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AGR2451 Lecture 5 - Notes (M. Raizada)
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------------------------------------------------------------------Lecture 5 - Change I- “New Plant Traits from DNA Mutations”
Evolutionary Divergence of the Major
Eukaryotic Model Systems
Moss
Arabidopsis
Plants
Corn
Fungi
Nematode
Fungi
Arthropod
Fishes
Amphibians
Rodents
Primates
Animals
0
200
Precambrian
600
800
1000
1200
1400
time (million years)
400
Cambrian
1600
1800
*Fossil evidence (often much later than molecular clock data)
*Housekeeping/conserved nuclear or organellar genes
*Micro and macro DNA changes (introns, inversions, duplications)
summarized from Proc.R.Soc.Lond.B.(1999) 266: 163-171
Nature (1997) 389: 33-39
Change: Evolution of Land Plant Phenotypes (see
Labs)
•Plants, unlike animals came onto land only once -- all
land plants related
•there are >250,00 species of land plants, most
flowering plants
Flowering Monocots
(65,000 sp. - eg. the grasses:
corn, rice, wheat, barley, rye)
Flowering Dicots
(170,000 sp. - eg. Arabidopsis,
tomato, potato, peaches, canola)
Wind pollen
Corn
Arabidopsis
130200
Fruits, mya?
Gymnosperms
(720 sp. - eg. conifers)
-SeedSeedless vascular
(eg. ferns - 11,000 sp.)
Roots
Bryophytes
(eg. moss -9500 sp.)
Stomates
Surface wax
Freshwater
Green Algae
Vascular
tissue (sugar
water, etc.)
Onto dry land;
secondary
metabolite
>450
mya
Land ecosystems,
human civilization
Model Research
Species
For Plant
Geneticists
Slide
5.2
1. By mutating ancestral genes, single-celled eukaryotes have created
multicellular organisms with novel, divergent traits. However, all
organisms share a common set of genes. Why??
Functions of genes in Arabidopsis (weed, Mustard)
-Transcription
16.9% 3,018 genes
-Protein synthesis
4.1% 730
-Protein fate (modifications, 9.9% 1,766
Folding, compartment targeting)
-Signalling
10.4% 1,855
(incl coordination of multiple cell types)
-Intracellular transport
(between compartments)
-Metabolism
-Plant defence
-Growth
-Transport
Source: TAGI (2000) Nature 408, 796-814
8.3% 1,472
22.5%
11.5%
11.7%
4.8%
assigned
total
4,009
2,055
2,079
849
---------17,833
25,498
Why?? Because all cells must carry out basic functions
such as transcription, protein synthesis and making
plasma membranes. These are called “housekeeping
Slide 1
genes”.
Slide 5.3
• Despite dramatic phenotype changes, a key concept
is that all organisms are remarkably related at
the molecular level in the protein coding regions:
•this may be the greatest discovery in Biology in the
last 50 years!!
eg. >30% of human genes may have a functional
counterpart in yeast (fungus) after 1.4
billion years of evolution
•Obvious related proteins between species pairs:
Human -Fruit fly
61%
Human-Worm
43%
Human-Yeast (fungus)
46%
•~52% of Arabidopsis (plant) genes have a
recognizable DNA/protein sequence to genes
of fruit flies, worms, fungus and humans
Source: IHGSC (2001) Nature 409, 860-921
•out of 289 human disease genes, 48% were
signficantly related to Arabidopsis genes!!
•17 human disease genes are more similar to
Arabidopsis genes than yeast, fruit fly or worm
eg. Hereditary deafness, MYO15
Cystic fibrosis, ABCC7
Source: TAGI (2000) Nature 408, 796-814
•The genetic codes of different plants are very
related to one another.
Why is relatedness advantageous to research in agriculture?
Slide 5.4
Conservation of DNA (Genotype) During Evolution
•sometimes, DNA/amino acid sequences have diverged, but
when the 3-dimensional shapes of proteins from distant
organisms are compared, they have the same shape and perform
a related function
•natural selection selects for protein shape and
function regardless of the encoding DNA sequence
•not only are DNA/protein sequences related, but the linear
order of genes may be shared between more closely related
species (=chromosomal synteny): demo
eg.mouse-cat-human
eg. rice-corn-wheat-barley-oat-sorghum (cereals)
eg. tomato-potato-tobacco-canola-Arabidopsis
•this suggests that during evolution, not only genes,
but entire chromosomal segments were conserved:
Moore, Devos, Wang and Gale (1995)
Current Biology 5, 737-739
Current Biology Publishing Group, (UK)
Grass synteny chromosome map
Slide 5.5
2. If proteins are so highly conserved across species, then
why are there such dramatic differences between species
even closely-related species (humans to chimpanzees or
turfgrass to corn)?
Asked another way, are all mutations equal in their effect?
To breed each of the following new traits, in what type of gene
and location within that gene should mutations be selected for?
-to recognize a new pathogen?
-to make a leaf bigger in size?
-to create a plant with 5 fewer leaves?
-to cause 1000 new genes (responsible for drought tolerance)
to be induced by a new stimulus such as heat?
-to change the amount of starch in a seed?
-to add a sugar group (-OH) onto a plant toxin to detoxify it
for human consumption?
Slide 5.6
To answer the previous questions posed:
•Though proteins and thus DNA coding regions may be
conserved, the regulatory regions are not. Small changes
in regulatory regions can lead to dramatic changes in
phenotype quickly. This is important in plant breeding.
•Small changes in signalling molecules (transcription
factor binding sites, receptor-ligand recognition, hormone
dose) can also lead to dramatic changes in phenotype.
Case Study: Maize evolved from its wild relative, Teosinte.
The two plants can interbreed (same species), yet their shoot
architecture is dramatically different. Mutations in only 1
major gene, Tb1, is responsible for this change.
Slide 5.7
Teosinte vs. Maize
Tb1 gene
QuickTime™ and a
GIF decompressor
are needed to see this picture.
TB1 is a signalling protein, which regulates the number of
vegetative branches produced by a plant. Comparing the
Tb1 gene between teosinte and maize,most of the mutations
are in the regulatory region (as well as in the intron), not
the exons. Changes in the regulation and dose of the mRNA
likely explain the differences in plant architecture.
Indigenous people in Mexico selected for mutations in the
regulatory region of Tb1 over a period of >300 years.
In addition to mutations in the regulatory regions, small amino
acid changes at the binding sites of proteins (eg. enzyme-substrate
binding site,or transcription factor binding site) can lead to
dramatic changes in phenotype.
Slide 5.8
3. Do mutations happen randomly or are they
targetted to certain genes or certain parts of genes?
In the case of Tb1, if mutations occur randomly,
why are there so few mutations between Teosinte and
modern maize in the exons of Tb1?
Natural Selection is the “filter” that
the environment places on
a phenotype, thus selecting
for or against mutations
in the genotype. demo
example-Dubautia (sunflower family) includes
28 species in Hawaii and California
-Rainfall diversity 40cm-1230 cm/year
-Result: natural selection on leaf size
-Is natural selection active or passive?
Most mutations have no effect (neutral) and hence
From Biology of Plants p.164
they simply build-up over generationsP.(eg.
inEvert
introns
and
Raven, R.
and S.Eichhorn
Worth Publishers, New York, 1992
in the DNA between genes on a chromosome)
Slide 1
Slide 5.9
4. Natural Selection vs. Human Selection
•Natural selection took place over 1.4-1.6 billion years for
plants in complex ecosystems, with competition from
predators, struggle over resources with other
plants. Plants were not selected for to serve humans, but
rather to deter animals or
use them for seed dispersal.
•Human selection on plants has been the exact opposite: It
has taken place only for >10,000 years, for the benefit of the
human herbivore, in a monoculture ecosystem
with much less competition. What are the consequences of
these differences?
From Raven
Slide
5.10
International
Seed Banks
•Mutations selected by human selection
by farmers are a much more valuable
resource for crop breeding than random
mutations,or arguably, mutations selected
by natural selection. Hundreds of
thousands of these
varieties exist in seedbanks around the
world and are
used in breeding programs to introduce
new traits.
•Many of these farmer-selected mutations
are likely in
regulatory regions of genes, signalling
proteins and enzyme binding sites.
The Seedbank at The International Maize and
Wheat Improvement Center (CIMMYT), Mexico
•novel alleles caused
drought tolerance,
cold resistance,
disease resistance,
pest tolerance
Raizada
Slide 5.11
5. What causes the (random) DNA mutations?
i) Point mutations, short insertions and deletions.
eg. G to A. These are caused by mistakes during
DNA replication.
ii). Parasitic DNA -- DNA parasites that duplicate themselves and
“jump” into genes and between genes (called transposons,
retroelements, or mobile elements)
Walbot and Petrov (2001) PNAS 98, 8163-8164
National Academy Sci. Press, USA, Washington, DC
gene
gene
gene
•ancient jumping genes may have given rise to introns
•highly repeated blocks of mobile elements are called
heterochromatin (gene-rich blocks = euchromatin)
•examples of mobile elements in humans:
SINEs
1.6 million copies
LINEs
868,000 copies Source IHGSC (2001) Nature 409, 860-921
•in humans and corn, 80-90% of genome consists of
mobile element parasites (“junk DNA”)
•mobile elements can carry new regulatory
information or jump into gene switches
(very important in plant evolution), and hence have
created new alleles for plant evolution
Slide 5.12
Consequences of Parasitic DNA (Mobile Genes)
•dilemma: corn, rice, wheat have highly related genes,
similar # of genes (50-60,000) but the total amount of
DNA in their genomes is very different:
Rice
450 million base pairs
Corn
2,600 million bp
Wheat
12,200 million bp
(all haploid)
Why??
•these genomes vary in the amount of “junk DNA”
they have due to a high copy number DNA parasites
•therefore, mobile DNA is responsible for genome
expansion by creating blocks intergenic “junk DNA”
blocks. **DNA quantity does not correlate with
complexity in multicellular organisms.**
Example of a corn jumping gene jumping in and out:
demo
Pigmentation Gene
Transposon
Insertion
Excision
(Reversion)
Source: M.Raizada
Slide 5.13
Lecture 5 - Concept Summary
1. Proteins are conserved across evolution, especially
“housekeeping proteins”. Most important concept!!
2. Even between non-housekeeping genes, the proteins
they encode maintain their 3-D structures (only 1000
unique folds).
3. Though proteins and thus DNA coding regions may be
conserved, the regulatory regions are not. Small changes
in regulatory regions can lead to dramatic changes in
phenotype quickly. This is important in plant breeding.
4. Small changes in signalling molecules (transcription
factor binding sites, receptor-ligand recognition, hormone
dose) can also lead to dramatic changes in phenotype.
5. Small amino acid changes at the binding sites of proteins
(eg. enzyme-substrate binding site,or transcription factor
binding site) can lead to dramatic changes in phenotype.
6. DNA mutations occur randomly. Mutations with no
effect can accumulate. Mutations with phenotypic effects
can be selected by natural selection or human (breeding)
selection and these new mutations can spread through the
population.
7. Two mechanisms responsible for creating DNA mutations
are spontaneous nucleotide “point mutations” and
the insertion and excision of parasitic mobile DNA
elements (“jumping genes”)
Slide 5.14