Annual Review of Plant Biology - Volume 49, 1998

In this review, we address the phylogenetic and structural relationships between light-responsive promoter regions from a range of plant genes, that could explain both their common dependence on specific photoreceptor-associated transduction pathways and their functional versatility. The well-known multipartite light-responsive elements (LREs) of flowering plants share sequences very similar to motifs in the promoters of orthologous genes from conifers, ferns, and mosses, whose genes are expressed in absence of light. Therefore, composite LREs have apparently evolved from cis-regulatory units involved in other promoter functions, a notion with significant implications to our understanding of the structural and functional organization of angiosperm LREs.

Carotenoids are integral and essential components of the photosynthetic membranes in all plants. Within the past few years, genes encoding nearly all of the enzymes required for the biosynthesis of these indispensable pigments have been identified. This review focuses on recent findings as to the structure and function of these genes and the enzymes they encode. Three topics of current interest are also discussed: the source of isopentenyl pyrophosphate for carotenoid biosynthesis, the progress and possibilities of metabolic engineering of plants to alter carotenoid content and composition, and the compartmentation and association of the carotenogenic enzymes. A speculative schematic model of carotenogenic enzyme complexes is presented to help frame and provoke insightful questions leading to future experimentation.

After a long period of little change, the basic concepts of lignin biosynthesis have been challenged by new results from genetic modification of lignin content and composition. New techniques for making directed genetic changes in plants, as well as improvements in the analytical techniques used to determine lignin content and composition in plant cell walls, have been used in experimental tests of the accepted lignin biosynthetic pathway. The lignins obtained from genetically modified plants have shown unexpected properties, and these findings have extended the known range of variation in lignin content and composition. These results argue that the accepted lignin biosynthetic pathway is either incomplete or incorrect, or both; and also suggest that plants may have a high level of metabolic plasticity in the formation of lignins. If this is so, the properties of novel lignins could be of significant scientific and practical interest.

Desaturation of a fatty acid first involves the enzymatic removal of a hydrogen from a methylene group in an acyl chain, a highly energy-demanding step that requires an activated oxygen intermediate. Two types of desaturases have been identified, one soluble and the other membrane-bound, that have different consensus motifs. Database searching for these motifs reveals that these enzymes belong to two distinct multifunctional classes, each of which includes desaturases, hydroxylases, and epoxidases that act on fatty acids or other substrates. The soluble class has a consensus motif consisting of carboxylates and histidines that coordinate an active site diiron cluster. The integral membrane class contains a different consensus motif composed of histidines. Biochemical and structural similarities between the integral membrane enzymes suggest that this class also uses a diiron cluster for catalysis. Soluble and membrane enzymes have been successfully re-engineered for substrate specificity and reaction outcome. It is anticipated that rational design of these enzymes will result in new and desired activities that may form the basis for improved oil crops.

Contaminated soils and waters pose a major environmental and human health problem, which may be partially solved by the emerging phytoremediation technology. This cost-effective plant-based approach to remediation takes advantage of the remarkable ability of plants to concentrate elements and compounds from the environment and to metabolize various molecules in their tissues. Toxic heavy metals and organic pollutants are the major targets for phytoremediation. In recent years, knowledge of the physiological and molecular mechanisms of phytoremediation began to emerge together with biological and engineering strategies designed to optimize and improve phytoremediation. In addition, several field trials confirmed the feasibility of using plants for environmental cleanup. This review concentrates on the most developed subsets of phytoremediation technology and on the biological mechanisms that make phytoremediation work.

This review summarizes current knowledge about genes whose products function in the transport of various cationic macronutrients (K, Ca) and micronutrients (Cu, Fe, Mn, and Zn) in plants. Such genes have been identified on the basis of function, via complementation of yeast mutants, or on the basis of sequence similarity, via database analysis, degenerate PCR, or low stringency hybridization. Not surprisingly, many of these genes belong to previously described transporter families, including those encoding Shaker-type K⁺ channels, P-type ATPases, and Nramp proteins. ZIP, a novel cation transporter family first identified in plants, also seems to be ubiquitous; members of this family are found in protozoa, yeast, nematodes, and humans. Emerging information on where in the plant each transporter functions and how each is controlled in response to nutrient availability may allow creation of food crops with enhanced mineral content as well as crops that bioaccumulate or exclude toxic metals.

Calmodulin is a small Ca²⁺-binding protein that acts to transduce second messenger signals into a wide array of cellular responses. Plant calmodulins share many structural and functional features with their homologs from animals and yeast, but the expression of multiple protein isoforms appears to be a distinctive feature of higher plants. Calmodulin acts by binding to short peptide sequences within target proteins, thereby inducing structural changes, which alters their activities in response to changes in intracellular Ca²⁺ concentration. The spectrum of plant calmodulin-binding proteins shares some overlap with that found in animals, but a growing number of calmodulin-regulated proteins in plants appear to be unique. Ca²⁺-binding and enzymatic activation properties of calmodulin are discussed emphasizing the functional linkages between these processes and the diverse pathways that are dependent on Ca²⁺ signaling.

While the concept of H⁺-coupling has dominated studies of energy-dependent organic solute transport in plants for over two decades, recent studies have demonstrated the existence of a group of organic solute transporters, belonging to the ATP-binding cassette (ABC) superfamily, that are directly energized by MgATP rather than by a transmembrane H⁺-electrochemical potential difference. Originally identified in microbial and animal cells, the ABC superfamily is one of the largest and most widespread protein families known. Competent in the transport of a broad range of substances including sugars, peptides, alkaloids, inorganic anions, and lipids, all ABC transporters are constituted of one or two copies each of an integral membrane sector and cytosolically oriented ATP-binding domain. To date, two major subclasses, the multidrug resistance-associated proteins (MRPs) and multidrug resistance proteins (MDRs) (so named because of the phenotypes conferred by their animal prototypes), have been identified molecularly in plants. However, only the MRPs have been defined functionally. This review therefore focuses on the functional capabilities, energetics, organization, and regulation of the plant MRPs. Otherwise known as GS-X pumps, or glutathione-conjugate or multispecific organic anion Mg²⁺-ATPases, the MRPs are considered to participate in the transport of exogenous and endogenous amphipathic anions and glutathionated compounds from the cytosol into the vacuole. Encoded by a multigene family and possessing a unique domain organization, the types of processes that likely converge and depend on plant MRPs include herbicide detoxification, cell pigmentation, the alleviation of oxidative damage, and the storage of antimicrobial compounds. Additional functional capabilities might include channel regulation or activity, and/or the transport of heavy metal chelates. The identification of the MRPs, in particular, and the demonstration of a central role for ABC transporters, in general, in plant function not only provide fresh insights into the molecular basis of energy-dependent solute transport but also offer the prospect for manipulating and investigating many fundamental processes that have hitherto evaded analysis at the transport level.