Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids: III. Binding properties of two specific proteolytic digestion products of the protein (G32P1I and G32P1III)

Brief treatment of gene 32 protein with proteolytic enzymes produces two specific digestion products in good yield (Moise & Hosoda, 1976). One, representing the native protein with ~60 amino acid residues removed from the C-terminus, is G32P¹I. The other, for which ~20 amino acid residues have been removed from the N-terminus in addition to the 60 residues from the C-terminus, is G32P¹III. Both of these specific “core” fragments of gene 32 protein have been isolated and purified, and their binding properties to single-stranded oligo- and polynucleotides have been studied. We find that the binding properties of G32P¹I are relatively little changed from those characteristic of the native gene 32 protein: (1) the apparent binding constants to short (l = 2 to 8) oligonucleotides are independent of lattice length and essentially independent of base and sugar composition, but do show an increased salt dependence of binding relative to that of the native protein; (2) the intrinsic association constants (K) for polynucleotides binding in the co-operative mode show the same binding specificities as seen with the native protein, but with absolute values increased two to fourfold; (3) the polynucleotide binding co-operativity parameter (ω^?2 × 10³) and the binding site size (n ～-7 nucleotide residues) are the same as for the native protein; (4) essentially the entire salt dependence of the net affinity (Kω) remains in K. However, unlike native gene 32 protein, G32P¹I can melt native DNA to equilibrium (Hosoda et al., 1974; Greve et al., 1978); this suggests that the kinetic pathways for DNA melting by these two species must differ, since the changes in equilibrium binding parameters measured here are far too small to account for the differences in melting behavior. In contrast to G32P¹I, for G32P¹III we find that: (1) binding is non-cooperative (ω ～-1); (2) the binding site size (n) for the protein has decreased by one to two nucleotide residues relative to that characteristic of the native protein and G32P¹I; (3) binding to short (l = 2 to 8) oligonucleotides is length and salt concentration dependent; (4) while binding to polynucleotides continues to show approximately the same base composition dependence as the native protein, the absolute values of K are somewhat different and the salt concentration dependencies of K are less. Polynucleotide ultraviolet light and circular dichroism spectra obtained in the presence of G32P¹I and G32P¹III are indistinguishable from those measured with the native protein at similar binding densities, indicating that all three protein species distort the polynucleotide lattice to comparable extents.These results are combined with the equilibrium binding data for native gene 32 protein (Kowalczykowski et al., 1980a: Newport et al., 1980) to obtain further insight into the molecular details of the interactions of this protein with its nucleic acid binding substrates.     

Nucleic acid binding properties of Escherichia coli ribosomal protein S1. I. Structure and interactions of binding site I.

Escherichia coli ribosomal protein S1 plays a central role in initiation of protein synthesis, perhaps via participation in the binding of messenger RNA to the ribosome. S1 protein has two nucleic acid binding sites with very different properties: site I binds either single-stranded DNA or RNA, while site II binds single-stranded RNA only (Draper et al., 1977). The nucleic acid binding properties of these sites have been explored using the quenching of intrinsic protein fluorescence which results from binding of oligo- and polynucleotides, and are reported in this and the accompanying paper (Draper &; von Hippel, 1978).Site I has been studied primarily using DNA oligomers and polymers, and has been found to have the following properties. (1) The intrinsic binding constant (K) of site I for poly(dA) and poly(dC) is ~3 × 10⁶m^?1 at 0.12 m-Na⁺, and the site size (n, the number of nucleotide residues covered per S1 bound) is 5.1 ± 1.0 residues. (2) Binding of site I to polynucleotides is non-co-operative. (3) The K value for binding of S1 to single-stranded polynucleotides is ~10³ larger than K for binding to double-stranded polynucleotides, meaning that S1 (via site I) is a potential “melting” or “double-helix destabilizing” protein. (4) The dependence of log K on log [Na⁺] is linear, and analysis of the data according to Record et al. (1976) shows that two basic residues in site I form charge-charge interactions with two DNA phosphates. In addition, a major part of the binding free energy of site I with the nucleic acid chain appears to involve non-electrostatic interactions. (5) Oligonucleotides bound in site II somewhat weaken the binding affinity of site I. (6) Binding affin is virtually independent of base and sugar composition of the nucleic acid ligand; in fact, the total absence of the base appears to have little effect on the binding, since the association constant for 2′-deoxyribose 5′-phosphate is approximately the same as that for dAMP or dCMP. (7) Two molecules of d(ApA) can bind to site I, suggesting the presence of two “subsites” within site I. (8) Iodide quenching experiments with S1-oligonucleotide complexes show differential exposure of tryptophans in and near the subsites of site I, depending upon whether neither, one, or both subsites are complexed with an oligonucleotide.     

Interaction between the adenovirus DNA-binding protein and double-stranded DNA.

DNA-binding protein was characterized by previous investigators as a single-stranded DNA-binding protein analogous to the gene 32 protein of phage T4 (Van der Vliet &; Levine, 1973; Sugawara et al., 1977). In the studies presented here the interactions between natural and synthetic polynucleotides and the DNA-binding protein of adenovirus 2-infected HeLa cells have been examined. Polynucleotide melting techniques revealed a tight yet dissociable binding to the helix structure of double-stranded DNA. In addition, binding and filter binding competition experiments at high DNA to protein ratios revealed a specific binding to double-stranded DNA termini with a dissociation constant of 1 × 10^?9 to 2 × 10^?9m. The ability of DNA-binding protein to bind to heat-denatured viral DNA was confirmed but the binding to double-stranded DNA termini was more specific on a molar basis. DNA-binding protein can recognize both flush and staggered ends of double-stranded DNA molecules.     

Immunoreactivity in a Cellular Immune Reaction of Lymphocytes preabsorbed on Cell Monolayers

SELECTIVE removal from non-immune lymphoid cell populations, of lymphocytes involved ultimately in production of antibody against haptenic determinants, has been demonstrated^1,2 using the particular haptenic group coupled to an inert substrate. In a series of preliminary experiments, we have used monolayer cultures of fibroblast cells to remove lymphocytes, from a population of non-immune lymph node cells, capable of reacting against cellular antigens represented in the monolayer culture. Our test system in these experiments is the in vitro graft reaction model of Ginsburg³ as modified by Berke et al.⁴.     

Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids: II. Specificity of binding to DNA and RNA

In this paper we examine the specificity of the co-operative binding (in the polynucleotide mode) of bacteriophage T4-coded gene 32 protein to synthetic and natural single-stranded nucleic acids differing in base composition and sugar type. It is shown by competition experiments in a tight-binding (low salt) environment that there is a high degree of binding specificity under these (protein-limiting) conditions, with one type of nucleic acid lattice binding gene 32 protein to saturation before any binding to the competing lattice takes place; it is also shown that the same differential specificities apply at high salt concentrations. Procedures developed in the preceding paper (Kowalczykowski et al., 1980) are used to measure the net binding affinities (Kω) of gene 32 protein to a variety of polynucleotides, as well as to determine individual values of K and ω for some systems. For all polynucleotides, virtually the entire specificity and salt dependence of binding of Kω appears to be in K. In ~0.2 m-NaCl, the net binding affinities (Kω) range from ~10⁶ to ~10¹¹m^?1; in order of increasing affinities we find: poly(rC) < poly(rU) < poly(rA) < poly(dA) < poly(dC) < poly(dU) < poly(rI) < poly(dI) < poly-(dT). In general, Kω for a particular homopolyribonucleotide at constant salt concentration is 10¹ to 10⁴smaller than Kω for the corresponding homopoly-deoxyribopolynucleotide. Values of Kω for randomly copolymerized polynucleotides and for natural DNA fall at the compositionally weighted average of the values for the individual homopolynucleotides (except for poly(dT), which appears to bind somewhat tighter), indicating that the net affinity represents the sum of the binding free energy contributions of the individual nucleotides. It is shown that these results, on a competition basis under physiological salt conditions, can account quantitatively for the autogenous regulation of the synthesis of gene 32 protein at the translational level (Russel et al., 1976; Lemaire et al., 1978). In addition, these results suggest possible mechanisms by which gene 32 messenger RNA might be specifically recognized (by gene 32 protein) and functionally discriminated from the other mRNAs of phage T4.     

The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. II. The binding of the pancreatic trypsin inhibitor and of isoleucine-valine and of sequentially related peptides to trypsinogen and to p-guanidinobenzoate-trypsinogen.

p-Guanidinobenzoate-trypsinogen is transformed into a trypsin-like conformation upon binding of Ile-Val as evidenced by specific changes in its circular dichroism spectrum. By means of this signal the association constants for the binding of a variety of peptides sequentially analogous to either the bovine trypsin N-terminus or to the N-terminal activation peptide sequences of several trypsinogens have been determined at different Ca²⁺ concentrations. Ile-Val and Ile-Val-Gly exhibit the strongest binding affinity of all peptides investigated. Replacement of the first isoleucine or of the second valine residue by other amino acids considerably reduces the peptide affinity. Discussion of these is based on the known spatial arrangement of the Ile16-Val17-Gly18 N-terminus and of the Ile-Val dipeptide in the Ile16 cleft (crystal structures of bovine trypsin and of the trypsinogen-PTI³-Ile-Val complex; Bode et al., 1978). The free energies of binding of the first and of the second peptide residue are almost additive indicating independency between both subsites. The third residue, glycine, does not significantly contribute to binding. The peptide analogues of various trypsinogen N-termini exhibit no measurable affinity for the Ile 16 cleft.The equilibrium constant for the binding of PTI to trypsinogen and the affinity of Ile-Val for the resulting binary complex have been determined in the presence and absence of Ca²⁺, using the competitive PTI-binding to α-chymotrypsin. These competition experiments allow the estimation of the standard free-energy changes due to the conformational transition of trypsinogen into a trypsin-like state (+43 kJ mol^?1, 20 °C; stabilization of the “activation domain”; Fehlhammer et al., 1977), due to the binding of the trypsin N-terminus (—55 kJ mol^?1) and of the peptide analogues (e.g. Ile-Val; ?28 kJ mol^?1) into the preformed Ile 16 cleft, and due to the specific burying of the covalently linked pGB group in the fixed specificity pocket (— 39 kJ mol^?1). This pocket is co-operatively linked with the Ile 16 cleft according to a free-energy change coupling of —43 kJ mol^?1.     

An alternative view of mammalian DNA sequence organization: I. Repetitive sequence interspersion in Syrian hamster DNA: A model system

The biochemical and biophysical techniques originally introduced by Davidson et al. (1973) and Graham et al. (1974) for the determination of the general organization and length of repetitive and non-repetitive sequences in eukaryotic DNA have been extended and modified. Improvements in the experimental methods employed in these pioneering works have led to novel interpretations and conclusions about mammalian DNA sequence organization. In what is commonly referred to as an interspersion experiment, the average spacing of repetitive DNA regions is inferred from the length dependence of hydroxyapatite binding of radio-labeled tracer DNAs reassociated with an excess of short 200 nucleotide repetitive sequence driver DNA. Studies on Syrian hamster DNA, using an improved procedure for conducting interspersion experiments, suggest that either a frequent cluster in the distribution of non-repetitive DNA sequence lengths occurs at 7200 (±2000) nucleotides or that repetitive sequences are randomly spaced on a number average basis. In contrast, measurements obtained using the traditional methods suggest that a frequent cluster in the distribution of non-repetitive DNA sequence lengths occurs at approximately 1000 nucleotides. When reassociations were conducted at elevated temperatures, to allow only well-matched repetitive sequences to hybridize, the amount of DNA operationally observed as “repetitive” was reduced. Interspersion experiments conducted with Syrian hamster DNA at a reassociation temperature of 75 °C yielded data similar to those obtained by Manning et al. (1975) for Drosophila melanogaster DNA reassociated at 60 °C.     

The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. The refined crystal structures of the bovine trypsinogen-pancreatic trypsin inhibitor complex and of its ternary complex with Ile-Val at 1.9 A resolution

The complex formed by bovine trypsinogen and the pancreatic trypsin inhibitor crystallizes in large crystals isomorphous with trypsin-PTI² complex crystals Rühlmann et al. 1973. X-ray diffraction data to 1.9 Å resolution were collected in the absence and presence of Ile-Val dipeptide. Both trypsinogen complex structures have been crystallographically refined, using the refined trypsin-PTI complex Huber et al. 1974a as a starting model. The final R values are 0.25 and 0.26, respectively. The mean main-chain atom deviations between the three complex structures are about 0.15 Å. In contrast, the mean deviation between the complexed and the free trypsinogen Fehlhammer et al. 1977 is 0.28 Å, reflecting the influence of crystal packing and complexation. The trypsinogen component adopts a trypsin-like conformation upon PTI binding: The Asp194 side-chain turns around and the activation domain becomes rigid, forming the specificity pocket and the Ile16 binding cleft. The specific interactions between PTI and trypsin are also observed in the trypsinogen complex. As in free trypsinogen, the N-terminus including residues Val10 to Gly18 is mobile and sticks out into solution. Apart from the different arrangement of the N-termini in the two complexes, the only significant, but minor structural difference is the enhanced thermal mobility of the autolysis loop in the trypsinogen complex. Upon binding of the Ile-Val dipeptide, the autolysis loop becomes fixed as in the trypsin complex. The Ile-Val position is identical in the ternary and the trypsin complex.     

Effect of BCG on Friend Disease Virus in Mice

NONSPECIFIC stimulation of the reticulo-endothelial system and resistance against tumorigenesis are produced by injection of attenuated Mycobacterium bovis (BCG). Biozzi et al.¹ demonstrated resistance to Ehrlich's ascites tumour in BCG-immune mice and Halpern et al.² showed that such immunization effected control of T-8 tumours in rats. Further, at least partial control of other tumours^3–6 has been effected by this procedure in mice and hamsters.     

Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities

Nucleosome positions on the DNA are determined by the intrinsic affinities of histone proteins to a given DNA sequence and by the ATP-dependent activities of chromatin remodeling complexes that can translocate nucleosomes with respect to the DNA. Here, we report a theoretical approach that takes into account both contributions. In the theoretical analysis two types of experiments have been considered: in vitro experiments with a single reconstituted nucleosome and in vivo genome-scale mapping of nucleosome positions. The effect of chromatin remodelers was described by iteratively redistributing the nucleosomes according to certain rules until a new steady state was reached. Three major classes of remodeler activities were identified: (i) the establishment of a regular nucleosome spacing in the vicinity of a strong positioning signal acting as a boundary, (ii) the enrichment/depletion of nucleosomes through amplification of intrinsic DNA-sequence-encoded signals and (iii) the removal of nucleosomes from high-affinity binding sites. From an analysis of data for nucleosome positions in resting and activated human CD4⁺ T cells [Schones et al., Cell 132, p. 887] it was concluded that the redistribution of a nucleosome map to a new state is greatly facilitated if the remodeler complex translocates the nucleosome with a preferred directionality.     

Type 3 IP3 receptors driving oncogenesis

Type 3 Inositol 1,4,5-trisphosphate (IP₃) receptors (IP₃R3s) have been identified as anti-oncogenic channels by propelling pro-apoptotic Ca²⁺ signals to mitochondria. Yet, recent studies (Rezuchova et al, Cell Death Dis, 2019; Ueasilamongkol et al, Hepathology, 2019; Guerra et al, Gut, 2019) revealed that IP₃R3 upregulation drives oncogenesis via ER-mitochondrial Ca²⁺ crosstalk, adding complexity to IP₃R3’s role in cancer.     

Abscisic acid and CO2 signalling via calcium sensitivity priming in guard cells, new CDPK mutant phenotypes and a method for improved resolution of stomatal stimulus-response analyses

Background

Stomatal guard cells are the regulators of gas exchange between plants and the atmosphere. Ca²⁺-dependent and Ca²⁺-independent mechanisms function in these responses. Key stomatal regulation mechanisms, including plasma membrane and vacuolar ion channels have been identified and are regulated by the free cytosolic Ca²⁺ concentration ([Ca²⁺]_cyt).

Scope

Here we show that CO₂-induced stomatal closing is strongly impaired under conditions that prevent intracellular Ca²⁺ elevations. Moreover, Ca²⁺ oscillation-induced stomatal closing is partially impaired in knock-out mutations in several guard cell-expressed Ca²⁺-dependent protein kinases (CDPKs) here, including the cpk4cpk11 double and cpk10 mutants; however, abscisic acid-regulated stomatal movements remain relatively intact in the cpk4cpk11 and cpk10 mutants. We further discuss diverse studies of Ca²⁺ signalling in guard cells, discuss apparent peculiarities, and pose novel open questions. The recently proposed Ca²⁺ sensitivity priming model could account for many of the findings in the field. Recent research shows that the stomatal closing stimuli abscisic acid and CO₂ enhance the sensitivity of stomatal closing mechanisms to intracellular Ca²⁺, which has been termed ‘calcium sensitivity priming’. The genome of the reference plant Arabidopsis thaliana encodes for over 250 Ca²⁺-sensing proteins, giving rise to the question, how can specificity in Ca²⁺ responses be achieved? Calcium sensitivity priming could provide a key mechanism contributing to specificity in eukaryotic Ca²⁺ signal transduction, a topic of central interest in cell signalling research. In this article we further propose an individual stomatal tracking method for improved analyses of stimulus-regulated stomatal movements in Arabidopsis guard cells that reduces noise and increases fidelity in stimulus-regulated stomatal aperture responses ( Box 1). This method is recommended for stomatal response research, in parallel to previously adopted blind analyses, due to the relatively small and diverse sizes of stomatal apertures in the reference plant Arabidopsis thaliana.

Box 1. Improved resolution of stimulus-induced stomatal movements in guard cells by tracking of individual stomatal apertures

Arabidopsis guard cells have become a prime model system for analysing signal transduction, since early research combining genetic and ion channel analyses in this system (Ichida et al., 1997; Pei et al., 1997, 1998; Roelfsema and Prins, 1997). Arabidopsis stomata are small relative to other stomatal model systems and stomatal apertures of various plant types including Arabidopsis are known to show variability in the size of individual stomatal complexes and also variability in the opening apertures of stomata of similar size in a given leaf (Gorton et al., 1988; Mott and Buckley, 2000; Mott and Peak, 2007). Thus stomatal aperture measurements are expected to show a clear degree of statistical variation. Use of blind experiments, in which the genotype and, when possible, the stimulus being applied to guard cells is unknown to the experimenter (Murata et al., 2001) has been employed by several laboratories, has become a standard in the field and has aided in addressing the above limitations of the range of stomatal aperture sizes found under any given condition.Research in our laboratory has shown that a major additional improvement in experiments can be made, by adding imaging of the same individual stomatal apertures over time (Allen et al., 2001; Mori et al., 2006; Vahisalu et al., 2008; Siegel et al., 2009), while performing blind experiments. In such ‘stomatal tracking’ experiments the lower side of a leaf is attached to a glass coverslip in an extracellular incubation medium (Webb et al., 2001; Young et al., 2006). The mesophyll and upper leaf epidermis are removed surgically for better optical resolution of stomatal apertures in the intact lower leaf epidermis (Young et al., 2006). For stimulus-induced stomatal closing analyses, a field of well-opened stomata is located and images are captured (e.g. using Scion Image software) for later analyses and data storage. The bottom (dry side) of coverslips can be marked with colour marker pens to label grids in the regions where apertures where imaged, for finding these same stomata subsequently if needed. Images of the same stomatal apertures are taken over time and can be stored for later analyses of individual stomatal apertures and for deposition of image files. While this approach has been used as a standard for imposed Ca²⁺ oscillation studies (Allen et al., 2001; Mori et al., 2006; Vahisalu et al., 2008; Fig. 4), we have found that this method also substantially improves stomatal movement response analyses to any given stimulus (Siegel et al., 2009; see Figs 1 and 4 and, Box Fig. 1). For example, while individual stomata are known to have diverse apertures (e.g. Box Fig. 1C), the relative responses of wide open stomata and smaller stomatal apertures to ABA or to CO₂ were comparable (Fig. 1 and Box Fig. 1; Siegel et al., 2009). Note that this method has previously been proposed and used in Vicia faba (Gorton et al., 1988), for which stomata exhibit relatively weak ABA and CO₂ responses, compared with, for example, Arabidopsis. We propose that this simple image-capturing approach, together with blind analyses, be used as a standard for stomatal response research in arabidopsis. Our research experience with this method shows that this approach will aid in greatly improving resolution and robustness and in defining the functions of individual Ca²⁺-independent and Ca²⁺-dependent components and mechanisms in stomatal response analyses. Open in a separate windowBox Fig. 1.ABA-induced stomatal closing of individually tracked stomatal apertures. (A) Average individually tracked stomatal apertures in the presence of 50 µm Ca²⁺ (open triangles) and in the presence of 200 nm free Ca²⁺ (open squares) in the bath solution from three experiments are shown and were normalized to the stomatal apertures at time = 0. (B, C) ABA-induced stomatal closing in the presence of 50 µm Ca²⁺ in five individually tracked stomatal apertures. In (A; open triangles) normalized stomatal apertures of the same stomata depicted in (B) and (C) are shown. Methods used in these experiments tracking individual stomatal apertures are described in Siegel et al. (2009). ABA-induced stomatal closing experiments are reproduced from Siegel et al. (2009) with permission of the publisher.     

2,3-Diphosphoglycerate Content of Human Arterial and Venous Blood

THE glycolytic intermediate, 2,3-diphosphoglycerate, is an intracellular regulator of the oxygen affinity of haemoglobin^1,2. At high altitudes there is a direct relationship between the decreased oxygen affinity of haemoglobin and the increased concentration of diphosphoglycerate in the blood³. This was explained by Benesch et al.⁴ and Chanutin et al.⁵, who found that the binding of diphosphoglycerate to haemoglobin reduces the oxygen affinity and by our finding that the concentration of diphosphoglycerate increases when the red cells are incubated under low oxygen tension^6,7, thereby releasing oxygen from haemoglobin. For the same reason, the oxygen tension is reduced during the circulation of blood from the pulmonary alveoli to the tissues; the decreased level of the diphosphoglycerate facilitates the binding of oxygen to haemoglobin in the pulmonary alveoli and the increased level of the diphosphoglycerate in the blood of the capillaries decreases the affinity of haemoglobin for oxygen. We have measured the amount of 2,3-diphosphoglycerate and other glycolytic intermediates in arterial and venous blood to test this supposition.     

Isolation and identification of homeobox genes from the human placenta including a novel member of the Distal-less family,DLX4

We have carried out a DNA binding site screen of a 32-week human placental cDNA library using a consensus homeodomain binding site as a probe. This study represents the first library screen carried out to isolate homeobox genes from the human placenta. We have shown that three homeobox genes known to be expressed in the embryo, HB24, GAX and MSX2 are also expressed in the placenta. We have also identified a novel homeobox gene, DLX4, that shows 85% sequence identity with the homeodomain encoded by the Drosophila Distal-less (Dll) gene. DLX4 therefore represents a new member of the Distal-less family of homeobox genes. This is the first evidence that members of the Distal-less family of homeobox genes are expressed in the placenta. Using fluorescence in situ hybridisation (FISH), DLX4 has been assigned to human chromosome 17q21–q22. This places DLX4 in the same region of chromosome 17 as another member of the Distal-less family, DLX3 (Scherer et al., 1995), and the HOX-B homeobox gene cluster (Acampora et al., 1989; Boncinelli et al., 1991). Members of the Distal-less family (DLX1 and DLX2; DLX5 and DLX6) are found as closely linked pairs on human chromosomes (Simeone et al., 1994). We predict that DLX3 and DLX4 are closely linked and have arisen through gene duplication and divergence from a common ancestral precursor.     

Phytochelatin Synthesis Is Essential for the Detoxification of Excess Zinc and Contributes Significantly to the Accumulation of Zinc

The synthesis of phytochelatins (PCs) is essential for the detoxification of nonessential metals and metalloids such as cadmium and arsenic in plants and a variety of other organisms. To our knowledge, no direct evidence for a role of PCs in essential metal homeostasis has been reported to date. Prompted by observations in Schizosaccharomyces pombe and Saccharomyces cerevisiae indicating a contribution of PC synthase expression to Zn²⁺ sequestration, we investigated a known PC-deficient Arabidopsis (Arabidopsis thaliana) mutant, cad1-3, and a newly isolated second strong allele, cad1-6, with respect to zinc (Zn) homeostasis. We found that in a medium with low cation content PC-deficient mutants show pronounced Zn²⁺ hypersensitivity. This phenotype is of comparable strength to the well-documented Cd²⁺ hypersensitivity of cad1 mutants. PC deficiency also results in significant reduction in root Zn accumulation. To be able to sensitively measure PC accumulation, we established an assay using capillary liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry of derivatized extracts. Plants grown under control conditions consistently showed PC2 accumulation. Analysis of plants treated with same-effect concentrations revealed that Zn²⁺-elicited PC2 accumulation in roots reached about 30% of the level of Cd²⁺-elicited PC2 accumulation. We conclude from these data that PC formation is essential for Zn²⁺ tolerance and provides driving force for the accumulation of Zn. This function might also help explain the mysterious occurrence of PC synthase genes throughout the plant kingdom and in a wide range of other organisms.Both essential and nonessential metal ions can be toxic when present in excess. Zinc (Zn) ions, for instance, are used in biological systems as catalytic or structural components in a myriad of proteins (Frausto da Silva and Williams, 2001). In humans, about 10% of genes encode Zn-dependent proteins (Andreini et al., 2006) and it is reasonable to postulate similar numbers for plants. When the Zn-buffering capacity of a cell is exceeded, however, aberrant binding of Zn ions to thiols or other functional groups can occur, which disrupts the function of proteins. Also, Zn ions can displace other essential metal ions from their binding sites (Krämer and Clemens, 2005). Toxicity thresholds for Zn were found to range between 100 and 300 μg g⁻¹ dry weight depending on plant species and physiological state (Marschner, 1995). Ions of the nonessential metal cadmium (Cd) have a high affinity for various functional groups in biological molecules, in particular thiols. When taken up into a cell they can inactivate proteins by uncontrolled binding or cause oxidative stress by depleting glutathione pools (Clemens, 2006a).Because of the potential toxicity of metal ions, all living systems possess mechanisms to tightly regulate the distribution of metal ions and to minimize damage under conditions of excess metal supply (Eide, 2006; Grotz and Guerinot, 2006). Principally, detoxification of excess metal ions is assumed to be achieved by efflux, sequestration, and chelation. For instance, in the past few years evidence has been reported for a contribution of AtMTP1 (At2g46800) to vacuolar sequestration of Zn²⁺ (Kobae et al., 2004; Desbrosses-Fonrouge et al., 2005) and of AtHMA4 (At2g19110) to effluxing Zn²⁺ (Mills et al., 2005). Furthermore, the Arabidopsis halleri ortholog of HMA4 is essential for Zn and Cd hypertolerance (Hanikenne et al., 2008). Loss of ZIF1, a transporter of the major facilitator superfamily, results in Zn²⁺ hypersensitivity in Arabidopsis (Arabidopsis thaliana; Haydon and Cobbett, 2007).The synthesis of phytochelatins (PCs), glutathione-derived metal-binding peptides, represents a major detoxification mechanism for Cd and arsenic (As) ions in various species. More recently, PCs have also been implicated in long-distance transport of Cd in the phloem (Mendoza-Cozatl et al., 2008). Formation of PCs is catalyzed by PC synthases (PCS) and genes encoding this enzyme have been cloned from plants, fungi, and nematodes (Clemens et al., 1999, 2001; Ha et al., 1999; Vatamaniuk et al., 1999, 2001). Mutant lines of Arabidopsis, Schizosaccharomyces pombe, or Caenorhabditis elegans that are deficient in PC synthesis show a severe loss of Cd and As tolerance (Clemens et al., 1999; Ha et al., 1999; Vatamaniuk et al., 2001). For other metal ions only minor effects have been reported (Cobbett and Goldsbrough, 2002). Arabidopsis cad1-3 mutant plants, which are defective in AtPCS1, showed about a 2-fold increase in copper (Cu) and mercury sensitivity and no significant increase in Zn sensitivity (Ha et al., 1999). S. pombe PCS-deficient mutants are slightly more Cu²⁺ sensitive than wild-type cells (Clemens et al., 1999). PC-metal complexes have been detected in plant cells only with Cd, silver, Cu, and As (Maitani et al., 1996; Schmöger et al., 2000) even though synthesis of PCs is activated by a wide range of metal ions both in vivo and in vitro (Grill et al., 1987; Vatamaniuk et al., 2000; Oven et al., 2002). Thus, the role of PC synthesis in metal detoxification has so far been seen as being confined to Cd and As (Cobbett and Goldsbrough, 2002). This, however, leaves the question as to why PCS genes are so widespread and why the enzyme is expressed constitutively throughout the plant (Rea et al., 2004). It is not clear how the sporadic need to sequester excess Cd or As ions could have provided the selective pressure to maintain PCS expression throughout the plant kingdom and beyond (Clemens, 2006b). One explanation could be the second enzymatic function of PCS, i.e. breakdown of glutathione conjugates (GS conjugates) to the corresponding β-glutamyl-Cys conjugates (Blum et al., 2007). The catalytic activity of bacterial PCS-like proteins is similar (Harada et al., 2004; Tsuji et al., 2004; Vivares et al., 2005). Another possibility is involvement of PC synthesis in essential metal homeostasis, which has been discussed occasionally (Steffens et al., 1986; Rauser, 1990; Steffens, 1990). As early as 1986, Steffens et al. suggested this based on the observation that small amounts of PCs were detectable in tomato (Solanum lycopersicum) cell cultures in the absence of excess metals. Similarly, Grill et al. reported the induction of PC synthesis by Cu and Zn ions after transfer of cultured cells into fresh medium. The amount of detectable PCs was correlated linearly with the Zn²⁺ concentration in the culture medium and an involvement of PC synthesis in metal homeostasis was proposed (Grill et al., 1987, 1988). However, no genetic evidence for such a role of PCs has been reported to date. Here we present evidence that PC formation indeed contributes significantly to Zn²⁺ detoxification in Arabidopsis and enhances Zn accumulation.     

A critical evaluation of the predicted and X-ray structures of α-Lactalbumin

The rapidly increasing availability of protein amino-acid sequences, many of which have been determined from the corresponding gene sequences, has intensified interest in the prediction of related protein structures when the three-dimensional structure of another member of the family is known. The study of bovine α-Lactalbumin provides a classic example in which the three-dimensional structure was predicted, first by Browneet al. (1969) and later by Warmeet al. (1974), from the three-dimensional structure of hen-egg-white lysozyme (Blakeet al., 1965), taking into account the striking relationship between the amino acid sequences of the two proteins. A comprehensive comparison of these models with the structure of baboon α-Lactalbumin derived from X-ray crystallography (Acharyaet al., 1989) is presented. The models mostly compare well with the experimentally determined structure except in the flexible C-terminal region of the molecule (rms deviation on C^α of residues 1–95, 1.1 Å).     

Crystalline aggregation of a proteolytic fragment of the major head protein of bacteriophage T4.

An analysis has been made of the composition and structure of the two types of sheets assembled from material from dissociated bacteriophage T2 (Poglazov &; Mesyhanzhinov, 1967) and T4 capsids. Serological techniques have been used to show that both types of sheet are assembled from proteolytic fragment of P23¹, the major capsid constituent. The two types of sheets have been found to interconvert depending on the concentration of Mg²⁺ ions in the buffer. Computer modelling experiments show that the “hexagonal” and “rectangular” morphologies observed in the negative stain are due to in-register and staggered associations, respectively, of a single basic hexagonal lattice. Analysis by polyacrylamide gel electrophoresis of samples of sheets and dissociated capsids, together with previous results from immune electron microscopy (Kistler et al., 1978), suggest that hexamers of the proteolytic fragment are derived conservatively from capsomers of the phage head.The value of this proteolytic P23 fragment has been twofold: (1) it has proved to be a useful peptide in the ongoing primary sequence determination of P23 and (2) antibodies raised against it have been employed to follow the fate of P23 antigenic sites during various steps of phage capsid maturation (Kistler et al., 1978).     

Lack of Differences in Serum Binding of Calcium in Cystic Fibrosis,Carriers and Controls

Attempts have been made to detect carriers for cystic fibrosis (CF) by some means other than genetic inference from affected children to their otherwise normal parents¹. The ability to detect CF carriers would result in substantial advances in genetic counselling. Moreover, an assay by which heterozygotes are identifiable must involve a parameter close to the elusive primary gene abnormality. Accordingly the paper by Fitz-patrick et al.² in which serum binding of tracer amounts of calcium (determined by equilibrium dialysis) of CF > heterozygotes > controls was a potentially significant report. We were, however, sceptical about data in which healthy carrier individuals demonstrated so great a difference from normal (an increase in serum binding of ⁴⁵Ca in heterozygotes over controls of 65 ± 11%) for a clearly nonspecific characteristic. As we have substantial serum and salivary electrophoretic data³ in which no consistent protein differences were apparent in carriers and because we wondered about the biological explanation of the findings of Fitzpatrick et al.², we decided to repeat their serum binding of calcium experiments. We repeated the reported procedures as closely as possible. We also assayed calcium binding with the additional buffer and salt concentration conditions described below. Sera from different individuals [N (controls = 30; N (heterozygotes) = 31; N (CF) = 33] were used in 4 experiments.     

Chicken liver ribosomes: Characterization of cross-reaction and inhibition of some functions by antibodies prepared against Escherichia coli ribosomal proteins L7 and L12

Antibodies prepared in rabbits against Escherichia coli ribosomal proteins L7/L12 are reported to be immunologically cross-reactive with some ribosomal proteins on the 60 S subunit of eukaryote ribosomes (Wool & Stöffler, 1974; Stöffler et al., 1974). We have confirmed these reports and extended this finding to a detailed study of the functional properties of eukaryote ribosomes which are affected by these cross-reacting antibodies. We report here the partial reactions in protein synthesis that are inhibited by the anti-L7/L12 IgG (immunoglobulin G) preparations using a chicken liver system. The following reactions were inhibited: EF-1 (elongation factor 1) dependent binding of aminoacyl-tRNA to ribosomes and GTP hydrolysis; EF-2 dependent binding of nucleotide to ribosomes and GTP hydrolysis; binding of [¹⁴C]ADP-ribosyl · EF-2 to ribosomes. This last reaction is more sensitive to the antibody inhibition than the corresponding nucleotide binding reaction. We show that the inhibitions were not simply non-specific precipitation of ribosomes by IgG, in that monovalent Fabs were also inhibitory, and peptidyl transferase activity was not inhibited. The functions inhibited with the IgG preparations in the chicken liver system are analogous to those inhibited in the homologous E. coli system. Thus the cross-reacting protein is functionally as well as immunologically conserved.