Transcript The Plant Cell - Molecular and Cell Biology

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Mendel forever
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The data
Expt. 1. Form of seed. -- From 253 hybrids 7324 seeds were
obtained in the second trial year. Among them were 5474
round or roundish ones and 1850 angular wrinkled ones.
Therefrom the ratio 2.96:1 is deduced.
Expt. 2. Color of albumen. -- 258 plants yielded 8023 seeds, 6022
yellow, and 2001 green; their ratio, therefore, is as 3.01:1.
Expt. 3. Color of the seed-coats. -- Among 929 plants, 705 bore
violet-red flowers and gray-brown seed-coats; 224 had white
flowers and white seed-coats, giving the proportion 3.15:1.
Expt. 4. Form of pods. -- Of 1181 plants, 882 had them simply
inflated, and in 299 they were constricted. Resulting ratio,
2.95:1.
Expt. 5. Color of the unripe pods. -- The number of trial plants was
580, of which 428 had green pods and 152 yellow ones.
Consequently these stand in the ratio of 2.82:1.
Expt. 6. Position of flowers. -- Among 858 cases 651 had
inflorescences axial and 207 terminal. Ratio, 3.14:1.
Expt. 7. Length of stem. -- Out of 1064 plants, in 787 cases the stem
was long, and in 277 short. Hence a mutual ratio of 2.84:1. In
this experiment the dwarfed plants were carefully lifted and
transferred to a special bed. This precaution was necessary,
as otherwise they would have perished through being
overgrown by their tall relatives. Even in their quite young state
they can be easily picked out by their compact growth and
thick dark-green foliage.
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Sweet
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Mendel's dwarfing gene: cDNAs from the Le
alleles and function of the expressed proteins
Martin et al. Proc. Natl. Acad. Sci. USA Vol. 94, pp. 8907-8911
Four alleles of the Le locus known:
Le > le-3 > le > led.
“gibberellins”
The stature of Le mutants can be restored
by application of GA1, but not by
GA20
Herr Mendel, meet Drs. Beadle and Tatum
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Mendel's green cotyledon gene encodes a positive
regulator of the chlorophyll-degrading pathway
Sato et al. PNAS August 28, 2007 vol. 104 14169-14174
“Mendel's Green Cotyledon Mutation Is a Stay-Green Mutation.
The pea strain JI2775 has a defect on the I locus and presents
green cotyledons in mature seeds …. And also retains
greenness of leaves during leaf senescence, suggesting that
JI2775 is a stay-green mutant and that the I gene functions in
Chl degradation both in cotyledons during seed maturation and
in true leaves during senescence
Also see Armstead, et al. (2007) Science 315, 73
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1866 – 2007 – ∞
Solely on the basis of statistical analysis of plant crosses, and a full
century before the discovery of the structure of DNA, the chemical
nature of mutations, the “central dogma (fact) of molecular biology,”
the notion that genes code for enzymes (or enzyme subunits) – in
essense, before the discovery of anything at all relevant to what is
being studied here – Mendel correctly determined that differenced
between plants in traits such as seed shape, plant height, and seed
color are determined by discrete entities that behave in a distinct,
specific way during meiosis, and during ontogeny.
Nearly 150 years later, molecular genetic and biochemical analysis has
shown that Mendelian inheritance of the traits Mendel studied is, in
precise agreement with his model (take THAT, Karl Nägeli and your
stupid apomixing Hieracium; grrrrrrr), due to specific lesions
(mutations) in single genes coding for enzymes directly involved in
the development of the traits that Mendel studied. Furthermore, the
nature of the lesions conclusively explains the recessive nature of
the alleles Mendel studied.
These examples offer wonderful case studies in the effect of genotype
on phenotype.
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“It’s All in the Genes”
New York Times, 5/2/04
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Gene  phenotype
Other genes  epistasis  variable
expressivity (sickle-cell anemia)
The environment  “norm of reaction” 
variable penetrance (BRCA1-induced
breast cancer)
Epigenetic effects
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Plant epigenetics 1:
mitotically, but not meiotically
resistant inheritance
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Persephone, the Greek goddess of Spring
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A bit of plant biology – the seeming
paradox of vernalization
“Vernalization is the process by which prolonged exposure
to cold temperatures promotes flowering.
Monocarpic species senesce after flowering and setting
seed. … Plants that require vernalization to flower thus
typically require two seasons to complete the life cycle
and are usually classified as biennials or winter annuals.
Many winter annuals and biennials become established in
the fall, taking advantage of the cool and moist
conditions optimal for their growth. The vernalization
requirement of such plants prevents flowering until
spring has actually arrived. ”
R. Amasino The Plant Cell 16:2553-2559 (2004)
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Vernalization
A) A biennial cabbage (Brassica
oleracea) variety with an obligate
vernalization requirement that had been
growing for five years without cold
exposure. The small plant in my
daughter's hands is a summer-annual
variety of B. oleracea that flowers
rapidly without vernalization.
(B) and (C) Summer annual and
vernalization-requiring types of henbane
(B) and Arabidopsis (C). In both
examples, a single-dominant gene is
responsible for the vernalizationrequiring habit. All plants were grown in
long days (inductive photoperiods)
without vernalization. The rapidflowering summer annuals (which have
initiated flowering) are at left and the
winter-annual types at right.
R. Amasino The Plant Cell 16:2553-2559 (2004)
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“I think it is reasonable to refer to the
vernalization-induced, mitotically stable
acquisition of the competence to flower as
an epigenetic switch because it is a
change that can be propagated through
cell divisions in the absence of the
inducing signal.”
R. Amasino The Plant Cell 16:2553-2559 (2004)
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“The vernalization-mediated repression of
FLC is epigenetic in the sense discussed
above: The repressed state of FLC is
maintained after vernalized plants are
returned to warm growing conditions.
Thus, in Arabidopsis, vernalization
provides competence to flower by
repressing the expression of a flowering
repressor. As expected, FLC expression
is on again in the next generation. This
resetting of the epigenetic switch during
passage to the next generation is
reminiscent of genomic imprinting in
animals. But the unique aspect of this
switch is that the on-to-off direction of the
switch is set by perception of the
environment, whereas the off-to-on
direction is set by passage to the next
generation.”
R. Amasino The Plant Cell 16:2553-2559 (2004)
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Tragic memories
“… some might argue that the term epigenetic
should be used only for changes that
persist from one generation to the next.
This of course does not happen in the
case of vernalization; if it did, a biennial
would only be a biennial for one
generation.
One of Lysenko's false claims was that the
vernalized state was heritable; that is, a
vernalized plant would transmit the rapidflowering trait to the next generation. This
fit the Marxist ideology that the
environment of the members of a Marxist
society could produce heritable changes
in attitude, and, thus, if the proper
environment was provided, future
generations would consist of improved
citizens. Lysenko's efforts to obtain or
fabricate results that supported a political
ideology and, with the assistance of
Stalin's regime, to force others to accept
his views had disastrous consequences
for Russian genetics.”
R. Amasino The Plant Cell 16:2553-2559 (2004)
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Plant epigenetics 2:
mitotically and meiotically
resistant inheritance
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Maize (corn) – Zea mays
Maize is monoecious – distinct
male (tassel) and female (“corn
silk”) flowers on the same plant.
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Courtesy of Prof. Jay Hollick, MCB Department
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?!!!
R. Alexander Brink, 1950
Vicky Chandler, Jay Hollick
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What is going on?
1.
2.
3.
4.
5.
The green maize plant is not
outcrossing, it is selfing.
The red allele is
incompletely penetrant,
except when in a
homozygous state.
This is actually two-locus
inheritance, and the green
locus exhibits full dominant
epistasis to the red locus.
This is actually two-locus
inheritance, and the green
locus exhibits full recessive
epistasis to the red locus.
Mmmmm … Milla …
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What IS going on
This is paramutation:
a meiotically heritable change in
the phenotype of a plant that
results not from the physical
alteration of the primary
DNA sequence of the
underlying genes, but from
an effect on their
expression.
Recall Mendel’s “compromise that
the two alleles of a gene
reach in a heterozygous
organism for the life of a
plant.”
In this case, the compromise is
not reached. The Pl’ allele
somehow causes the
epigenetic silencing of the Pl
allele – silencing that
persists through meiosis.
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Transcriptional Regulation of Anthocyanins
Courtesy of Prof. Jay Hollick, MCB Department
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Other genes involved in maize pigment
synthesis can be paramutated
Courtesy of Prof. Jay Hollick, MCB Department
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A critical aspect of the paramutation process – one
that is shared by many epigenetic processes
It is sensitive to the environment:
paramutation can be variably expressive (in other words,
the extent of paramutation can vary, and how variable
it is can be specified by the environment).
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Genetics 140 1379-1387
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Grandpaternal seedling conditions
32C LL
Genetics 140 1379-1387
22C LL
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Three processes
Vernalization:
Environment 
epigenetic state that
is mitotically heritable
Paramutation
“Dialog” of two alleles 
epigenetic state that
is meiotically heritable
and sensitive to the
environment
Transgenerational memory of stress:
environment  epigenetic state that is meiotically heritable
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Transgeneration memory of stress in plants –
Barbara Hohn et al. Nature 442, 1046-1049
“Owing to their sessile nature, plants are constantly exposed to a
multitude of environmental stresses to which they react with a
battery of responses. …Here we show that in Arabidopsis thaliana
plants treated with short-wavelength radiation (ultraviolet-C) or
flagellin (an elicitor of plant defences6), somatic homologous
recombination of a transgenic reporter is increased in the treated
population and these increased levels of homologous recombination
persist in the subsequent, untreated generations. The epigenetic
trait of enhanced homologous recombination could be transmitted
through both the maternal and the paternal crossing partner, and
proved to be dominant. The increase of the hyper-recombination
state in generations subsequent to the treated generation was
independent of the presence of the transgenic allele (the
recombination substrate under consideration) in the treated plant.
We conclude that environmental factors lead to increased genomic
flexibility even in successive, untreated generations, and may
increase the potential for adaptation.”
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1.
Plants are engineered to have a
“reporter gene” – if the gene undergoes
recombination, blue sectors appear.
2.
Irradiation of the plants increases the
number of blue sectors (not surprising).
3.
Most surprisingly, the offspring of the
irradiated plants show increased
recombination frequency.
Molinier et al. Nature 442, 1046-1049
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Great-grand-grand-children
Molinier et al. Nature 442, 1046-1049
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Hmmmmmmmmmmmm
“Influences of the environment on the plant genome have
been documented, [and] have been interpreted as
'genomic shock'. Here we demonstrated that
environmental influences, specifically ultraviolet radiation
and a bacterial elicitor, change the flexibility of the plant
genome in somatic tissue of treated plants and in
somatic tissue of their progeny. As these influences
persist in the entire population of plants, the basis for
the change is epigenetic rather than genetic. Plants
carrying the transgene locus do not have to face the
environmental challenges themselves in order to
transmit the epigenetic change to the offspring; the
stimulus for an increase of recombination can be
imposed in trans by a single treated parent.”
Molinier et al. Nature 442, 1046-1049
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Epigenetics:
from phenomenon to mechanism
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An important point
Paramutation and across-generation
memory of stress are both epigenetic
phenomena: the loci they affect do not
change DNA sequence.
This does not mean, however, that the
mediators of these epigenetic effects are
fundamentally “magical” – there are
genes, the products of which are required
for epigenetic effects.
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From screen …
To mechanism:
Hollick and Chandler
Genetics, Vol. 157, 369-378
Alleman et al.
Nature 442, 295-298
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Arabidopsis thaliana
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Some mutations that affect flower
structure
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S. Jacobsen and E. Meyerowitz
“Superman”
Wild-type flower: 6 stamens (♂).
superman null mutations: 12 stamens.
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S. Jacobsen, UCLA
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No comment on the nomenclature
There are two ways to mutate the
SUPERMAN gene and get the same
phenotype (12 stamens):
1. Just delete the gene.
2. Keep the gene as it and METHYLATE it!
The methylated form is an “epi-allele” of
SUPERMAN and is called clark kent.
S. Jacobsen, UCLA
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S. Jacobsen, UCLA
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Suppressors of clark kent
clk-st
S. Jacobsen, UCLA
Suppressor mutants:
Cmt3 (the DNMT)
or
kyp (kryptonite)
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kyp (kryptonite) codes for an H3K9
histone methyltransferase!
Jackson et al. (Jacobsen) Nature 416: 556-560 (2002).
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From plants to mice
Chandler (2007) Cell 128: 641
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An evolutionary perspective
Mikula (1995) Genetics 140 1379-1387
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And now, to conclude the section
on “classical” genetics – a realworld perspective on the
complexity of life
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Emery and Clayton (2005) “The Mentality of
Crows: Convergent Evolution of Intelligence in
Corvids and Apes” Science 306: 1903
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Weir et al. (2002) Science 297: 981
“Many animals use tools, but their understanding
of physical forces or causal relations is unclear.
Primates are considered the most versatile and
complex tool users, but observations of New
Caledonian crows (Corvus moneduloides) raise
the possibility that these birds may rival
nonhuman primates in tool-related cognitive
capabilities. We report here an experiment
inspired by the observation that a captive female
spontaneously bent a piece of straight wire into
a hook and successfully used it to lift a bucket
containing food from a vertical pipe.”
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No comment
“The male rarely attempted this task and
never bent the wire. He observed the
female bending the wire and stole the food
from her in three trials.”
Weir et al. (2002) Science 297: 981.
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An actual e-mail
Hey Professor Urnov, This is X from your MCB 140
course at Berkeley. How are you doing and how
are things at Sangamo? I hope things are going
well for you. As for me, [after] graduat[ing] from
Berkeley I have moved back home to X.
I have am also considering a career in Y and am
currently applying. I was wondering if you'd be
willing to provide a letter of reference for me. If
possible, please let me know so that I can properly
send you the materials necesary for doing so.
Thank you. Sincerely,
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An actual application
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A two-step solution
1.
2. Horace Judson The Eighth Day of
Creation; Steven Jay Gould The
Mismeasure of Man
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Next
1. No office hours today.
2. Review session 7 pm (sharp) – 9 pm –
will feature practice midterm and lots of
“clicking” – answers to homework will be
given – Thursday, Oct. 4, Dwinelle 155
3. Answers to previous midterm and to
homeworks will be posted shortly
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