Justin K. M. Roberts

Proteomics and a future generation of plant molecular biologists

Proteomic methods are required for the study of many different aspects of plant function. Important issues in proteomics include the molecular complexity of proteins, given that there are hundreds of thousands of chemically and physically distinct proteins in plants, and the context of protein functions with respect to both genomes and the environment. Available genomic and gene sequences greatly simplify the identification of proteins using improved techniques of mass spectrometry. This improved capability has led to much discussion on proteomes, and some experimentation using proteomic methodologies aimed at modest numbers of proteins. The scale of proteomics is open, for the number of proteins and genes considered at any one time is as dependent on the nature of the scientific question posed as on technical resources and capabilities. We know just enough about plant proteomes to imagine the breathtaking scope of our ignorance. There are tremendous opportunities for new molecular biologists to define the nature of the protein machines that transduce genetic and environmental information, and transform simple energy and matter, to give plants.

Identification of a nucleic acid binding domain in eukaryotic initiation factor eIFiso4G from wheat.

Higher plants have two complexes that bind the m7G-cap structure of mRNA and mediate interactions between mRNA and ribosomal subunits, designated eIF4F and eIFiso4F. Both complexes contain a small subunit that binds the 5′-cap structure of mRNA, and a large subunit, eIF4G or eIFiso4G, that binds other translation factors and RNA. Sequence-specific proteases were used to cleave native cap-binding complexes into structural domains, which were purified by affinity chromatography. We show here that eIFiso4G contains a central protease-resistant domain that binds specifically to nucleic acids. This domain spans Gln170 to Glu443 and includes four of the six homology blocks shared by eIFiso4G and eIF4G. A slightly shorter overlapping sequence, from Gly202 to Lys445, had no nucleic acid binding activity, indicating that the N-terminal end of the nucleic acid binding site lies within Gln170 to Arg201. The binding of the central domain and native eIFiso4F to RNA homopolymers and double- and single-stranded DNAs was studied. Both molecules had highest affinity for poly(G) and recognized single- and double-stranded sequences.

HIGH-RESOLUTION NMR METHODS FOR STUDY OF HIGHER PLANTS

Publisher Summary This chapter describes the means to obtain high-resolution nuclear magnetic resonance (NMR) data from living plant cells and tissues. High resolution NMR spectroscopy can provide plant biologists with information on the types of low-molecular-weight metabolites in plant cells, their relative concentrations, their mobility, and their interactions with other species such as H + or paramagnetic ions. The chapter focuses on one-dimensional NMR. The most important magnetic isotopes in biological NMR are 1 H, 13 C, 15 N, and 31 P. The term high resolution NMR implies observation of distinct signals in spectra. The distinct signals can reflect different chemical groups; this effect is the chemical shift, and the spectral axis is generally labeled “chemical shift.” NMR probes are aluminum-bodied cylinders inserted into the magnet bore. They contain a coil of copper wire or foil that surrounds the sample tube. The expense of NMR reflects technological effort aimed at overcoming the inherent insensitivity of the method. NMR signals can readily be obtained from metabolites present at 10 -3 M.

Cytoplasmic malate levels in maize root tips during K+ ion uptake determined by 13C-NMR spectroscopy

13C-NMR spectroscopy was used to determine the level of cytoplasmic malate in maize root tips that exhibited different rates of malate synthesis. Intracellular malate was 13C-labeled at carbons 1 and 4 by perfusing root tips with 5 nM H13CO3-. This labeling reflects the activities of phosphoenolpyruvate carboxylase and malate dehydrogenase (production of [4-13C]malate), and fumarase (scrambling of 13C-label between C1 and C4 of malate). In vivo 13C-NMR spectra contained a clearly resolved resonance from cytoplasmic [4-13C]malate, while the resonance from cytoplasmic [1-13C]malate overlapped with others. After 90 min of H13CO3- treatment, 13C-labeling of organic acid pools had reached steady-state. Thereafter, the ratios [13C]malate/[12C + 13C]malate and [1-13C]malate/[4-13C]malate in tissue extracts remained constant; evidence is presented that these ratios were the same for both cytoplasmic and total cellular malate. Hence, the intensity of the cytoplasmic [4-13C]malate signal was proportional to the amount of cytoplasmic malate in root tips. Potassium sulfate stimulate malate synthesis in maize root tips, relative to root tips perfused with HCO3- alone; total cellular malate doubled after approx. 1 h of 5 mM K2SO4-treatment. Cytoplasmic malate increased from approx. 3.5 mM to approx. 7.5 mM within 45 min of the onset of K2SO4-treatment, declining slightly thereafter. The possible effects of these changing cytoplasmic malate concentration on the enzymes involved in malate metabolism are discussed.

Sucrose Cycling in Heterotrophic Plant Cell Metabolism: First Step Towards an Experimental Model

Sucrose is the cornerstone of higher plant metabolism. Produced by photosynthesis, sucrose is the main substrate for respiration and biosynthesis. The emerging idea is that sucrose may act as regulator of its own metabolism, characterized in particular by a permanent process of degradation and formation. This sucrose turnover may control several important physiological functions. Of particular concern is an energy dependent cycle involving the hexokinase. This report presents an experimental approach to define quantitatively physiological states of suspension-cultured plant cells wih reference to their sucrose content and respiration rate. Sucrose depletion of normal cells incubated in a medium devoid of sugar is measured in vivo using 13C and respiration is simultaneously recorded. Results obtained with sucrose-storing cells and Arabidopsis thaliana show that respiration rate is closely linked to the available sucrose. Sucrose-depleted cells offer a stable model to study the bioenergetics of the process.

Observation of uridine triphosphate:glucose-1-phosphate uridylyltransferase activity in maize root tips by saturation transfer 31P-NMR. Estimation of cytoplasmic PPi

Saturation transfer 31P nuclear magnetic resonance was used to estimate the unidirectional rate of phosphorus exchange between Glc-1-P and UDPGlc in maize root tips. The rate was determined to be approx. 4 mumol.min-1 per g fresh weight. This estimated rate is much higher than net rates of other reactions in glucose metabolism (e.g., more than 10-times faster than the maximal glycolytic flux in this tissue). Furthermore, exchange between Glc-1-P and UDPGlc was not significantly inhibited by the metabolic poison KCN. We conclude that the unidirectional rate of conversion of Glc-1P to UDPGlc is much faster than the net rate of UDPGlc synthesis--the UTP:Glc-1-P uridylyltransferase reaction is near-equilibrium in vivo. From the equilibrium constant for this transferase reaction and the concentrations of Glc-1-P, UTP and UDPGlc, the level of cytoplasmic PPi was estimated to be approx. 10 nmol.g-1.