Myers Lecture 4 Eukaryotes Fall06

8/2/2019 Myers Lecture 4 Eukaryotes Fall06

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4HumanBiology2AMyersLecture4: TheEukaryoticGenomeand itsExpression

What use are the genome sequences?

Can deduce most of the biochemical capabilities of a bacterial

species (which genes are present and which are absent are both

important for understanding the biology of each species)

Development of antibacterial drugs and vaccines is greatly

accelerated because coat proteins and other targets are known

DNA tests can be done to determine whether a strain carries

pathogenic versions of particular genes

Strains (especially of Streptomyces species) that produce

antibiotics and other valuable proteins or chemicals can be

identified much more quickly

Many environmental applications


Environmental DNA sequencing

Take uncultured, unseparated biological material from an

interesting site

Soil, water, polluted area

Human site (gums, gut, throat, etc.)

Filter out all organisms that are not bacterial species

Sequence the bacterial DNA as a pool (i.e., dont separate outdifferent bacterial species before sequencing)

Analyze the sequences to determine which species and/or

which types of genes are present in the pool

> 99% of bacterial species are not culturable


Sequenced genomic DNA from biofilm at toxic waste site

Collected about 76 Mb of sequence

Acid mine studyIron Mountain, CA (waste from iron mining)

Nature 438, 37-43 (March 2004)


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Superfund site

Discharging >1 ton of toxic metals/day

(pH


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Eukaryotes vs. prokaryotes

Life: The Science of Biology.

8th Edition. Sinauer Press.

Note: these numbers are not correct:

The smallest (free-living) prokaryotic genome is about 10 6 bp in length

The smallest eukaryotic genomes are about 10 7 bp in length (e,g Saccharomyces cerevisiae [Bakers yeast]genome is 12 Mb)


We now know the complete genome sequences of more

than 100 eukaryotic organisms

A product of The Human Genome Project (begun in 1990)


Uses of genome sequences

Key concept

Functions of many genes can be deduced by comparing the

DNA sequences in different organisms

Why?

Genes that encode proteins with the same or similar functions

in different organisms have similar DNA sequences(this is because all organisms are evolutionarily related, i.e., they all

share a common ancestry)

So: if you know the function of a gene in one organism(based

on experiments), you can guess the function of a gene of similarsequence in another organism


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Complete genome sequences:

This is for the fruit fly, but the proportions are similar for humans

1. identify all the genes in an organism

2. allow classification of most genes into functional categories


50% of the human genome is composed of repetitive sequences

Much of the genome of higher animals is repetitive. Over time, it has become clear that much of this DNAconsists of mobile DNA elements (transposons) or their fossils.

--------- 45% (!!)

1. Small repeats

MicrosatellitesMinisatellites

(simple sequencerepeats)

2. Larger repeats

Gene family membersSegmental duplications (5% of the human genome)Range from several kb to many thousands of kb


Eukaryotic genes vary tremendously in size

Molecular Biology of the Cell.

4th Edition. Garland Science.

Some genes are even larger. The dystrophin gene (which is mutated in

boys with Duchenne muscular dystrophy) is more than 2 million base pairs inlength.

26 exons, 9,000 nucleotide-long

mature mRNA, 2,351 amino acids

in the protein3 exons, 600 nucleotide-longmature mRNA, 146 amino acids in

the protein


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Prokaryotes Eukaryotes




Potential points for regulating gene expression in eukaryotes




How eukaryotes control the expression oftheir genes

1. Transcription

2. Splicing

3. RNA stability (we wont discuss)

4. RNA editing

5. Translational and post-translational


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1. Eukaryotic transcription

Many similarities to prokaryotic transcription

Same directionality, precursors, etc.

RNA polymerase(s) = transcribing enzyme

But very important differences

Many sequence-specific transcription factors

RNA polymerase and promoters are more complex

Many different long-distance transcriptional elements

Enhancers, silencers

Can be >500,000 bp away from promoter

DNA is covered with histone (and other) proteins

Provides a global regulation mechanism

Chromatin = histone/DNA complex

Chromatin is modified +/- transcription


Eukaryotic promoters have RNA polymerase and regulatory protein binding

sites

Long-distance elements can be upstream, downstream and within a gene

Control regions for eukaryotic genes






looping

DNA binding proteins regulate transcription of genes


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(another version)


Genes that need to be expressed at the same time

often share a common regulatory protein



Example:

Genes needed by cells

to respond to stress


The globin gene familyIts genes are differentially expressed at different times during development

There are many gene families in higher eukaryotes

Humans: About half our genes are members of families

Multiple proteins related in sequence and function

Arose during evolution from common ancestral genesLife: The Science of Biology.



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Slightly different proteins are made from each gene

Why?

Fetal -globin genes (G and A)bind O2 more strongly than doesadult -globin

This allows O2 from mothershemoglobin in the placenta to bepicked up by the fetushemoglobin




Eukaryotic DNA in the nucleus is complexed

with histones to form chromatin

Open chromatin

Genes transcribed

Closed chromatin

Genes turned off

Histone

octamers






2. Splicing




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How do enzymes know where to cut and splice?




Splicing in more detail




Alternative splicingAllows a tremendous increase in diversity of proteins from a smaller number of genes




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4. RNA editing

For some genes, the RNA sequence can be changed after transcription (= RNA editing)




5. Translational and post-translational regulation

Rate of translation is highly regulated -- many mRNAs dont gettranslated non-stop, but are held until protein is needed

Example: Regulation of ferritin, an iron storage protein

When iron is low, a translational repressor proteinbinds to ferritin mRNA and prevents translation

When iron levels rise, excess iron binds to therepressor and alters its structure, causing it to detachfrom the mRNA, allowing translation


Low iron

Dont need ferritin

High iron

Need ferritin




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The lifetime of proteins is controlled by the proteasome

Regulating the lifetime of a protein is a way to control its actions

Myers Lecture 4 Eukaryotes Fall06

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