Prescott’s Microbiology, 9th Edition
15
Eukaryotic and Archaeal Genome Replication and
Expression
CHAPTER OVERVIEW
This chapter deals with replication of cells and DNA across the three domains of life: eukaryotic, archaeal and
eubacterial. A comparison and contrast of the mechanisms used in genomic architecture and its expression suggest
that in spite of the fact that the archaea resemble bacteria, they are quite distinct and likely more closely related to
eukaryotes. The processes of DNA replication and genome structure resemble eubacteria as the studied archaea
possess circular chromosomes and have some operon arrangement, but also include some elements seen in
eukaryotes such as multiple origins of replication and introns. The promoters of archaeal genes have elements which
resemble elements found in eukaryotic promoters such as the TATA box. In addition, a mechanism of posttranscriptional regulation via antisense RNA is seen in the archaea as well as in eukaryotes. Further studies among
the diverse archaea will likely reveal more similarities to eukaryotes and contrasts to eubacteria.
LEARNING OUTCOMES
After reading this chapter you should be able to:
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create a table or concept map that illustrates the differences in eukaryotic, archaeal, and bacterial
genome structure and organization
distinguish the replicons of eukaryotes and archaeal cells from bacterial replicons
compare and contrast the replisomes of eukaryotes, archaeal cells, and bacterial cells
construct a model to demonstrate the role of telomerase in the replication of eukaryotic chromosomes
compare and contrast gene structure of eukaryotic, archaeal, and bacterial cells
create a table to distinguish eukaryotic, archaeal, and bacterial promoters, RNA polymerases, and
transcription factors
discuss the modifications made to eukaryotic mRNA molecules during and after synthesis
differentiate the structure of eukaryotic, archaeal, and bacterial ribosomes
identify the initiator tRNA used by eukaryotic and archaeal cells
discuss the role of molecular chaperones in eukaryotic and archaeal cells
create a concept map or table that distinguishes the translocation and secretion systems observed in the
three domains of life
list the steps at which eukaryotic and archaeal cells can regulate cellular processes
explain why the separation in time and space of transcription and translation in eukaryotic cells is
important to the possible regulatory mechanisms used
write a paragraph comparing the mechanisms by which eukaryotic and bacterial regulatory proteins
control transcription
discuss the importance of small RNA molecules in regulating gene expression in eukaryotes
CHAPTER OUTLINE
I.
Why Consider Eukaryotic and Archaeal Genetics Together?
A. Evolutionary histories of eukaryotes and archaea are intertwined.
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Prescott’s Microbiology, 9th Edition
B.
In many ways the similarities of the archaea and eukaryotes outnumber those between the archaea and
eubacteria particularly in the areas of how they replicate and express their genomes.
II. DNA Replication
A. DNA replication is accomplished by a large complex of proteins called the replisome
B. DNA Replication in Eukaryotes
1. Replication of the large and multiple chromosomes is initiated at multiple sites
2. Origins of replication are marked by an origin of replication complex (ORC) that recruits replication
proteins
3. Three polymerases are used in eukaryotes
a. Polymerase  primase synthesizes a primer made of RNA
b. Polymerase carries out leading strand synthesis
c. Polymerase carries out lagging strand synthesis
4.
Telomeres and telomerases are used to protect the ends of linear DNA molecules
a. Telomeres are a protein-DNA complex
b. Telomerase uses an internal RNA template to add a Guanine rich tail to the chromosome
C. DNA Replication in archaea
1. Archaeal chromosomes are circular and similar in size to eubacterial chromosomes
2. Some archaea have multiple origins of replication
3. Some archaea have histones associated with their chromosomes like eukaryotes
4. Replisomes of archaea have replisomes that contain a primase and DNA polymerase (PolB) that is
similar to the eukaryotic replisome
a. The archaeal primase is uniquely heterodimeric with a catalytic and regulatory subunit
b. Some archaea, Euryarchaeota, utilize pol B plus a unique polymerase, Pol D.
III. Transcription
A. Transcription in eukaryotes
1.
Eukaryotic genes are monocistronic and contain their own promoters
2.
Many eukaryotic genes have polypeptide coding exons, interposed with non-coding regions
called introns
3. Eukaryotes utilize 3 RNA polymerases
a. RNA Pol II transcribes mRNA
b. RNA Pol I transcribes rRNA
c. RNA Pol III transcribes tRNA
4.
Transcription initiation in Eukaryotes
a. RNA Pol II must be recruited to a promoter which often contains a “TATA” box
b. Transcription factors such as the TBP (TATA binding protein) orient RNA Pol II
5.
From pre-mRNA to mRNA is a unique eukaryotic process
a. A cap of 7-methyl guanosine is added to the 5’ end of the transcript
b. Introns are spliced out by a protein complex known as the spliceosome
c. A tail of poly adenosine (poly a) is added to the 3’ end
B. Transcription in archaea
1. Archaea have a single RNA polymerase that is similar to eukaryotic Pol II
2. Many archaeal genes are arranged as operons and produce polycistronic mRNA
3. Archaeal promoters have elements similar to eukaryotes and a TATA box
4. Two transcription factors are used to recruit RNA polymerase
a. TBP, a TATA binding protein
b. TFB helps to initiatiate transcription
5. A third element, TFE, then binds to form the open complex
IV. Translation and Protein Maturation and Localization
A. Bacterial translation uses 2 ribosomal subunits , a large 70s and a smaller 16s
1. Shine-Delgarno sequence helps position ribosome to starting codon
2. Initiator codon-fMet is added to P site on the ribosome
B. Eukaryotic Translation
1. Eukaryotic ribosomes are larger and require more initiation factors
2. Initiation involves interaction of the 5’ and 3’ ends of the RNA
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
C.
D.
E.
V.
3. 43s complex binds and then finds a start codon
4. Translation elongation is similar to eubacteria
5. Translation termination uses a single release factor (eRF) rather than the 3 seen in eubacteria
Protein folding in eukaryotes
1.
Aided by molecular chaperones that are homologous to those seen in eubacteria
2.
Chaperones vary by size and are also known as heat shock proteins (HSPs)
Protein localization and secretion in eukaryotes
1.
Proteins translocated into the endoplasmic reticulum by the Sec system
2.
Sec proteins of eukaryotes have homologues in both Archaea and eubacteria
3.
Proteins are trafficked between the ER, Golgi, and plasma membrane by vesicular transport
directed by a signal peptide
4.
Localization of proteins into the mitochondria or chloroplasts involves systems related to bacterial
membrane proteins
Translation, protein maturation, and protein localization in Archaea
1.
Transcription and translation are coupled in the cytoplasm as in bacteria
2.
Some archaea possess a Shine-Delgarno sequence while others do not.
3.
Polycistronic mRNA has translation initiated at initiation sites for each polypeptide
4.
Elongation factors are similar to those seen in eubacteria and eukaryotes.
5.
Archaea utilize a single release factor to terminate translation just as eukaryotes do.
6.
Archaea utilize molecular chaperones to fold nascent proteins with homologues to those
seen in bacteria and eukaryotes with the exception of the hsp90 and hsp100 homolgues.
7.
Archaea use the Sec and Tat pathways to translocate proteins.
a. The Sec pathway is similar to the eukaryotic homologues.
b. Only cotranslational translocation has been observed to date.
Regulation of Cellular Processes
A. Regulation of transcription initiation in eukaryotes
1. Regulator sites on promoters
a. Activators bind enhancers or activation sites
b. Repressors bind silencer sites
c. Elements exert influence by modulating transcription factors, histone modifying enzymes ,
and chromatin remodeling enzymes.
B. Other regulatory mechanism in eukaryotes
1. Antisense RNAs are used in eukaryotes to block translation
2.
Micro RNAs can complex to target a particular mRNA to block translation
3.
Small interfering RNAs (siRNA) can form localized heterochromatin to block transcription
C. Regulation of transcription initiation in archaea
1. Repressor proteins operate under 2 mechanisms
a. Some bind an operator sequence and repress transcription like eubacteria
b. Others localize the TATA box and exclude archaeal transcription factors
2. Histones can effectively block or moderate transcription
CRITICAL THINKING
1.
Using table 15.3 as a guide, comment on the possible evolutionary lineage of the RNA polymerases.
Which came first and why do you think so?
2.
Name some of the problems that might be encountered by trying to express archaeal genes in a eubacterial cell.
Would a yeast cell be a better alternative? Why or why not?
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.
Prescott’s Microbiology, 9th Edition
3.
Comment on the existence of homologous molecular chaperones used in to assist protein folding
across all three domains.
CONCEPT MAPPING CHALLENGE
Prepare a concept map that compares and contrasts the similarities and differences between eubacteria,
archaea, and eukaryotes. Be sure to include the areas of: inititation of DNA replication, transcription
inititation, translation, translation regulation and protein translocation and folding.
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© 2014 by McGraw-Hill Education. This is proprietary material solely for authorized instructor use. Not authorized for sale or distribution in any
manner. This document may not be copied, scanned, duplicated, forwarded, distributed, or posted on a website, in whole or part.