In vitro and in vivo detection of microbial gene expression in bioactivated scaffolds seeded with cyanobacteria.

Dermal replacement materials bioactivated with cyanobacteria have shown promising potential for wound regeneration. To date, extraction of cyanobacteria RNA from seeded scaffolds has not been described. The aim of this study was to develop a method to isolate total RNA from bioactivated scaffolds and to propose a new approach in determining living bacteria based on real-time PCR. Transgenic Synechococcus sp. PCC 7002 (tSyn7002) were seeded in liquid cultures or scaffolds for dermal regeneration in vitro and in vivo for 7 days. RNA was extracted with a 260/280 ratio of ≥2. The small subunit of the 30S ribosome in prokaryotes (16S) and RNAse P protein (rnpA) were validated as reference transcripts for PCR analysis. Gene expression patterns differed in vitro and in vivo. Expression of 16S was significantly upregulated in scaffolds in vitro, as compared to liquid cultures, whilst rnpA expression was comparable. In vivo, both 16S and rnpA showed reduced expression compared to in vitro (16S: in vivo Ct value 13.21 ± 0.32, in vitro 12.44 ± 0.42; rnpA in vivo Ct value 19.87 ± 0.41, in vitro 17.75 ± 1.41). Overall, the results demonstrate rnpA and 16S expression after 7 days of implantation in vitro and in vivo, proving the presence of living bacteria embedded in scaffolds using qPCR.

Roles of Tetratricopeptide Repeat Proteins in Biogenesis of the Photosynthetic Apparatus.

Biosynthesis of the photosynthetic apparatus is a complex operation, which includes the concerted synthesis and assembly of lipids, pigments and metal cofactors, and dozens of proteins. Research conducted in recent years has shown that these processes, as well as the stabilization and repair of this molecular machinery, are facilitated by transiently acting regulatory proteins, many of which belong to the superfamily of helical repeat proteins. Here, we focus on one of its families in photoautotrophic model organisms, the tetratricopeptide repeat (TPR) proteins, which participate in almost all of these steps and are crucial for biogenesis of the thylakoid membrane.

Characterization of the cyanobacterial ycf37: mutation decreases the photosystem I content.

We have constructed and analysed a cyanobacterial mutant that lacks the putative homologue of ycf37, the chloroplast open reading frame 37, which is conserved in different algae, but missing in the plastome of higher plants. In this report we show that Ycf37 of Synechocystis sp. PCC 6803 contains three tetratrico-peptide repeat (TPR) units resembling the structural organization of Ycf3, a protein that has been suggested to function as a chaperone during photosystem (PS) I complex formation. We demonstrate a light-activated transcript accumulation of this gene. Inactivation of ycf37 leads to a lower PSI/PSII ratio and a higher phycocyanin/chlorophyll ratio in Synechocystis cells. The observed alterations in the ycf37 mutants and the structural organization of the gene product suggest a functional role in PSI stability or assembly.

Intron-specific RNA binding proteins in the chloroplast of the green alga Chlamydomonas reinhardtii.

Mitochondria and chloroplasts both contain group II introns which are believed to be the ancestors of nuclear spliceosomal introns. We used the mitochondrial group II intron rI1 from the green alga Scenedesmus obliquus for biochemical characterization of intron-specific RNA binding proteins. rI1 is correctly spliced from a chloroplast precursor RNA when integrated into the chloroplast genome of Chlamydomonas reinhardtii. Glycerol gradients revealed the sedimentation profile of transcripts containing intron rI1 in native C. reinhardtii extracts and in deproteinized RNA preparations, thus indicating the association of rI1 containing transcripts with high molecular weight ribonucleoprotein complexes in vivo. Furthermore, the specific binding of a 61 kDa protein and a 31 kDa protein with the conserved domain IV was demonstrated using a set of intron derivatives for in vitro RNA binding experiments. We propose that we have biochemically characterized 'general splicing factors', which enable the successful splicing even of mitochondrial introns in chloroplasts.

cis- and trans-Acting determinants for translation of psbD mRNA in Chlamydomonas reinhardtii.

Chloroplast translation is mediated by nucleus-encoded factors that interact with distinct cis-acting RNA elements. A U-rich sequence within the 5' untranslated region of the psbD mRNA has previously been shown to be required for its translation in Chlamydomonas reinhardtii. By using UV cross-linking assays, we have identified a 40-kDa RNA binding protein, which binds to the wild-type psbD leader, but is unable to recognize a nonfunctional leader mutant lacking the U-rich motif. RNA binding is restored in a chloroplast cis-acting suppressor. The functions of several site-directed psbD leader mutants were analyzed with transgenic C. reinhardtii chloroplasts and the in vitro RNA binding assay. A clear correlation between photosynthetic activity and the capability to bind RNA by the 40-kDa protein was observed. Furthermore, the data obtained suggest that the poly(U) region serves as a molecular spacer between two previously characterized cis-acting elements, which are involved in RNA stabilization and translation. RNA-protein complex formation depends on the nuclear Nac2 gene product that is part of a protein complex required for the stabilization of the psbD mRNA. The sedimentation properties of the 40-kDa RNA binding protein suggest that it interacts directly with this Nac2 complex and, as a result, links processes of chloroplast RNA metabolism and translation.

The Nac2 gene of Chlamydomonas encodes a chloroplast TPR-like protein involved in psbD mRNA stability.

The psbD mRNA, which encodes the D2 reaction center polypeptide of photosystem II, is one of the most abundant chloroplast mRNAs. We have used genomic complementation to isolate the nuclear Nac2 gene, which is required for the stable accumulation of the psbD mRNA in Chlamydomonas reinhardtii. Nac2 encodes a hydrophilic polypeptide of 1385 amino acids with nine tetratricopeptide-like repeats (TPRs) in its C-terminal half. Cell fractionation studies indicate that the Nac2 protein is localized in the stromal compartment of the chloroplast. It is part of a high molecular weight complex that is associated with non-polysomal RNA. Change of a conserved alanine residue of the fourth TPR motif by site-directed mutagenesis leads to aggregation of Nac2 protein and completely abrogates its function, indicating that this TPR is important for proper folding of the protein and for psbD mRNA stability, processing and/or translation.

The unicellular green alga Chlamydomonas reinhardtii as an experimental system to study chloroplast RNA metabolism.

Chloroplasts are typical organelles of photoautotrophic eukaryotic cells which drive a variety of functions, including photosynthesis. For many years the unicellular green alga Chlamydomonas reinhardtii has served as an experimental organism for studying photosynthetic processes. The recent development of molecular tools for this organism together with efficient methods of genetic analysis and the availability of many photosynthesis mutants has now made this alga a powerful model system for the analysis of chloroplast biogenesis. For example, techniques have been developed to transfer recombinant DNA into both the nuclear and the chloroplast genome. This allows both complementation tests and analyses of gene functions in vivo. Moreover, site-specific DNA recombinations in the chloroplast allow targeted gene disruption experiments which enable a "reverse genetics" to be performed. The potential of the algal system for the study of chloroplast biogenesis is illustrated in this review by the description of regulatory systems of gene expression involved in organelle biogenesis. One example concerns the regulation of trans-splicing of chloroplast mRNAs, a process which is controlled by both multiple nuclear- and chloroplast-encoded factors. The second example involves the stabilization of chloroplast mRNAs. The available data lead us predict distinct RNA elements, which interact with trans-acting factors to protect the RNA against nucleolytic attacks.

Mutations at three different nuclear loci of Chlamydomonas suppress a defect in chloroplast psbD mRNA accumulation.

In the photosynthetic chloroplast mutant PRB2A of Chlamydomonas reinhardtii the psbD mRNA is unstable. Three strains were isolated, in which the underlying site-directed mutation within the psbD 5' UTR (untranslated region) is suppressed. In all three suppressors, psbD RNA levels and RNA 5' maturation are restored to a varying extent, suggesting a tight coupling of RNA stabilization and 5' processing. Expression of the psbA gene is not compromised in these strains. Genetic crosses revealed that the suppressor mutations affect three unlinked nuclear loci, which may encode new factors involved in psbD gene expression.

Identification of cis-acting RNA leader elements required for chloroplast psbD gene expression in Chlamydomonas.

The psbD mRNA of Chlamydomonas reinhardtii is one of the most abundant chloroplast transcripts and encodes the photosystem II reaction center polypeptide D2. This RNA exists in two forms with 5' untranslated regions of 74 and 47 nucleotides. The shorter form, which is associated with polysomes, is likely to result from processing of the larger RNA. Using site-directed mutagenesis and biolistic transformation, we have identified two major RNA stability determinants within the first 12 nucleotides at the 5' end and near position -30 relative to the AUG initiation codon of psbD. Insertion of a polyguanosine tract at position -60 did not appreciably interfere with translation of psbD mRNA. The same poly(G) insertion in the nac2-26 mutant, which is known to be deficient in psbD mRNA accumulation, stabilized the psbD RNA. However, the shorter psbD RNA did not accumulate, and the other psbD RNAs were not translated. Two other elements were found to affect translation but not RNA stability. The first comprises a highly U-rich sequence (positions -20 to -15), and the second, called PRB1 (positions -14 to -11), is complementary to the 3' end of the 16S rRNA. Changing the PRB1 sequence from GGAG to AAAG had no detectable effect on psbD mRNA translation. However, changing this sequence to CCUC led to a fourfold diminished rate of D2 synthesis and accumulation. When the psbD initiation codon was changed to AUA or AUU, D2 synthesis was no longer detected, and psbD RNA accumulated to wild-type levels. The singular organization of the psbD 5' untranslated region could play an important role in the control of initiation of psbD mRNA translation.

Transcripts containing the 5' untranslated regions of the plastid genes psbA and psbB from higher plants are unstable in Chlamydomonas reinhardtii chloroplasts.

The 5' regions of chloroplast genes contain cis-acting regulatory elements including promoters, and determinants of RNA stability and translation. In this work I examined whether the 5' regions of the spinach psbB and the wheat psbA genes can drive the expression of an aadA reporter gene in chloroplasts of the unicellar green alga Chlamydomonas reinhardtii. Both plant 5' sequences confer aadA-dependent, spectinomycin resistance on Escherichia coli, but not on the alga following integration into its chloroplast genome. Northern and run-on transcription analyses reveal that the plant promotors are active in C. reinhardtii but that the resulting chimeric transcripts are unstable. Therefore, the data suggest differences between higher plants and green algae with respect to the molecular mechanisms underlying plastid RNA metabolism.

Determinants for stability of the chloroplast psbD RNA are located within its short leader region in Chlamydomonas reinhardtii.

Stability of the chloroplast psbD mRNA encoding the D2 protein of the photosystem II reaction center is drastically decreased in the nuclear photosynthetic mutant nac2-26 of Chlamydomonas reinhardtii. Using biolistic transformation and genetic crosses we have introduced chimeric genes consisting of the psbD leader fused to a reporter gene into the chloroplast in both wild-type and mutant nuclear backgrounds. The chimeric message is destabilized in the latter, but not in the former case, indicating that the 74 nt psbD leader includes one of the target sites for psbD RNA degradation in the absence of wild-type NAC2 function. Increased instability of the psbD leader in mutant versus wild-type chloroplast lysates is also demonstrated in vitro and the primary cleavage sites have been mapped. The instability of the psbD RNA in the mutant correlates with the loss of binding of a 47 kDa protein to the psbD leader RNA, suggesting that this factor acts as message stabilizer in wild-type.

The 54 kDa RNA-binding protein from mustard chloroplasts mediates endonucleolytic transcript 3' end formation in vitro.

A 54 kDa protein from mustard chloroplasts was previously shown to interact specifically with a conserved U-rich sequence element in RNA derived from the 3' flanking regions of the plastid trnK and rps16 genes, which code for tRNA(Lys) and ribosomal protein CS19, respectively (Nickelsen and Link, 1991). This RNA-binding protein has now been purified by affinity chromatography on heparin Sepharose and poly(U) Sepharose. In vitro processing experiments and nuclease S1 analyses of the processing products revealed that the 54 kDa polypeptide is an endonuclease. The in vitro cleavage sites are consistent with the positions of corresponding transcript in vivo 3' ends downstream of trnK and rps16, suggesting that RNA 3' end formation takes place endonucleolytically also in vivo.

RNA-protein interactions at transcript 3' ends and evidence for trnK-psbA cotranscription in mustard chloroplasts.

In vitro transcripts from the 3' flanking regions of mustard chloroplast genes were tested for protein binding in a chloroplast extract. Efficient and sequence-specific RNA-protein interaction was detected with transcripts of the genes trnK, rps16 and trnH, but not with the 3' terminal region of trnQ RNA. The transacting component required for specific complex formation is probably a single 54 kDa polypeptide. The protein-binding region of the rps16 3' terminal region was mapped and compared with that of the trnK transcript determined previously. Both regions reveal a conserved 7-mer UUUAUCU followed by a stretch of U residues. Deletion of the trnK 3' U cluster resulted in more than 80% reduction in the binding activity, and after deletion of both the U stretch and the 7-mer motif no binding at all was detectable. RNase protection experiments indicate that the protein-binding regions of both the rps16 and trnK transcripts correlate with the positions of in vivo 3' ends, suggesting an essential role for the 54 kDa binding protein in RNA 3' end formation. In the case of the trnK gene, evidence was obtained for read-through transcripts that extend into the psbA coding region, thus pointing to the possibility of trnK-psbA cotranscription.

Interaction of a 3' RNA region of the mustard trnK gene with chloroplast proteins.

The 3' flanking region of the chloroplast trnK gene for tRNALys of mustard contains a palindromic sequence previously implicated with transcription termination and/or processing of the precursor RNA. Here we have investigated whether RNA sequences from the trnK 3' region are capable of interacting with chloroplast proteins in vitro. We find specific binding to an RNA region which is located further downstream from the palindromic sequence. The approximate length and position of this 3' binding region is reflected by a 41 nt spanning RNA segment which is protected against RNase T1 digestion by chloroplast protein(s). Competition experiments and sequence analyses suggest that U residues play an essential role in the RNA-protein interaction. Only a small number of proteins, possibly one single species, is in contact with the trnK 3' RNA.

Local intranasal immunotherapy with high-dose polymerized ragweed extract.

Thirty-one ragweed-allergic patients received preseasonal local intranasal immunotherapy (LNIT) with high doses of gluteraldehyde-polymerized ragweed extract (average total dose 544 micrograms antigen E). Minimal side effects were reported during treatment and did not interfere with the dosing schedule. During the ragweed pollen season, LNIT-treated patients had lower symptom scores for sneezing, rhinorrhea and nasal congestion than a comparable group of untreated ragweed-allergic patients. There was no difference in ragweed-induced eye symptoms between the two groups. Secretory ragweed-specific IgA and IgG rose following LNIT treatment. Absolute antibody titers and changes in titers did not correlate with clinical improvement. LNIT with the polymerized ragweed did not block the seasonal rise in serum ragweed-specific IgE. These results suggest that LNIT with high-dose polymerized ragweed extract is a safe, simple and effective form of immunotherapy.

Lack of correlation between titers of serum allergen-specific IgE and symptoms in untreated patients with seasonal allergic rhinitis.

In five ragweed seasons and three grass pollen seasons, preseason and postseason ragweed-specific serum IgE and nasal secretory-specific IgE and IgA have been measured in untreated patients with seasonal allergic rhinitis. There was no consistent correlation between severity of rhinitis, as measured by symptom/medication scores during the season, and either absolute or changes in antibody titers. These findings suggest that antibody levels are only one of the factors that determine symptom severity.

Local nasal immunotherapy: efficacy of low-dose aqueous ragweed extract.

In previous studies preseasonal local nasal immunotherapy (LNIT) with moderate doses of aqueous ragweed extract (mean total dose 59 micrograms of AgE and 139 micrograms of AgE) was an effective treatment for ragweed hay fever; however, local adverse reactions during therapy were common. This study evaluated the clinical and immunologic responses to LNIT by use of lower doses of aqueous ragweed extract in order to minimize these adverse reactions. Patients were administered preseasonal LNIT for 7 wk and received a mean total dose of 4.7 micrograms of AgE. During the ragweed season, symptom/medication scores (SMS) of the treated patients were equivalent to SMS of untreated patients. Serum ragweed-specific IgE and nasal secretory ragweed-specific IgA rose slightly in the treated patients but not to the extent observed in previous studies. After the ragweed season treated and untreated patients had a substantial increase in serum ragweed IgE antibody titers. No correlation could be found between antibody responses and SMS. This study indicates that LNIT with lower doses of aqueous ragweed extract is clinically ineffective.

Local nasal immunotherapy for ragweed-allergic rhinitis. III. A second year of treatment.

In 1979, pre-seasonal local nasal immunotherapy (LNIT) was found to be an effective treatment for ragweed hay fever. In 1980, this study was continued to evaluate the clinical and immunologic responses of a second year of LNIT. Patients received either pre-seasonal treatment with an unmodified ragweed extract (RW) or a polymerized ragweed extract (PRW), or no treatment. The results of the second year of treatment were the same as the first year. Adverse reactions were significantly higher in the RW-treated group than in the PRW-treated group (P less than 0.001). Symptom/medication scores (SMS) in the RW-treated group were significantly lower than in the control group (P less than 0.005). Although SMS in the PRW-treated group were lower than in the control group, this difference was not significant. The immunologic response was evaluated by measurements of serum (S) RW-specific IgE and IgG and nasal secretory (NS) RW-specific IgE, IgG, and IgA. After treatment, serum IgE titres and secretory IgA titres rose in the RW-treated patients. Nasal secretory-IgG and NS-IgA titres increased with PRW treatment. The only immunologic response observed in the control group was a rise in S-IgE titres after the ragweed season. There was no substantial difference in immunologic measurements observed in the 1979 and 1980 seasons, except that the pre-treatment NS-IgE level was higher in 1980 (P less than 0.02). No significant correlations were found between antibody response and SMS. This study supports the efficacy of LNIT but does not support the protective role for NS-ragweed-specific IgA or IgG.