Biology Reference
In-Depth Information
[78]
. Since excess salinity is a common problem in soils
around the world, the experimental results could have real-
world applications to agriculture. To define a timeframe in
which plants should be treated, the first step was to run
a time course experiment with microarray analyses per-
formed at multiple time points after exposure to high salt
media. It was found that a substantial change in the
expression of a large number of transcription factors
occurred after 1 hour of exposure to high salt. This time
point was then selected for the analysis of six individual
cell types and four developmental stages isolated through
FACS sorting and microdissection. The remarkable finding
was that far more genes were differentially regulated within
individual cell types and/or developmental stages than
across all cell types and developmental stages. Moreover,
with the heightened resolution this approach afforded, there
were about eight times as many genes identified as being
responsive to salt stress than had been previously identified
using entire organs or whole plants
[78]
. This strongly
suggested that even though salt is equally toxic to all cells,
differential responses have evolved that are beneficial to the
organism as a whole.
So what are the genes that respond to salt doing, and
why is their expression regulated in a tissue-specific
manner? Some answers are emerging. A striking morpho-
logical change that occurs upon encountering a high-
salinity environment is swelling of the cells in the cortex.
This could be an effort by the root to lower the salt
concentration through dilution in the cortex cells. Within
the cortex, a set of genes that regulates cell expansion were
specifically downregulated upon salt stress
[79]
. Similarly,
root hair elongation is aborted upon exposure to salt, which
could be an effort to reduce salt uptake. Genes involved in
root hair outgrowth are downregulated specifically in the
root epidermis
[79]
.
Similar approaches have been used to analyze the
response at the level of individual cell types and devel-
opmental stages of growth in low iron or after nitrogen
stimulation
[80,81]
. In the former, a gene named
POPEYE whose expression is enriched in the pericycle
when grown under iron deficiency conditions was shown
to be required for root growth in low iron conditions. It
encodes a transcription factor of the bHLH family, and
through ChIP-chip analysis it was found to bind the
promoters of a set of genes involved in metal ion
homeostasis
[81]
. It also is co-regulated with a second
gene named BRUTUS, which when mutated results in
faster-growing roots under iron deficiency conditions.
Both POPEYE and BRUTUS are able to interact with
other bHLH proteins, suggesting that they act as
a complex
[81]
. Thus, a gene regulatory network active in
the response to low iron has begun to emerge with
a transcription factor complex upstream of a set of genes
involved in iron homeostasis.
A Major Challenge: The Transition
to Flowering
The transition from vegetative growth to reproductive
development imposes dramatic changes upon the devel-
opmental programs within the shoot apex. The fertilization
process takes place in flowers and has to be exquisitely
timed with respect to the right season and circumstances,
and the production of flowers and seeds that result from
successful fertilization instead of photosynthetic leaves
imposes physiological demands on the plant. In perennial
plants, this decision is made on a subpopulation of shoot
nodes, but annuals such as Arabidopsis undergo an all-or-
none transition to flowering, heightening the importance of
proper timing of this process. For these reasons, the floral
transition is controlled by the integration of many endog-
enous and environmental cues. Genes controlling flowering
time were among the first described by Arabidopsis
geneticists
[82]
, and the collective effort of numerous
groups has led to a molecular genetic dissection of flow-
ering time control, where separate genetic pathways were
shown to mediate the effect of day length, light quality and
exposure to cold periods, all converging on the transcrip-
tional activity of a few 'floral pathway integrator' genes
encoding transcription factors
[83]
. The pathway integra-
tors mediate the transition to flowering and later activate
floral meristem identity genes, which change the develop-
mental program of shoot meristems to allow the production
of patterned floral organs
which are modified leaves
[84]
.
Over the last decade many molecular details on how the
perception of environmental inputs is transferred to the
activity of floral pathway integrator genes have been
elucidated, and for an updated account of this work we refer
the reader to recent reviews
[85,86]
. This work has clarified
the structure of five separate pathways that control flow-
ering. (1) The photoperiod pathway utilizes rhythmic
stimulation of expression conveyed by the circadian clock
(see Chapter 21) in combination with direct light inputs to
activate, in long days, the CONSTANS (CO) transcription
factor in leaves. CO contributes to the activation of the
floral pathway integrator FT, constituting a mobile signal
that can move to the shoot apex and induce the floral
transition. (2) FT is also regulated by the transcriptional
repressor FLC, whose abundance decreases in prolonged
cold periods due to local changes in chromatin structure.
(3) FLC abundance is also regulated by general factors
involved in chromatin modification and/or RNA process-
ing, which fall into the 'autonomous pathway' that could
monitor developmental age. (4) Increases in ambient
temperature promote flowering and feed into FT abun-
dance. (5) The plant hormone gibberellic acid and high
sugar levels facilitate the induction of pathway integrators
in the meristem. These factors may read out a variety of
endogenous cues related to aging and carbohydrate status.
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