Annual Review of Plant Biology - Volume 54, 2003

Many disease resistance (R) proteins of plants detect the presence of disease-causing bacteria, viruses, or fungi by recognizing specific pathogen effector molecules that are produced during the infection process. Effectors are often pathogen proteins that probably evolved to subvert various host processes for promotion of the pathogen life cycle. Five classes of effector-specific R proteins are known, and their sequences suggest roles in both effector recognition and signal transduction. Although some R proteins may act as primary receptors of pathogen effector proteins, most appear to play indirect roles in this process. The functions of various R proteins require phosphorylation, protein degradation, or specific localization within the host cell. Some signaling components are shared by many R gene pathways whereas others appear to be pathway specific. New technologies arising from the genomics and proteomics revolution will greatly expand our ability to investigate the role of R proteins in plant disease resistance.

Phosphorylation and dephosphorylation of a protein often serve as an “on-and-off” switch in the regulation of cellular activities. Recent studies demonstrate the involvement of protein phosphorylation in almost all signaling pathways in plants. A significant portion of the sequenced Arabidopsis genome encodes protein kinases and protein phosphatases that catalyze reversible phosphorylation. For optimal regulation, kinases and phosphatases must strike a balance in any given cell. Only a very small fraction of the thousands of protein kinases and phosphatases in plants has been studied experimentally. Nevertheless, the available results have demonstrated critical functions for these enzymes in plant growth and development. While serine/threonine phosphorylation is widely accepted as a predominant modification of plant proteins, the function of tyrosine phosphorylation, despite its overwhelming importance in animal systems, had been largely neglected until recently when tyrosine phosphatases (PTPs) were characterized from plants. This review focuses on the structure, regulation, and function of protein phosphatases in higher plants.

Peroxiredoxins (Prxs) are abundant low-efficiency peroxidases located in distinct cell compartments including the chloroplast and mitochondrion. They are grouped into four clans based on their structural and biochemical properties. The catalytic center contains a cysteinyl residue that reduces diverse peroxides and is regenerated via intramolecular or intermolecular thiol-disulfide-reactions and finally by electron donors such as thioredoxins and glutaredoxins. Prxs show a complex regulation by endogenous and environmental stimuli at both the transcript and protein levels. In addition to their role in antioxidant defense in photosynthesis, respiration, and stress response, they may also be involved in modulating redox signaling during development and adaptation.

Nitric oxide (NO) is a small highly diffusible gas and a ubiquitous bioactive molecule. Its chemical properties make NO a versatile signal molecule that functions through interactions with cellular targets via either redox or additive chemistry. In plants, NO plays a role in a broad spectrum of pathophysiological and developmental processes. Although nitric oxide synthase (NOS)-dependent NO production has been reported in plants, no gene, cDNA, or protein has been isolated to date. In parallel, precise and regulated NO production can be measured from the activity of the ubiquitous enzyme nitrate reductase (NR). In addition to endogenous NO formation, high NO emissions are observed from fertilized soils, but their effects on the physiology of plants are largely unknown. Many environmental and hormonal stimuli are transmitted either directly or indirectly by NO signaling cascades. The ability of NO to act simultaneously on several unrelated biochemical nodes and its redox homeostatic properties suggest that it might be a synchronizing molecule in plants.

Brassinosteroids (BRs) are steroid hormones that regulate the growth and development of plants. Detailed study of the biosynthesis of brassinolide, a C28 BR, revealed that two parallel routes, the early and late C-6 oxidation pathways, are connected at multiple steps and also are linked to the early C-22 oxidation pathway. Thus, BR biosynthetic pathways are highly networked. Furthermore, the biosynthesis of C27 BRs was shown to proceed in a similar way to that of C28 BRs. Information on enzymes and genes involved in the BR biosynthesis, as well as their regulation, has been obtained using BR-deficient and BR-insensitive mutants. In addition, the biosynthesis of sterols, which were recently recognized not only as precursors of BRs and membrane constituents, but also as modulators of plant development, is discussed. Various metabolic reactions of BRs including epimerization, oxidation, and conjugation are also summarized.

The COP9 signalosome (CSN) is a multiprotein complex that was initially identified in plants as a repressor of photomorphogenesis. It is now known to play major roles in several other developmental pathways, from auxin response to flower development. Furthermore, the COP9 signalosome shares homologies with the lid sibcomplex of the proteasome and is evolutionarily conserved from fission yeast to humans. It is important for the proper development of virtually all higher eukaryotes. In recent years, significant progress has been made in unraveling the molecular, cellular, and physiological mode of action of the COP9 signalosome. This review discusses our current understanding of the COP9 signalosome function with particular emphasis on its recently defined role in modulating a wide variety of cellular processes by regulating specific protein degradation events.

Cellular and whole organism iron homeostasis must be balanced to supply enough iron for metabolism and to avoid excessive, toxic levels. To perform iron uptake from the environment, iron distribution to various organs and tissues, and iron intracellular compartmentalization, various membranes must be crossed by this metal. The uptake and transport of iron under physiological conditions require particular processes such as chelation or reduction because ferric iron has a very low solubility. The molecular actors involved in iron acquisition from the soil have recently been characterized. A few candidates belonging to various gene families are hypothesized to play major roles in iron distribution throughout the plant. All these transport activities are tightly regulated at transcriptional and posttranslational levels, according to the iron status of the plant. These coordinated regulations result from an integration of local and long-distance transduction pathways.

Plants, green algae, and cyanobacteria synthesize storage polysaccharides by a similar ADPglucose-based pathway. Plant starch metabolism can be distinguished from that of bacterial glycogen by the presence of multiple forms of enzyme activities for each step of the pathway. This multiplicity does not coincide with any functional redundancy, as each form has seemingly acquired a distinctive and conserved role in starch metabolism. Comparisons of phenotypes generated by debranching enzyme-defective mutants in Escherichia coli and plants suggest that enzymes previously thought to be involved in polysaccharide degradation have been recruited during evolution to serve a particular purpose in starch biosynthesis. Speculations have been made that link this recruitment to the appearance of semicrystalline starch in photosynthetic eukaryotes. Besides the common core pathway, other enzymes of malto-oligosaccharide metabolism are required for normal starch metabolism. However, according to the genetic and physiological system under study, these enzymes may have acquired distinctive roles.

Cell division in plants is controlled by the activity of cyclin-dependent kinase (CDK) complexes. Although this basic mechanism is conserved with all other eukaryotes, plants show novel features of cell-cycle control in the molecules involved and their regulation, including novel CDKs showing strong transcriptional regulation in mitosis. Plant development is characterized by indeterminate growth and reiteration of organogenesis and is therefore intimately associated with cell division. This may explain why plants have a large number of cell-cycle regulators that appear to have overlapping and distinct functions. Here we review the recent considerable progress in understanding how core cell-cycle regulators are involved in integrating and coordinating cell division at the molecular level.

Phospholipids are emerging as novel second messengers in plant cells. They are rapidly formed in response to a variety of stimuli via the activation of lipid kinases or phospholipases. These lipid signals can activate enzymes or recruit proteins to membranes via distinct lipid-binding domains, where the local increase in concentration promotes interactions and downstream signaling. Here, the latest developments in phospholipid-based signaling are discussed, including the lipid kinases and phospholipases that are activated, the signals they produce, the domains that bind them, the downstream targets that contain them and the processes they control.

Comprehensive studies in grasses show that gibberellins (GAs) play a role as a florigen. For Lolium temulentum, which flowers in response to a single long day (LD), GAs are a transmitted signal, their content increasing in the leaf early in the LD and then, hours later, at the shoot apex. There is a continuous trail of evidence of hormonal action of these GAs for L. temulentum and support for a similar role in the flowering of other LD-responsive temperate grasses and cereals. A characteristic of the initial flowering responses of grasses and cereals is their limited stem elongation. Interestingly, it is GAs with low effectiveness for stem elongation, GA5 and GA6, that reach the shoot apex and, structurally, are probably not degraded by 2-oxidase enzymes. By contrast, GA1 and GA4 cause stem elongation, may be inactive for floral evocation, and do not reach the vegetative shoot apex apparently because of susceptibility to degradation. However, GA4 can be florally active if protected against 2-oxidases either structurally or by using a 2-oxidase inhibitor. Later in inflorescence development, GA1 and GA4 can be detected at the shoot apex and are florally active if applied. The 2-oxidase restricting accessibility to the apex has probably declined at this time so there is a second florigenic, LD-regulated GA action. A growing body of molecular evidence supporting these actions of GA may provide a future basis for manipulating flowering of grasses and cereals.

In this review we focus on photosynthetic behavior of overwintering evergreens with an emphasis on both the acclimative responses of photosynthesis to cold and the winter behavior of photosynthesis in conifers. Photosynthetic acclimation is discussed in terms of the requirement for a balance between the energy absorbed through largely temperature-insensitive photochemical processes and the energy used for temperature-sensitive biochemical processes and growth. Cold acclimation transforms the xanthophyll-mediated nonphotochemical antenna quenching of absorbed light from a short-term dynamic response to a long-term sustained quenching for the whole winter period. This acclimative response helps protect the evergreen foliage from photooxidative damage during the winter when photosynthesis is restricted or prevented by low temperatures. Although the molecular mechanisms behind the sustained winter excitation quenching are largely unknown, it does involve major alterations in the organization and composition of the photosystem II antenna. In addition, photosystem I may play an important role in overwintering evergreens not only by quenching absorbed light photochemically via its support of cyclic electron transport at low temperatures, but also by nonphotochemical quenching of absorbed light irrespective of temperature. The possible role of photosystem II reaction centers in nonphotochemical quenching of absorbed energy in overwintering evergreens is also discussed. Processes like chlororespiration and cyclic electron transport may also be important for maintaining the functional integrity of the photosynthetic apparatus of overwintering evergreens both during periods of thawing in winter and during recovery from winter stress in spring. We suggest that the photosynthetic acclimation responses of overwintering evergreens represent specific evolutionary adaptations for plant species that invest in the long-term maintenance of leaf structure in cold climatic zones as exemplified by the boreal forests of the Northern Hemisphere.

Future advances in plant genomics will make it possible to scan a genome for polymorphisms associated with qualitative and quantitative traits. Before this potential can be realized, we must understand the nature of linkage disequilibrium (LD) within a genome. LD, the nonrandom association of alleles at different loci, plays an integral role in association mapping, and determines the resolution of an association study. Recently, association mapping has been exploited to dissect quantitative trait loci (QTL). With the exception of maize and Arabidopsis, little research has been conducted on LD in plants. The mating system of the species (selfing versus outcrossing), and phenomena such as population structure and recombination hot spots, can strongly influence patterns of LD. The basic patterns of LD in plants will be better understood as more species are analyzed.

In the present genomics era, powerful reverse-genetic strategies are needed to elucidate gene and protein function in the context of a whole organism. However, most current techniques lack the generality and high-throughput potential of descriptive genomic approaches, such as those that rely on microarray hybridization. For example, in plant research, effective insertional mutagenesis and transgenic methods are limited to relatively few species or are inefficient. Fortunately, single-nucleotide changes can be induced in any plant by using traditional chemical mutagens, and progress has been made in efficiently detecting changes. Because base substitutions in proteins provide allelic series, and not just knockouts, this strategy can yield refined insights into protein function. Here, we review recent progress that has been made in genome-wide screening for point mutations and natural variation in plants. Its general applicability leads to the expectation that traditional mutagenesis followed by high-throughput detection will become increasingly important for plant functional genomics.

Because the plant epidermis is readily accessible and consists of few cell types on most organs, the epidermis has become a well-studied model for cell differentiation and cell patterning in plants. Recent advances in our understanding of the development of three epidermal cell types, trichomes, root hairs, and stomata, allow a comparison of the underlying patterning mechanisms. In Arabidopsis, trichome development and root epidermal patterning use a common mechanism involving closely related cell fate transcription factors and a similar lateral inhibition signaling pathway. Yet the resulting patterns differ substantially, primarily due to the influence of a prepattern derived from subepidermal cortical cells in root epidermal patterning. Stomatal patterning uses a contrasting mechanism based primarily on control of the orientation of cell divisions that also involves an inhibitory signaling pathway. This review focuses on comparing and contrasting these patterning pathways to identify and illustrate general themes that may be broadly applicable to other systems. Where these pathways occur in the same tissue, interaction and competition between these pathways is also discussed.

Transfer cells are plant cells with secondary wall ingrowths. These cells are ubiquitous, occurring in all plant taxonomic groups and in algae and fungi. Transfer cells form from differentiated cells across developmental windows and in response to stress. They are considered to play a central role in nutrient distribution by facilitating high rates of transport at bottlenecks for apo-/symplasmic solute exchange. These properties are conferred by their unique structural features—an invaginated secondary wall ensheathed by an amplified area of plasma membrane enriched in a suite of solute transporters. Recent development of transfer cell experimental systems, combined with technologies to image the three-dimensional structure of wall ingrowths, is allowing identification of inductive and regulatory signals, discovery of sequential processes involved in their differentiation, and a search for transfer cell identity genes. A model of key events in differentiation of a transfer cell is presented to highlight areas for future investigation.

The study of chloroplast movement made a quantum leap at the beginning of the twenty-first century. Research based on reverse-genetic approaches using targeted mutants has brought new concepts to this field. One of the most exciting findings has been the discovery of photoreceptors for both accumulation and avoidance responses in Arabidopsis and in the fern Adiantum. Evidence for the adaptive advantage of chloroplast avoidance movements in plant survival has also been found. Additional discoveries include mechano-stress-induced chloroplast movement in ferns and mosses, and microtubule-mediated chloroplast movement in the moss Physcomitrella. The possible ecological significance of chloroplast movement is discussed in the final part of this review.

Cryptochromes are photosensory receptors mediating light regulation of growth and development in plants. Since the isolation of the Arabidopsis CRY1 gene in 1993, cryptochromes have been found in every multicellular eukaryote examined. Most plant cryptochromes have a chromophore-binding domain that shares similar structure with DNA photolyase, and a carboxyl terminal extension that contains a DQXVP-acidic-STAES (DAS) domain conserved from moss, to fern, to angiosperm. In Arabidopsis, cryptochromes are nuclear proteins that mediate light control of stem elongation, leaf expansion, photoperiodic flowering, and the circadian clock. Cryptochromes may act by interacting with proteins such as phytochromes, COP1, and clock proteins, or/and chromatin and DNA. Recent studies suggest that cryptochromes undergo a blue light–dependent phosphorylation that affects the conformation, intermolecular interactions, physiological activities, and protein abundance of the photoreceptors.

Four proteins have been identified recently as diiron carboxylate proteins on the basis of conservation of six amino acids (four carboxylate residues and two histidines) constituting an iron-binding motif. Unlike previously identified proteins with this motif, biochemical studies indicate that each of these proteins is membrane bound, although homology modeling rules out a transmembrane mode of binding. Therefore, the predicted structure of each protein [the alternative oxidase (AOX), the plastid terminal oxidase (PTOX), the diiron 5-demethoxyquinone hydroxylase (DMQ hydroxylase), and the aerobic Mg-protoporphyrin IX monomethylester hydroxylase (MME hydroxylase)] is that of a protein bound monotopically to one leaflet of the membrane bilayer. Three of these enzymes utilize a quinol substrate, with two oxidizing the quinol (AOX and PTOX) and one hydroxylating it (DMQ hydroxylase). MME hydroxylase is involved in synthesis of the isocyclic ring of chlorophyll. Two enzymes are involved in respiration (AOX and, indirectly, the diiron DMQ hydroxylase through ubiquinone biosynthesis) and two in photosynthesis, through their roles in carotenoid and chlorophyll biosynthesis (PTOX and MME hydroxylase, respectively). We discuss what is known about each enzyme as well as our expectations based on their identification as interfacially bound proteins with a diiron carboxylate active site.