ABI3 finding that it can impart desiccation stress

ABI3 (Abscisic acid
insensitive 3), a homologue of maize viviparous
1 (VP1), was identified in mutant background insensitive to ABA hormone.

Earlier designated as a seed specific transcription factor 1-3, ABI3 has now emerged as a general regulator in
cellular maturation and plant developmental processes such as quiescence of
shoot apex meristem, plastid differentiation, regulation of flowering time,
etc.4, 5. ABI3 was also found at the juncture of ABA-auxin
signaling crosstalk during seed germination, lateral root initiation and stress
physiology 6-8. In recent years, role of ABI3 has stretched beyond
developmental aspects to abiotic stress response. Ectopic expression of ABI3 in
Arabidopsis thaliana imparted higher
tolerance to freezing temperature 9 A breakthrough revelation of ABI3 mediated stress
response was the finding that it can impart desiccation stress tolerance to the
non-seed bearing system of Physcomitrella
patens 10. In consonance, our previous work has established role
of ABI3 as a key player in dehydration stress response in Arabidopsis thaliana11. ABI3
was found to mediate dehydration stress response by regulating expression of
several genes including the CRUCIFERIN
group of genes and the osmo-tolerance imparting Late Embryogenesis Abundant
(LEA) genes.

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ABI3 is a multi-domain protein
belonging to the AFL (ABI3/ FUSCA3/
LEAFY COTYLEDON 2) family of B3-domain containing transcription
factors. ABI3, FUS3 and LEC2 are known to form a signalling
network which regulates seed maturation and dormancy 12, 13. In addition to the B3 DNA binding domain, the ABI3
protein has three other domains: the acidic A1 domain and two other basic
domains B1 and B2 which facilitate nuclear localization and mediate
protein-protein interaction especially with bZIP factors 14-17.  Interestingly, the B3 domain of ABI3 is known
to bind to three different consensus sequences, the Sph/RY element (CATGCA), to
G-box/ABREs (GACGTG) and the AuxRE (TGTCTC) depending on different
physiological and developmental cues 8, 14, 18, 19 .It is possible that the ability of B3 domain of
ABI3 to bind to different cis-elements
under various physiological conditions imparts the multifaceted roles of ABI3
in plant stress and developmental responses. Such diversity in the role of ABI3
requires a robust and well-orchestrated signalling network which maintains the
spatio-temporal regulation of ABI3.

During seed dormancy, ABI3
is interdependently regulated by phyto-hormones auxin and ABA. ABA is known to
directly regulate ABI3, whereas auxin mediates its function through auxin
response factor 10 (ARF10) and 16 (ARF16) 7.  In addition
to ARF mediated regulation in seed physiology, ABI3 is known to be regulated by
FUS3, LEC1 and LEC2 during seed maturation 20-22. Interestingly, apart from being regulated by a
plethora of other factors, ABI3 along with FUS3 is known to form a feedback
loop, regulating its own expression during seed development 23. Additionally, ABI3 is also regulated by CHD1-like
protein CHR5 and CHD3-like protein PICKLE (PKL) where former induces active
chromatin state by reducing nucleosome occupancy during transcription, while
latter represses ABI3 expression via H3 K27 trimethylation post germination 24, 25. Apart from transcriptional regulation, ABI3 is
also known to be regulated post-transcriptionally and post-translationally.

ABI3 protein level is regulated by ABI3 Interacting Protein (AIP2), an E3
ligase, which ubiquitinates and represses ABI3 activity 26. Post-transcriptional regulation of ABI3 involves
the presence of lengthy 5′-UTR in the ABI3 gene, which negatively affects ABI3
expression 27. Moreover, splice variants of ABI3 homologs were
identified in both dicotyledonous and monocotyledonous plants suggesting an
important role of alternative splicing in ABI3 expression 28-30 .

The diverse modes of ABI3 regulation mentioned
above, indicate the significance of this gene product in various plant
signalling pathways and necessitates understanding the mechanisms of ABI3
regulation in utmost details. Understanding gene regulation in a eukaryotic
system has the additional complexity at the level of chromatin. Chromatin
organization at the upstream regulatory region of genes is one of the rate
determining step for transcriptional activity in eukaryotes 31-33. Chromatin structure is regulated by two
aspects- i) the physical signature and ii) the chemical state of the
nucleosomes. Physical signature of chromatin implies the distribution of
nucleosomes at a gene locus, which can either be strongly or loosely
positioned. Whereas chemical states of nucleosome signifies presence of post
translational modifications on histone residues such as acetylation, methylation
and phosphorylation, among others 34.

Such chemical modifications can prime the locus to either a transcriptionally
repressed or transcriptionally activated state. A transcriptionally active gene
is defined by presence of loosely compacted chromatin structure and presence of
histone modifications associated with active chromatin such as H3 K9ac, H3
K27ac, H3 K4me3 etc. For transcription activation the physical signature of chromatin
needs to alter as well and such alterations are often based on the chemical
modifications. Nucleosomes occluding important regulatory elements at the
promoter region of a gene need to expose the required sequences for
transcriptional activation in presence of inducible cues 35, 36.

In the present work we have aimed to decode the
genetic aspects and the chromatin modifications that are essentially involved
in regulating ABI3 gene expression in response to dehydration stress and stress
recovery. We have shown how nucleosomes at the ABI3 locus occlude important regulatory
cis-elements during transcriptionally
repressed state of the gene, which get repositioned during transcription
activation. This process involves several histone modifications that bring in
the necessary alterations in the chromatin landscape. We have further dissected
out two important cis-elements that
play a regulatory role in ABI3 expression during dehydration stress and subsequent
recovery phases.