Global population increases and climate change underscore the need for better comprehension of how plants acquire and process nutrients such as iron. Using cell type-specific transcriptional profiling, we identified a pericycle-specific iron deficiency response and a bHLH transcription factor, POPEYE (PYE), that may play an important role in this response. Functional analysis of PYE suggests that it positively regulates growth and development under iron-deficient conditions. Chromatin immunoprecipitation-on-chip analysis and transcriptional profiling reveal that PYE helps maintain iron homeostasis by regulating the expression of known iron homeostasis genes and other genes involved in transcription, development, and stress response. PYE interacts with PYE homologs, including IAA-Leu Resistant3 (ILR3), another bHLH transcription factor that is involved in metal ion homeostasis. Moreover, ILR3 interacts with a third protein, BRUTUS (BTS), a putative E3 ligase protein, with metal ion binding and DNA binding domains, which negatively regulates the response to iron deficiency. PYE and BTS expression is also tightly coregulated. We propose that interactions among PYE, PYE homologs, and BTS are important for maintaining iron homeostasis under low iron conditions.

Little is known about the way developmental cues affect how cells interpret their environment. We characterized the transcriptional response to high salinity of different cell layers and developmental stages of the Arabidopsis root and found that transcriptional responses are highly constrained by developmental parameters. These transcriptional changes lead to the differential regulation of specific biological functions in subsets of cell layers, several of which correspond to observable physiological changes. We showed that known stress pathways primarily control semiubiquitous responses and used mutants that disrupt epidermal patterning to reveal cell-layer-specific and inter-cell-layer effects. By performing a similar analysis using iron deprivation, we identified common cell-type-specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions.

Iron uptake and metabolism are tightly regulated in both plants and animals. In Arabidopsis (Arabidopsis thaliana), BRUTUS (BTS), which contains three hemerythrin (HHE) domains and a Really Interesting New Gene (RING) domain, interacts with basic helix-loop-helix transcription factors that are capable of forming heterodimers with POPEYE (PYE), a positive regulator of the iron deficiency response. BTS has been shown to have E3 ligase capacity and to play a role in root growth, rhizosphere acidification, and iron reductase activity in response to iron deprivation. To further characterize the function of this protein, we examined the expression pattern of recombinant ProBTS::b-GLUCURONIDASE and found that it is expressed in developing embryos and other reproductive tissues, corresponding with its apparent role in reproductive growth and development. Our findings also indicate that the interactions between BTS and PYE-like (PYEL) basic helix-loop-helix transcription factors occur within the nucleus and are dependent on the presence of the RING domain. We provide evidence that BTS facilitates 26S proteasome-mediated degradation of PYEL proteins in the absence of iron. We also determined that, upon binding iron at the HHE domains, BTS is destabilized and that this destabilization relies on specific residues within the HHE domains. This study reveals an important and unique mechanism for plant iron homeostasis whereby an E3 ubiquitin ligase may posttranslationally control components of the transcriptional regulatory network involved in the iron deficiency response.

Pathogen resistance ( R ) genes of the NBS-LRR class (for nucleotide binding site and leucine-rich repeat) are found in many plant species and confer resistance to a diverse spectrum of pathogens. Little is known about the mechanisms that drive NBS-LRR gene evolution in the host-pathogen arms race. We cloned the RPP8 gene (for resistance to Peronospora parasitica ) and compared the structure of alleles at this locus in resistant Landsberg erecta (L er -0) and susceptible Columbia (Col-0) accessions. RPP8-L er encodes an NBS-LRR protein with a putative N-terminal leucine zipper and is more closely related to previously cloned R genes that confer resistance to bacterial pathogens than it is to other known RPP genes. The RPP8 haplotype in L er -0 contains the functional RPP8-L er gene and a nonfunctional homolog, RPH8A. In contrast, the rpp8 locus in Col-0 contains a single chimeric gene, which was likely derived from unequal crossing over between RPP8-L er and RPH8A ancestors within a L er -like haplotype. Sequence divergence among RPP8 family members has been accelerated by positive selection on the putative ligand binding region in the LRRs. These observations indicate that NBS-LRR molecular evolution is driven by the same mechanisms that promote rapid sequence diversification among other genes involved in non-self-recognition. INTRODUCTIONA broad range of microorganisms have evolved the ability to use plants as a nutritional resource, and plants in turn have evolved multiple lines of defense against pathogen invasion (Hammond-Kosack and Jones, 1996a). Inducible defenses are mediated through gene-for-gene systems in which the plant carrying a particular resistance ( R ) gene allele responds to pathogens carrying a matching avirulence ( avr ) gene (Flor, 1971). Most plants contain large collections of highly specific R genes, which are thought to encode specialized receptors that recognize avr gene-dependent elicitors (Keen, 1990). If the R gene or the corresponding avr gene is not functional, then recognition does not occur, defenses are not activated, and the plant is susceptible to infection. Thus, pathogens can circumvent gene-for-gene resistance by alteration or loss of avr genes. This places the host under selective pressure to evolve new recognition capabilities. avr gene mutations and deletions occur at high frequency in nature (van Kan et al., 1991;Rohe et al., 1995;Sweigard et al., 1995;Joosten et al., 1997), but the host's response in this evolutionary arms race is not well understood.Two themes have emerged from recent molecular characterization of R genes. R genes are often members of tightly linked multigene families, which can be functionally diversified (Hammond-Kosack and Jones, 1996b). A second, somewhat unexpected generality is that all R genes characterized to date, with one exception (Martin et al., 1993), encode proteins with long stretches of leucine-rich repeats (LRRs) . LRRs are present in a wide variety of proteins and participate in protein-protein interactions and ligand binding (Kobe ...

Pathogen resistance ( R ) genes of the NBS-LRR class (for nucleotide binding site and leucine-rich repeat) are found in many plant species and confer resistance to a diverse spectrum of pathogens. Little is known about the mechanisms that drive NBS-LRR gene evolution in the host-pathogen arms race. We cloned the RPP8 gene (for resistance to Peronospora parasitica ) and compared the structure of alleles at this locus in resistant Landsberg erecta (L er -0) and susceptible Columbia (Col-0) accessions. RPP8-L er encodes an NBS-LRR protein with a putative N-terminal leucine zipper and is more closely related to previously cloned R genes that confer resistance to bacterial pathogens than it is to other known RPP genes. The RPP8 haplotype in L er -0 contains the functional RPP8-L er gene and a nonfunctional homolog, RPH8A. In contrast, the rpp8 locus in Col-0 contains a single chimeric gene, which was likely derived from unequal crossing over between RPP8-L er and RPH8A ancestors within a L er -like haplotype. Sequence divergence among RPP8 family members has been accelerated by positive selection on the putative ligand binding region in the LRRs. These observations indicate that NBS-LRR molecular evolution is driven by the same mechanisms that promote rapid sequence diversification among other genes involved in non-self-recognition. INTRODUCTIONA broad range of microorganisms have evolved the ability to use plants as a nutritional resource, and plants in turn have evolved multiple lines of defense against pathogen invasion (Hammond-Kosack and Jones, 1996a). Inducible defenses are mediated through gene-for-gene systems in which the plant carrying a particular resistance ( R ) gene allele responds to pathogens carrying a matching avirulence ( avr ) gene (Flor, 1971). Most plants contain large collections of highly specific R genes, which are thought to encode specialized receptors that recognize avr gene-dependent elicitors (Keen, 1990). If the R gene or the corresponding avr gene is not functional, then recognition does not occur, defenses are not activated, and the plant is susceptible to infection. Thus, pathogens can circumvent gene-for-gene resistance by alteration or loss of avr genes. This places the host under selective pressure to evolve new recognition capabilities. avr gene mutations and deletions occur at high frequency in nature (van Kan et al., 1991;Rohe et al., 1995;Sweigard et al., 1995;Joosten et al., 1997), but the host's response in this evolutionary arms race is not well understood.Two themes have emerged from recent molecular characterization of R genes. R genes are often members of tightly linked multigene families, which can be functionally diversified (Hammond-Kosack and Jones, 1996b). A second, somewhat unexpected generality is that all R genes characterized to date, with one exception (Martin et al., 1993), encode proteins with long stretches of leucine-rich repeats (LRRs) . LRRs are present in a wide variety of proteins and participate in protein-protein interactions and ligand binding (Kobe ...

Symbiotic nitrogen fixation is one of the most promising and immediate alternatives to the overuse of polluting nitrogen fertilizers for improving plant nutrition. At the core of this process are a number of metalloproteins that catalyze and provide energy for the conversion of atmospheric nitrogen to ammonia, eliminate free radicals produced by this process, and create the microaerobic conditions required by these reactions. In legumes, metal cofactors are provided to endosymbiotic rhizobia within root nodule cortical cells. However, low metal bioavailability is prevalent in most soils types, resulting in widespread plant metal deficiency and decreased nitrogen fixation capabilities. As a result, renewed efforts have been undertaken to identify the mechanisms governing metal delivery from soil to the rhizobia, and to determine how metals are used in the nodule and how they are recycled once the nodule is no longer functional. This effort is being aided by improved legume molecular biology tools (genome projects, mutant collections, and transformation methods), in addition to state-of-the-art metal visualization systems.

Complex gene regulatory networks are composed of genes, noncoding RNAs, proteins, metabolites, and signaling components. The availability of genome-wide mutagenesis libraries; large-scale transcriptome, proteome, and metabalome data sets; and new high-throughput methods that uncover protein interactions underscores the need for mathematical modeling techniques that better enable scientists to synthesize these large amounts of information and to understand the properties of these biological systems. Systems biology approaches can allow researchers to move beyond a reductionist approach and to both integrate and comprehend the interactions of multiple components within these systems. Descriptive and mathematical models for gene regulatory networks can reveal emergent properties of these plant systems. This review highlights methods that researchers are using to obtain large-scale data sets, and examples of gene regulatory networks modeled with these data. Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed.

Iron (Fe) metabolism and the plant immune system are both critical for plant vigor in natural ecosystems and for reliable agricultural productivity. Mechanistic studies of plant iron homeostasis and plant immunity have traditionally been carried out in isolation from each other; however, our growing understanding of both processes has uncovered significant connections. For example, iron plays a critical role in the generation of reactive oxygen intermediates during immunity and has been recently implicated as a critical factor for immune-initiated cell death via ferroptosis. Moreover, plant iron stress triggers immune activation, suggesting that sensing of iron depletion is a mechanism by which plants recognize a pathogen threat. The iron deficiency response engages hormone signaling sectors that are also utilized for plant immune signaling, providing a probable explanation for iron-immunity cross-talk. Finally, interference with iron acquisition by pathogens might be a critical component of the immune response. Efforts to address the global burden of iron deficiency-related anemia, have focused on classical breeding and transgenic approaches to develop crops biofortified for iron content. However, our improved mechanistic understanding of plant iron metabolism suggests that such alterations could promote or impede plant immunity, depending on the nature of the alteration and the virulence strategy of the pathogen. Effects of iron biofortification on disease resistance should be evaluated while developing plants for iron biofortification.