Project description:Comparison of gene expression between cna-2 phb-13 phv-11, cna-2 phb-13 phv-11 rev-6, and wild type (Col er-2) in 0.5 mm root tips of Arabidopsis.
Project description:Total mRNA was extracted from the root tips (2-3 mm from the root apex) of wild-type plants (Col-0 accession) and med16-2 mutants grown under low and high phosphate conditions 4 days after germination, using and sequenced by RNA-seq methodology.
Project description:Functional divergence of transcription factors (TFs) has driven cellular and organismal complexity throughout evolution, but its mechanistic drivers remain poorly understood. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two functionally diverged paralogs in the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of TFs. We show that virtually all genes bound by PHB ( ~ 99%) are also bound by CNA, ruling out occupation of distinct sets of genes as a mechanism of functional divergence. Further, genes bound and regulated by both paralogs are almost always regulated in the same direction, ruling out opposite regulation of shared targets as a mechanistic driver. Functional divergence of CNA and PHB instead results from differential usage of shared binding sites, with hundreds of uniquely regulated genes emerging from a commonly bound genetic network. Regulation of a given gene by CNA or PHB is thus a function of whether a bound site is considered ‘responsive’ versus ‘non-responsive’ by each paralog. Discrimination between responsive and non-responsive sites is controlled, at least in part, by their lipid binding START domain. This suggests a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes from a shared network architecture. Taken together, our study identifies a mechanism of HD-ZIPIII TF paralog divergence and proposes the ubiquitously distributed START evolutionary module as a driver of functional divergence.
Project description:Total mRNA was extracted from the root tips (10 mm from the root apex) of wild-type plants (Col-0 accession) and stop1 mutants grown 5 days after germination under optimum conditions and then transferred for 16 hours to low phosphate(Pi), low pH, Al and Fe excess mediums.
Project description:Transcriptional profiling of C. perfringens 13 strain compared with strain 13∆cpe1786 erm after growth in minimal medium with 0.5 mM cystine.
Project description:Transcriptionnal profiling of C. perfringens 13 strain comparing growth in minimal medium with 1 mM homocysteine with growth in minimal medium with 0.5 mM cystine.
Project description:Throughout evolution, the duplication and functional divergence of transcription factors (TFs) has driven cellular and organismal complexity. Mechanisms by which paralogous TFs functionally diverge are thus of broad interest yet remain poorly understood. One well-established mechanism underlying TF divergence is the occupation and regulation of distinct sets of genes. Here we test for new mechanisms using CORONA (CNA) and PHABULOSA (PHB), two representative members of the CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) family of plant TFs. CNA and PHB have largely overlapping binding profiles yet each paralog has hundreds of uniquely regulated targets. Regulation of a given gene thus depends on whether its local binding site is considered primed (inactive) or regulated (active) by CNA or PHB. This decision appears to be controlled, at least in part, by their lipid binding START domain, proposing a model in which HD-ZIPIII TFs use information integrated by their START domain to generate paralog-specific transcriptional outcomes at commonly bound genes. Taken together, our study identifies a new mechanism of TF paralog divergence and proposes the ubiquitously distributed START evolutionary module as a driver of functional divergence.
Project description:The class III HD-ZIP transcription factors regulate vascular patterning in Arabidopsis thaliana roots. In this expression study we compare the expression profile of the cna-2 phb-13 phv-11 and cna-2 phb-13 phv-11 rev-6 mutants to their wild type. The results are presented in PHABULOSA mediates an auxin signaling loop to regulate vascular patterning in Arabidopsis by Christina Joy Müller, Ana Elisa Valdés, Guodong Wang, Prashanth Ramachandran, Lisa Beste, Daniel Uddenberg, and Annelie Carlsbecker, accepted for publication in Plant Physiology Nov. 2015. Plant vascular tissues, xylem and phloem, differentiate in distinct patterns from procambial cells as an integral transport system for water, sugars and signaling molecules. Procambium formation is promoted by high auxin levels activating class III homeodomain leucine zipper (HD-ZIP III) transcription factors (TFs). In the root of Arabidopsis thaliana, HD-ZIP III TFs dose-dependently govern the patterning of the xylem axis, with higher levels promoting metaxylem cell identity in the central axis and lower levels protoxylem at its flanks. It is, however, unclear by what mechanisms the HD-ZIP III TFs control xylem axis patterning. Here we present data suggesting that an important mechanism is their ability to moderate auxin response. We found that changes in HD-ZIP III TF levels affect the expression of genes encoding core auxin response molecules. We show that one of the HD-ZIP III TFs, PHABULOSA, directly binds the promoter of both MONOPTEROS/AUXIN RESPONSE FACTOR5 (MP/ARF5), a key factor in vascular formation, and IAA20, encoding an AUX/IAA protein which is stable in the presence of auxin and able to interact with and repress MP activity. The double mutant of IAA20 and its closest homologue IAA30 forms ectopic protoxylem, while overexpression of IAA30 causes discontinuous protoxylem and occasional ectopic metaxylem, similar to a weak loss-of-function mp-mutant. Our results provide evidence that HD-ZIP III TFs directly affect auxin response and mediate a feed forward loop formed by MP and IAA20 that may focus and stabilize auxin response during vascular patterning and differentiation of xylem cell types.
