Reconstruction of source water using the δ18O of tree ring phenylglucosazone: A potential tool in paleoclimate studies

The oxygen isotope ratios of tree ring cellulose have a great potential as proxy for the oxygen isotope ratios of source water, which is related to climate. However, source water isotopic signatures can be masked by plant physiological and biochemical processes during cellulose synthesis. To minimize biochemical effects in the recording of source water, we modified the cellulose molecule to phenylglucosazone, which only has oxygen attached to carbon 3–6 (O_C3–6) of the cellulose glucose moieties, thus eliminating the oxygen attached to carbon 2 of the cellulose glucose moieties (O_C-2). Here we developed a method to use small amounts of inter and intra-annual tree ring cellulose for phenylglucosazone synthesis. Using this new method we tested if the oxygen isotope ratios of source water reconstructed from tree ring phenylglucosazone (δ¹⁸O_sw^PG) and the observed source water (δ¹⁸O_sw^obs) would have a better agreement than those reconstructed from the tree ring cellulose molecule. Annual tree ring samples were obtained from Pinus sylvestris (1997–2003) (Finland) and Picea abies (1971–1992) (Switzerland) and intra-annual tree ring samples were obtained from Pinus radiata (October 2004–March 2006) (New Zealand), each near a meteorological station where precipitation and relative humidity (RH) were measured periodically. The δ¹⁸O of tree ring cellulose and tree ring phenylglucosazone for each of the three species were then used to back calculate the δ¹⁸O of source water according to a previous published empirical equation. As expected, the δ¹⁸O of tree ring phenylglucosazone was superior than cellulose in the reconstruction of source water available to the plant. Deviation between δ¹⁸O_sw^PG and δ¹⁸O_sw^obs was in part correlated with variation in atmospheric relative humidity (RH) which was not observed for the cellulose molecule. We conclude that this new method can be applicable to inter and intra-annual tree ring studies and that the use of the tree ring phenylglucosazone will significantly improve the quality of paleoclimate studies.     

Genetic and physical map of a P1 miniplasmid

The prophage form of bacteriophage P1 is a unit-copy plasmid which is maintained with great fidelity in its Escherichia coli host. The plasmid maintenance functions of P1 are clustered in one region of the genome. An 11.5-kilobase fragment from this region has been cloned into a lambda delta att vector and promotes stable unit-copy plasmid maintenance. The properties of the lambda vector facilitated the isolation of deletion mutants affecting the P1 DNA. Twenty-eight deletion mutants were isolated, and their lesions were mapped by physical techniques. The genetic properties of the mutants with respect to plasmid replication, stability of plasmid maintenance, and ability to exert incompatibility effects against P1 and P7 plasmids were determined. These properties, along with those of several subfragments of the P1 insert cloned into high-copy-number plasmid vectors, allow the construction of an unambiguous genetic and physical map of the maintenance functions. A region of less than 3 kilobases, the rep region, is essential for plasmid replication and contains the incA incompatibility determinant within an 800-base-pair segment. Immediately adjacent to rep is a second region of approximately 3 kilobases which is required for stable plasmid maintenance, but not replication. This region, par, contains a second incompatibility element incB which is approximately 1 kilobase in size. The par region appears to specify equipartition of plasmid copies to daughter cells during cell division.     

Characterization of the binding sites of c1 repressor of bacteriophage P1. Evidence for multiple asymmetric sites

The repressor of bacteriophage P1, encoded by the c1 gene, is responsible for maintaining a P1 prophage in the lysogenic state. In this paper we present: (1) the sequence of the rightmost 943 base-pairs of the P1 genetic map that includes the 5'-terminal 224 base-pairs of the c1 gene plus its upstream region; (2) the construction of a plasmid that directs the production of approximately 5% of the cell's protein as P1 repressor; (3) a deletion analysis that establishes the startpoint of P1 repressor translation; (4) filter binding experiments that demonstrate that P1 repressor binds to several regions upstream from the c1 gene; (5) DNase I footprint experiments that directly identify two of the P1 repressor binding sites. Sequences very similar to the identified binding sites occur in at least 11 sites in P1, in most cases near functions known, or likely, to be controlled by repressor. From these sites we have derived the consensus binding site sequence ATTGCTCTAATAAATTT. We suggest that, unlike other phage operators, the P1 repressor binding sites lack rotational symmetry.     

Irregular structure of the HIV fusion peptide in membranes demonstrated by solid-state NMR and MD simulations

To better understand peptide-induced membrane fusion at a molecular level, we set out to determine the structure of the fusogenic peptide FP23 from the HIV-1 protein gp41 when bound to a lipid bilayer. An established solid-state ¹⁹F nuclear magnetic resonance (NMR) approach was used to collect local orientational constraints from a series of CF₃-phenylglycine-labeled peptide analogues in macroscopically aligned membranes. Fusion assays showed that these ¹⁹F-labels did not significantly affect peptide function. The NMR spectra were characteristic of well-behaved samples, without any signs of heterogeneity or peptide aggregation at 1:300 in 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC). We can conclude from these NMR data that FP23 has a well-defined (time-averaged) conformation and undergoes lateral diffusion in the bilayer plane, presumably as a monomer or small oligomer. Attempts to evaluate its conformation in terms of various secondary structures, however, showed that FP23 does not form any type of regular helix or β-strand. Therefore, all-atom molecular dynamics (MD) simulations were carried out using the orientational NMR constraints as pseudo-forces to drive the peptide into a stable alignment and structure. The resulting picture suggests that FP23 can adopt multiple β-turns and insert obliquely into the membrane. Such irregular conformation explains why the structure of the fusion peptide could not be reliably determined by any biophysical method so far.     

Photosynthesis of F(1) Hybrids between C(4) and C(3)-C(4) Species of Flaveria

Photosynthetic characteristics were studied in several F₁ hybrids between C₄ and C₃-C₄ species of Flaveria. Stable carbon isotope ratios, O₂ inhibition of apparent photosynthesis, and phosphoenolpyruvate carboxylase activities in the hybrids were similar to the means for the parents. Values of CO₂ compensation concentrations were nearer to those of the C₄ parent and apparent photosynthesis was below that of both parents, being only 60 and 74% of that of the lowest (C₃-C₄) parent in two experiments. Reductions of CO₂ compensation concentration and O₂ inhibition of apparent photosynthesis as well as increases in carbon isotope ratios and phosphoenolpyruvate carboxylase activities compared to values in C₃-C₄ species suggest transfer of a limited degree of C₄ photosynthesis to the F₁ hybrids. However, the lower apparent photosynthesis of the hybrids suggests that transfer of C₄ characteristics to non-C₄ species is detrimental unless characteristics associated with C₄ photosynthesis are fully developed. There was a highly significant negative correlation (r = −0.90) between CO₂ compensation concentration and the logarithm of phosphoenolpyruvate carboxylase activity in the parents and hybrids, suggesting involvement of this enzyme in controlling the CO₂ compensation concentration. Although bundle-sheath cells were more developed in leaves of hybrids than in C₃-C₄ parents, they appeared to contain lower quantities of organelles than those of the C₄ parent. Reduced quantities of organelles in bundle-sheath cells could indicate incomplete compartmentation of partial pathways of the C₄ cycle in the hybrids. This may mean that the reduction of CO₂ compensation and O₂ inhibition of apparent photosynthesis relative to the C₃-C₄ parents is less dependent on fully developed Kranz anatomy than is increased apparent photosynthesis.     

Two Essential Arginine Residues in the T Components of Energy-Coupling Factor Transporters

Energy-coupling factor (ECF) transporters, a recently discovered class of importers of micronutrients, are composed of a substrate-specific transmembrane component (S component) and a conserved energy-coupling module consisting of a transmembrane protein (T component) and pairs of ABC ATPases (A proteins). Based on utilization of a dedicated (subclass I) or shared (subclass II) energy-coupling module, ECF systems fall into two subclasses. The T components are the least-characterized proteins of ECF importers, and their function is essentially unknown. Using RcBioN and LmEcfT, the T units of the subclass I biotin transporter (RcBioMNY) of a gram-negative bacterium and of the subclass II folate, pantothenate, and riboflavin transporters of a lactic acid bacterium, respectively, we analyzed the role of two strongly conserved short motifs, each containing an arginine residue. Individual replacement of the two Arg residues in RcBioN reduced ATPase activity, an indicator of the transporter function, by two-thirds without affecting the modular assembly of the RcBioMNY complex. A double Arg-to-Glu replacement destroyed the complex and abolished ATPase activity. The corresponding single mutation in motif II of LmEcfT, as well as a double mutation, led to loss of the T unit from the subclass II ECF transporters and inactivated these systems. A single Arg-to-Glu replacement in motif I, however, abolished vitamin uptake activity without affecting assembly of the modules. Our results indicate that the conserved motif I in T components is essential for intramolecular signaling and, in cooperation with motif II, for subunit assembly of modular ECF transporters.Energy-coupling factor (ECF) transporters are a recently discovered novel class of importers of micronutrients in prokaryotes (9, 12, 13, 20). They are composed of a conserved energy-coupling module consisting of a transmembrane protein (T component) and pairs of ATP-binding cassette-containing proteins (A proteins), as well as an S unit (S component) through which substrate specificity is conveyed. S components represent a group of highly diverse small integral membrane proteins with predicted or experimentally established individual specificity for transition metal ions, B vitamins or their precursors, biotin, lipoate, and intermediates of salvage pathways. A link between substrate specificity and S components has been experimentally demonstrated in the case of CbiMN (Co²⁺) and NikMN (Ni²⁺) (13), RibU (riboflavin) (4, 6, 19), BioY (biotin) (9), FolT (folate) (8, 12), and ThiT (thiamine) (8, 12, 14). Based on utilization of a dedicated or shared AAT module, ECF transporters fall into two subclasses. Members of subclass I are encoded by operons containing one or two ABC ATPase genes, a T-component gene, and an S-component gene (12). RcBioMNY, the biotin transporter of Rhodobacter capsulatus, is the prototype of these systems. Previous work has established that the solitary BioY (S component) can function as a low-affinity transporter. It is converted into a high-affinity system in the presence of the AAT module BioMN (9). Notably, the majority of ECF transporters belong to subclass II. These promiscuous systems are widespread in the Firmicutes and also occur in members of the Thermotogales lineage and in archaea (12). In general, the cells contain a single ecfA1A2T operon and a number of genes for S units that are scattered around the genome. Cooccurrence of subclass I and subclass II ECF transporters is found in archaeal and bacterial species. The bioinformatic prediction for subclass II systems suggesting that several diverse S components interact with the same EcfA1A2T module has recently been confirmed experimentally for folate, riboflavin, and thiamine transporters of Bacillus subtilis, Lactobacillus casei, and Leuconostoc mesenteroides and for the hypothetical pantothenate transporter of L. mesenteroides (12).The modular composition of ECF transporters poses questions about their oligomeric structure, the specificity of subunit recognition, and the intersubunit signaling that couples substrate uptake to ATP hydrolysis by the ABC ATPase domains. These issues are essentially unsolved for any ECF transporter.In the present study, we confirm the predicted role of L. mesenteroides PanT (LmPanT) as a pantothenate-specific S component that functionally interacts with the LmEcfA1A2T module. The main focus is on the role of the T components, which are the least-characterized proteins of ECF importers. T proteins have moderately similar primary structures. Two 3-amino-acid signatures with Ala-Arg-Gly as the consensus sequence in the C-terminal part are the most conserved feature in the T units. Using RcBioMNY as a member of subclass I and LmEcfA1A2T plus LmFolT, LmPanT, or LmRibU as representatives of subclass II ECF transporters, we obtained evidence that replacement of either of the Arg residues in the T proteins strongly reduces or abolishes activity of the systems. While double mutations interfered with complex stability in each case, single replacements of the Arg residue in motif I did not have a marked impact on stability of the complexes, suggesting that this residue is important primarily for intramolecular signaling in both subclasses of ECF transporters.     

Prediction of beta-turns in proteins using neural networks

The use of neural networks to improve empirical secondary structure prediction is explored with regard to the identification of the position and conformational class of beta-turns, a four-residue chain reversal. Recently an algorithm was developed for beta-turn predictions based on the empirical approach of Chou and Fasman using different parameters for three classes (I, II and non-specific) of beta-turns. In this paper, using the same data, an alternative approach to derive an empirical prediction method is used based on neural networks which is a general learning algorithm extensively used in artificial intelligence. Thus the results of the two approaches can be compared. The most severe test of prediction accuracy is the percentage of turn predictions that are correct and the neural network gives an overall improvement from 20.6% to 26.0%. The proportion of correctly predicted residues is 71%, compared to a chance level of about 58%. Thus neural networks provide a method of obtaining more accurate predictions from empirical data than a simpler method of deriving propensities.