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Biochemistry & Molecular Biology of Plants

Review from ACTA Physiologiae Plantarum (APP)

This is the first edition and a new concept of textbook dealing with plant biochemistry accompanied by molecular and functional context of plant biochemical components and processes. According to editors own opinion the book was organized around the elements required for life: membranes, energy, metabolism and reproduction. The fact the fifth element fundamental for life -information processing and storage was also included. In other words this is the book of plant biochemistry and molecular biology with necessary elements of plant physiology.

The book is written by a team of 53 prominent authors widely known in plant science with the leadership of main editors (two of them were president of the ASPP) and accompanied by numerous groups of reviewers. Despite the fact that the book was written by so many authors it is easy to read because of unified text and page design as well as illustrations selection and composition. It could be clearly seen that it is common work of good scientists, professional editors and illustrators. In the text numerous boxes have been included presenting analytical methods and their specific application to solve biochemical or biological problem being presented in the book. It is also supplemented with detailed index and with references for illustrations presented inside.

The book is divided into five parts dealing with main aspects of plant functioning: (cell) Compartments, Cell reproduction, Energy flow, Metabolic and developmental integration and finally Plant environment and agriculture, and comprises in total 24 separated chapters.

Chapter 1. Cell membranes and membranous organelles
In this part the general features and molecular organization of membranes as well as the architecture and functions of such different membranous organelles and structures like endoplasmatic reticulum, Golgi apparatus, vacuoles, nucleus, peroxisomes, plastids and mitochondria are described.

Chapter 2. The cell wall
Surprisingly big attention is paid to the cell wall composition, structure and function. The role of the cell wall is precisely characterized by the authors; "In living cells, the cell wall constrains the rate and direction of cell growth, exerting a profound influence on plant development and morphology". From the chapter the cell wall is arising as a dynamic compartment that changes throughout the life of the cell although in some cells the protoplast disintegrates during development, and the mature cell consists entirely of cell wall.

Chapter 3. Membrane transport
The following topics have been described in the chapter: overview of membrane transport, organization of transport at plant membranes, pumps, carriers, general properties of ion channels, ion channels in action and water transport through aquaporins. In addition some theoretical bases of the processes under study (water electro-chemical potential of solutes, membrane potential, hyperpolarization and Donnan potential, proton motive force) as well as main experimental methods used in the study (micromanipulation and microinjections, measurements of voltage dependence of ion transport, as a function of electric potential and also the membrane water permeability as related to osmotic properties of cell solutes)

Chapter 4. Protein sorting and vesicle transport
The importance of the subject is well characterized when taking in account that plant cell may content 5 to 10 thousands different polypeptide sequences and billions of individual protein molecules. In properly functioning cell all these proteins must be directed to proper metabolic cell compartments, cytoplasm structures and membrane systems. Another problem being rather of philosophical nature is that all the proteinous traffic has to be regulated by mechanisms being also of protein nature, what means that only small part of proteins may be engaged in the protein sorting. In the chapter both general rules of protein transport as well as the transport directed to specific organelles are described. In the second part of the chapter the vesicle formation and sorting as well as the taking up proteins from surrounding environment and delivering them to proper cell compartments was presented.

Chapter 5. The cytoskeleton
From the chapter the cytoskeleton arises as the system enabling the cell to organize its components spatially, keeping some of them in fixed finely defined locations of the cell while others are moving (sometimes along precisely defined paths) to attain optimal positions. In the chapter few specific experimental methods were described. First one is based on the use of polarized light microscopy to visualize polar constructed cytoskeleton, while the second visualizes cytoskeleton using fluorescent labeling and the application of confocal microscope and the last based on very fast criofixation of samples
preventing water crystallization. A special attention was put on the mitotic spindle microfibrile, which directs (sorts) of particular chromosomes to one of new cells.

Chapter 6. Nucleic acids
The chapter gives rather typical (thought clearly presented with the use of numerous and finely prepared diagrams, photos and graphs) information concerning biosynthesis of nucleotides and nucleic acids, as well as their structure and function. Both nuclear and plastid genomes are described.

Chapter 7. Genome organization and expression
The chapter is focused on the informational organization of the genes within chromosomes. The idea of the chapter it that all information encoded in thousands of genes requires (even in simple organisms) some sort of organization. The first organizational level is the chromosome, but with so many genes and so few chromosomes a vast array of genes must reside any one chromosome. The most important question is how all of these genes are organized and their expression precisely orchestrated with the cell differentiation and plant development.

Chapter 8. Amino acids
This is typical biochemical chapter describing the pathways of particular amino acid biosynthesis. This group of compounds besides their obvious role in protein synthesis performs key functions in both primary and secondary plant metabolism. Some of them participate in nitrogen assimilation and transport; others are the precursors of numerous secondary products as phytohormones or compounds involved in plant defense. This chapter highlights examples of combined molecular, biochemical and genetic approaches define the pathways and regulatory mechanisms of amino acids biosynthesis in plants. A special role of auxotrophic mutants in the process is also presented.

Chapter 9. Protein synthesis, assembly, and degradation
The title of chapter precisely defines its topic. As author mentions "it is not surprising that protein synthesis is central to cell growth, differentiation and reproduction". Hence the following stages have been described: transcription, translation (in all three cell compartments - i.e. in cytoplasm, in chloroplasts and also in mitochondria), posttranslational modification of proteins, folding of proteins, function of chaperons, and finally protein degradation.

Chapter 10. Lipids
The term lipids includes a wide variety of fatty acid-derived compounds, as well as many pigments and secondary compounds that are metabolically unrelated to fatty acid metabolism. The subtitles of the chapter clearly stress main conclusions followed from the chapter: lipids have diverse role in plants, fatty acids biosynthesis in plants is similar to that in bacteria, plants contain a soluble, plastid-localized stearoyl-ACP desaturase, more than 200 fatty acids occur in plants, unusual fatty acids occur almost exclusively in seed oils and may serve a defense function, membrane lipid synthesis requires a complex collaboration between cell compartments, membrane lipid composition affects plant form and function, membrane lipid composition can influence plant cell responses to freezing, membrane and storage lipids often have distinct compositions, edible oils can be improved by metabolic engineering^ biodegradable plastics can be produced in plants.

Chapter 11. Cell division regulation
Contrary to cell growth and most of biochemical processes that are of continuous nature cell division proceeds in discrete incremental steps. Thus the cell division process has to be regulated on the other way. Specific role is played by specific checkpoints permitting or not the mitosis to continue. In the chapter a whole cell cycle is described, starting from DNA replication, then prereplicative state and finally mitosis. Biological consequences of the mitosis like shoot meristems and other organ formation, root cell speciation, growth of plants and finally totipotency both in natural and during plant in vitro sterile cultures are also presented.

Chapters 12. (Photosynthesis), 13. (Carbohydrate metabolism) and 14. (Respiration and photorespiration)
These are three typical chapters of greater part entitled Energy flow. In chapter 12 main aspects of the photosynthetic reduction of carbon dioxide i.e. light harvesting, C3, C4 and CAM pathways and their biochemical details are presented. From our point of view this chapter ought be completed with some relations between photosynthesis, assimilate translocation and crop forming, however we understand that it is not a book of plant physiology.

In the chapter 13 main carbohydrate metabolism pathways have been described. A special attention was focused on biosynthesis and decay of starch (both amylose and amylopectin), sucrose and monosaccharides as well as other processes leading to the following stages of respiration (the citric acid cycle) or connected to nitrate and sulfate reduction.

Chapter 14 is devoted to aerobic oxidation of metabolites mentioned above, as well as to photorespiration - a unique process taking place in plants and related to oxidative properties of the Rubisco. The citric acid cycle has been overviewed not only as an energy source but also as the pathway for biosynthesis and degradation of numerous amino acids, ammonia assimilation and other metabolic paths. A remarkable part of the chapter describes function of the mitochondria.

Chapter 15. Long-distance transport
One can say that there is not many biochemistry and molecular biology in the long - distance transport between spatially distinct but nutritionally interdependent plant regions. In fact in prevailed volume of the chapter rather physical phenomena are presented like convection, diffusion, water potential as providing a thermodynamic basis for water movement, surface tension and cohesion-tension mechanism of water movement and finally rather rarely met in this kind of books - cavitation process. Generally this is probably the most physiological chapter in the entire book.

Chapter 16. Nitrogen and sulfur
The common feature of the both elements is that they are uptaken from the soil in highly oxidized form. To be incorporated into biotic compounds (amino acids, amines components of NA structure etc.) they have to be reduced as highly as through 8 oxidation levels (sulfur from +6 to -2 and nitrogen from +5 to -3). The reduction needs a big amount of metabolic energy and both ATP and reduced form of nucleotides supply. This is why the incorporation of both elements into plant organism tightly connected with main energy turnover processes and cycles. The nitrogen assimilation is described in details taking in account the fundamental rule of the element and a relatively high its contents in plant cells. The biochemistry as well as molecular processes accompanying the assimilation processes is described here in details.

Chapter 17. Biosynthesis of hormones and elicitor molecules
Authors distinguished 9 groups of plant hormones (gibberellins, ABA, ethylene, zeatin, IAA, brassinolide, jasmonic acid, salicylic acid and spermidine) but according to our opinion this classification reflects in part author's subjective point of view. Each of these compounds has its own particular properties, so the pathways regulating their production and degradation are quite diverse and have been elucidated by synergistic use of many disciplines, including chemistry, biochemistry, plant physiology, genetics and, more recently, molecular genetics. The most powerful tool have been plants being an auxotrophic mutants and transgenic technology permitting regulation of the expression of genes involved in plant hormones biosynthesis and degradation. All these problems were precisely highlighted in the chapter and supplied also with physiological action mode of particular plant hormones and presentation of the hormones as a tool in pathogenesis process as well as in signal-exchanging between future symbiotic cells of bacteria and root hair in Papilionaceae.

Chapter 18. Signal perception and transduction
This part of plant biology is developing very fast during last years. This is for the editors decided to involve in the bookseparate part devoting to this problem. According to the author's own words "Plant cells are constantly bombarded with information to which they must react.signal transduction research contributes to all aspects of plant science, linking many fields of study.." In the chapter such subjects like variability and nature of the signals, signal receptors, ion channels working as intracellular receptors, phytochromes and cryptochrome as a group of specific light receptors, G-proteins and a share of phospholipids in cell signaling, cyclic nucleotides, calcium as a signaling intermediate, protein kinases, are discussed.

Chapter 19. Reproductive development
The generative development appears to be the most fundamental plant process. Though reproduction is a typical process of physiological nature being not often met in typical books of plant physiology, in the book recent developments in genetics, molecular biology, and biochemistry of flower induction and evocation have been highlighted. In the beginning of the chapter authors presented some flowering induction factors but there is not many new information. We can agree that the photoperiod is the most often met flowering stimulator but in temperate climate regions also vernalization is an important flower-controlling factor. Authors give however detailed study of the molecular and genetic processes accompanying (or maybe controlling rather) flower induction in Arabidopsis thaliana on the basis of use of numerous developmental mutants of the plant. These genetic researches are strongly supported by in vitro cultures, specially the haploid and dihaploid homozygous plants culture, which simplify the genetic control of plant flowering. In the chapter some "side" problems like self-incompatibility, pollen grain germination, seed formation, filling with storage materials, as well as the embryo maturation and desiccation are elaborated.

Chapter 20. Senescence and programmed cell death
The death of specific cells (at specific time point) is an essential part of the growth and development of many eucariotic organisms, including plants and animals. Cell death can be an important component of the plant response to biotic and abiotic stresses. In the chapter both main types of regulated plant cell death - programmed cell death (PCD) and hypersensitivity reaction (HE) is detailed. Special authors attention was paid to the physiological, anatomical but mainly genetic and molecular mechanisms leading cells to senescence or death. This is somewhat surprising when cells activate their own genes to induce their transcripts which in short time period kill the cell, what means that death signaling coming from cell surrounding environment but employs cell own killing mechanisms. As previously, some plant mutants have been used to elucidate particular events accompanying cell senescence and death as well as the process as playing fundamental role in such "practice" problem like remobilization and reutilization of the cell organic components as new storage material for the rest of organism. Finally the role of plant hormones and the oxygen free radicals in plant senescence and death is detailed here.

Chapter 21. Responses to plant pathogens
This chapter is first one belonging to last part of the book concerning selected agricultural aspects of the main theme. Here the following topics have been discussed: ways in which plant pathogens cause disease, plant defense system, genetic basis of plant-pathogen interactions, R genes and R gene-mediated disease resistance, biochemistry of plant defense reactions, systemic plants defense responses, control of plant pathogens by genetic engineering.

Chapter 22. Responses to abiotic stresses
This chapter completes the last one on the same way as abiotic stresses complete biotic ones. It is worth to note that often in other book the both group of stresses are described in common because of partly common biochemical mechanisms of their action and plant defensive reactions. In the chapter authors took in account such stress factors like water deficit, salinity, frost, flooding, oxygen deficit, oxidative stress, ozone, and heat stress, which were detailed with respect to their mechanism and the influence to plant crop yields and the mechanisms of counteraction by plants.

Chapter 23. Molecular physiology of mineral nutrient acquisition, transport and utilization
This chapter focuses on recent findings concerning the molecular physiology of macro- and micronutrient transport as well as the strategies plants use to tolerate stressful soil environment such as toxic concentrations of some metal ions. With this respect the chapter is typical but the topics are supplemented with theory of the kinetics of ion uptake and transport.

Chapter 24. Natural products (secondary metabolites) On almost 70 pages the extensive list of numerous plant secondary metabolites is presented. These unique compounds play important role both in plant organisms and in medicine. Some of the compounds have been known and used for thousands of years; others were discovered in last years. In the last chapter these secondary metabolites were categorized and then described in details. Authors distinguished following groups of the plant secondary metabolites: terpenoids, alkaloids, phenolic compounds, lignins, favonoids, coumarins and derivatives.

In the final remark we would like to express our opinion that the book presented here is directed at advanced students and professionals in the plant sciences: molecular biologists, botanists, biochemists, or those in the horticultural or agricultural sciences. It was really good idea that with helps of the American Society of Plant Physiolgists such a valuable book was prepared. This is really rich source of information and guide to the literature for scientists. According to our opinion this book should be translated into Polish.

F. Dubert (Krakow), W, Filek (Krakow)

© Copyright American Society of Plant Biologists 2013 (All Rights Reserved)