Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase, as a Novel Regulator of Root Meristem Maintenance

Pu, Yunting; Walley, Justin W.; Shen, Zhouxin; Lang, Michelle; Briggs, Steven P.; Estelle, Mark; Kelley, Dior R.

doi:10.1074/mcp.ra119.001378

Cited by 18 publications

(20 citation statements)

References 74 publications

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“…The predicted truncated protein would be similar to previously reported C-terminal domain mutations of phyB which reduce its biological activity (Qiu et al, 2019;Wagner and Quail, 1995;Wagner et al, 1996;Matsushita et al, 2003).…”

Section: R a F Tsupporting

confidence: 81%

“…The missing 'T' nucleotide at position 3,370 in the PHYB cDNA, converts a leucine codon to a premature stop codon that likely results in a truncation of 48 amino acids from its C-terminal domain ( Figure 4A). Other C-terminal module disruptions to the PHYB protein have been reported to disrupt PHYB activity through various mechanisms (Rockwell et al, 2006;Qiu et al, 2019;Wagner and Quail, 1995).…”

Section: Discussionmentioning

confidence: 99%

“…Previous studies have shown that the dimerization of the PHYB C-terminal domain is essential for its accumulation in subnuclear photobodies as well as its interaction with PIFs driving their photoactivated degradation (Chen et al, 2003;Qiu et al, 2019). The catalytic ATP-binding domain of PHYB contains four conserved subdomains named N, G1, F, and G2 that are essential for its Histidine Kinase Related Domain mediated dimerization (Yeh and Lagarias, 1998;Qiu et al, 2019;Schneider-Poetsch et al, 1991). The slim shady allele of PHYB we have discovered contains an indel that would result in a truncation of the entire G2 subdomain, which would likely generate a loss of function allele.…”

Section: Discussionmentioning

confidence: 99%

“…Plant hormone gibberellins also contribute towards hypocotyl elongation by modulating PIF activity and stability (De Lucas et al, 2008;Feng et al, 2008;Li et al, 2016). While auxin can rapidly regulate gene expression D R A F T at the transcript and protein level (Bargmann et al, 2014;Nemhauser et al, 2006;Clark et al, 2019;Pu et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

Dash

McEwan²,

Montes

et al. 2021

Preprint

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Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin rapid changes in transcript and protein abundance occur in hypocotyls and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin-regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady, in an annotated insertion line in IMMUNOREGULATORY RNA-BINDING PROTEIN (IRR). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T-DNA allele of IRR found that it had a wild-type hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid-auxin-phytochrome (BAP) regulatory module compared to wild-type, including transcription factors that regulate brassinosteroid, auxin and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence and transcriptomics data for SALK_015201C we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase-related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb-9 confirmed that slim shady is a mutant allele of PHYB. This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T-DNA stocks.

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Section: R a F Tsupporting

confidence: 81%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

Dash

McEwan²,

Montes

et al. 2021

Preprint

Self Cite

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“…Additionally, transcriptional changes in Arabidopsis seedlings have been well documented . Initial characterization of auxin responsive proteomes in seedlings and roots identified proteins that are responsive 6–24 h after auxin treatment, but further studies of the auxin‐regulated proteome are needed to generate a more comprehensive view of auxin mediated gene expression …”

mentioning

confidence: 99%

Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings

et al. 2019

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It is known that auxin induces rapid gene expression changes throughout plant development, but how these transcriptional responses relate to changes in protein abundance is not well characterized. This report identifies early auxin responsive proteins in whole Arabidopsis seedlings using an isobaric tags for relative and absolute quantification‐based quantitative proteomics approach. Approximately 25% of the detected proteins (1045 out of 4257 proteins) are auxin responsive, which is in line with the central role of auxin in the regulation of plant growth and development. Several well‐known auxin pathway proteins are identified as differentially expressed, validating this quantitative proteomics approach. Additionally, functional categorization of these auxin responsive proteins indicates that rapid and complex metabolic changes occur in seedlings in response to auxin, including lipid metabolism. Altogether, these data describe novel auxin‐regulated proteins and are an excellent resource for identifying new downstream signaling components related to auxin‐mediated plant growth and development.

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slim shady is a novel allele of PHYTOCHROME B present in the T‐DNA line SALK_015201

Dash

McEwan²,

Montes

et al. 2021

Plant Direct

Self Cite

View full text Add to dashboard Cite

Auxin is a hormone that is required for hypocotyl elongation during seedling development. In response to auxin, rapid changes in transcript and protein abundance occur in hypocotyls, and some auxin responsive gene expression is linked to hypocotyl growth. To functionally validate proteomic studies, a reverse genetics screen was performed on mutants in auxin‐regulated proteins to identify novel regulators of plant growth. This uncovered a long hypocotyl mutant, which we called slim shady , in an annotated insertion line in IMMUNOREGULATORY RNA‐BINDING PROTEIN ( IRR ). Overexpression of the IRR gene failed to rescue the slim shady phenotype and characterization of a second T‐DNA allele of IRR found that it had a wild‐type (WT) hypocotyl length. The slim shady mutant has an elevated expression of numerous genes associated with the brassinosteroid‐auxin‐phytochrome (BAP) regulatory module compared to WT, including transcription factors that regulate brassinosteroid, auxin, and phytochrome pathways. Additionally, slim shady seedlings fail to exhibit a strong transcriptional response to auxin. Using whole genome sequence data and genetic complementation analysis with SALK_015201C, we determined that a novel single nucleotide polymorphism in PHYTOCHROME B was responsible for the slim shady phenotype. This is predicted to induce a frameshift and premature stop codon at leucine 1125, within the histidine kinase‐related domain of the carboxy terminus of PHYB, which is required for phytochrome signaling and function. Genetic complementation analyses with phyb‐9 confirmed that slim shady is a mutant allele of PHYB . This study advances our understanding of the molecular mechanisms in seedling development, by furthering our understanding of how light signaling is linked to auxin‐dependent cell elongation. Furthermore, this study highlights the importance of confirming the genetic identity of research material before attributing phenotypes to known mutations sourced from T‐DNA stocks.

show abstract

Quantitative Early Auxin Root Proteomics Identifies GAUT10, a Galacturonosyltransferase, as a Novel Regulator of Root Meristem Maintenance

Cited by 18 publications

References 74 publications

slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

slim shadyis a novel allele of PHYTOCHROME B present in the T-DNA line SALK_015201

Auxin Induces Widespread Proteome Remodeling in Arabidopsis Seedlings

slim shady is a novel allele of PHYTOCHROME B present in the T‐DNA line SALK_015201

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