Biology Reference
In-Depth Information
recently also with data for B. distachyon, is equipped with NetworkCom-
parer tool which permits comparative cross-species co-expression analysis
et al., 2011
). Shortly, the tool accepts a gene as a query and searches for
networks that show similar gene family composition across the eight plant
species. The entry for the analysis was At2g37040 (AtPAL1) from Arabidop-
sis and the tool found the most similar networks in the other seven species,
including Brachypodium. The output is shown in
Table II
, where the results
are sorted by the number a given family is present in AtPAL1-like networks
across the eight species.
Thus, the comparative analysis correctly identified major components
of the lignin biosynthesis pathway (marked in bold letters) as being the
most relevant and displayed putative functional homologs from other
species (
Table II
). For example, a functional homolog of Arabidopsis
At1g15950 (CCR1) in Brachypodium is most likely Bradi1g18020, as
these two genes belong to the same pfam family and are components of
very similar co-expression networks. The platform is using pfam to clas-
sify genes into gene families (
http://pfam.sanger.ac.uk/
;
Finn et al., 2008
).
While the pfam classification is quite rough (e.g. C3H and C4H have been
assigned to one pfam: p450), the tool was designed to compare distinctive
species, where strong divergence of functional homologs could impair
comparative analysis. In addition to finding known components of the
lignin biosynthesis pathway, the several other families are persistently
appearing across different species, suggesting their involvement (
Table II
).
These include:
Myb_DNA_binding: MYB63 and MYB7 transcription factors from Arabi-
dopsis. While MYB63 is a known regulator of lignin biosynthesis (
Zhou
et al., 2009
), the analysis suggests MYB7 to be involved as well. The table
also lists BrachypodiumMYBs Bradi5g20130, Bradi4g36210, Bradi1g10470
and Bradi2g47590 as putative functional homologs.
Pkinase (present in seven species) and Pkinase_Tyr (present in six species)
correspond to serine/threonine and tyrosine kinases, respectively. While no
kinase-mediated signalling has been associated with lignin biosynthesis,
every biological process requires coordination with the environment, often
mediated by kinases. However, one should keep in mind that both kinase
families contain more than 2000 genes, resulting in ubiquitous presence of
those families in the co-expression network.
Abhydrolase_1 and Abhydrolase_3 are described as alpha/beta hydrolase
fold catalytic site containing proteins which are found in a very wide range
of enzymes, such as proteases, lipases, peroxidases, esterases, epoxide
hydrolases and dehalogenases.
