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Nematocidal activity of natural polyphenols from bryophytes and their derivatives.

The nematocidal in vitro activity of three natural perotetins (phenolic bisbibenzyiethers) and eleven diphenyl ethers used as synthetic precursors has been assayed using two different experimental models, Caenorhabditis elegans and Nippostrongylus brasiliensis. Nine compounds showed some activity against C. elegans and nine against N. brasiliensis. For the former model, three compounds displayed an activity similar to that of the standards, whereas for N. brasiliensis none of the tested compounds was as active as the standards. From the in vitro results, five compounds (3, 4, 8, 9, 13) could be selected as lead compounds to continue the search for improved activity.

Animals↗

Positive and negative tropic curvature induced by microbeam irradiation of protonemal tip cells of the moss Ceratodon purpureus.

The photoreceptor phytochrome mediates tropic responses in protonemata of the moss Ceratodon purpureus. Under standard conditions the tip cells grow towards unilateral red light, or perpendicular to the electrical vector of polarized light. In this study the response of tip cells to partial irradiation of the apical region was analysed using a microbeam apparatus. The fluence response curve gave an unexpected pattern: whereas a 15-min microbeam with light intensities around 3 micro mol m (-2) s (-1) induced a growth curvature towards the irradiated side, higher light intensities around 100 micro mol m (-2) s (-1) caused a negative response, the cells grew away from the irradiated side. This avoidance response is explained by two effects: the light intensity is high enough to induce photoconversion into the active Pfr form of phytochrome, not only on the irradiated but also on the non-irradiated side by stray light. At the same time, the strong light on the irradiated side acts antagonistically to Pfr. As a result of this inhibition, the growth direction is moved to the light-avoiding side. Such a Pfr-independent mechanism might be important for the phototropic response to distinguish between the light-directed and light-avoiding side under unilateral light.

Bryopsida↗

High throughput cryopreservation of 140,000 Physcomitrella patens mutants.

A high throughput protocol was established to preserve 140,000 mutants of a moss, Physcomitrella patens, a model plant for functional genomics studies, over liquid nitrogen. Regarding the reliable long-term storage of diverse mutant phenotypes, as well as time and cost effectiveness, each working step was optimized: 1) plant preparation, 2) freezing regime, cryogenic conditions, 3) regrowth after thawing. A prerequisite for maximum regrowth was a 1-week preculture of chopped plant material on a supplemented medium prior to freezing. Cryo vials as preculture vessels resulted in identical regrowth rates, compared to petri dishes. The cryo vial type had a significant influence on regrowth rates. A cooling rate of - 1 degrees C/min down to - 35 degrees C with a 10 min holding time before transferring plants to - 152 degrees C was the most suitable freezing regime. This protocol allows a cryopreservation of 1100 plants during a 5-day working week, practicable by one person. For more than 650 cryopreserved mutants a maximum regrowth rate of 100 % was obtained, independently of mutant phenotypes.

Bryopsida↗

Molecular phylogeography of the moss Tortula muralis Hedw (Pottiaceae) based on chloroplast rps4 gene sequence data.

Tortula muralis is a moss species of cosmopolitan distribution, for which we present chloroplast rps4 sequence data. The sequences provided a sufficiently high degree of divergence ( h = 0.878, theta = 0.00989 +/- 0.0000106, a total of 18 haplotypes for 49 accessions) for the degree of differentiation between regions from different continents to be investigated. In fact, 18.53 % of the variation found corresponded to differences between these regions, while 81.43 % was attributed to intra-region differences. Only the Japanese area differed significantly from other regions. Some haplotypes are found on several continents, while others are restricted to certain areas. Six of the seven sequenced plants from Japan belong to a haplotype only found there. The phylogenetic analysis suggests that Tortula muralis might be paraphyletic, with Tortula vahliana nested within the Tortula muralis clade. At present, it is not clear whether gene flow between the different clades of Tortula muralis is a continuing process or whether Tortula muralis is an example of cryptic speciation.

Analysis of Variance↗

Representation and high-quality annotation of the Physcomitrella patens transcriptome demonstrates a high proportion of proteins involved in metabolism in mosses.

To gain insight into the transcriptome of the well-used plant model system Physcomitrella patens, several EST sequencing projects have been undertaken. We have clustered, assembled, and annotated all publicly available EST and CDS sequences in order to represent the transcriptome of this non-seed plant. Here, we present our fully annotated knowledge resource for the Physcomitrella patens transcriptome, integrating annotation from the production process of the clustered sequences and from a high-quality annotation pipeline developed during this study. Each transcript is represented as an entity containing full annotations and GO term associations. The whole production, filtering, clustering, and annotation process is being modelled and results in seven datasets, representing the annotated Physcomitrella transcriptome from different perspectives. We were able to annotate 63.4 % of the 26 123 virtual transcripts. The transcript archetype, as covered by our clustered data, is compared to a compilation based on all available Physcomitrella full length CDS. The distribution of the gene ontology annotations (GOA) for the virtual transcriptome of Physcomitrella patens demonstrates consistency in the ratios of the core molecular functions among the plant GOA. However, the metabolism subcategory is over-represented in bryophytes as compared to seed plants. This observation can be taken as an indicator for the wealth of alternative metabolic pathways in moss in comparison to spermatophytes. All resources presented in this study have been made available to the scientific community through a suite of user-friendly web interfaces via www.cosmoss.org and form the basis for assembly and annotation of the moss genome, which will be sequenced in 2005.

3' Untranslated Regions↗

An RNAi system in Physcomitrella patens with an internal marker for silencing allows for rapid identification of loss of function phenotypes.

RNAi is a powerful method for generating loss of function mutants, especially for targeting genes belonging to large gene families. We have recently shown that RNAi functions in the moss Physcomitrella patens. We obtained stable lines that show constitutive silencing of a nuclearly localized GFP:GUS fusion protein (NLS:GFP:GUS). However, lines that display silencing of the protein do not necessarily have reduced transcript levels. Therefore, a system has been developed that silences the NLS:GFP:GUS reporter construct at the same time as it silences a gene of interest. Gateway (Invitrogen) recombination cassettes were incorporated into these vectors to facilitate cloning of many different cDNA sequences. In addition, vectors were generated that contain genomic moss DNA sequence information to increase the production of stable moss lines. Transformation with these constructs results in strong silencing within 24 h and is stable for at least a month after transformation. FtsZ2-1, whose loss of function phenotype is known, was incorporated as a test case for analyzing phenotypes. One hundred per cent of regenerating colonies that have silenced GFP exhibit a loss of function FtsZ2-1 phenotype, validating the use of this system to assay phenotypes for plant genes of unknown function.

Blotting, Northern↗

Identification and characterisation of a bryophyte polyphenol oxidase encoding gene from Physcomitrella patens.

Polyphenol oxidases (PPO) are enzymes of secondary plant metabolism that catalyse the oxidation of polyphenols to quinones. Because of their ubiquitous appearance in the plant kingdom, an important role is assumed; however, the exact physiological function of PPOs remains unclear. In this work, the identification, cloning, and characterisation of a bryophyte PPO from the moss Physcomitrella patens is presented. PPO activity from protein extracts was determined polarographically after activation by SDS. Four Physcomitrella ESTs with homologies to known plant PPOs were selected from publicly accessible databases, and PCR experiments demonstrated that they belong to the same gene, named Pp_ppo1. The identified cDNA was found to be 2402 bp long, containing a single open reading frame of 1611 bp encoding for a 536 amino acid protein with a molecular mass of 60.1 kDa. Cloning and sequencing of a genomic part of Pp_ppo1 revealed the presence of a 94-bp intron. The time course of Pp_ppo1 gene expression in liquid culture was monitored by real time RT-PCR, revealing increasing transcription levels until the 4th day, a maximum between the 4th and the 8th day, and decreasing transcription until the 12th day. A comparison of the deduced amino acid sequence of Pp_ppo1 with seed plant PPOs revealed similarities such as the presence of two highly conserved copper-binding domains and a similar pattern of hydrophobic regions, but also differences such as a stronger membrane association and a shorter signal sequence, thus reflecting the phylogenetic distance of Physcomitrella from seed plants.

Amino Acid Sequence↗

Glyco-engineering of moss lacking plant-specific sugar residues.

The commercial production of complex pharmaceutical proteins from human origin in plants is currently limited through differences in protein N-glycosylation pattern between plants and humans. On the one hand, plant-specific alpha(1,3)-fucose and beta(1,2)-xylose residues were shown to bear strong immunogenic potential. On the other hand, terminal beta(1,4)-galactose, a sugar common on N-glycans of pharmaceutically relevant proteins, e.g., antibodies, is missing in plant N-glycan structures. For safe and flexible production of pharmaceutical proteins, the humanisation of plant protein N-glycosylation is essential. Here, we present an approach that combines avoidance of plant-specific and introduction of human glycan structures. Transgenic strains of the moss Physcomitrella patens were created in which the alpha(1,3)-fucosyltransferase and beta(1,2)-xylosyltransferase genes were knocked out by targeted insertion of the human beta(1,4)-galactosyltransferase coding sequence in both of the plant genes (knockin). The transgenics lacked alpha(1,3)-fucose and beta(1,2)-xylose residues, whereas beta(1,4)-galactose residues appeared on protein N-glycans. Despite these significant biochemical changes, the plants did not differ from wild type with regard to overall morphology under standard cultivation conditions. Furthermore, the glyco-engineered plants secreted a transiently expressed recombinant human protein, the vascular endothelial growth factor, in the same concentration as unmodified moss, indicating that the performed changes in glycosylation did not impair the secretory pathway of the moss. The combined knockout/knockin approach presented here, leads to a new generation of engineered moss and towards the safe and flexible production of correctly processed pharmaceutical proteins with humanised N-glycosylation profiles.

Base Sequence↗

Isolation of mutant lines with decreased numbers of chloroplasts per cell from a tagged mutant library of the moss Physcomitrella patens.

Eleven mutant lines exhibiting decreased numbers of chloroplasts per cell were isolated from 8 800 tagged mutant lines of Physcomitrella patens by microscopic observations. Chloronema subapical cells in wild-type plants had a mean of 48 chloroplasts, whereas chloroplast numbers in subapical cells in mutant lines 215 and 222 decreased to 75 % of that in the wild type. Seven mutant lines - 473, 122, 221, 129, 492, 207, and 138 - had about half as many chloroplasts as the wild type. Mutant line 11 had a few remarkably enlarged chloroplasts, and mutant line 347 had chloroplasts of various sizes. Whereas the cell volume was the same as in the wild type in mutant lines 222, 473, 221, 129, 492, and 207, the cell volume of the other mutants increased. The chloroplast number of leaf cells was the same as that of chloronema cells in each mutant line when gametophores could be formed. Treatment with ampicillin decreased the number of chloroplasts in all mutant lines. Southern hybridization using DNA in tags as probes showed that only one insertion occurred in mutant lines 473 and 221. To determine whether the tagged DNA inserted into the known genes for plastid division, we isolated the PpMinD1, PpMinD2, and PpMinE1 genes. Genomic polymerase chain reaction analysis showed that the PpFtsZ and PpMinD/E genes were not disrupted by the insertion of the tags in mutant lines 11 and 347, respectively.

Base Sequence↗

Large-scale analysis of 73 329 physcomitrella plants transformed with different gene disruption libraries: production parameters and mutant phenotypes.

Gene targeting in the moss Physcomitrella patens has created a new platform for plant functional genomics. We produced a mutant collection of 73 329 Physcomitrella plants and evaluated the phenotype of each transformant in comparison to wild type Physcomitrella. Production parameters and morphological changes in 16 categories, such as plant structure, colour, coverage with gametophores, cell shape, etc., were listed and all data were compiled in a database (mossDB). Our mutant collection consists of at least 1804 auxotrophic mutants which showed growth defects on minimal Knop medium but were rescued on supplemented medium. 8129 haploid and 11 068 polyploid transformants had morphological alterations. 9 % of the haploid transformants had deviations in the leaf shape, 7 % developed less gametophores or had a different leaf cell shape. Other morphological deviations in plant structure, colour, and uniformity of leaves on a moss colony were less frequently observed. Preculture conditions of the plant material and the cDNA library (representing genes from either protonema, gametophore or sporophyte tissue) used to transform Physcomitrella had an effect on the number of transformants per transformation. We found correlations between ploidy level and plant morphology and growth rate on Knop medium. In haploid transformants correlations between the percentage of plants with specific phenotypes and the cDNA library used for transformation were detected. The number of different cDNAs present during transformation had no effect on the number of transformants per transformation, but it had an effect on the overall percentage of plants with phenotypic deviations. We conclude that by linking incoming molecular, proteome, and metabolome data of the transformants in the future, the database mossDB will be a valuable biological resource for systems biology.

Bryopsida↗

Transcript profiling in plastid arginine tRNA-CCG gene knockout moss: construction of Physcomitrella patens plastid DNA microarray.

The moss Physcomitrella patens is a newly established model plant that is widely used for the characterization of gene function by targeted gene knockout or over-expression. The target gene disruption occurs in both the nuclear and chloroplast genomes. We applied DNA microarray technology to the P. patens plastid genome for large-scale analysis of transcripts. A microarray was constructed containing 108 DNA fragments to detect all annotated plastid genes. We analyzed the transcript profile in a knockout transformant for the arginine tRNA gene, trnR-CCG, and confirmed previous results that rbcL and psaI transcripts accumulate in similar levels to wild-type moss, and accD transcript level is higher than those of wild-type moss. Additionally, the plastid DNA microarray revealed that most plastid genes were expressed at similar levels in wild-type and transformant mosses. This indicates that trnR-CCG is not essential for the expression of plastid genes.

Base Sequence↗

The family of CONSTANS-like genes in Physcomitrella patens.

The CONSTANS (CO) gene plays a central role in the regulation of flowering time in Arabidopsis, and is a member of a family of 17 CO-like genes. CO and CO-like genes have been found in all flowering plants, but not in yeast and animals. To address the question of the origin of CO, we analysed this gene family in the moss Physcomitrella patens, a phylogenetically distant organism. Database searches in EST libraries that almost completely covered the Physcomitrella transcriptome, and Southern blotting, identified only three genes that had all of the hallmarks of CO. Further analysis demonstrated that these are most similar to CO-like genes AtCOL3/AtCOL4/AtCOL5, a group of Arabidopsis genes closely related to, but distinct from CO, suggesting that the CO branch of the AtCOL phylogeny does not exist in the Physcomitrella genome. Since 17 COL genes occur in Arabidopsis and only three closely related and two distantly related genes were found in Physcomitrella, the family of CO-like proteins appears to be smaller in Physcomitrella than in Arabidopsis, in agreement with observations made with other gene families. The data also indicate that CO-like genes must have existed in the common ancestor of bryophytes and flowering plants, and that CO originated in the group of CO-like genes represented by AtCOL3/AtCOL4/AtCOL5. Furthermore, expression of the three closely related Physcomitrella homologues is regulated by light, suggesting that the role of CO in flowering time control was probably derived from an ancestral function in light signal transduction.

Amino Acid Sequence↗

Image analysis supported moss cell disruption in photo-bioreactors.

Diverse methods for the disruption of cell entanglements and pellets of the moss Physcomitrella patens were tested in order to improve the homogeneity of suspension cultures. The morphological characterization of the moss was carried out by means of image analysis. Selected morphological parameters were defined and compared to the reduction of the carbon dioxide fixation, and the released pigments after cell disruption. The size control of the moss entanglements based on the rotor stator principle allowed a focused shear stress, avoiding a severe reduction in the photosynthesis. Batch cultures of P. patens in a 30.0-l pilot tubular photo-bioreactor with cell disruption showed no significant variation in growth rate and a delayed cell differentiation, when compared to undisrupted cultures. A highly controlled photoautotrophic culture of P. patens in a scalable photo-bioreactor was established, contributing to the development required for the future use of mosses as producers of relevant heterologous proteins.

Algorithms↗

Isolation and characterization of new MIKC*-Type MADS-box genes from the moss Physcomitrella patens.

MADS-box genes encode for a large family of transcription-regulating proteins, which were isolated from all groups of eukaryotic organisms. The plant-specific MIKC-type MADS-box genes have been intensively analyzed for their roles in controlling developmental processes. Well-known are the MADS-box genes acting as homeotic selector genes in the differentiation of whorls of floral organs in seed plants. The MADS-box gene family has also been studied in non-flowering plants, such as lycophytes, pteridophytes, and bryophytes. The analysis of MADS-box genes in the moss Physcomitrella patens led to the identification of a new class of MIKC-type genes, designated as MIKC*-type genes. The MIKC*-type genes possess a number of structural features which clearly distinguish them from the already known MIKC-type genes. Recently, orthologues of the Physcomitrella MIKC*-type genes were found in Arabidopsis thaliana, demonstrating the conservation of these genes in tracheophytes. Here, we report the isolation of two new MIKC*-type MADS-box genes from Physcomitrella. Structural features and expression patterns of these genes were analyzed. The contribution of our findings to a better understanding of the evolution of MIKC*-type genes in land plants is discussed.

Amino Acid Sequence↗

Molecular tools to study Physcomitrella patens.

The moss Physcomitrella patens has become a suitable model plant system for the analysis of diverse aspects of modern plant biology. The research strategies have been influenced by the implementation of state-of-the-art cell culture and molecular biology techniques. The forthcoming completion of the Physcomitrella genome sequencing project will generate many open questions, the examination of which will rely on a diverse set of molecular tools. Within this article, we intend to introduce the essential cell culture and molecular biology techniques which have been adopted in recent years to make Physcomitrella amenable to a wide range of genetic analyses. Many research groups have made valuable contributions to improve the methodology for the study of Physcomitrella. We would like to apologise to all colleagues whose important contributions could not be cited within this manuscript.

Bioreactors↗

Is the Rehydrin TrDr3 from Tortula ruralis associated with tolerance to cold, salinity, and reduced pH? Physiological evaluation of the TrDr3-orthologue, HdeD from Escherichia coli in response to abiotic stress.

We have employed EST analysis in the resurrection moss Tortula ruralis to discover genes that control vegetative desiccation tolerance and describe the characterization of the EST-derived cDNA TrDr3 ( Tortula ruralis desiccation-stress related). The deduced polypeptide TRDR3 has a predicted molecular mass of 25.5 kDa, predicted pI of 6.7, and six transmembrane helical domains. Preliminary expression analyses demonstrate that the TrDr3 transcript ratio increases in response to slow desiccation relative to the hydrated control in both total and polysomal mRNA (mRNP fraction), which classifies TrDr3 as a rehydrin. Bioinformatic searches of the electronic databases reveal that Tortula TRDR3 shares significant similarities to the hdeD gene product ( HNS- dependent expression) from Escherichia coli. The function of the HdeD protein in E. coli is unknown, but it is postulated to be involved in a mechanism of acid stress defence. To establish the role of E. coli HdeD in abiotic stress tolerance, we determined the log survival percentage from shaking cultures of wild-type bacteria and the isogenic hdeD deletion strain (Delta hdeD) in the presence of low temperature (28 degrees C), elevated NaCl (5 % (w/v)), or decreased pH (4.5), or all treatments simultaneously. The Delta hdeD deletion strain was less sensitive, as compared to wild-type E. coli, in response to decreased pH ( p > 0.009), and the combination of all three stresses ( p > 0.0001).

Acclimatization↗

Moss systems biology en route: phytohormones in Physcomitrella development.

The moss Physcomitrella patens has become a powerful model system in modern plant biology. Highly standardized cell culture techniques, as well as the necessary tools for computational biology, functional genomics and proteomics have been established. Large EST collections are available and the complete moss genome will be released soon. A simple body plan and the small number of different cell types in Physcomitrella facilitate the study of developmental processes. In the filamentous juvenile moss tissue, developmental decisions rely on the differentiation of single cells. Developmental steps are controlled by distinct phytohormones and integration of environmental signals. Especially the phytohormones auxin, cytokinin, and abscisic acid have distinct effects on early moss development. In this article, we review current knowledge about phytohormone influences on early moss development in an attempt to fully unravel the complex regulatory signal transduction networks underlying the developmental decisions of single plant cells in a holistic systems biology approach.

Abscisic Acid↗

Moss biology and phytohormones--cytokinins in Physcomitrella.

Mosses present several advantages for the analysis of phytohormone physiology. Their enormous regeneration capacity, the possibility of controlling their whole life cycle under in vitro culture conditions, as well as the small number of cell types facilitate studies of hormone homeostasis. This review focuses on the metabolism and biosynthesis of cytokinins, mostly summarising data obtained using the moss Physcomitrella patens (Hedw.) B.S.G. which has served as a model system for cytokinin research for many years. A comparison of metabolic differences with respect to seed plants is presented, pointing out an important role of adenosine kinase for the formation of nucleotides during cytokinin interconversion in Physcomitrella. Results on cytokinin biosynthesis in Physcomitrella are summarised with respect to the OVE mutants, which can be considered unique in the plant kingdom due to their strong overproduction of cytokinins. The OVE phenotype is correlated with both increased activity in early stages of cytokinin biosynthesis as well as increased conversion of cytokinin riboside to the base. Cytokinin interconverting reactions can contribute to the increased levels of cytokinins in OVE mutants. Further studies on hormone physiology in moss will help to complete our understanding of hormonal homeostasis by elucidating the situation in an evolutionary early embryophyte.

Adenosine Kinase↗