'Genome order index' should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve

Background  

The Z-curve is a three dimensional representation of DNA sequences proposed over a decade ago and has been extensively applied to sequence segmentation, horizontal gene transfer detection, and sequence analysis. Based on the Z-curve, a "genome order index," was proposed, which is defined as S = a ²+ c ²+t ²+g ², where a, c, t, and g are the nucleotide frequencies of A, C, T, and G, respectively. This index was found to be smaller than 1/3 for almost all tested genomes, which was taken as support for the existence of a constraint on genome composition. A geometric explanation for this constraint has been suggested. Each genome was represented by a point P whose distance from the four faces of a regular tetrahedron was given by the frequencies a, c, t, and g. They claimed that an inscribed sphere of radius r = 1/ contains almost all points corresponding to various genomes, implying that S <r ². The distribution of the points P obtained by S was studied using the Z-curve.     

On the relationship between leaf anatomy and CO2 diffusion through the mesophyll of hypostomatous leaves

Internal conductances to CO₂ transfer from the stomatal cavity to sites of carboxylation (g_i) in hypostomatous sun-and shade-grown leaves of citrus, peach and Macadamia trees (Lloyd et al. 1992) were related to anatomical characteristics of mesophyll tissues. There was a consistent relationship between absorptance of photosynthetically active radiation and chlorophyll concentration (mmol m^?2) for all leaves, including sclerophyllous Macadamia, whose transmittance was high despite its relatively thick leaves. In thin peach leaves, which had high g_i, the chloro-plast volume and mesophyll surface area exposed to intercellular air spaces (ias) per unit leaf area were similar to those in the thicker leaves of the evergreen species. Peach leaves, however, had the lowest leaf dry weight per area (D/a), the lowest tissue density (T_d) and the highest chloro-plast surface area (S_c) exposed to ias. There were negative correlations between g_i and leaf thickness or D/a, but positive correlations between g_i and S_c or S_c/T_d. We developed a one-dimensional diffusion model which partitioned g_i into a gaseous diffusion conductance through the ias (g_ias) plus a liquid-phase conductance through mesophyll cell walls (g_cw). The model accounted for a significant amount of variation (r₂=0.80) in measured g_i by incorporating both components. The g_ias component was related to the one-dimensional path-length for diffusion across the mesophyll and so was greater in thinner peach leaves than in leaves of evergreen species. The g_cw component was related to tissue density and to the degree of chloroplast exposure to the ias. Thus the negative correlations between g_i and leaf thickness or D/a related to g_ias whereas positive correlations between g_i and S_c or S_c/T_d, related to g_cw. The g_cw was consistently lower than g_ias, and thus represented a greater constraint on CO₂ diffusion in the mesophylls of these hypostomatous species.     

Focus Issue on Calcium Signaling: Analyses of a Gravistimulation-Specific Ca2+ Signature in Arabidopsis using Parabolic Flights

Gravity is a critical environmental factor affecting the morphology and functions of organisms on the Earth. Plants sense changes in the gravity vector (gravistimulation) and regulate their growth direction accordingly. In Arabidopsis (Arabidopsis thaliana) seedlings, gravistimulation, achieved by rotating the specimens under the ambient 1g of the Earth, is known to induce a biphasic (transient and sustained) increase in cytoplasmic calcium concentration ([Ca2+]_c). However, the [Ca2+]_c increase genuinely caused by gravistimulation has not been identified because gravistimulation is generally accompanied by rotation of specimens on the ground (1g), adding an additional mechanical signal to the treatment. Here, we demonstrate a gravistimulation-specific Ca²⁺ response in Arabidopsis seedlings by separating rotation from gravistimulation by using the microgravity (less than 10⁻⁴g) conditions provided by parabolic flights. Gravistimulation without rotating the specimen caused a sustained [Ca2+]_c increase, which corresponds closely to the second sustained [Ca2+]_c increase observed in ground experiments. The [Ca2+]_c increases were analyzed under a variety of gravity intensities (e.g. 0.5g, 1.5g, or 2g) combined with rapid switching between hypergravity and microgravity, demonstrating that Arabidopsis seedlings possess a very rapid gravity-sensing mechanism linearly transducing a wide range of gravitational changes (0.5g–2g) into Ca²⁺ signals on a subsecond time scale.Calcium ion (Ca²⁺) functions as an intracellular second messenger in many signaling pathways in plants (White and Broadley, 2003; Hetherington and Brownlee, 2004; McAinsh and Pittman, 2009; Spalding and Harper, 2011). Endogenous and exogenous signals are spatiotemporally encoded by changing the free cytoplasmic concentration of Ca²⁺ ([Ca2+]_c), which in turn triggers [Ca2+]_c-dependent downstream signaling (Sanders et al., 2002; Dodd et al., 2010). A variety of [Ca2+]_c increases induced by diverse environmental and developmental stimuli are reported, such as phytohormones (Allen et al., 2000), temperature (Plieth et al., 1999; Dodd et al., 2006), and touch (Knight et al., 1991; Monshausen et al., 2009). The [Ca2+]_c increase couples each stimulus and appropriate physiological responses. In the Ca²⁺ signaling pathways, the stimulus-specific [Ca2+]_c pattern (e.g. amplitude and oscillation) provide the critical information for cellular signaling (Scrase-Field and Knight, 2003; Dodd et al., 2010). Therefore, identification of the stimulus-specific [Ca2+]_c signature is crucial for an understanding of the intracellular signaling pathways and physiological responses triggered by each stimulus, as shown in the case of cold acclimation (Knight et al., 1996; Knight and Knight, 2000).Plants often exhibit biphasic [Ca2+]_c increases in response to environmental stimuli. Thus, slow cooling causes a fast [Ca2+]_c transient followed by a second, extended [Ca2+]_c increase in Arabidopsis (Arabidopsis thaliana; Plieth et al., 1999; Knight and Knight, 2000). The Ca²⁺ channel blocker lanthanum (La³⁺) attenuated the fast transient but not the following increase (Knight and Knight, 2000), suggesting that these two [Ca2+]_c peaks have different origins. Similarly, hypoosmotic shock caused a biphasic [Ca2+]_c increase in tobacco (Nicotiana tabacum) suspension-culture cells (Takahashi et al., 1997; Cessna et al., 1998). The first [Ca2+]_c peak was inhibited by gadolinium (Gd³⁺), La³⁺, and the Ca²⁺ chelator EGTA (Takahashi et al., 1997; Cessna et al., 1998), whereas the second [Ca2+]_c increase was inhibited by the intracellular Ca²⁺ store-depleting agent caffeine but not by EGTA (Cessna et al., 1998). The amplitude of the first [Ca2+]_c peak affected the amplitude of the second increase and vice versa (Cessna et al., 1998). These results suggest that even though the two [Ca2+]_c peaks originate from different Ca²⁺ fluxes (e.g. Ca²⁺ influx through the plasma membrane and Ca²⁺ release from subcellular stores, respectively), they are closely interrelated, showing the importance of the kinetic and pharmacological analyses of these [Ca2+]_c increases.Changes in the gravity vector (gravistimulation) could work as crucial environmental stimuli in plants and are generally achieved by rotating the specimens (e.g. +180°) in ground experiments. Use of Arabidopsis seedlings expressing apoaequorin, a Ca²⁺-reporting photoprotein (Plieth and Trewavas, 2002; Toyota et al., 2008a), has revealed that gravistimulation induces a biphasic [Ca2+]_c increase that may be involved in the sensory pathway for gravity perception/response (Pickard, 2007; Toyota and Gilroy, 2013) and the intracellular distribution of auxin transporters (Benjamins et al., 2003; Zhang et al., 2011). These two Ca²⁺ changes have different characteristics. The first transient [Ca2+]_c increase depends on the rotational velocity but not angle, whereas the second sustained [Ca2+]_c increase depends on the rotational angle but not velocity. The first [Ca2+]_c transient was inhibited by Gd³⁺, La³⁺, and the Ca²⁺ chelator 1,2-bis(2-aminophenoxy)ethane-N,N,N′,N′-tetraacetic acid but not by ruthenium red (RR), whereas the second sustained [Ca2+]_c increase was inhibited by all these chemicals. These results suggest that the first transient and second sustained [Ca2+]_c increases are related to the rotational stimulation and the gravistimulation, respectively, and are mediated by distinct molecular mechanisms (Toyota et al., 2008a). However, it has not been demonstrated directly that the second sustained [Ca2+]_c increase is induced solely by gravistimulation; it could be influenced by other factors, such as an interaction with the first transient [Ca2+]_c increase (Cessna et al., 1998), vibration, and/or deformation of plants during the rotation.To elucidate the genuine Ca²⁺ signature in response to gravistimulation in plants, we separated rotation and gravistimulation under microgravity (μg; less than 10⁻⁴g) conditions provided by parabolic flight (PF). Using this approach, we were able to apply rotation and gravistimulation to plants separately (Fig. 1). When Arabidopsis seedlings were rotated +180° under μg conditions, the [Ca2+]_c response to the rotation was transient and almost totally attenuated in a few seconds. Gravistimulation (transition from μg to 1.5g) was then applied to these prerotated specimens at the terminating phase of the PF. This gravistimulation without simultaneous rotation induced a sustained [Ca2+]_c increase. The kinetic properties of this sustained [Ca2+]_c increase were examined under different gravity intensities (0.5g–2g) and sequences of gravity intensity changes (Fig. 2A). This analysis revealed that gravistimulation-specific Ca²⁺ response has an almost linear dependency on gravitational acceleration (0.5g–2g) and an extremely rapid responsiveness of less than 1 s.Open in a separate windowFigure 1.Diagram of the experimental procedures for applying separately rotation and gravistimulation to Arabidopsis seedlings. Rotatory stimulation (green arrow) was applied by rotating the seedlings 180° under μg conditions, and 1.5g 180° rotation gravistimulation (blue arrow) was applied to the prerotated seedlings after μg.Open in a separate windowFigure 2.Acceleration, temperature, humidity, and pressure in an aircraft during flight experiments. A, Accelerations along x, y, and z axes in the aircraft during PF. The direction of flight (FWD) and coordinates (x, y, and z) are indicated in the bottom graph. The inset shows an enlargement of the acceleration along the z axis (gravitational acceleration) during μg conditions lasting for approximately 20 s. B, Temperature, humidity, and pressure in the aircraft during PF. Shaded areas in graphs denote the μg condition.     

A study on the relationship between leaf conductance,CO2 concentration and carboxylation rate in various species

Leaf conductance g_L is strongly influenced by environmental factors like CO₂, irradiance and air humidity. According to Ball et al. (1987), g_L is correlated with an index calculated as the product of net CO₂ exchange rate A and ambient water vapour concentration W_a, divided by ambient CO₂ concentration c_a. However, this empirical model does not apply to high values of g_L observed at c_a below CO₂ compensation concentration . Therefore, we applied modified indices in which A is replaced by estimates for the rate of carboxylation. Such estimates, P₁ and P₂, were determined by adding to A the quotient of and the sum of gas phase resistance r_g and intracellular resistance for CO₂ exchange r_i, P₁ = A+/(r_g + r_i), or the quotient of and r_i, P₂ = A + /r_i. If P₂ is chosen, c_a in the Ball index has to be replaced by the intercellular CO₂ concentration c_i. By using the modified indices P₁·W_a/c_a and P₂·W_a/c_i, we analysed data from the C₃ species Nicotiana tabacum and Nicotiana plumbaginifolia, the C₃–C₄ intermediate species Diplotaxis tenuifolia, and the C₄ species Zea mays. The data were collected at widely varying levels of irradiance and CO₂ concentration. For all species uniform relationships between g_L and the new indices were found for the whole range of CO₂ concentrations below and above . Correlations between g_L and P₁·W_a/c_a were closer than those between g_L and P₂·W_a/c_i because P₁/c_a implicitly contains g_L. Highly significant correlations were also obtained for the relationships between g_L and the ratios P₁/c_a and P₂/c_i.     

Graphic analysis of codon usage strategy in 1490 human proteins

The frequencies of bases A (adenine), C (cytosine), G (guanine), and T (thymine) occurring in codon positioni, denoted bya _i ,c _i ,g _i , andt _i , respectively (i=1, 2, 3), have been calculated and diagrammatized for the 1490 human proteins in the codon usage table for primate genes compiled recently. Based on the characteristic graphs thus obtained, an overall picture of codon base distribution has been provided, and the relevant biological implication discussed. For the first codon position, it is shown in most cases that G is the most dominant base, and that the relationshipg ₁>a ₁>c ₁>t ₁ generally holds true. For the second codon position, A is generally the most dominant base and G is the one with the least occurrence frequently, with the relationship ofa ₂>t ₂>c ₂>g ₂. As to the third codon position, the values ofg ₃+c ₃ vary from 0.27 to 1, roughly keeping the relationship ofc ₃>g ₃>a ₃=t ₃ for the majority of cases. Interestingly, if the average frequencies for bases A, C, G, and T are defined as , respectively, we find that is valid almost without exception. Such a characteristic inequality might reflect some inherent rule of codon usage, although its biological implications is unclear. An important advantage by introducing graphic methods is to make it possible to catch essential features from a huge amount of data by a direct and intuitive examination. The method used here allows one to see means and variances, and also spot outliers. This is particularly useful for finding and classifying similarity patterns and relationships in data sets of long sequences, such as DNA coding sequences. The current method also holds a great potential for the study of molecular evolution from the viewpoint of genetic code whose data have been accumulated rapidly and are to continue growth at a much faster pace.On sabbatical leave from Department of Physics, Tianjin University, Tianjin, China.     

The origin of split EPR signals in the Ca2+-depleted Photosystem II

A light-driven reaction model for the Ca²⁺-depleted Photosystem (PS) II is proposed to explain the split signal observed in electron paramagnetic resonance (EPR) spectra based on a comparison of EPR assignments with recent x-ray structural data. The split signal has a splitting linewidth of 160 G at around g = 2 and is seen upon illumination of the Ca²⁺-depleted PS II in the S₂ state associated with complete or partial disappearance of the S₂ state multiline signal. Another g=2 broad ESR signal with a 110 G linewidth was produced by 245 K illumination for a short period in the Ca²⁺-depleted PS II in S₁ state. At the same time a normal Y_Z^· radical signal was also efficiently trapped. The g=2 broad signal is attributed to an intermediate S₁X^· state in equilibrium with the trapped Y_Z^· radical. Comparison with x-ray structural data suggests that one of the split signals (doublet signal) is attributable to interaction between His 190 and the Y_Z^· radical, and other signals is attributable to interaction between His 337 and the manganese cluster, providing further clues as to the mechanism of water oxidation in photosynthetic oxygen evolution.     

X-ray crystal structures of the copper(II), nickel(II) and silver(I) complexes of a 17-membered dibenzo macrocycle with a N3S2 donor set

The copper(II), nickel(II) and silver(I) complexes of the pentadentate 17-membered macrocycle 1, 12, 15-triaza-3, 4:9, 10-dibenzo-5,8-dithiacycloheptadecane (L¹) have been prepared as perchlorates and characterized by X-ray crystallography. The N₃S₂ ligand uses all donor atoms for complexation. The copper coordination is square pyramidal with one sulfur atom in the axial site. Ni(II) displays an octahedral coordination by an interaction with a water molecule. The Ag(I) coordination is best described as a distorted pentagonal bipyramid. In [CuL¹]²⁺ the 1, 4, 7-triazaheptane fragment of L¹ is meridionally coordinated, but facially in [NiL¹(H₂O)]²⁺ and intermediate in [AgL¹](ClO₄). Crystal data for [CuL¹](ClO₄)₂: monoclinic, space group P2₁/n, a = 13.153(8), b = 11.951(5), c = 17.880(8)Å, β = 110.29(4)°, Z = 4, R = 0.086 for 2732 independent reflections with I 2σ(I); [NiL¹(H₂O)](ClO₄)₂: monoclinic, P2₁/a, a = 10.771(2), b= 16.157(2), c = 15.286(2) Å, β =93.08(1)°, Z = 4, R = 0.085 for 1464 independent reflections with I 2σ(I); [AgL¹](ClO₄): monoclinic, P2₁/n, a = 12.708(9), b = 9.483(7), c = 19.569(13) Å, β= 103.95(6)°, Z = 4, R = 0.039 for 3600 independent reflections with I 2σ(I).     

Conformational studies of peptides: Crystal and molecular structures of L-3,4-dehydroproline and its t-butoxycarbonyl and acetyl amide derivatives

The crystal structures of L -3,4-dehydroproline, t-butoxycarbonyl-L -3,4-dehydroproline amide, and acetyl-L -3,4-dehydroproline amide have been determined. L -3,4-Dehydroproline is orthorhombic with a = 16.756, b = 5.870, c = 5.275 Å, and Z = 4; t-butoxycarbonyl-L -3,4-dehydroproline amide is orthorhombic with a = 6.448, b = 8.602, c = 21.710 Å, and Z = 4; acetyl-L -3,4-dehydroproline amide is monoclinic with a = 4.788, b = 10.880, c = 7.785 Å, β = 105.25°, and Z = 2. The final R value for the L -3,4-dehydroproline is 0.046 based on 529 reflections; for t-butoxycarbonyl-L -3,4-dehydroproline amide, 0.050 based on 792 reflections; and for acetyl-L -3,4-dehydroproline amide, 0.058 based on 632 reflections. The structures clearly establish that the free amino acid exists in the zwitterionic form in the crystalline state. The molecular conformations of the t-Boc and acetyl derivatives consist of two planes: one involving the primary amide and the other the remaining atoms of the molecule. The acetyl-L -3,4-dehydroproline amide contains a tertiary amide bond in the cis conformation. To the best of our knowledge, this is the first example of a cis bond in an acetyl derivative of an amino acid or peptide. At variance with the previously reported proline amides, which present ? and ψ values corresponding to those of a right-handed α-helical conformation (conformation A), the t-Boc and acetyl derivatives both have ? and ψ values corresponding to a collagenlike conformation (conformation F).     

Polymorphism in V k 10 genes encoding L chains of antibodies bearing the Ars-A and A48 cross-reactive idiotypes

p-azophenylarsonate-specific antibodies of A/J mice which bear the Ars-A cross-reactive idiotype utilize the V _K–Ars–A gene segment, a member of the V _K 10 family. Southern hybridization of genomic DNA from several inbred strains using a probe from the 5 flanking region of the V _K–Ars–A gene demonstrated three patterns of restrictio fragment length polymorphisms (RFLP). Six genes corresponding to hybridizing bands were obtained from DNA libraries of C.AKR, PERU and A/J mice, and nucleotide sequence comparisons revealed two allelic groups: AKRI (Igk-V10.1 ^a ), AJ1 (Igk-V10.1 ^b ) and PERU1 (Igk-V10.1 ^c ); AKR2 (Igk-V10.2 ^a ), AJ2 (Igk-V10.2 ^b ), and PERU2 (Igk-V10.2 ^c ).The Igk-V10.1 ^b gene of the A/J strain is the V _k–Ars–A gene used in Ars-A idiotype-positive antibodies. The product of the C.AKR allele (Igk-V10.1 ^a ) contained four amino acid substitutions in CDR3 as compared with Igk-V10.1 ^b . These substitutions probably explain the failure of AKR mice and other strains with the same V_K10 RFLP pattern to provide in genetic crosses a L chain which, together with the A/J V _H–ArsA gene product, form Ars-A idiotype-positive antibodies. Also, the nucleotide sequence identity between the Igk-V10.1 ^c and Igk-V10.1 ^b alleles and the Igk-V10.2 ^c and Igk-V10.2 ^b alleles is significantly greater than that seen in comparisons with the Igk-V10.1 ^a and Igk-V10.2 ^a alleles, respectively, suggesting an evolutionary pathway similar to that of the linked Igk-J locus.BALB/c antibodies bearing the A48 regulatory idiotype contain L chains encoded by the BALB/c Igk-V10.1 ^b and Igk-V10.2 ^b alleles. Strongly A48 idiotype-positive antibodies utilize the Igk-V10.1 ^b chain, and weakly A48-positive antibodies use the Igk-V10.2 ^b L chain. The possible effects of amino acid substitutions specified by the Igk-V10.1 ^a , Igk-V10.1 ^c , Igk-V10.2 ^a , and Igk-V10.2 ^c alleles on their ability to provide L chains used in A48 idiotype-positive are discussed.The locus name, Igk-V28 (D'Hoostelaere et al. 1988), will be used in this report in place of the name, Igk-VSer, used in the original publications (Goldrick et al. 1985; Boyd et al. 1986; Gottlieb et al. 1986; Ponath et al. 1988). The four alleles described at the Igk-VSer locus (Igk-VSer ^a , Igk-VSer ^b , Igk-VSer ^c , and Igk-VSer ^d ) are referred to as Igk-V28 ^a , Igk-V28 ^b , Igk-V28 ^c , and Igk-V28 ^d , respectively.The nucleotide sequence data reported in this paper have been submitted to GenBank nucleotide sequence database and have been assigned the accession numbers M54903, M54904, M54905, M54906, M54907, and M54908. Address correspondence and offprint requests to : P. D. Gottlieb.     

Constrained C-terminal hexapeptide neurotensin analogues containing a 3-oxoindolizidine skeleton

Summary In order to enforce different spatial orientations in the C-terminal hexapeptide of neurotensin (NT_8–13) and to gain information about the importance of the 10–11 peptide bond for binding to NT receptors, the Pro¹⁰-Tyr¹¹ fragment has been replaced with (2R,8S,8aR)-, (2S,8S,8aR)-, (2S,8S,8aS)-, (2S,8R,8aS)- and (2R,8R,8aS)-8-amino-2-benzyl-3-oxoindolizidine-2-carboxylic acid. Molecular dynamics calculations and energy minimization studies have shown that, contrarily to the Pro-Tyr moiety, none of these indolizidines display a tendency to adopt type I and III -turns, but those having (8S,8aR) or (8R,8aS) stereochemistry essentially adopt extended conformations and the (8S,8aS) stereoisomer prefers a nonstandard folding. The four diastereomeric NT_8–13 analogues incorporating (8S,8aR) or (8R,8aS) indolizidines displayed binding affinities for the brain NT receptor similar to that of [Ala¹¹]-NT_8–13 and only five- to ninefold lower than that of the corresponding analogue, [Phe¹¹]NT_8–13. Although this slight decrease could be attributed to differences in conformational behavior between these constrained NT_8–13 analogues and [Phe¹¹]NT_8–13 or NT_8–13, it is not clear whether the -turn around Pro¹⁰-AA¹¹ (AA=Phe, Tyr) is conserved upon receptor binding. An excessive restriction in the motions of the aromatic side chain, imposed by the highly steric constraint of the indolizidine moiety, emerges as an alternative explanation. The findings reported here demonstrate the possibility of replacing the Pro¹⁰-Tyr¹¹ dipeptide in NT_8–13 with a non-peptide residue without affecting considerably the affinity for brain NT receptors.     

Electron paramagnetic resonance and Mössbauer spectroscopy of intact mitochondria from respiring <Emphasis Type="Italic">Saccharomyces cerevisiae</Emphasis>

Mitochondria from respiring cells were isolated under anaerobic conditions. Microscopic images were largely devoid of contaminants, and samples consumed O₂ in an NADH-dependent manner. Protein and metal concentrations of packed mitochondria were determined, as was the percentage of external void volume. Samples were similarly packed into electron paramagnetic resonance tubes, either in the as-isolated state or after exposure to various reagents. Analyses revealed two signals originating from species that could be removed by chelation, including rhombic Fe³⁺ (g = 4.3) and aqueous Mn²⁺ ions (g = 2.00 with Mn-based hyperfine). Three S = 5/2 signals from Fe³⁺ hemes were observed, probably arising from cytochrome c peroxidase and the a₃:Cu_b site of cytochrome c oxidase. Three Fe/S-based signals were observed, with averaged g values of 1.94, 1.90 and 2.01. These probably arise, respectively, from the [Fe₂S₂]⁺ cluster of succinate dehydrogenase, the [Fe₂S₂]⁺ cluster of the Rieske protein of cytochrome bc ₁, and the [Fe₃S₄]⁺ cluster of aconitase, homoaconitase or succinate dehydrogenase. Also observed was a low-intensity isotropic g = 2.00 signal arising from organic-based radicals, and a broad signal with g _ave = 2.02. Mössbauer spectra of intact mitochondria were dominated by signals from Fe₄S₄ clusters (60–85% of Fe). The major feature in as-isolated samples, and in samples treated with ethylenebis(oxyethylenenitrilo)tetraacetic acid, dithionite or O₂, was a quadrupole doublet with ΔE _Q = 1.15 mm/s and δ = 0.45 mm/s, assigned to [Fe₄S₄]²⁺ clusters. Substantial high-spin non-heme Fe²⁺ (up to 20%) and Fe³⁺ (up to 15%) species were observed. The distribution of Fe was qualitatively similar to that suggested by the mitochondrial proteome.     

Identification of self-incompatibility genotypes of almond by allele-specific PCR analysis

In almond, gametophytic self-incompatibility is controlled by a single multiallelic locus (S-locus). In styles, the products of S-alleles are ribonucleases, the S-RNases. Cultivated almond in California have four predominant S-alleles (S ^a, S ^b, S ^c, S ^d). We previously reported the cDNA cloning of three of these alleles, namely S ^b, S ^c and S ^d. In this paper we report the cloning and DNA sequence analysis of the S ^a allele. The S^a-RNase displays approximately 55% similarity at the amino-acid level with other almond S-RNases (S^b, S^c, and S^d) and this similarity was lower than that observed among the S^b, S^c and S^d-RNases. Using the cDNA sequence, a PCR-based identification system using genomic DNA was developed for each of the S-RNase alleles. Five almond cultivars with known self-incompatibility (SI) geno-types were analyzed. Common sequences among four S-alleles were used to create four primers, which, when used as sets, amplify DNA bands of unique size that corresponded to each of the four almond S-alleles; S ^a (602 bp), S ^b (1083 bp), S ^c (221 bp) and S ^d (343 bp). All PCR products obtained from genomic DNA isolated from the five almond cultivars were cloned and their DNA sequence obtained. The nucleotide sequence of these genomic DNA fragments matched the corresponding S-allele cDNA sequence in every case. The amplified products obtained for the S ^a- and S ^b-alleles were both longer than that expected for the coding region, revealing the presence of an intron of 84 bp in the S ^a-allele and 556 bp in the S ^b-allele. Both introns are present within the site of the hypervariable region common in S-RNases from the Rosaceae family and which may be important for S specificity. The exon portions of the genomic DNA sequences were completely consistent with the cDNA sequence of the corresponding S-allele. A useful application of these primers would be to identify the S-genotype of progeny in a breeding program, new varieties in an almond nursery, or new grower selections at the seedling stage. Received: 21 June 1999 / Accepted: 15 November 1999     

Purification of the photosynthetic reaction center from <Emphasis Type="Italic">Heliobacterium modesticaldum</Emphasis>

We have developed a purification protocol for photoactive reaction centers (HbRC) from Heliobacterium modesticaldum. HbRCs were purified from solubilized membranes in two sequential chromatographic steps, resulting in the isolation of a fraction containing a single polypeptide, which was identified as PshA by LC–MS/MS of tryptic peptides. All polypeptides reported earlier as unknown proteins (in Heinnickel et al., Biochemistry 45:6756–6764, 2006; Romberger et al., Photosynth Res 104:293–303, 2010) are now identified by mass spectrometry to be the membrane-bound cytochrome c ₅₅₃ and four different ABC-type transporters. The purified PshA homodimer binds the following pigments: 20 bacteriochlorophyll (BChl) g, two BChl g′, two 8¹-OH-Chl a _F, and one 4,4′-diaponeurosporene. It lacks the PshB polypeptide binding the F_A and F_B [4Fe–4S] clusters. It is active in charge separation and exhibits a trapping time of 23 ps, as judged by time-resolved fluorescence studies. The charge recombination rate of the P₈₀₀ ⁺F_X⁻ state is 10–15 ms, as seen before. The purified HbRC core was able to reduce cyanobacterial flavodoxin in the light, exhibiting a K _M of 10 μM and a k _cat of 9.5 s⁻¹ under near-saturating light. There are ~1.6 menaquinones per HbRC in the purified complex. Illumination of frozen HbRC in the presence of dithionite can cause creation of a radical at g = 2.0046, but this is not a semiquinone. Furthermore, we show that high-purity HbRCs are very stable in anoxic conditions and even remain active in the presence of oxygen under low light.     

Isolation of membrane bound light-harvesting-complexes from the dinoflagellates Heterocapsa pygmaea and Prorocentrum minimum

We have isolated Chl a-Chl c-carotenoid binding proteins from the dinoflagellates Prorocentrum minimum and Heterocapsa pygmaea grown under high (500 mol m^–2 s^–1, HL) and low (35 mol m^–2 s^–1, LL) light conditions. We compared various isolation procedures of membrane bound light harvesting complexes (LHCs) and assayed the functionality of the solubilized proteins by determining the energy transfer efficiency from the accessory pigments to Chl a by means of fluorescence excitation spectra. The identity of the newly isolated protein-complexes were confirmed by immunological cross-reactions with antibodies raised against the previously described membrane bound Chl a-c proteins (Boczar et al. (1980) FEBS Lett 120: 243–247). Spectroscopic analysis demonstrated the relatedness of these proteins with the recently described Chl-a-c ₂-peridinin (ACP) binding protein (Hiller et al. (1993) Photochem Photobiol 57: 125–131; Iglesias Prieto et al. (1993) Phil Trans R Soc London B 338: 381–392). The water-soluble peridinin-Chl a binding-protein (PCP) was not detectable in P. minimum. Two functional forms of ACP with different pigmentation were isolated. A variant of ACP which was isolated from high-light grown cells, that specifically binds increased amounts of diadinoxanthin was compared to the previously described ACPs that bind proportionately more peridinin.Abbreviations ACP Chl a-Chl c-peridinin binding protein - AEBSF 4-(2-aminoethyl)-benzenesulfonyl fluoride hydrochloride - DDM dodecyl -d maltoside - Deriphat 160 N-lauryl-beta-iminopropionic acid - HEPES (N-2-hydroxyethylpiparizine-N-2-ethanesulphonic acid) - HL high light (500 mol m^–2 s^–1) - LL low light (35 mol m^–2 s^–1) - ₇₃₀ fluorescence yield (emission at 730 nm) - PCP peridinin-Chl a-binding protein - PMSF phenyl-methyl-sulfonyl-fluoride - PS I Photosystem I - PS II Photosystem II     

Molecular recognition between 4a<Emphasis Type="Italic">S/R</Emphasis>-galanthamine diastereoisomers and α-cyclodextrin

Molecular recognition between 4aS/R-galanthamine diastereoisomers (1: 4aS-galanthamine; 2: 4aR-galanthamine) and -cyclodextrin (-CD) were studied by use of docking and molecular dynamics (MD) simulation approaches. The binding energy of constructed 2···-CD complexes is ~17 kcal mol^–1 lower than that of 1···-CD, implying a stronger binding ability of 2 with -CD than that of 1. The theoretical modeling result is consistent with our previous CZE result, which demonstrated that -CD is an efficient chiral additive for separating 1 and 2. The modeling result also indicates that both hydrophobic interaction and H-bond force may work as major factors for molecular recognition between the galanthamine diastereoisomers and -CD. Figure Chemical structures of 4aS-galanthamine (left) and 4aR-galanthamine (right)Abbreviations Galanthamine 4aS,6R,8aS-4a,5,9,10,11,12-Hexahydroxy-3-methoxy-11-methyl-6H-benzofuro[3a,3,2-e,f]benzazepin-6-ol     

Iridoids from Pedicularis verticillata and Their Anti‐Complementary Activity

Three new iridoids named as pediverticilatasin A – C ( 1 – 3 , resp.), together with five known iridoids ( 4 – 8 , resp.) were isolated from the whole plants of Pedicularis verticillata. The structures of three new compounds were identified as (1S,7R)‐1‐ethoxy‐1,5,6,7‐tetrahydro‐7‐hydroxy‐7‐methylcyclopenta[c]pyran‐4(3H)‐one ( 1 ), (1S,4aS,7R,7aS)‐1‐ethoxy‐1,4a,5,6,7,7a‐hexahydro‐7‐hydroxy‐7‐methylcyclopenta[c]pyran‐4‐carboxylic acid ( 2 ), (1S,4aS,7R,7aS)‐1‐ethoxy‐1,4a,5,6,7,7a‐hexahydro‐7‐hydroxy‐7‐methylcyclopenta[c]pyran‐4‐carbaldehyde ( 3 ). Their structures were elucidated on the basis of spectroscopic methods and compared with the NMR spectra data in the literature. All compounds were evaluated for their anti‐complementary activity on the classical pathway of the complement system in vitro. Among which, compounds 1 , 3 , and 6 exhibited anti‐complementary effects with CH₅₀ values ranging from 0.43 to 1.72 mm , which are plausible candidates for developing potent anti‐complementary agents.     

The boundary layer and the apparent responses of stomatal conductance to wind speed and to the mole fractions of CO2 and water vapour in the air

The experiments and simulations reported in this paper show that, for stomata sensitive to both CO₂ and water vapour concentrations, responses of stomatal conductance (g^w_s) to boundary layer thickness have two components, one resulting from changes in intercellular CO₂ concentration (χ^c_i) and another from changes in leaf surface water vapour saturation deficit (D^w_s). The experiments and simulations also show that the boundary layer conductance (g^w_b) can significantly alter the apparent response of g^w_s to ambient air CO₂ mole fraction (χ^c_a) and water vapour mole fraction (χ^w_a). Because of the feedback loop involved the responses of g^w_s for χ^c_a and χ^w_a each include responses to both χ^c_i and D^w_s. The boundary layer alters the state of the variables sensed by the guard cells—i.e. χ^c_i and D^w_s—and so it is a source of feedback. Thus, when scaling up from responses of stomata to the response of g^w_s for a whole leaf, the effect of the boundary layer must be considered. The results indicate that, for given responses of g^w_s to χ^c_i and D^w_s, the apparent responses of g^w_s to D^w_a and χ^c_a depend on the size of the leaf and wind speed, showing that this effect of the boundary layer should be considered when comparing data measured under different conditions, or with different methods.     

Synthesis of 3-fluoro-6-S-(2-S-pyridyl) nucleosides as potential lead cytostatic agents

The 3-deoxy-3-fluoro-6-S-(2-S-pyridyl)-6-thio-β-d-glucopyranosyl nucleoside analogs 7 were prepared via two facile synthetic routes. Their precursors, 3-fluoro-6-thio-glucopyranosyl nucleosides 5a-e, were obtained by the sequence of deacetylation of 3-deoxy-3-fluoro-β-d-glucopyranosyl nucleosides 2a-e, selective tosylation of the primary OH of 3 and finally treatment with potassium thioacetate. The desired thiolpyridine protected analogs 7a-c,f,g were obtained by the sequence of deacetylation of 5a-c followed by thiopyridinylation and/or condensation of the corresponding heterocyclic bases with the newly synthesized peracetylated 6-S-(2-S-pyridyl) sugar precursor 13, which was obtained via a novel synthetic route from glycosyl donor 12. None of the compounds 6 and 7 showed antiviral activity, but the 5-fluorouracil derivative 7c and particularly the uracil derivative 7b were endowed with an interesting and selective cytostatic action against a variety of murine and human tumor cell cultures.     

Enlarging the family of ferrocenylphosphine dinuclear rhodium complexes: synthesis and X-ray structure of a novel “A-frame”-type trimetallic Rh/Fe/Rh complex

The symmetrically substituted ligand 1,1^′-bis[di(5-methyl-2-furyl)phosphino]ferrocene (1) has been obtained from the bromophosphine BrP(Fu^Me)₂ and the dilithioferrocene/TMEDA adduct. The quantitative addition of this ferrocene derivative to the tetracarbonyl dimer [(CO)₄Rh₂{μ-(S^tBu)₂}] leads, through decarbonylation, to the dinuclear rhodium complex [(CO)₂Rh₂{μ-(S^tBu)₂}{μ-P,P-Fc[P(Fu^Me)₂]₂}] (2) in high yield. A X-ray structure [orthorhombic, space group P2₁2₁2₁; a=11.2982(2) Å, b=13.3165(3) Å, c=27.2687(7) Å] and the solution multinuclear NMR characterization are reported, which show that the rare “quasi-closed bridging” A-frame structure of the complex is rather similar to the one reported for [(CO)₂Rh₂{μ-(S^tBu)₂}{μ-P,P-dppf}] in solid state. However, in solution the furyl-containing ferrocenylphosphine complex presents a greater fluxionality, together with an electronic environment at phosphorus very different from the dppf analogue (δ_P=−10 and 27 ppm, respectively).