Chloroplast PNPase exists as a homo-multimer enzyme complex that is distinct from the Escherichia coli degradosome

In Escherichia coli, the exoribonuclease polynucleotide phosphorylase (PNPase), the endoribonuclease RNase E, a DEAD-RNA helicase and the glycolytic enzyme enolase are associated with a high molecular weight complex, the degradosome. This complex has an important role in processing and degradation of RNA. Chloroplasts contain an exoribonuclease homologous to E. coli PNPase. Size exclusion chromatography revealed that chloroplast PNPase elutes as a 580-600 kDa complex, suggesting that it can form an enzyme complex similar to the E. coli degradosome. Biochemical and mass-spectrometric analysis showed, however, that PNPase is the only protein associated with the 580-600 kDa complex. Similarly, a purified recombinant chloroplast PNPase also eluted as a 580-600 kDa complex after gel filtration chromatography. These results suggest that chloroplast PNPase exists as a homo-multimer complex. No other chloroplast proteins were found to associate with chloroplast PNPase during affinity chromatography. Database analysis of proteins homologous to E. coli RNase E revealed that chloroplast and cyanobacterial proteins lack the C-terminal domain of the E. coli protein that is involved in assembly of the degradosome. Together, our results suggest that PNPase does not form a degradosome-like complex in the chloroplast. Thus, RNA processing and degradation in this organelle differ in several respects from those in E. coli.

Polynucleotide phosphorylase functions as both an exonuclease and a poly(A) polymerase in spinach chloroplasts

The molecular mechanism of mRNA degradation in the chloroplast consists of sequential events including endonucleolytic cleavage, the addition of poly(A)-rich sequences to the endonucleolytic cleavage products, and exonucleolytic degradation by polynucleotide phosphorylase (PNPase). In Escherichia coli, polyadenylation is performed mainly by poly(A)-polymerase (PAP) I or by PNPase in its absence. While trying to purify the chloroplast PAP by following in vitro polyadenylation activity, it was found to copurify with PNPase and indeed could not be separated from it. Purified PNPase was able to polyadenylate RNA molecules with an activity similar to that of lysed chloroplasts. Both activities use ADP much more effectively than ATP and are inhibited by stem-loop structures. The activity of PNPase was directed to RNA degradation or polymerization by manipulating physiologically relevant concentrations of P(i) and ADP. As expected of a phosphorylase, P(i) enhanced degradation, whereas ADP inhibited degradation and enhanced polymerization. In addition, searching the complete Arabidopsis genome revealed several putative PAPs, none of which were preceded by a typical chloroplast transit peptide. These results suggest that there is no enzyme similar to E. coli PAP I in spinach chloroplasts and that polyadenylation and exonucleolytic degradation of RNA in spinach chloroplasts are performed by one enzyme, PNPase.

Retrospective clinical investigation of the impact of early treatment of children with Down's syndrome according to Castillo-Morales

BACKGROUND

Infants and toddlers with Down's syndrome are treated at the Department of Orthodontics, University of Frankfurt/Main only when the tongue protrudes over the lower lip, hindering mouth closure. No plate therapy is applied in patients with less tongue protrusion. This study aimed to assess objectively the treatment effects of stimulation plate therapy after Castillo-Morales at this early stage of development.

PATIENTS AND METHOD

The follow-up covered 33 children, 20 of whom showed no mouth closure with the tongue resting protrusively on the lower lip at first examination at the age of 8 months. These 20 children received orthodontic treatment based on a stimulation plate. The parents were advised to insert the plate four times a day for about half an hour respectively. The overall treatment time was ca. 2 years. The second group (13 children) received no early treatment, as the functional parameters were only slightly altered at the age of 7 months. At follow-up, the children of the treatment group were between 8.8 +/- 2.3, and those of the control group 8.9 +/- 3.0 years old. The children underwent clinical examination; the parents answered a questionnaire. Additionally, study casts and intraoral photographs were taken along with frontal and profile photographs. The factors assessed were various functions, dentition, facial development, and subjective rating of the parents.

RESULTS

In contrast to the initial findings, no difference between the two groups was found at follow-up.

CONCLUSION

Early treatment using a stimulation plate thus appears to mitigate or even normalize the initially more severe dysfunctions recorded in the study group as compared to the controls.

The complex case--unforeseeable findings and interdisciplinary treatment

Orthodontic treatment is described in a case requiring an early treatment start due to disturbed eruption in the upper front, with displacement of an upper central incisor, tongue dysfunction and Class III tendency. The further course revealed additional problems which had been unforeseeable at treatment onset: ankylosis of the lower left first molar and dehiscences in the lower front. Treatment duration was very long due to treatment measures overlapping. The interdisciplinary treatment measures are outlined and the difficulties posed by contractual guidelines are pointed out.

Insertion of polydeoxyadenosine-rich sequences into an intergenic region increases transcription in Chlamydomonas reinhardtii chloroplasts

In this study, chloroplast transformation in Chlamydomonas reinhardtii was used to insert a tract of polydeoxyadenosine, which is known to influence DNA structure and transcription in other systems, between the 3' end of the atpB gene, encoding the beta-subunit of the chloroplast ATP synthase, and a downstream chimeric gene, aadA, encoding antibiotic resistance. Run-on transcription and RNA analyses revealed that in cells containing (dA)40 and (dAAAGGG)8, aadA was transcribed at a higher rate, and its RNA accumulated to a relatively high level. It is concluded that poly(dA/dT) can function in the chloroplast as a transcription enhancer element. Therefore, the insertion of poly(dA/dT) sequence into the intergenic region of a multicistronic transcription unit may modulate gene expression at the transcriptional level.

Biomass steam gasification--an extensive parametric modeling study

A model for steam gasification of biomass was developed by applying thermodynamic equilibrium calculations. With this model, the simulation of a decentralized combined heat and power station based on a dual fluidized-bed steam gasifier was carried out. Fuel composition (ultimate analysis and moisture content) and the operating parameters, temperature and amount of gasification agent, were varied over a wide range. Their influences on amount, composition, and heating value of product gas and process efficiencies were evaluated. It was shown that the accuracy of an equilibrium model for the gas composition is sufficient for thermodynamic considerations. Net electric efficiency of about 20% can be expected with a rather simple process. Sensitivity analysis showed that gasification temperature and fuel oxygen content were the most significant parameters determining the chemical efficiency of the gasification.

Hepatic cholesterol metabolism and resistance to dietary cholesterol in LXRbeta-deficient mice

The nuclear oxysterol-receptor paralogues LXRalpha and LXRbeta share a high degree of amino acid identity and bind endogenous oxysterol ligands with similar affinities. While LXRalpha has been established as an important regulator of cholesterol catabolism in cholesterol-fed mice, little is known about the function of LXRbeta in vivo. We have generated mouse lines with targeted disruptions of each of these LXR receptors and have compared their responses to dietary cholesterol. Serum and hepatic cholesterol levels and lipoprotein profiles of cholesterol-fed animals revealed no significant differences between LXRbeta(-/-) and wild-type mice. Steady-state mRNA levels of 3-hydroxy-3-methylglutaryl coenzyme A reductase, farnesyl diphosphate synthase, and squalene synthase were increased in LXRbeta(-/-) mice compared with LXRbeta(+/+) mice, when fed standard chow. The mRNA levels for cholesterol 7alpha-hydroxylase, oxysterol 7alpha-hydroxylase, sterol 12alpha-hydroxylase, and sterol 27-hydroxylase, respectively, were comparable in these strains, both on standard and 2% cholesterol chow. Our results indicate that LXRbeta(-/-) mice - in contrast to LXRalpha(-/-) mice - maintain their resistance to dietary cholesterol, despite subtle effects on the expression of genes coding for enzymes involved in lipid metabolism. Thus, our data indicate that LXRbeta has no complete overlapping function compared with LXRalpha in the liver.

Adapting the waterproof BMS-96 diode array for isodose determination of dynamic beams

We report the application of the Schuster BMS-96 waterproof linear diode array for isodose determination of dynamic beams. The array recorded beam profiles correctly, while depth dose distributions of dynamic beams with large variations in dose rate were registered erroneously. The deviations could be eliminated by appropriate software modifications. Until the software is revised, true isodoses can be obtained by rescaling each individual profile to the depth dose curve as measured with a single ionization chamber. After the corrections presented in the paper, isodoses interpolated from these corrected data sets agreed with ionization chamber measurements within 1-2%.

[Mesial temporal sclerosis syndrome in adult patients]

Magnetic resonance imaging (MRI) has become an essential tool in the work-up of epilepsy. Since its appearance it has been possible to identify pathologies, such as hippocampal sclerosis (HS), that had previously only been detected by histopathological assays. The aim of this study was to analyze the clinical manifestations, EEG and the outcome of patients with HS as shown by MRI. We revised the clinical histories of 384 outpatients from the Epilepsy Center, Ramos Mejía Hospital, who had been studied by MRI. Thirty five of them (15.5%) had a diagnosis of HS, based on the structural changes observed on the images. Six patients were excluded because of incomplete clinical data. Therefore, we studied 29 patients including 15 men. The mean age was 32.7 +/- 10.2 years (range: 19-58). All of them had partial seizures. Ten subjects had had febrile convulsions (34.5%) in childhood. Neurological examination was normal in all subjects. Interictal EEG showed focal abnormalities that were coincident in their location with the MRI abnormalities in 16 patients (55.1%). Fourteen patients (48.3%) showed right side hippocampal lesions on MRI, thirteen on the left side (44.9%) and 2 bilateral HS (6.8%). Twenty-seven patients (93.1%) had intractable epilepsy. Anterior temporal lobectomy was performed in 3 subjects with good outcome. The identification of these patients who present certain clinical and MRI characteristics, provides an opportunity to define the mesial temporal sclerosis syndrome. This could benefit patients in their prognosis and for specific treatments.

RNA-binding characteristics of the chloroplast S1-like ribosomal protein CS1

The chloroplast ribosomal protein CS1, the homolog of the bacterial ribosomal protein S1, is believed to be involved in the process of ribosome binding to mRNA during translation. Since translation control is an important step in chloroplast gene expression, and in order to study initiation complex formation, we studied the RNA-binding properties of CS1 protein. We found that most of the CS1 protein in spinach chloroplast co-purified with the 30S ribosomal subunit. The relative binding affinity of RNA to CS1 was determined using the UV-crosslinking competition assay. CS1 protein binds the ribohomopolymer poly(U) with a relatively high binding affinity. Very low binding affinities were obtained for the other ribohomopolymers, poly(G), poly(A) and poly(C). In addition, no specific binding of CS1, either in the 30S complex or as a recombinant purified protein, was obtained to the 5'-untranslated region of the mRNA in comparison to the other parts. RNA-binding experiments, in which the N- and C-termini of the protein were analyzed, revealed that the RNA-binding site is located in the C-terminus half of the protein. These results suggest that CS1 does not direct the 30S complex to the initiation codon of the translation site by specific binding to the 5'-untranslated region. In bacteria, specific binding is derived by base pairing between 16S rRNA and the Shine-Dalagarno sequences. In the chloroplast, nuclear encoded and gene-specific translation factors may be involved in the determination of specific binding of the 30S subunit to the initiator codon.

Variability in Time and Space of Meloidogyne incognita Fall Population Density in Cotton Fields

Three cotton fields infested with Meloidogyne incognita were intensively sampled in the fall for 3 years (1996 to 1998) to determine if intensive sampling for M. incognita, for which spatial location is important, was necessary every year in a continuous cotton system. Two composite soil samples (20 cores each), taken over an area covering one-third of the field length and two rows wide, were averaged to represent that area (row-location combination). Each field (except one) had 24 areas assayed for changes in M. incognita population density (Pf) over a 3-year period. At all three sites, Pf was higher during fall 1998 than fall 1996. There were no differences in Pf between rows within a year or between years (no. row x year interaction) at any of the sites. At all three sites, there was a consistent difference each year in Pf among locations in a field (no. year x location interaction). At each area, M. incognital/500 cm(3) was labeled for one of four Pf classes: <250, 250 to 999, 1,000 to 2,499, and >/= 2,500. Management of root-knot nematode would likely be altered as classification changed. The areas that were reclassified by two classes or more after 1 and 2 years ranged from 0 to 29% and 25 to 54%, respectively. The risk of underestimating Pf of M. incognita was higher in one site 2 years after the initial intensive sampling procedure, whereas in another site there was little change in Pf 2 years after initial sampling. Sampling frequency will need to be decided on a field-by-field basis.

Organotypic cultures of gingival cells: an epithelial model to assess putative local effects of orthodontic plate and occlusal splint materials under more tissue-like conditions

This article explores whether organotypic cultures of immortalized gingival keratinocytes constitute a suitable model for assessing the epithelial cell compatibility of two groups of dental resins, each of them representing one group used in orthodontics and temporo-mandibular disorders (TMD) therapy under conditions more closely resembling the actual tissue situation. The resins were tested with the agar diffusion assay (ADA) in conventional monolayer and organotypic cultures. Compared to the control exhibiting a neutral red destaining index of 3, the index of 4 obtained after exposure of monolayers to one soft permanent resin (Durabase) indicated the presence of a non-lytic but physiologically active substance. In contrast, the adaptation of the ADA to organotypic cultures revealed no apparent lesions at the epithelial surface by performing scanning electron microscopy, while histoarchitecture indicated the development of stratified surface epithelia. This was substantiated by undamaged cells in the uppermost cell layers and by the preservation of cell-to-cell contacts. Furthermore, indirect immunofluorescence for Ki-67 and the cytokeratins ck 14 and ck4 revealed that cell proliferation and epithelial structure were maintained, while differentiation was enhanced, possibly increasing epithelial resistance. The results obtained from the organotypic cultures suggest that (i) cell-affecting effects of materials visible in monolayer cultures may not be seen in epithelia resembling that in vivo and that (ii) enhanced differentiation may be associated with increased stability of the epithelial cells. Thus, organotypic cultures of gingival cells constitute a tissue model allowing short-term tissue compatibility studies of dental materials and rendering a potential candidate also for long-term studies.

Processing and degradation of chloroplast mRNA

The conversion of genetic information stored in DNA into a protein product proceeds through the obligatory intermediate of messenger RNA. The steady-state level of an mRNA is determined by its relative synthesis and degradation rates, i.e., an interplay between transcriptional regulation and control of RNA stability. When the biological status of an organism requires that a gene product's abundance varies as a function of developmental stage, environmental factors or intracellular signals, increased or decreased RNA stability can be the determining factor. RNA stability and processing have long been known as important regulatory points in chloroplast gene expression. Here we summarize current knowledge and prospects relevant to these processes, emphasizing biochemical data. The extensive literature on nuclear mutations affecting chloroplast RNA metabolism is reviewed in another article in this volume (Barkan and Goldschmidt-Clermont, this issue).

Polyadenylation of three classes of chloroplast RNA in Chlamydomonas reinhadtii

Three classes of RNA, represented by atpB and petD mRNAs, Arg and Glu tRNAs, and 5S rRNA, were found to exist in polyadenylated form in Chlamydomonas reinhardtii chloroplasts. Sequence analysis of cDNA clones derived from reverse transcriptase-polymerase chain reaction protocols used to select polyadenylated RNAs revealed that, at least for the mRNAs and tRNAs, there are three apparent types of polyadenylation. In the first case, the poly(A) tail is added at or near the mature 3' end, even when this follows a strong secondary structure. In the second case, the tail is added to pre-mRNA or pre-tRNA, suggesting a possible competition between polyadenylation and RNA-processing pathways. Finally, in all cases, the poly(A) tail can be added internally, possibly as a part of an RNA-decay pathway. The tails found in Chlamydomonas chloroplasts differ from those of spinach chloroplasts in adenine content, being nearly homopolymeric (>98% adenine) versus 70% in spinach, and are similar in length to those of Escherichia coli, being mostly between 20 and 50 nt. In vitro assays using a Chlamydomonas chloroplast protein extract showed that a 3' end A25 tail was sufficient to stimulate rapid degradation of atpB RNA in vitro, with a lesser effect for petD, and only minor effects on trnE. We therefore propose that polyadenylation contributes to mRNA degradation in Chlamydomonas chloroplasts, but that its effect may vary.

Characterization of the E.coli poly(A) polymerase: nucleotide specificity, RNA-binding affinities and RNA structure dependence

Polyadenylation of RNA molecules in bacteria and chloroplasts has been implicated as part of the RNA degradation pathway. The polyadenylation reaction is performed in Escherichia coli mainly by the enzyme poly(A) polymerase I (PAP I). In order to understand the molecular mechanism of RNA poly-adenylation in bacteria, we characterized the biochemical properties of this reaction in vitro using the purified enzyme. Unlike the PAP from yeast nucleus, which is specific for ATP, E.coli PAP I can use all four nucleotide triphosphates as substrates for addition of long ribohomopolymers to RNA. PAP I displays a high binding activity to poly(U), poly(C) and poly(A) ribohomopolymers, but not to poly(G). The 3'-ends of most of the mRNA molecules in bacteria are characterized by a stem-loop structure. We show here that in vitro PAP I activity is inhibited by a stem-loop structure. A tail of two to six nucleo-tides located 3' to the stem-loop structure is sufficient to overcome this inhibition. These results suggest that the stem-loop structure located in most of the mRNA 3'-ends may function as an inhibitor of poly-adenylation and degradation of the corresponding RNA molecule. However, RNA 3'-ends produced by endonucleolytic cleavage by RNase E in single-strand regions of mRNA molecules may serve as efficient substrates for polyadenylation that direct these molecules for rapid exonucleolytic degradation.

Comparison of Variable and Single-Rate Applications of Aldicarb on Cotton Yield in Fields Infested with Meloidogyne incognita

Variable-rate applications of the nematicide aldicarb were compared to producer standard rates in eight field tests over 3 years. Test areas (308 to 1,015 m long) were divided into eight or five blocks. Each block contained two plots with a variable-rate treatment (VRT) of aldicarb and a producer standard treatment (PST) of aldicarb. Each VRT plot was divided into three subunits and intensively sampled for Meloidogyne incognita in either the fall or spring before planting. Rates of aldicarb were assigned to each subunit for VRT based on M. incognita population density. In three of the eight tests, VRT resulted in either higher yield or similar yields, but less nematicide applied. In two tests there were no differences between PST and VRT in yields or average rates of aldicarb applied. In three tests, VRT used more aldicarb (>0.17 kg a.i./ha difference) than PST and yields were not significantly different between treatments. In two of the cases where VRT was superior to PST, the producer's rate of aldicarb was judged to be either too low or too high for the average M. incognita density present in the field. In all three cases where PST was superior to VRT, perennial weeds were an important factor also limiting yield. Variable-rate application of aldicarb did not consistently provide for higher yields or lower nematicide usage than standard application rates.

Altering the 3 UTR endonucleolytic cleavage site of a Chlamydomonas chloroplast mRNA affects 3-end maturation in vitro but not in vivo

The 3' ends of chloroplast mRNAs are produced by the processing of longer precursors. The 3' ends of most plastid mRNAs are located at, or several nucleotides downstream of, stem-loop structures, which act as 3'-end-processing signals and RNA stability elements. In chloroplasts of the green alga Chlamydomonas reinhardtii, 3'-end maturation of atpB mRNA involves endonucleolytic cleavage of the pre-mRNA at an AU-rich site located about 10 nucleotides downstream of the stem-loop structure. This cleavage is followed by exonucleolytic resection to generate the mature 3' end. In order to define critical nucleotides of the endonucleolytic cleavage site, we mutated its sequence. Incubation of synthetic atpB pre-RNAs containing these mutations in a chloroplast protein extract resulted in the accumulation of 3'-end-processed products. However, in two cases where the AU-rich sequence of this site was replaced with a GC-rich one, the 3' end of the stable processing product differed from that of the wild-type product. To examine whether these mutations affected atpB mRNA processing or accumulation in vivo, the endogenous 3' UTR was replaced with mutated sequences by biolistic transformation of Chlamydomonas chloroplasts. Analysis of the resulting strains revealed that the accumulation of atpB mRNA was approximately equal to that of wild-type cells, and that a wild-type atpB 3' end was generated. These results imply that Chlamydomonas atpB 3' processing parallels the situation with other endonucleases such as Escherichia coli RNAse E, where specific sequences are required for correct in vitro processing, but in vivo these mutations can be overcome.