The Genetics of
Viruses and Prokaryotes
The Genetics of Viruses and Prokaryotes
Probing the Nature of Genes
Viruses: Reproduction and Recombination
Prokaryotes: Reproduction and Recombination
Regulation of Gene Expression in Prokaryotes
Control of Transcription in Viruses
Prokaryotic Genomes
Probing the Nature of Genes
Prokaryotes and viruses have advantages for the study of genetics:
§ They have small genomes.
§ They quickly produce large numbers of individuals.
§ They are usually ________ making genetic analyses easier.
Probing the Nature of Genes
The ease of use of bacteria and viruses in genetic research has propelled the
science of genetics and molecular biology during the last 50 years.
Prokaryotes continue to play a central role as tools for biotechnology and for
research on eukaryotes.
Prokaryotes play important ecological roles, including the cycling of
elements.
Many prokaryotes and viruses are pathogens.
Viruses: Reproduction and Recombination
Most viruses are composed of a ________ ________ and a few proteins.
Viruses are________ (noncellular) and do not metabolize energy.
Viruses do not produce ATP or conduct fermentation, cell respiration, or
photosynthesis.
Viruses can reproduce only in systems that do perform these functions: living
cells.
Viruses: Reproduction and Recombination
The tobacco mosaic virus was the first virus to be discovered in the 1890s,
but it was not crystallized until the 1930s.
In the 1950s, direct observation by electron microscopes showed how much
viruses differ from bacteria.
The simplest ________ agents are viroids, which are made up only of genetic
material.
-the following note is not on the slides-if you are reading this carefully,
before class, come up to me and if you are the first one to say the phrase that
pays Are prions infectious agents simpler than viroids?" you will be rewarded.-
Viruses: Reproduction and Recombination
Viruses are obligate intracellular ________ that develop and reproduce only
within living cells of specific hosts.
Viruses reproduce using the host's synthetic machinery and usually destroy the
host cell in the process.
The host cell releases progeny viruses, which then infect new hosts.
Outside the cell, the individual viral particles are called virions.
Viruses: Reproduction and Recombination
Virion genetic material is either DNA or RNA and is generally surrounded by a
capsid, or protein coat.
Characteristic shapes are determined by the protein coat.
Viruses are unaffected by antibiotics because they lack the cell wall
structure and ribosomal biochemistry of bacteria.
Viruses: Reproduction and Recombination
Viruses are described according to four different criteria:
§ Whether the genome is DNA or RNA
§ Whether the nucleic acid is single-stranded or double-stranded
§ Whether the shape of the virion is a simple or complex crystal
§ Whether or not the virion is surrounded by a membrane
Viruses: Reproduction and Recombination
Viruses that infect bacteria are called bacteriophage.
________ recognize their host by means of specific binding between proteins in
the capsid and receptor proteins on the host's cell.
The virions are equipped with tail assemblies that inject the phage's nucleic
acid into the host cell.
Viruses: Reproduction and Recombination
The virus may reproduce immediately and kill the host, or postpone
reproduction by integrating its nucleic acid into the host's genome.
There are two types of reproductive cycles: the lytic cycle and the lysogenic
cycle.
Viruses: Reproduction and Recombination
In the lytic cycle, the infected bacterium lyses, releasing the progeny phage.
Phage that only have lytic cycles are called virulent viruses.
The phage nucleic acid takes over the host's synthetic machinery in two
stages: early and late stage.
Viruses: Reproduction and Recombination
The viral genome contains a promoter sequence that attracts host RNA
polymerase.
In the early stage, viral genes adjacent to the promoter are transcribed.
Early gene products often include proteins that shut down host transcription and
stimulate viral genome replication.
In the late stage, viral late genes code for the protein coat and an enzyme
that causes host cell lysis, resulting in viral release.
Viruses: Reproduction and Recombination
In the lysogenic cycle, the host cell does not lyse, but harbors the viral
nucleic acid for many generations.
Bacteria harboring phage that are not lytic are called lysogenic bacteria.
The viruses are called ________ viruses.
Viruses: Reproduction and Recombination
Lysogenic bacteria have a molecule of noninfective phage DNA called a prophage
inserted into their chromosome.
Under some conditions, the prophage replicates during the bacterium's normal
reproductive cycle without otherwise harming the bacterium.
Certain conditions will activate the prophage, initiating a lytic cycle that
results in the release of a large number of free phage.
Viruses: Reproduction and Recombination
Lytic bacteriophage destroy their bacterial hosts, and thus might be useful in
treating diseases caused by bacteria.
Early work by D'Herelle showed that phage could be used to control some
bacterial diseases.
Rise of antibiotics reduced interest in phage therapy, but it may become
useful again, as bacteria become resistant to antibiotics.
Viruses: Reproduction and Recombination
Animal viruses are diverse.
Arboviruses infect both insects and vertebrates. The virus passes from
arthropod to vertebrate via an insect bite. The arthropod is a vector (carrier).
Animal viruses include those that are just particles of protein surrounding a
nucleic acid core as well as those that have a membrane derived from that of the
host.
Some animal viruses have DNA, and some have RNA, but all have small genomes.
Viruses: Reproduction and Recombination
Animal viruses enter cells in three different ways:
§ Endocytosis of a naked virion
§ Endocytosis of a membrane-encased virus
§ Fusion of a membrane-encased virus with the cell's membrane
The life cycles of influenza virus and HIV illustrate two styles of infection
and reproduction.
Viruses: Reproduction and Recombination
Plant viruses can be transmitted in two ways:
§ Horizontal transmission is the spread of viruses from one plant to another.
§ Vertical transmission is the transfer of viruses from parent plant to
offspring.
Viruses: Reproduction and Recombination
To infect a plant cell, the virus must penetrate a ________ ________ and
________________ Insects are possible vectors. A virion-laden insect feeding
on a plant can penetrate the cell wall and insert the virus.
Another means of infection is contact between damaged tissue of an infected
and a noninfected plant.
Viruses: Reproduction and Recombination
Vertical transmission can occur through vegetative or sexual reproduction.
Once inside a plant cell, viruses can spread by moving through plasmodesmata,
the cytoplasmic connections between cells.
The viruses bind with special proteins that assist their travel through the
otherwise too narrow plasmodesmata pores.
Prokaryotes: Reproduction and Recombination
Unlike viruses, bacteria and archaea are living cells that carry out basic
cellular functions.
The division of single cells into two identical offspring produces clones, or
genetically identical individuals.
If a number of cells are spread on a semisolid medium containing agar,
individual cells give rise to clearly visible colonies.
Prokaryotes: Reproduction and Recombination
In 1946, Lederberg and Tatum demonstrated the exchange of DNA between two
living bacteria.
This exchange is called________
The physical contact required for conjugation is initiated by a ________ which
is a fine projection produced by the donor cell.
The DNA transfers through a thin cytoplasmic bridge called a conjugation tube.
Once the DNA fragment is inside the recipient cell, it recombines with
homologous genes.
Prokaryotes: Reproduction and Recombination
Transformation of bacteria occurs when bacteria take up extracellular DNA and
incorporate it.
More than 75 years ago, Frederick Griffith obtained the first evidence for
transfer of genes between bacteria.
Prokaryotes: Reproduction and Recombination
In ________ viruses carry genes from one cell to another
During the lytic cycle, some bacteriophage package a host bacterium's DNA in
capsids, or viral protein coats.
Cells infected by such viruses get a segment of another bacterium's DNA, not
the viral DNA.
In transduction, this bacterial DNA recombines with the chromosomal DNA of the
host and alters its genetic composition.
Prokaryotes: Reproduction and Recombination
Plasmids are small, circular chromosomes found in many bacteria.
Each plasmid replicates separately from the primary chromosome.
Plasmids move between bacterial cells during conjugation.
Different types of plasmids are classified according to the kinds of genes
they carry.
Some plasmids (metabolic factors) carry genes for unusual metabolic functions,
such as degrading oils from oil spills.
Prokaryotes: Reproduction and Recombination
Fertility factors (F factors) are plasmids that carry genes for conjugation.
Around 25 genes, including the ones responsible for the pilus, are on the F
factor plasmid.
Bacteria with this plasmid are called F+.
On occasion, this F plasmid inserts into the main chromosome.
When this occurs, chromosomal genes can be transferred during conjugation.
Prokaryotes: Reproduction and Recombination
Some plasmids are resistance factors (R factors) and carry genes that code for
proteins that protect the bacteria.
Antibiotic resistance genes interfere with antibiotic activity or transport.
Research found that resistance to an entire spectrum of antibiotics could be
transferred by conjugation.
This finding raised the warning that inappropriate use of antibiotics may lead
to their becoming ineffective.
Prokaryotes: Reproduction and Recombination
Segments of chromosomes or plastids that can move into other genes within a
cell are called transposable elements.
The movement of these t________ elements into other genes disrupts normal
function.
Long transposable elements (about 5000 base pairs), which include one or more
genes, are called transposons.
Transposons have contributed to the evolution of plasmids, and there is some
evidence that R factors developed antibiotic resistance through transposons.
Regulation of Gene Expression in Prokaryotes
Prokaryotes can conserve energy and resources by making proteins only when
they are needed.
Cells can regulate protein synthesis by several methods:
§ Block transcription of the gene that codes for a protein
§ Hydrolyze the mRNA after it is made
§ Prevent translation of mRNA at the ribosome
§ Hydrolyze the protein after it is made
§ Inhibit the function of the protein
Regulation of Gene Expression in Prokaryotes
E. coli prefers glucose as an energy source, but can use lactose if glucose is
low.
Three enzymes are required for lactose metabolism.
Presence of lactose stimulates production of these enzymes. Lactose is
an________
The enzymes that are produced are said to be inducible.
Enzymes that are made all the time are said to be constitutive.
Regulation of Gene Expression in Prokaryotes
There are two basic ways of regulating the rate of a metabolic pathway:
§ Allosteric regulation
§ Regulation of protein synthesis
Regulation of Gene Expression in Prokaryotes
Structural genes specify the primary structures (amino acid sequence) of a
protein molecule.
The three structural genes involved in lactose metabolism are adjacent to each
other on the E. coli chromosome.
All are ________ together when a single promoter binds RNA polymerase.
When these enzymes are not needed, the mRNA synthesis must be shut down, using
the operon mechanism.
Regulation of Gene Expression in Prokaryotes
Prokaryotes shut down transcription by placing an obstacle between the
promoter and its structural genes, called the operator.
If a specific protein, the repressor, binds to the operator, it creates an
obstacle, and RNA polymerase is blocked from transcribing the structural genes.
When the repressor is not attached to the operator, mRNA synthesis proceeds.
The whole unit of genes and their DNA controls is called an operon.
Regulation of Gene Expression in Prokaryotes
The ________ for the three lactose-metabolizing enzymes is called the lac
operon.
The repressor protein has two binding sites: one for the operator and the
other for inducers.
Binding of the repressor by the inducer molecules (lactose) changes the shape
of the repressor by allosteric modification.
The change in shape prevents the repressor from binding to the operator.
Thus, RNA polymerase can bind to the promoter and start gene transcription of
the lac operon.
Regulation of Gene Expression in Prokaryotes
If the concentration of the inducer (lactose) drops, the functioning repressor
binds the operator, and the enzymes for lactose metabolism are not synthesized.
If the concentration of lactose rises, the repressor itself is bound and does
not bind the operator. The enzymes for lactose metabolism are synthesized.
Regulation of Gene Expression in Prokaryotes
The repressor protein is coded for by the regulatory gene.
The regulatory gene that codes for the lac repressor is the i (inducibility)
gene.
The i gene is located near the lac structural genes. However, not all
regulatory genes are near the operons they control.
Regulatory genes like i have their own promoter, called pi.
The i gene is expressed constitutively (expression is constant).
Regulation of Gene Expression in Prokaryotes
Summary of the lac operon control:
§ When no inducer (lactose) is present, lac is off.
§ The regulator protein (repressor) turns the operon off.
§ The i gene produces the repressor.
§ The operator and promoter are DNA sequences that are binding sites for
regulatory proteins.
§ Adding inducer (lactose) turns the operon on.
Regulation of Gene Expression in Prokaryotes
If synthesis of an enzyme can be turned off, it is said to be________
The trp operon in E. coli is repressible.
In the absence of tryptophan, RNA polymerase transcribes the trp operon,
leading to production of enzymes that synthesize tryptophan.
When tryptophan is present, it binds to a repressor, which becomes active.
The repressor binds to the operator of the trp operon, blocking production of
enzymes for tryptophan synthesis.
Regulation of Gene Expression in Prokaryotes
The molecule that binds and activates a repressor is called a corepressor.
The corepressor may be the end product of the operon (as in the case of
tryptophan), or an analog.
In inducible systems, an inducer from the cell's environment prevents a
repressor from blocking transcription.
In repressible systems, a corepressor produced by the cell activates a
repressor, enabling it to block transcription.
Regulation of Gene Expression in Prokaryotes
Another way to regulate transcription is to make the promoter sequence of the
operon work more efficiently.
When glucose is high, even when lactose is available, the lac operon fails to
transcribe frequently.
When glucose is low, and lactose is available, lac structural genes are
transcribed.
Low glucose levels cause elevated levels of cyclic AMP (cAMP).
Regulation of Gene Expression in Prokaryotes
When glucose is low and cAMP is high, cAMP binds to a protein called CRP.
The CRPcAMP complex binds the DNA just upstream of the promoter.
Binding of this site makes it easier for RNA polymerase to bind the promoter
and thus increases rates of transcription.
Regulation of Gene Expression in Prokaryotes
When glucose is abundant, cAMP levels drop.
The CRPcAMP complex does not form.
Without the CRPcAMP complex, RNA polymerase cannot bind to the promoter
efficiently.
The lac structural genes are not transcribed.
This is called catabolite repression.
Control of Transcription in Viruses
Viruses also have gene regulation mechanisms.
Bacteriophage l is a temperate phage, meaning that it can undergo either a
lytic or a lysogenic cycle.
When host bacteria are growing in rich medium, the prophage remains lysogenic;
when the host is less healthy, the prophage becomes lytic.
A "genetic switch" determines the prophage behavior.
Control of Transcription in Viruses
Two regulatory proteins, cI and Cro, compete for two operator/promoter sites
on phage DNA.
One operator controls the lytic gene activities; the other, lysogenic cycles.
The two regulatory proteins have opposite effects on the two operators.
cI represses the lytic operator/promoter and activates the lysogenic
operator/promoter.
Cro activates the lytic operator/promoter and represses the lysogenic
operator/promoter.
The relative concentrations of cI and Cro determine the outcome.
Prokaryotic Genomes
Viral genomes were the first to be sequenced.
Three types of information can be obtained from a genomic sequence:
§ Open reading frames can be recognized by promoter regions and start and stop
codons.
§ Amino acid sequences can be deduced from the DNA sequence.
§ Gene control sequences of promoters and terminators can be identified.
Prokaryotic Genomes
Functional genomics is the assignment of roles to the products of genes
described by genomic sequencing.
Haemophilus influenzae has a circular chromosome of 1,830,137 base pairs and
1,743 protein-coding regions.
When it was sequenced, 42 percent of the genes coded for proteins with unknown
functions.
Roles for most of the unknown proteins have now been identified by a process
known as annotation.
Prokaryotic Genomes
Comparative genomics involves the comparison of genome sequences of different
organisms.
In addition to the sequences for H. influenzae, those for Mycoplasma
genitalium (580,070 base pairs) and E. coli (4,639,211 base pairs) have been
completed.
Prokaryotic Genomes
Scientists are discovering genes for proteins in prokaryotes that cause
infectious diseases.
These are potential targets for new drugs.
New vaccines may be possible as cell surface antigen coding genes are
discovered.
Prokaryotic Genomes
There are some universal genes needed by all organisms, such as those coding
for an ATP binding site.
M. genitalium has just 470 genes, the smallest known genome.
Using mutagens to knock out genes, scientists have determined that M.
genitalium can survive in the laboratory with just ________ genes.
This number is termed the "minimal essential genome."
Animation 13.1 The lac Operon
Animation 13.2 The trp Operon
Video 13-01