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IN BRIEF
Breaking Down the Complex Regulatory Web Underlying
Lignin Biosynthesis
Vascular plants would not dominate the
terrestrial ecosystem today if they had not
evolved the ability to synthesize lignin. Lignin,
the second most abundant biological material
on earth (after cellulose), helps vascular plants
stand upright and serves as a scaffold for
water and nutrient transport systems, enabling vascular plants to tower over their
bryophyte relatives. Lignin is one of the most
difficult biopolymers to degrade, making it an
excellent barrier to pests and pathogens.
Unfortunately, lignin also interferes with efforts
to extract sugars from plant cellulose to
convert them to biofuels, and it represents
the major barrier to efficient extraction of
cellulose fibers for pulp and paper production
(Novaes et al., 2010). Thus, while lignin is
indispensible to vascular plants, much time
and money is spent trying to get rid of it.
Lignin is a complex material primarily comprising so-called monolignol subunits, mainly
derived from coniferyl alcohol (which forms
guaiacyl units after polymerization), and sinapyl alcohol (which forms syringyl units after
polymerization), as well as smaller amounts of
phenylpropanoid aldehydes, acetates, esters,
and other compounds. While some lignin
biosynthetic enzymes and associated transcription factors have been identified and
manipulated to alter lignin content and/or
composition, and genomics-based descriptions of lignin pathway genes are available,
the genetic pathway regulating lignin formation remains to be fully elucidated. Powerful
techniques have now been developed to
elucidate the regulatory pathways underlying
lignin formation in the energy crop switchgrass (Panicum virgatum) and wood formation
(in general) in poplar (Populus trichocarpa).
Shen et al. (2013) employed two systems
to identify candidate genes for lignin biosynthesis in the complex switchgrass genome:
the fourth internode region of mature tillers,
which contains a wide range of lignification
and lignified tissue types, and suspension cells
capable of undergoing lignification (see figure). They compared all available putative
switchgrass unique transcript sequences
www.plantcell.org/cgi/doi/10.1105/tpc.113.251111
Induced (+) and noninduced (2) switchgrass suspension cells harvested at days 1 and 7 and stained
with phloroglucinol. The red color indicates the presence of lignin. (Reprinted from Shen et al. [2013], Figure 2B.)
to known Arabidopsis thaliana sequences
involved in lignin biosynthesis and tested their
expression in internodes and suspension
cells using microarray analysis. Protein
sequence alignment and phylogenetic analysis were used to identify candidate genes,
which were tested using RNA silencing,
culminating in the identification of candidate
genes encoding enzymes involved in the early
steps of the currently accepted monolignol
biosynthesis pathway and the construction
of a more detailed putative pathway to
monolignols in switchgrass.
Lin et al. (2013) set out to identify
a regulatory hierarchy underlying wood
formation, specifically, the network of genes
targeted by Secondary Wall-Associated NAC
Domain-B1 (SND1-B1), a transcription factor
affecting wood formation in poplar. First, they
developed a differentiating xylem protoplast
system from poplar stems, which is no small
feat, since wood-forming cells are generally
resistant to protoplast isolation. Protoplasts
were transfected with SND1-B1 and differentially expressed genes identified using RNA
sequencing. The authors inferred direct interactions between SND1-B1 and the identified genes by integrating time-course RNA
sequencing data and top-down graphical
Gaussian modeling–based algorithms. To
verify these inferred interactions in vivo, they
developed an antibody-based chromatin im-
munoprecipitation method for wood-forming
cells, which is also a difficult task, as these
cells are highly recalcitrant to nuclear and
chromatin isolation. Chromatin immunoprecipitation analysis of differentiating
xylem and the production of stably transgenic P. trichocarpa helped confirm the
functions of the identified genes.
By combining robust genetic and cell culture
techniques, much can be learned about the
material that helps vascular plants stand tall
and interferes with their utilization.
Jennifer Lockhart
Science Editor
[email protected]
REFERENCES
Lin, Y.C., Li, W., Sun, Y.-H., Kumari, S., Wei,
H., Li, Q., Tunlaya-Anukit, S., Sederoff, R.R.,
and Chiang, V.L. (2013). SND1 transcription
factor–directed quantitative functional hierarchical genetic regulatory network in wood formation
in Populus trichocarpa. Plant Cell 25: doi/
10.1105/tpc.113.117697.
Novaes, E., Kirst, M., Chiang, V., Winter-Sederoff,
H., and Sederoff, R. (2010). Lignin and biomass:
A negative correlation for wood formation and
lignin content in trees. Plant Physiol. 154: 555–561.
Shen, et al. (2013). A genomics approach to
deciphering lignin biosynthesis in switchgrass
(Panicum virgatum). Plant Cell 25: doi/10.1105/
tpc.113.118828.
The Plant Cell Preview, www.aspb.org ã 2013 American Society of Plant Biologists. All rights reserved.
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Breaking Down the Complex Regulatory Web Underlying Lignin Biosynthesis
Jennifer Lockhart
Plant Cell; originally published online November 27, 2013;
DOI 10.1105/tpc.113.251111
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