Plant Biochemistry

Caroline Bowsher, Alyson Tobin

• Publisher: Garland Science
• Year: 2021
• ISBN:
  9781000327953
• Edition: 2
• Topic: Sciences biologiques
• Subtopic: Biochimie

Plant Biochemistry focuses on the molecular and cellular aspects of each major metabolic pathway and sets these within the context of the whole plant. Using examples from biomedical, environmental, industrial and agricultural applications, it shows how a fundamental understanding of plant biochemistry can be used to address real-world issues. It illustrates how plants impact human activity and success, in terms of their importance as a food supply and as raw materials for industrial and pharmaceutical products, and considers how humans can benefit from exploiting plant biochemical pathways.

All chapters in this second edition have been substantially revised to incorporate the latest research developments, and case studies include updates on progress in developing novel plants and plant products. The artwork, now in full color, superbly illustrates the key concepts and mechanisms presented throughout.

Key features:

• Presents each topic from the cellular level to the ecological and environmental levels, placing it in the context of the whole plant.
• Biochemical pathways are represented as route maps, showing how one reaction interacts with another both within and across pathways.
• Includes comprehensive reading lists with descriptive notes to enable students to conduct their own research into topics they wish to explore further
• The wide-ranging approach of this book emphasizes the importance of teaching and learning plant biochemical pathways within the framework of what the pathway does and why it is needed.
• Illustrates the fundamental significance of plants, in terms of their importance as a food supply, as raw materials and as sources of novel products.

Plant Biochemistry is invaluable to undergraduate students who wish to gain insight into the relevance of plant metabolism in relation to current research questions and world challenges. It should also prove to be a suitable reference text for graduates and researchers who are new to the topic or who wish to broaden their understanding of the range of biochemical pathways in plants.

1

Introduction to Plant Biochemistry

Plants are present in all aspects of our everyday life. They provide our food, produce the oxygen that we breathe, and serve as raw materials in many of our clothes and buildings, and in the manufacture of biofuels, drugs, dyes, perfumes, and pesticides. Land plants have existed for over 400 million years, and the first flowering plants (angiosperms) evolved about 135–190 million years ago. Through their continued evolution, they have acquired an enormous diversity of form and physiology that has enabled them to colonize a wide range of habitats successfully. There are currently thought to be between 250,000 and 400,000 angiosperm species, and they survive on all continents, from the Arctic to the Antarctic, and in all manner of environments, from deserts to flooded plains. Such a breadth of environments means that plants also survive a wide range of temperatures.

Despite the diversity and prevalence of plants, modern agriculture relies on just a few species to provide much of the human diet. Indeed, just six crop plants—wheat, rice, corn, potatoes, sweet potatoes, and manioc—provide, directly or indirectly (i.e. after having been fed to animals), over 80% of the total calories consumed by humans. Although these plants are rich in carbohydrates, to ensure a balanced diet, proteins can be provided by legumes, including beans, peas, lentils, peanuts, and soybeans, while additional vitamins and minerals are provided by leafy vegetables, such as lettuce, cabbage, and spinach. Finally, fats are provided by the seeds and fruits of plants such as sunflowers, peanuts, canola, and olives. Although other crops are of great importance to humans, including sugar cane, sugar beet, barley, sorghum, coconut, and bananas, it is clear that we currently use only a tiny proportion of the available plant species in our daily diet. As the world’s population continues to grow, there is an increasing demand not only for food but also for the raw materials that plants supply. To meet this demand, we need to be able to maximize the production of plant products by improving existing crops and developing novel crops. Consequently, an important aim of plant biochemical research is to discover how plants produce and control the production of these valuable food and non-food products. We hope that reading this book will provide you with insights into our current knowledge of plant biochemistry.

The biochemistry of plants is sufficiently distinctive to merit separate treatment from that of other organisms. This is for two main reasons. First, the sessile plant cannot avoid environmental stress or predation by moving away, and second, plants are autotrophic, and their resources are relatively simple (e.g. inorganic nutrients, light, water, and CO₂) and frequently in short supply. Consequently, plant biochemical pathways tend to be particularly flexible and responsive to changes in the plant’s environment, both as a survival mechanism and as a means of making optimum use of limited resources. Throughout this book, examples of plants’ responses to their environment and the challenges the environment presents will be considered. As we shall see, a recurring feature of plant biochemical pathways is the existence of isoenzymes—enzymes that carry out essentially identical reactions yet differ in their regulatory properties and subcellular locations. For example, many enzymes are duplicated between plastids and cytoplasm [e.g. in ammonium assimilation (Chapter 8), glycolytic reactions (Chapter 6), and reactions that produce precursors for terpenoid biosynthesis (Chapter 12)]. One function of these isoenzymes is to add flexibility to the biochemical pathway. It is almost as if this duplicity of function provides a safety net whereby a metabolic bypass may occur should stress produce an untoward effect on one compartment. The second major feature that marks out plant biochemistry is the autotrophic nature of plants—hence, even respiratory pathways such as the tricarboxylic acid cycle, which are primarily catabolic in non-photosynthetic organisms, serve an anabolic function in plants, providing carbon skeletons for biosynthesis (Chapter 6). A good example where both of these key features coincide to enable plants to survive is that of the secondary metabolic pathways leading to the biosynthesis of alkaloids (Chapter 10), phenolics (Chapter 11), and terpenoids (Chapter 12), where the environmental stress imposed by herbivory, in particular, has led to the evolution of increasingly complex biochemical pathways, resulting in a chemical arms race, with plants producing a massive array of defensive chemicals as a means of deterring potential herbivores. This, of course, presents a significant drain on the photosynthetic productivity of a plant, yet biochemical pathways are sustained as a survival mechanism.

As you will find in any biochemistry textbook, we have presented the metabolic pathways rather like a route map to show how one reaction follows another. However, it is important to see these pathways as dynamic and fluid processes that do not operate in isolation and are responsive to considerably fluctuating conditions, both in their immediate vicinity (i.e. cellular or subcellular) and in the wider (i.e. whole plant–environment interactions) environment. To understand specifically not just the route map but also the flux and regulation, i.e. the dynamic nature of the pathways, what is being produced/degraded, and how this is balanced according to the needs of the plant, biochemists have developed a wealth of methods. In recent years, there has been a move away from the reductionist approach, whereby biochemical reactions were only ever investigated at the level of single proteins in isolation. Current progress is taking place through a more holistic, or systems-based, approach, which offers a realistic hope of understanding the interlinking processes of biochemical and gene regulation in relation to the function and metabolism of the whole plant. We have introduced and explained some current methodologies that provide a greater understanding of the biochemistry of the whole plant (Chapter 2). Indeed, a theme of this book is to set biochemistry within the context of the function and response of the whole plant, where we have been able to do so. In several chapters, you may find the boxes to be particularly useful in this respect.

Many biochemical pathways in plants, as in other eukaryotes, show cellular and subcellular compartmentation, with enzymes localized in distinct compartments (Chapter 2). It is important to understand plant cell structure in order to fully understand this compartmentation, and in Chapter 3, therefore, we introduce the structural aspects of plant cells. This topic serves as a reminder of the significant contribution that compartmentation makes to the regulation and control of biochemical pathways. Compartmentation is often essential as a means of preventing unwanted reactions from taking place, that is, by isolating enzymes from potential substrates that might otherwise be converted to toxic products. Nevertheless, many biochemical pathways are distributed among a number of different subcellular compartments. Photorespiration, which involves reactions that take place in chloroplasts, peroxisomes, cytosol, and mitochondria, is a good example of a highly compartmentalized pathway. In pathways such as this, there is a need for substrates and products to be moved across membranes, which provides additional control points that need to be considered when investigating the regulation of a pathway. Specific metabolite translocator proteins, which serve to carry metabolites across cell membranes, are, therefore, introduced in Chapter 2 and are further discussed in the context of photosynthesis (Chapter 5), respiration (Chapter 6), carbohydrate metabolism (Chapter 7), nitrogen and sulfur assimilation (Chapter 8), and fatty acid biosynthesis (Chapter 9).

The autotrophic nature of plant biochemistry is introduced in the two photosynthesis chapters (Chapter 4, Light Reactions of Photosynthesis, and Chapter 5, Photosynthetic Carbon Assimilation). Chapter 5 also illustrates, once again, the environmental influences on plant biochemical pathways, whereby the more complex carbon concentrating pathways of C₄ photosynthesis and Crassulacean acid metabolism are thought to have evolved in response to limited CO₂ concentrations and a reduction in water availability, respectively.

Autotrophy is not just about gaining carbon; it also involves the acquisition of other major minerals that are needed for plant growth and development. Hence nitrogen and sulfur assimilation (Chapter 8) are just as essential a part of autotrophy as carbon assimilation. The way in which plants acquire and reduce inorganic nitrogen is another good example of how environmental conditions influence plant biochemistry. As explained in Chapter 8, the form of inorganic nitrogen that is assimilated by a plant depends not only on the plant species but also on the conditions of the soil, with anaerobic and acidic soils being primarily colonized by plants that are adapted to using ammonium as their nitrogen source. In contrast, most agricultural soils contain the bulk of their nitrogen as nitrates; hence, in most crop species (with the noted exception of rice and legumes), nitrogen assimilation begins with the uptake and reduction of nitrate, while plants living in acid bogs and shrubby heathlands are generally better adapted to the uptake and assimilation of ammonium. Other plants, such as legumes, have co-evolved with symbiotic bacteria to acquire their nitrogen from free atmospheric nitrogen, with the bacteria releasing ammonium for the plant, which, in turn, supplies the bacteria with organic acids for respiration.

In plants, respiration involves the combined operation of glycolysis, the oxidative pentose phosphate pathway, the tricarboxylic acid cycle, and the mitochondrial electron transport chain, and respiration serves both a catabolic and a biosynthetic function (Chapter 6). Respiration is a highly flexible process that allows plants to respond to varying environmental conditions and to change their photosynthetic and photorespiratory activity. For example, plant glycolysis is unique in having dual locations, in the cytosol and the plastids. Plant glycolysis also uses alternative enzymes to supplement or even replace those conventionally present, ensuring metabolic flexibility and allowing glycolysis to proceed and the plant to survive under varying and potentially stressful environmental and/or nutritional conditions. Furthermore, plant mitochondria possess a branched electron transport chain that provides a mechanism for varying adenosine triphosphate (ATP) production in response to metabolic demands, in some cases supplementing the chloroplast to support carbon assimilation. For example, the possession of an alternative respiratory pathway, in addition to the conventional cytochrome pathway, enables plants to respire at high rates without the usual respiratory control by adenosine diphosphate (ADP) that would otherwise limit respiration. This pathway has been particularly successful, as we shall see, in some plants where high rates of carbohydrate oxidation result in heat production and volatilization of scents to attract pollinating flies (e.g. Arum lilies, Chapter 6).

Carbohydrates are the main respiratory substrate in most plant tissues (Chapter 7). They are also an important source of carbon skeletons for the biosynthesis of many organic molecules in a plant, for example, amino acids, lipids, and structural carbohydrates. Plant carbohydrate biosynthesis is highly compartmentalized, with the two major storage carbohydrates of sucrose and starch being synthesized in the cytosol and plastids, respectively. Starch is generally used for relatively long-term storage of carbohydrates, while sucrose is soluble and readily transported from tissue to tissue and cell to cell. The balance between the biosynthesis, transport, and utilization of carbohydrates has to be regulated to ensure that there is an adequate supply of carbohydrates for both photosynthetic and non-photosynthetic tissue. Consequently, carbohydrate metabolism is a highly regulated process with a number of feedback controls that serve to control and coordinate the supply and demand of source and sink tissue. The presence of isoenzymes adds further flexibility to the pathways for sucrose and starch metabolism, as explained in Chapter 7.

Lipids are not only essential to the structure of cells; they also serve as important respiratory substrates in certain plant tissues (e.g. oily seeds). Fats, oils, some hormones and pigments, and most non-protein membrane components are lipids. A saponifiable lipid is made of a glycerol backbone and fatty acids. Fatty acids are carboxylic acids with long-chain hydrocarbon side groups. The type of fatty acid that is made, in terms of chain length and degree of saturation, will determine the type of lipid produced. Similarly, the type of fatty acid incorporated into the glycerol backbone influences the type of lipid. Finally, the location where the fatty acids are built into lipids will influence the combination of fatty acids and the type of lipid produced. In Chapter 9, we focus on fatty acid biosynthesis and the lipids arising as a result of this. We further discuss the subsequent release of energy from lipids when they are metabolized. Fatty acid and lipid metabolism in plants have a number of features in common with other organisms. Again, in plants, fatty acid and lipid metabolism is more complex than in other organisms because of their cellular compartmentation. By necessity, lipid pools must be moved around to meet metabolic demands (Chapter 9).

This book illustrates some of the ways in which plants have exploited the full range of possibilities offered by carbon chemistry to flourish on this planet. The study of the numerous synthetic pathways present in plants, which entails unraveling the structures of intermediates and end products and characterizing the enzymes involved, is a challenge for the modern plant biochemist. With the toolkits of today’s chemists, it is at last possible to explore the fascinating range of processes that underlie the success of plants.

The topics covered in this book clearly demonstrate that plants and their biochemistry have a direct impact on human activity and success, both in terms of their importance as a food supply and as raw materials for fibers and other industrial and pharmaceutical products. With the world’s population growing and currently estimated to reach 9–10 billion by 2050, it is predicted that food will be in increasingly limited supply. There is an abundance of unused land on the earth, and much of it is nutrient-poor; the challenge is to develop effective strategies to exploit these areas. Both increased productivity in current areas of agricultural land and the successful cultivation of crops in more stressful environments (e.g. saline or mineral-deficient soils) will be needed to meet the growing demand for crops. Knowledge of the biochemistry of plants will provide us with the opportunity to try to develop the means to address at least some of these issues. Understanding the limits, controls, and potential sites for improvement of existing biochemical pathways will make it possible to significantly improve the productivity and versatility of plants. We will also be able to modify existing pathways and introduce novel pathways to produce new plant products.

2

Approaches to Understanding Metabolic Pathways

Key Concepts

• A range of techniques, including chromatography, electrophoresis, and the use of radioisotopes, are available to study metabolic pathways.
• The functions of individual genes and enzymes can be studied by analyzing mutant and transgenic plants.
• Omics platforms, including transcriptomics, proteomics, and metabolomics, can provide an understanding of entire biological systems.
• Plant metabolism is diverse, flexible, and robust because plants cannot move away from environmental stress or predators.
• Developments in system biology approaches o...