Supplemental text
Description of selected TF and TR families in Chlamydomonas
SBP TF family in Chlamydomonas: SQUAMOSA promoter-binding proteins (SBPs)
form a major family of plant-specific TFs involved in diverse processes like leaf and
glume development in maize, shoot development in Arabidopsis, or fruit ripening in
tomato (Wang et al. 2005; Wu & Poethig 2006; Manning et al. 2006) and have also been
shown to affect cryptochrome-mediated blue light signaling in Physcomitrella (Riese et
al. 2008). SBPs harbor a highly conserved, ~74 amino acid long DNA-binding domain,
known as the SBP domain, which contains two zinc-binding sites formed by eight
conserved Cys or His residues. Our analysis identified 21 SBP genes in Chlamydomonas
which is close to the number observed in angiosperms (17-29 genes). Notable, however,
only 13 SBP genes were found in Physcomitrella. In Chlamydomonas the COPPER
RESPONSE REGULATOR 1 gene encodes an SBP domain protein that is required for
both activating and repressing target genes of a copper- and hypoxia-sensing pathway
through binding to the GTAC core of the copper response element of CYC6 and CPX1
promoters (Kropat et al. 2005b). The Crr1 SBP domain also recognizes a GTACcontaining sequence of the Arabidopsis AP1 promoter that is a known binding site of a
member of the SBP TF family. Chlamydomonas Crr1 is most similar to a subgroup of the
SBP domain proteins from Arabidopsis that include SPL1, SPL7, and SPL12 (Kropat et
al. 2005a).
Jumonji TR family in Chlamydomonas: This family is divided into three super-clades
conserved in all plants. PoGO 6 contains only members of land plants while all remaining
PoGOs have members of all lineages (supplemental Figure 7). In seed plants, Jumonji
factors control various processes including chromatin remodeling and flowering time
(Noh et al. 2004). The role of Jumonji factors in Chlamydomonas is not known at
present, however, they might be important for synchronizing gene expression through
chromatin remodeling, e.g. as a response to a change in light availability.
SET TR family in Chlamydomonas: SET-domain proteins are also well conserved
across plants. We identified eight clusters from algae to angiosperms from which four
also include genes from red algae. SET proteins are involved in controlling circadian
rhythm, epigenetic imprinting and reproduction (Ng et al. 2007). A SET-domain protein,
ASHR3 from Arabidopsis, has recently been reported to interact with a TF of the bHLH
family, called ABORTED MICROSPRES (AMS), which is involved in anther and
stamen development (Thorstensen et al. 2007). It is thus possible that SET TRs and
bHLH proteins also interact in Chlamydomonas.
MicroRNAs in Chlamydomonas
miRNAs are ~22-nucleotide-long non-coding RNAs that can control gene expression
through post-transcriptional regulatory mechanisms including mRNA degradation or
inhibition of efficient translation. In angiosperms miRNAs regulate – by controlling TF
genes – various developmental processes or the response to environmental factors and
stresses (Reinhart et al. 2002; Mallory et al. 2004; Jones-Rhoades & Bartel 2004).
miRNAs have recently also been identified in Chlamydomonas. Among the predicted
miRNA targets many genes have a role in metabolism and physiological processes,
whereas TFs were underrepresented. Moreover, the miRNAs from Chlamydomonas had
no orthologues in any plant or animal species, indicating that they evolved independently
in the lineages leading to animals, angiosperms, and green algae (Zhao et al. 2007; Siomi
& Siomi 2007; Molnar et al. 2007).
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