Biomedical subjects

Christian S Hardtke

Publications and source records attributed to Christian S Hardtke.

12 recordsLinked to original sources

PubMed2007

Hidden branches: developments in root system architecture.

The root system is fundamentally important for plant growth and survival because of its role in water and nutrient uptake. Therefore, plants rely on modulation of root system architecture (RSA) to respond to a changing soil environment. Although RSA is a highly plastic trait and varies both between and among species, the basic root system morphology and its plasticity are controlled by inherent genetic factors. These mediate the modification of RSA, mostly at the level of root branching, in response to a suite of biotic and abiotic factors. Recent progress in the understanding of the molecular basis of these responses suggests that they largely feed through hormone homeostasis and signaling pathways. Novel factors implicated in the regulation of RSA in response to the myriad endogenous and exogenous signals are also increasingly isolated through alternative approaches such as quantitative trait locus analysis.

Adaptation, Physiological↗

PubMed2006

Opposite root growth phenotypes of hy5 versus hy5 hyh mutants correlate with increased constitutive auxin signaling.

The Arabidopsis transcription factor HY5 controls light-induced gene expression downstream of photoreceptors and plays an important role in the switch of seedling shoots from dark-adapted to light-adapted development. In addition, HY5 has been implicated in plant hormone signaling, accounting for the accelerated root system growth phenotype of hy5 mutants. Mutants in the close HY5 homolog HYH resemble wild-type, despite the largely similar expression patterns and levels of HY5 and HYH, and the functional equivalence of the respective proteins. Moreover, the relative contribution of HYH to the overall activity of the gene pair is increased by an alternative HYH transcript, which encodes a stabilized protein. Consistent with the enhanced root system growth observed in hy5 loss-of-function mutants, constitutively overexpressed alternative HYH inhibits root system growth. Paradoxically, however, in double mutants carrying hy5 and hyh null alleles, the hy5 root growth phenotype is suppressed rather than enhanced. Even more surprisingly, compared to wild-type, root system growth is diminished in hy5 hyh double mutants. In addition, the double mutants display novel shoot phenotypes that are absent from either single mutant. These include cotyledon fusions and defective vasculature, which are typical for mutants in genes involved in the transcriptional response to the plant hormone auxin. Indeed, many auxin-responsive and auxin signaling genes are misexpressed in hy5 mutants, and at a higher number and magnitude in hy5 hyh mutants. Therefore, auxin-induced transcription is constitutively activated at different levels in the two mutant backgrounds. Our data support the hypothesis that the opposite root system phenotypes of hy5 single and hy5 hyh double mutants represent the morphological response to a quantitative gradient in the same molecular process, that is gradually increased constitutive auxin signaling. The data also suggest that HY5 and HYH are important negative regulators of auxin signaling amplitude in embryogenesis and seedling development.

Alternative Splicing↗

PubMed2006

BRX mediates feedback between brassinosteroid levels and auxin signalling in root growth.

Brassinosteroid and auxin decisively influence plant development, and overlapping transcriptional responses to these phytohormones suggest an interaction between the two pathways. However, whether this reflects direct feedback or merely parallel inputs on common targets is unclear. Here we show that in Arabidopsis roots, this interaction is mediated by BREVIS RADIX (BRX), which is required for optimal root growth. We demonstrate that the brx phenotype results from a root-specific deficiency of brassinosteroid and is due to reduced, BRX-dependent expression of a rate-limiting enzyme in brassinosteroid biosynthesis. Unexpectedly, this deficiency affects the root expression level of approximately 15% of all Arabidopsis genes, but the transcriptome profile can be restored to wild type by brassinosteroid treatment. Thus, proper brassinosteroid levels are required for the correct expression of many more genes than previously suspected. Moreover, embryonic or post-embryonic brassinosteroid application fully or partially, respectively, rescues the brx phenotype. Further, auxin-responsive gene expression is globally impaired in brx, demonstrating that brassinosteroid levels are rate-limiting for auxin-responsive transcription. BRX expression is strongly induced by auxin and mildly repressed by brassinolide, which means that BRX acts at the nexus of a feedback loop that maintains threshold brassinosteroid levels to permit optimal auxin action.

Arabidopsis↗

PubMed2006

Unequal genetic redundancies in Arabidopsis--a neglected phenomenon?

Genetic redundancy is a common phenomenon in Arabidopsis and is thought to be responsible for the absence of phenotypes in the majority of single loss-of-function mutants. In this review, we highlight an increasing number of examples in which redundancy between homologous genes is limited or absent despite functional equivalence of the respective proteins. In particular, we focus on cases of unequal redundancy, where the absence of a mutant phenotype in loss-of-function mutants of one gene contrasts with a strong phenotype in mutants of its homolog. In the double mutants, this phenotype is strongly enhanced. Possible explanations for such scenarios are discussed. We propose that the study of unequally redundant gene pairs offers a unique opportunity to understand global patterns of functional genome evolution.

Arabidopsis↗

PubMed2006

Characterization of the plant-specific BREVIS RADIX gene family reveals limited genetic redundancy despite high sequence conservation.

To date, the function of most genes in the Arabidopsis (Arabidopsis thaliana) genome is unknown. Here we present the first analysis of the novel, plant-specific BRX (BREVIS RADIX) gene family. BRX has been identified as a modulator of root growth through a naturally occurring loss-of-function allele. The biochemical function of BRX is enigmatic, however several domains in BRX are conserved in the proteins encoded by the related BRX-like (BRXL) genes. The similarity between Arabidopsis BRXL proteins within these domains ranges from 84% to 93%. Nevertheless, analysis of brx brx-like multiple mutants indicates that functional redundancy of BRXLs is limited. This results mainly from differences in protein activity, as demonstrated by assaying the propensity of constitutively expressed BRXL cDNAs to rescue the brx phenotype. Among the genes tested, only BRXL1 can replace BRX in this assay. Nevertheless, BRXL1 does not act redundantly with BRX in vivo, presumably because it is expressed at a much lower level than BRX. BRX and BRXL1 similarity is most pronounced in a characteristic tandem repeat domain, which we named BRX domain. One copy of this domain is also present in the PRAF (PH, RCC1, and FYVE)-like family proteins. The BRX domain mediates homotypic and heterotypic interactions within and between the BRX and PRAF protein families in yeast (Saccharomyces cerevisiae), and therefore likely represents a novel protein-protein interaction domain. The importance of this domain for BRX activity in planta is underscored by our finding that expression of the C-terminal fragment of BRX, comprising the two BRX domains, is largely sufficient to rescue the brx phenotype.

Alleles↗

PubMed2005

Root development--branching into novel spheres.

Recent progress in deciphering the genetics of Arabidopsis root development has been driven by the availability of novel molecular tools. For instance, combining enhancer trap lines and microarray analyses enabled the creation of an expression map for over 22000 genes at cellular resolution. Such expression profiles often suggest redundant action of homologous genes, which has indeed been observed for several pivotal factors that are required for the organization and maintenance of root meristems. Additional regulators of root development are also being identified by analysis of natural genetic variation. Moreover, microRNA control of gene expression has recently been implicated in root development, and progress has been made in understanding the interplay between environmental and genetic factors in root branching.

Arabidopsis↗

PubMed2004

Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root.

Mutant analysis has been tremendously successful in deciphering the genetics of plant development. However, less is known about the molecular basis of morphological variation within species, which is caused by naturally occurring alleles. In this study, we succeeded in isolating a novel regulator of root growth by exploiting natural genetic variation in the model plant Arabidopsis. Quantitative trait locus analysis of a cross between isogenized accessions revealed that a single locus is responsible for approximately 80% of the variance of the observed difference in root length. This gene, named BREVIS RADIX (BRX), controls the extent of cell proliferation and elongation in the growth zone of the root tip. We isolated BRX by positional cloning. BRX is a member of a small group of highly conserved genes, the BRX gene family, which is only found in multicellular plants. Analyses of Arabidopsis single and double mutants suggest that BRX is the only gene of this family with a role in root development. The BRX protein is nuclear localized and activates transcription in a heterologous yeast system, indicating that BRX family proteins represent a novel class of transcription factors. Thus, we have identified a novel regulatory factor controlling quantitative aspects of root growth.

Amino Acid Sequence↗

PubMed2004

The Arabidopsis transcription factor HY5 integrates light and hormone signaling pathways.

The role of the Arabidopsis transcription factor LONG HYPOCOTYL 5 (HY5) in promoting photomorphogenic development has been extensively characterized. Although the current model for HY5 action largely explains its role in this process, it does not adequately address the root phenotype observed in hy5 mutants. In our search for common mechanisms underlying all hy5 traits, we found that they are partly the result of an altered balance of signaling through the plant hormones auxin and cytokinin. hy5 mutants are resistant to cytokinin application, and double mutant analyses indicate that a decrease in auxin signaling moderates hy5 phenotypes. Microarray analyses and semiquantitative RT-PCR indicate that two negative regulators of auxin signaling, AUXIN RESISTANT 2 (AXR2)/INDOLE ACETIC ACID 7 (IAA7) and SOLITARY ROOT (SLR)/IAA14, are underexpressed in hy5 mutants. The promoters of these genes contain a putative HY5 binding site, and in line with this observation, HY5 can bind to the promoter of AXR2 in vitro. Increased AXR2 expression in a hy5 background partially rescues the elongated hypocotyl phenotype. In summary, it appears that auxin signaling is elevated in hy5 mutants because HY5 promotes the expression of negative regulators of auxin signaling, thereby linking hormone and light signaling pathways.

Arabidopsis↗

PubMed2004

Overlapping and non-redundant functions of the Arabidopsis auxin response factors MONOPTEROS and NONPHOTOTROPIC HYPOCOTYL 4.

Transcription factors of the auxin response factor (ARF) family have been implicated in auxin-dependent gene regulation, but little is known about the functions of individual ARFs in plants. Here, interaction assays, expression studies and combinations of multiple loss- and gain-of-function mutants were used to assess the roles of two ARFs, NONPHOTOTROPIC HYPOCOTYL 4 (NPH4/ARF7) and MONOPTEROS (MP/ARF5), in Arabidopsis development. Both MP and NPH4 interact strongly and selectively with themselves and with each other, and are expressed in vastly overlapping domains. We show that the regulatory properties of both genes are far more related than suggested by their single mutant phenotypes. NPH4 and MP are capable of controlling both axis formation in the embryo and auxin-dependent cell expansion. Interaction of MP and NPH4 in Arabidopsis plants is indicated by their joint requirement in a number of auxin responses and by synergistic effects associated with the co-overexpression of both genes. Finally, we demonstrate antagonistic interaction between ARF and Aux/IAA gene functions in Arabidopsis development. Overexpression of MP suppresses numerous defects associated with a gain-of-function mutation in BODENLOS (BDL)/IAA12. Together these results provide evidence for the biological relevance of ARF-ARF and ARF-Aux/IAA interaction in Arabidopsis plants and demonstrate that an individual ARF can act in both invariantly programmed pattern formation as well as in conditional responses to external signals.

Arabidopsis↗

PubMed2003

Dispatch. Gibberellin signaling: GRASs growing roots dispatch.

Gibberellins are important endogenous plant growth regulators. A new study has revealed an unexpected role for gibberellin-regulated transcription factors in promoting root growth; this depends on signaling from another plant hormone, auxin, suggesting that auxin promotes root growth by modulating the cellular response to gibberellins.

Gibberellins↗

PubMed2002

Evaluation and classification of RING-finger domains encoded by the Arabidopsis genome.

BACKGROUND: In computational analysis, the RING-finger domain is one of the most frequently detected domains in the Arabidopsis proteome. In fact, it is more abundant in Arabidopsis than in other eukaryotic genomes. However, computational analysis might classify ambiguous domains of the closely related PHD and LIM motifs as RING domains by mistake. Thus, we set out to define an ordered set of Arabidopsis RING domains by evaluating predicted domains on the basis of recent structural data. RESULTS: Inspection of the proteome with a current InterPro release predicts 446 RING domains. We evaluated each detected domain and as a result eliminated 59 false positives. The remaining 387 domains were grouped by cluster analysis and according to their metal-ligand arrangement. We further defined novel patterns for additional computational analyses of the proteome. They were based on recent structural data that enable discrimination between the related RING, PHD and LIM domains. These patterns allow us to predict with different degrees of certainty whether a particular domain is indeed likely to form a RING finger. CONCLUSIONS: In summary, 387 domains have a significant potential to form a RING-type cross-brace structure. Many of these RING domains overlap with predicted PHD domains; however, the RING domain signature mostly prevails. Thus, the abundance of PHD domains in Arabidopsis has been significantly overestimated. Cluster analysis of the RING domains defines groups of proteins, which frequently show significant similarity outside the RING domain. These groups document a common evolutionary origin of their members and potentially represent genes of overlapping functionality.

Amino Acid Motifs↗

PubMed2002

Biochemical evidence for ubiquitin ligase activity of the Arabidopsis COP1 interacting protein 8 (CIP8).

Arabidopsis COP1 is a negative regulator of photomorphogenesis, which targets HY5, a positive regulator of photomorphogenesis, for degradation via the proteasome pathway in the absence of light. COP1 and its interactive partner CIP8 both possess RING finger motifs, characteristic of some E3 ubiquitin ligases. Here we show that CIP8 promotes ubiquitin attachment to HY5 in E2-dependent fashion in vitro. CIP8 exhibits a strong interaction with the E2 enzyme AtUBC8 through its N-terminal domain. Phosphorylation of HY5 by casein kinase II requires the beta subunit 2, but does not affect HY5's susceptibility to ubiquitination. The RING domain of CIP8 is required but is not sufficient for ubiquitin ligase activity. Although the RING domain of CIP8 interacts with the RING domain of COP1, addition of recombinant COP1 fails to affect CIP8's ubiquitin ligase activity towards HY5 in vitro. However, recombinant COP1 can pull-down native CIP8 from the extract of dark-grown seedlings, but not from the extract of light-grown seedlings in a column-binding assay, implying a requirement for light-regulated modification in vivo. Our data suggest that CIP8 can form a minimal ubiquitin ligase in co-operation with the E2 enzyme AtUBC8. It is possible that the AtUBC8-CIP8 module might interact with COP1 in vivo, thereby participating in proteasome-mediated degradation of HY5.

Arabidopsis↗