Download study guide for Vlad

ENGL 299C
April 28, 2014
Below is an in-progress, "Science in the Classroom"-style study guide for Daniela Vlad et al., "Leaf shape
evolution through duplication, regulatory diversification, and loss of a homeobox gene" (Science 343:
780-783, 2014).
GLOSSARY
Term
Assay
Auxin
Brassicaceae
Concerted Evolution
Dissected Leaf
Eudicots
Gene Duplication
Genetic screen
Homeobox
Homeodomain
In Situ Hybridization
Interspecific gene
transfers
Lobed leaf
Meristem
Morphogenesis
Neofunctionalization
Organogenesis
Student-provided definition
A laboratory procedure that measures “the presence or amount or the
functional activity of a target entity” (Wikipedia) (x2)
Plant hormones that play central role in the development of plant bodies,
especially in the zone of elongation involved in plant growth (Wikipedia). (x4)
An angiosperm family that mainly consists of mustard plants (Wikipedia). (x2)
A process that may explain the observation that paralogous genes within one
species are more closely related to each other than to members of the same
gene family in another species, even though the gene duplication event
preceded the speciation event. (Wikipedia) (x2)
A leaf that is deeply divided into numerous segments (Dictionary.com)
also known as “true dicots”; a monophylectic group of dicots (seed with two
embryotic leaves) that has tricolpate pollen. Source: Plant Systematics 3rd
Edition-Judd et al. (x2)
Evolution where genes are amplified and production of gene-specific products
increases (Google)
an experimental technique used to identify and select for individuals who
possess a phenotype of interest (Wikipedia)
A 180 base pair sequence in DNA that codes for a binding domain. Is
important in controlling morphological patterns in animal, fungal, and plant
development. (Wikipedia/Freeman text). (x7)
the part of a protein (60 amino acids encoded by a homeobox) that attaches
(binds) to specific regulatory regions of the target genes. Genes in the
homeobox family are involved in a wide range of critical activities during
development. (Google/biology-online.org) (x2)
A type of hybridization (the process of forming a double stranded nucleic acid
from joining two complementary strands of DNA or RNA) that uses a labeled
complementary DNA or RNA strand to pinpoint the location of a specific DNA
or RNA sequence in a section of tissue Sources: Wiki and http://www.biologyonline.org/dictionary/Hybridization (x2)
The naturally occurring transmission of genetic information between
organisms, related or unrelated, circumventing parent-to-offspring
transmission (http://www.reference.md/files/D022/mD022761.html)
a leaf having deeply indented margins (Wikipedia)
Leading growth tissue in the majority of plants that is the source of all the
tissues in a plant (Wikipedia/Freeman text)
the origin and development of morphological characteristics (Wikipedia) (x3)
a mutation event when one gene copy takes on a new function not present in
ancestral genes after duplication. Source: Wiki (x3)
A stage of embryonic development when major organs develop. Source:
ENGL 299C
Ortholog
Paralogs
Phylogeny
Pleiotropy
Pluripotent
Primordia
RCO homeodomain
protein
Reporter Gene Assay
Serration
Stipule
Tandem gene
duplication
Taxonomy
Transgene
Wild Type
April 28, 2014
Biological Science 4th Edition-Freeman (x2)
Genes in different species that are similar because of vertical descent from the
same common ancestor (Wikipedia). (x5)
genes related by duplication within a genome. Orthologs retain the same
function in the course of evolution, whereas paralogs evolve new functions,
even if these are related to the original one.
(http://homepage.usask.ca/~ctl271/857/def_homolog.shtml) (x4)
Tree of evolution showing the path of evolution of species.
(Wikipedia/Freeman text)
When one gene has effects on numerous and seemingly unrelated phenotypic
traits. (Wikipedia/Freeman text) (x5)
a cell that still can divide into a multitude of cell types, but only into those
within a specific tissue
The earliest stage of an organ or tissue (Google)
Reduced complexity, protein structure that binds to DNA or RNA (e.g.
transcription factors). Gene associated with the formation of leaflets instead of
leaves. Wikipedia-en.wikipedia.org/wiki/Homeodomain_fold (x2)
a gene that researchers attach to a regulatory region or a gene of interest that
allows them to know whether the gene has been expressed in a cell or
organism. Source: Wiki (x2)
A formation that resembles the teeth of a saw. (Edges of a leaf in this study)
(merriam-webster) (x2)
a small leaflike appendage to a leaf, typically borne in pairs at the base of the
leaf stalk. (Google)
Indicated by sequencing read pairs, which map in abnormal orientations.
Through a combination of increased sequence coverage and abnormal
mapping. Wikipedia-http://en.wikipedia.org/wiki/Gene_duplication
Differentiating groups of organisms based on shared/unshared characteristics
(Wikipedia).
genetic material that has been transferred from one organism to another.
Source: Wiki (x4)
a strain, gene, or characteristic that prevails among individuals in natural
conditions, as distinct from an atypical mutant type. (Google) (x2)
PREVIOUS WORK
Ref #
1
2
3
4
Student-provided summary
Background information on how simple and dissected leaflets develop on the apical
meristem and is also used to realize that we don't know how genes develop these leaflets. (x2)
This paper analyzes the causes of proliferation of leaves into leaflets, which is one of the core
things Vlad et. al. focuses on in the paper. Specifically it talks about the effect of a certain gene
on the formation of compound leaves, which is very similar to Vlad et. al.'s research. (x3)
These scientists studied the generation of divergent leaf forms. They found that KNOX
proteins rely heavily on the PIN1 transporter and that this process is what drives the formation
of the two different leaf forms. (x4)
This paper revolves around the study of KNOX genes that affect the meristem. This is important
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April 28, 2014
because they make statements regarding the effect of the gene on the meristem that leads to
the production of leaflets, which is in the same place as the KNOX genes. (x2)
LMI1 (Late Meristem Identity 1) is a transcription factor that acts as a meristem identity
regulator. The specific time and place that the transcription factor LMI1 is activated is crucial for
meristem identity and leaf morphogenesis. To me this screams out as especially important
because a very large portion of Vlad et. al.'s paper uses results regarding the LMII genes, which
were what Saddic et. al. were investigating. (x6)
This reference is important because Vlad et. al.'s paper has a significant focus on how the plant
is devolved the RCO gene in an evolutionary split addressed in Beilstein et. al.'s paper. (x2)
This reference is attempting to determine the phylogeny of the family of plants Brassicacea. The
scientists determined that the 24 of the 25 species of plant in this family have a common
ancestor with each other. (x2)
A book describing the duplication of genes as a basis for molecular evolution. Used to show a
contrast between evolution through loss of genes as opposed to the duplication of genes. (x3)
This article outlines the genetics behind how Arabidopsis thaliana’s leaf form could have
changed from a more complex ancestor through the loss of expression at a homeobox (STM).
(x2)
A study that uses ablation to show that the early pattern of oriented growth leads to a specific
leaf shape and that the leaf base is the foundation for organizing leaf growth.
Pertains to a chemical called auxin. It helps make the important point that there are multiple
chemical signals in play in the formation of this plant structure, therefore giving the researchers
more variables to test for.
More information on morphogenesis in plants as well as application of heat maps to Daniela
Vlad et al.
This experiment studied the difference in plant leaf morphologies and noted that it had to do
with the presence of KNOX proteins. Having KNOX would cause the leaf to have a dissected
form, while not having any KNOX would cause the leaf to have a simple form.
Inspiration for the idea of transgenics in Daniela Vlad et. al. Review on pleiotropy as well as
evasion of pleiotropy in evolution to avoid deleterious effects.
Article proposing that the method of gene duplication affects how genes are passed on. Used as
a reference to propose more research.
FIGURES
Figure 1
 QUESTION: Is the RCO gene responsible for the complexity of leaves in C. hirsuta?
 EXPERIMENT (F-I): Knock out the RCO gene in C. hirsuta (G), then see whether adding back
the RCO gene (H) restores the phenotype of complex leaves.
 RATIONALE (F-I): If RCO is solely or largely responsible for the leaf complexity, then its
presence or absence will dictate whether the leaves are dissected or simple.
 RESULTS (F-I): RCO was necessary and sufficient for leaf complexity to develop in C. hirsuta.
Trying to restore the complexity with the highly similar gene ChLMI1 did not work.
 CONCLUSION: RCO is a primarily controller of leaf complexity. Its absence leads to simple
leaves as found in Arabidopsis.
ENGL 299C
April 28, 2014
Figure 2
 QUESTION: RCO's sequence is very similar to 2 other genes. Is its anatomical pattern of
expression (as opposed to its sequence) responsible for its effect on leaf shape?
 EXPERIMENT (A-L): Determine where expression of RCO and ChLMI1 is normally expressed
in developing C. hirsute plants.
 RATIONALE (A-L): If RCO's expression pattern (as opposed to its amino acid sequence)
mediates its effect on leaf shape, if should be expressed in locations that are distinct from
where ChLMI1 is expressed and that would allow it to affect leaf shape.
 RESULTS (A-L): RCO expression (A-D, I) was anatomically distinct from ChLMI1 expression (EG, J).
 EXPERIMENT (M-O): Determine leaf complexity in RCO mutants complemented with ChLMI1
under the control of the RCO promoter.
 RATIONALE (M-O): If expression pattern rather than amino acid sequence is most important
for RCO's effect, ChLMI1 should have the same effect when controlled by the RCO promoter.
 RESULTS (M-O): ChLMI1 controlled by the RCO restored leaf complexity.
 EXPERIMENT (P-R): Add RCO genes into Arabidopsis plants.
 RATIONALE (P-R): If RCO's presence in C. hirsuta explains why its leaves are shaped
differently than Arabidopsis leaves, adding RCO to Arabidopsis should make Arabidopsis
leaves more complex.
 RESULTS (P-R): Adding RCO to Arabidopsis made its leaves for C. hirsuta-like.
 CONCLUSION: RCO achieves its specific effects on leaf shape via its promoter, not via subtle
amino-acid sequence differences.
Figure 3
 QUESTION: Does RCO alter leaf shape by repressing growth at the boundary between
leaflets?
 EXPERIMENT (A-B): Determine auxin activity in wild-type (A) and RCO-lacking (B) C. hirsuta.
 RATIONALE (A-B): If RCO acts independently of auxin, auxin activity will be similar in the
wild-type and mutant.
 RESULTS (A-B): Auxin activity was similar in wild-type and mutant C. hirsuta.
 EXPERIMENT (C-H): Monitor cell proliferation in C. hirsuta with and without RCO.
 RATIONALE (C-H): If RCO suppresses growth at leaflet boundaries, these boundaries will
show less proliferation in the RCO-lacking mutant.
 RESULTS (C-H): There was less cell proliferation in the RCO-lacking mutant.
 CONCLUSION: RCO alters leaf shape by repressing growth at the boundary between leaflets.