Mutation analysis of Lhca1 antenna complex. Low energy absorption forms originate from pigment-pigment interactions

The light harvesting complex Lhca1, one of the four gene products comprising the photosystem I antenna system, has been analyzed by site-directed mutagenesis with the aim of determining the chromophore(s) responsible for its long wavelength chlorophyll spectral form, a specific characteristic of the LHCI antenna complex. A family of mutant proteins, each carrying a mutation at a single chlorophyll-binding residue, was obtained and characterized by biochemical and spectroscopic methods. A map of the chromophores bound to each of the 10 chlorophyll-binding sites was drawn, and the energy levels of the Q(y) transition were determined in most cases. When compared with Lhcb proteins previously analyzed, Lhca1 is characterized by stronger interactions between individual chromophores as detected by both biochemical and spectroscopic methods; most mutations, although targeted to a single residue, lead to the loss of more than one chromophore and of conservative CD signals typical of chlorophyll-chlorophyll interactions. The lower energy absorption form (686 nm at 100K, 688 nm at room temperature), which is responsible for the red-shifted emission components at 690 and 701 nm, typical of Lhca1, is associated with a chlorophyll a/chlorophyll a excitonic interaction originating from a pigment cluster localized in the protein domain situated between helix C and the helix A/helix B cross. This cluster includes chlorophylls bound to sites A5-B5-B6 and a xanthophyll bound to site L2.     

Sequencing of simple sequence repeat anchored polymerase chain reaction amplification products of Biomphalaria glabrata

Simple sequence repeat anchored polymerase chain reaction amplification (SSR-PCR) is a genetic typing technique based on primers anchored at the 5' or 3' ends of microsatellites, at high primer annealing temperatures. This technique has already been used in studies of genetic variability of several organisms, using different primer designs. In order to conduct a detailed study of the SSR-PCR genomic targets, we cloned and sequenced 20 unique amplification products of two commonly used primers, CAA(CT)6 and (CA)8RY, using Biomphalaria glabrata genomic DNA as template. The sequences obtained were novel B. glabrata genomic sequences. It was observed that 15 clones contained microsatellites between priming sites. Out of 40 clones, seven contained complex sequence repetitions. One of the repeats that appeared in six of the amplified fragments generated a single band in Southern analysis, indicating that the sequence was not widespread in the genome. Most of the annealing sites for the CAA(CT)6 primer contained only the six repeats found within the primer sequence. In conclusion, SSR-PCR is a useful genotyping technique. However, the premise of the SSR-PCR technique, verified with the CAA(CT)6 primer, could not be supported since the amplification products did not result necessarily from microsatellite loci amplification.     

Persistence of tertiary structure in 7.9 M guanidinium chloride: the case of endo-beta-1,3-glucanase from Pyrococcus furiosus

The Pyrococcus furiosus endo-beta-1,3-glucanase belongs to the subfamily of laminarinase, which can be classified as "all beta proteins" as confirmed by deconvolution of far-UV CD and FTIR spectra. The persistence of a significant amount of tertiary structure in 7.9 M GdmCl, as indicated by near-UV CD spectroscopy, accompanied by a red-shift of the maximum fluorescence emission wavelength is a peculiar property of this hyperthermophilic endoglucanase. The possibility to observe tertiary structure elements under extremely denaturing conditions is notable and is limited to only a few examples. The unusual resistance toward guanidinium chloride denaturation is paralleled by a notable stability at extremely low pH and at high temperature. The analysis of the protein spectral properties indicates that the secondary structure elements are preserved down to pH 1.0 and up to 90 degrees C at pH 7.4 and pH 3.0. The study of the conditions that determine the persistence of residual structure at high denaturant concentration and the examination of these structures are particularly interesting because these state(s) may be preliminary or coincident with the coalescence of protein aggregates or to the formation of amyloid-like fibrils, and they may serve as seeds of protein folding.     

A nonhydrolyzable reactive cAMP analogue, (S(p))-8-[(4-bromo-2,3-dioxobutyl)thio]adenosine 3',5'-cyclic S-(methyl)monophosphorothioate, irreversibly inactivates human platelet cGMP-inhibited cAMP phosphodiesterase at micromolar concentrations

We previously showed that 8-[(4-bromo-2,3-dioxobutyl)thio]adenosine 3',5'-cyclic monophosphate inactivates cAMP phosphodiesterase (PDE3A); however, millimolar concentrations were needed to inactivate PDE3A because of ongoing hydrolysis. We have now synthesized a nonhydrolyzable reactive cAMP analogue, (S(p))-8-[(4-bromo-2,3-dioxobutyl)thio]adenosine 3',5'-cyclic S-(methyl)monophosphorothioate (S(p)-8-BDB-TcAMPSMe). S(p)-8-BDB-TcAMPSMe inactivates PDE3A in a time-dependent, irreversible manner, exhibiting saturation kinetics with a k(max) of (19.5 +/- 0.3) x 10(-3) min(-1) and a K(I) of 3.5 +/- 0.3 muM. To ascertain whether S(p)-8-BDB-TcAMPSMe reacts in the active site, nonhydrolyzable analogues of the substrate cAMP, or the competitive inhibitor cGMP, were included to protect against the inactivation of PDE3A. The order of effectiveness of protectants in decreasing the rate of inactivation (with K(d) values in micromolar) is as follows: S(p)-cAMPS (18) > R(p)-cGMPS (560) and S(p)-cGMPS (1260) > 5'-AMP (17 660), R(p)-cAMPS (30 110), and 5'-GMP (42 170). We docked S(p)-8-BDB-TcAMPSMe into PDE3A, based on the structural model of PDE3A-cAMP and the kinetic data from site-directed mutants. The S(p)-8-BDB-TcAMPSMe fits into the active site in the model. These results suggest that inactivation of PDE3A by the affinity reagent is a consequence of reaction at the overlap between cAMP and cGMP binding regions in the active site. S(p)-8-BDB-TcAMPSMe has proven to be an effective active site-directed irreversible cAMP affinity label for platelet PDE3A and can be used to identify amino acids in the active site of PDE3A as well as in other cAMP phosphodiesterases.     

Bacterial discrimination by means of a universal array approach mediated by LDR (ligase detection reaction)

Background  

PCR amplification of bacterial 16S rRNA genes provides the most comprehensive and flexible means of sampling bacterial communities. Sequence analysis of these cloned fragments can provide a qualitative and quantitative insight of the microbial population under scrutiny although this approach is not suited to large-scale screenings. Other methods, such as denaturing gradient gel electrophoresis, heteroduplex or terminal restriction fragment analysis are rapid and therefore amenable to field-scale experiments. A very recent addition to these analytical tools is represented by microarray technology.     

Inhibitory effects of cocoa flavanols and procyanidin oligomers on free radical-induced erythrocyte hemolysis

Excessive peroxidation of biomembranes is thought to contribute to the initiation and progression of numerous degenerative diseases. The present study examined the inhibitory effects of a cocoa extract, individual cocoa flavanols (-)-epicatechin and (+)-catechin, and procyanidin oligomers (dimer to decamer) isolated from cocoa on rat erythrocyte hemolysis. In vitro, the flavanols and the procyanidin oligomers exhibited dose-dependent protection against 2,2'-azo-bis (2-amidinopropane) dihydrochloride (AAPH)-induced erythrocyte hemolysis between concentrations of 2.5 and 40 microM. Dimer, trimer, and tetramer showed the strongest inhibitory effects at 10 microM, 59.4%, 66.2%, 70.9%; 20 microM, 84.1%, 87.6%, 81.0%; and 40 microM, 90.2%, 88.9%, 78.6%, respectively. In a subsequent experiment, male Sprague-Dawley rats (approximately 200 g; n = 5-6) were given a 100-mg intragastric dose of a cocoa extract. Blood was collected over a 4-hr time period. Epicatechin and catechin, and the dimers (-)-epicatechin-(4beta>8)-epicatechin (Dimer B2) and (-)-epicatechin-(4beta>6)-epicatechin (Dimer B5) were detected in the plasma with concentrations of 6.4 microM, and 217.6, 248.2, and 55.4 nM, respectively. Plasma antioxidant capacity (as measured by the total antioxidant potential [TRAP] assay) was elevated (P < 0.05) between 30 and 240 min following the cocoa extract feeding. Erythrocytes obtained from the cocoa extract-fed animals showed an enhanced resistance to hemolysis (P < 0.05). This enhanced resistance was also observed when erythrocytes from animals fed the cocoa extract were mixed with plasma obtained from animals given water only. Conversely, plasma obtained from rats given the cocoa extract improved the resistance of erythrocytes obtained from rats given water only. These results show cocoa flavanols and procyanidins can provide membrane protective effects.     

The amino acid sequence of glutamate dehydrogenase fromPyrococcus furiosus, a hyperthermophilic archaebacterium

The complete amino acid sequence of glutamate dehydrogenase from the archaebacteriumPyrococcus furiosus has been determined. The sequence was reconstructed by automated sequence analysis of peptides obtained after cleavage with cyanogen bromide, Asp-N endoproteinase, trypsin, or pepsin. The enzyme subunit is composed of 420 amino acid residues yielding a molecular mass of 47,122 D. In the recently determined primary structure of glutamate dehydrogenase from another thermophilic archaebacterium,Sulfolobus solfataricus, the presence of some methylated lysines was detected and the possible role of this posttranslational modification in enhancing the thermostability of the enzyme was discussed (Maras, B., Consalvi, V., Chiaraluce, R., Politi, L., De Rosa, M., Bossa, F., Scandurra, R., and Barra, D. (1992),Eur. J. Biochem. 203, 81–87). In the primary structure reported here, such posttranslational modification has not been found, indicating that the role of lysine methylation should be revisited. Comparison of the sequence of glutamate dehydrogenase fromPyrococcus furiosus with that ofS. solfataricus shows a 43.7% similarity, thus indicating a common evolutionary pathway.     

Tissue graft rejection in mice

A tissue slice-to-kidney bed grafting system is used to study the mechanism of specific tissue rejection (in this case, rejection of liver tissue) over a series of histocompatibility barriers other than the H-2 barrier. Using the method described, it is possible to obtain a pattern or time-course picture of the immunological process, rather than a mean survival time. It is clear from histological observations of these patterns that, although there are considerable differences in numbers of liver grafts which survive for long period's across the several histocompatibility barriers studied, some grafts in almost every case survive the immunological challenge elicited by the genetic barriers. Grafts of liver tissue are therefore similar, but not identical, in survival patterns to grafts of tumor, ovary, and skin. These studies also indicate that immunological mechanisms controlling rejection of tissue over H barriers other than H-2 differ from those controlling rejection over the major histocompatibility barrier in the mouse.     

Reproductive cycles in littoral populations of Choromytilus meridionalis (Kr.) and Aulacomya ater (Molina) with a quantitative assessment of gamete production in the former

Changes in ovary weight and ovary smears of Choromytilus meridionalis (Kr.) and Aulacomya ater (Molina) showed the breeding season to extend throughout the spring and summer months (Aug.-Feb.). Release of gametes was intermittent with regeneration of the gonad after peak spawning periods. Populations spawned synchronously or asynchronously with an average of 50% of individuals spawning at any one time. The end of the breeding season was marked by gonad depletion and resorption of gametes. Gametogenesis followed rapidly and large quantities of reserve material were not deposited in the mantle during the winter months as in Mytilus edulis.The False Bay population of Choromytilus meridionalis has predominantly synchronous spawning and gamete production for two breeding seasons was calculated. The quantity of gametes released varied annually and was not significantly different in males and females. Mean gamete production was calculated as 1.17 × standing crop expressed as dry flesh weight, or 1.33 × energy value of the standing crop per annum.