Plant Genes, Genomes and Genetics

Erich Grotewold, Joseph Chappell, Elizabeth A. Kellogg

• Publisher: Wiley-Blackwell
• Year: 2015
• ISBN:
  9781118539361
• Edition: 1
• Topic: Biowissenschaften
• Subtopic: Genetik & Genomik

Plant Genes, Genomes and Genetics provides a comprehensive treatment of all aspects of plant gene expression. Unique in explaining the subject from a plant perspective, it highlights the importance of key processes, many first discovered in plants, that impact how plants develop and interact with the environment. This text covers topics ranging from plant genome structure and the key control points in how genes are expressed, to the mechanisms by which proteins are generated and how their activities are controlled and altered by posttranslational modifications.

Written by a highly respected team of specialists in plant biology with extensive experience in teaching at undergraduate and graduate level, this textbook will be invaluable for students and instructors alike. Plant Genes, Genomes and Genetics also includes:

• specific examples that highlight when and how plants operate differently from other organisms
• special sections that provide in-depth discussions of particular issues
• end-of-chapter problems to help students recapitulate the main concepts
• rich, full-colour illustrations and diagrams clearly showing important processes in plant gene expression
• a companion website with PowerPoint slides, downloadable figures, and answers to the questions posed in the book

Aimed at upper level undergraduates and graduate students in plant biology, this text is equally suited for advanced agronomy and crop science students inclined to understand molecular aspects of organismal phenomena. It is also an invaluable starting point for professionals entering the field of plant biology.

Part I

Plant Genomes and Genes

Chapter 1
Plant genetic material

1.1 DNA is the genetic material of all living organisms, including plants

Like all living organisms, plants use deoxyribonucleic acid (DNA) as their genetic material. DNA is a polymer that consists of alternating sugars and phosphates with nitrogenous bases attached to the sugar moiety. More specifically, the nucleotide building block of DNA is a deoxyribose sugar with a phosphate group attached to carbon 5 (C-5) and a nitrogenous base to carbon 1 (C-1). Phosphodiester bonds connect the C-5 phosphate group of one nucleotide to the carbon 3 (C-3) of another, creating the alternating sugar–phosphate backbone of the DNA molecule. This means that one end of the chain is terminated by a C-5 phosphate, and is known as the 5′ end, whereas the other end is terminated by a C-3 hydroxyl, and is known as the 3′ end (Figure 1.1a). The idea that DNA molecules have a polarity is one that will be revisited over and over throughout this book.

Figure 1.1 Structure of the DNA molecule. (a) Alternating phosphate and ribose groups make up the backbone of the DNA strand. The C-3 hydroxyl at the 3′ end is required for attaching new nucleotides to the chain, so the DNA strand always is extended from the 3′ end. The nitrogenous bases are attached to C-1 of the ribose. (b) The double helix, formed from two antiparallel strands of DNA. (c) The four nitrogenous bases and the hydrogen bonds between them. (a) and (c) Reece et al. (2011). (b) Adapted from Raven et al. (2011)

Only four nitrogenous bases are used in a DNA molecule. Two of these, cytosine (C) and thymine (T), have a single aromatic ring consisting of four carbons and two nitrogen groups, and are classified as pyrimidines. The other two, adenine (A) and guanine (G), each have a double ring consisting of a pyrimidine ring fused to a 5-membered, heterocyclic ring, and are classified as purines. The bases form a linear molecule, a strand of DNA that interacts with the nitrogenous bases on the other strand.

Two DNA polymers, or strands, together form the iconic double helix, a structure like a twisted ladder that has come to symbolize life and its historical continuity (Figure 1.1b). Even viruses, many of which have genomes of single-stranded nucleic acids, must eventually pass through a double-stranded stage to reproduce. The strands are held together by hydrogen bonds (H-bonds) between the nitrogenous bases, with two bonds between A and T, and three between G and C (Figure 1.1c). Since more H-bonds between bases hold them together more tightly, it is significantly easier to denature a DNA molecule with many A-T base pairs than one with many C-G base pairs. The pairing rules for DNA are largely inflexible: A forms H-bonds with T and G with C. The strands are arranged in antiparallel fashion, so that the 5′ end base of one strand pairs with the 3′ end base of the other, and vice versa.

The structure of DNA is not unique to plants, but rather is shared among all three domains of life (Eukarya, Bacteria, and Archaea), as well as by viruses. The patterns of covalent bonds and H-bonds can thus be studied in any organism, and indeed much of what we know about DNA structure was originally worked out in bacteria, which are unicellular and prokaryotic (lacking a nucleus).

The four bases (A, C, G and T) are not present in equal amounts and can vary between genomes, parts of genomes, and species. For example, the A+T content of the chloroplast genome, an organellar genome discussed later in Chapter 5, is variable, but generally greater than 50% of the total. In contrast, nuclear genes of many grasses are enriched in G+C, a bias that is particularly noticeable in maize.

In plants, the nucleotide bases may be modified by attachment of methyl (–CH₃) groups to particular sites. A common position for DNA methylation is on C-5 of C (Figure 1.2), although adenine methylation is also possible, particularly in bacteria, Archaea, and unicellular eukaryotes. This common modification of the DNA is known to affect transcription, and will be discussed in more detail in Chapter 12. While methylation is also common in mammals, it is relatively rare in yeast and in the fruit fly (Drosophila melanogaster). Other insects, however, have extensive DNA methylation, as is the case of honeybees. Many aspects of biotechnology exploit the basic structure of DNA, as described in the box “Working with DNA.”

Figure 1.2 Structures of cytosine and 5-methylcytosine. http://en.wikipedia.org/wiki/File:Cytosine_chemical_structure.svg. By Engineer gena (Own work) [Public domain], via Wikimedia Commons

---

Working with DNA: biotechnology takes advantage of the properties of the DNA molecule

The polymerase chain reaction (PCR), a method used extensively in biotechnology for generating large numbers of similar or identical DNA fragments, relies on repeatedly increasing the temperature to separate the DNA strands and then decreasing it to allow primers to bind. It is thus important to know the temperature at which the strands of particular DNA molecules separate; this is known as the melting temperature, or T_m, and corresponds to the temperature at which half the DNA molecules are single-stranded (melted) and half are double-stranded. The T_m is controlled by several factors, but a major one is the fraction of G-C base pairs. Because G-C pairs are held together by three H-bonds (rather than two as in A-T pairs), breaking them requires more energy input, such as higher temperatures. A rough equation for the T_m of a short (<20 base pairs, bp) strand of DNA is:

where T is the temperature in degrees Centigrade, A+T is the total number of A-T base pairs and G+C is the total number of G-C base pairs.

Assuming a random nucleotide distribution, this rough equation makes two assumptions. The first is that one strand of the DNA is bound to a membrane, as it would be for a Southern blot, and that the blot is being probed with a short oligonucleotide (a single-stranded DNA molecule, generally <100 nucleotides long; the Greek prefix oligo- means “few”). With one strand immobilized, the DNA melts at a lower temperature (about 8°C less) than it would in solution. The second assumption is that the concentration of salt (e.g., NaCl) is 0.9 M, and that there is no chemical in the solution that would interfere with the formation of H-bonds between the bases (such as formamide, HCONH₂). The melting temperature of DNA increases with the log₁₀ of the concentration of salt. This means that the higher the salt concentration, the more stable the DNA heteroduplex. It also decreases linearly with the concentration of formamide or other similar small molecules that interfere with DNA H-bond formation. Thus, a more complete equation is:

where M is the molar concentration of cations (Na⁺ in t...