 
they contain many operons. Polycistronic transcription in eukaryotes was first discovered 
in trypanosomes (1988), although these polycistronically transcribed genes do not 
represent operons in the true sense that they are not coregulated. Widespread operons in 
an animal were first discovered in the nematode, Caenorhabditis elegans, in 1993. 
Approximately 15% of genes in the genome of C. elegans occur in operons. Polycistronic 
transcription also has been described in other eukaryotes, including flatworms, algae, 
Drosophila, and humans. Nematode operons are transcribed to produce polycistronic 
initial transcripts that are co-transcriptionally processed to make monocistronic mRNAs. 
This is also true for the operons discovered in flatworms and primitive chordates. Another 
type of operon consists of gene clusters more like bacterial operons — they make 
polycistronic mRNAs that are translated in that form. They are found in flies and plants.  
Source: Blumenthal T. Operons in eukaryotes. Brief Funct Genomic Proteomic. 2004 
Nov;3(3):199-211 
Cutter AD, Agrawal AF. The evolutionary dynamics of operon distributions in eukaryote 
genomes. Genetics. 2010 Jun; 185(2):685-93. 
 
Components of an operon  
An operon is composed of two DNA elements: the regulatory sequences (such as, promoter 
and operator) and a set of genes that are co-regulated. The genes are called as structural 
genes. Promoter is a DNA sequence, lying upstream to the structural genes, to which RNA