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SOG1 is a crucial plant-specific NAC domain family transcription factor and functions as the central regulator of DNA damage response, acting downstream of ATM and ATR kinases. In this study, various in-silico approaches have been employed for the characterization of SOG1 transcription factor in a comparative manner with its orthologues from various plant species. Amino acid sequences of more than a hundred SOG1 or SOG1-like proteins were retrieved and their relationship was determined through phylogenetic and motif analyses. Various physiochemical properties and secondary structural components of SOG1 orthologues were determined in selective plant species including Arabidopsis thaliana , Oryza sativa , Amborella trichopoda , and Physcomitrella patens. Furthermore, fold recognition or threading and homology-based three-dimensional models of SOG1 were constructed followed by subsequent evaluation of quality and accuracy of the generated protein models. Finally, extensive DNA-Protein and Protein-Protein interaction studies were performed using the HADDOCK server to give an insight into the mechanism of how SOG1 binds with the promoter region of its target genes or interacts with other proteins to regulate the DNA damage responses in plants. Our docking analysis data have shown the molecular mechanism of SOG1′s binding with 5′-CTT(N) 7 AAG-3′ and 5′-(N) 4 GTCAA(N) 4 -3′ consensus sequences present in the promoter region of its target genes. Moreover, SOG1 physically interacts and forms a thermodynamically stable complex with NAC103 and BRCA1 proteins, which possibly serve as coactivators or mediators in the transcription regulatory network of SOG1. Overall, our in-silico study will provide meaningful information regarding the structural and functional characterization of the SOG1 transcription factor. [ABSTRACT FROM AUTHOR]

The strategies and experimental approaches that led the author to demonstrate the role of auxin in caulonema differentiation in the protonema of the moss Funaria hygrometrica are discussed. In stationary suspension cultures, the status of cell differentiation is regulated by inoculum cell density and auxin level. At low inoculum cell densities, 2-5 mM indole acetic acid (IAA) led to the differentiation of 65-70% caulonema filaments in 5-6 days. Caulonema can also differentiate in auxin-free medium if buffered at pH 5.0 after a lag of 6±1 days. The duration of lag can be manipulated and the cells are capable of responding to auxin at a higher level (3-10 mM) and produce about 20% caulonema after 3 days. This responsiveness or sensitivity to auxin can be enhanced further by growing cells in a nutrient-limited medium buffered at pH 5.0. In this medium, addition of 3 mM IAA led to the differentiation of 75-80% caulonema and rhizoids within 3 to 4 days. Work done in other laboratories has shown that auxin promotes caulonema differentiation in the moss Physcomitrella patens by positively regulating two basic helix-loop-helix type of transcription factor genes namely root hair defective six-like1 (PpRSL1) and PpRSL2 (Jang and Dolan 2011, New Phytologist 192: 319-327). [ABSTRACT FROM AUTHOR]

Abstract The wide use of Ag nanoparticles (Ag NPs) as antimicrobial agents has resulted in a massive release of Ag NPs into environment, such as water and soil. As bryophytes live ubiquitously in water and soil, their tolerance and response to Ag NPs could be employed as an indicator for the harm of Ag NPs to the environment. Herein, we report the study on the physiological and biochemical responses of bryophytes to Ag NPs with different surface coatings at the gametophyte stages: protonema and leafy gametophyte, by using Physcomitrella patens as a model system. We found that Ag NPs, including AgNPs-B (Ag NPs without surface coating), AgNPs-PVP (Ag NPs coated with poly (N -vinyl-2-pyrrolidone)) and AgNPs-Cit (Ag NPs coated with citrate), were toxic to P. patens in terms of growth and development of the gametophyte. The toxicity was closely related to the concentration and surface coating of Ag NPs, and the growth stage of P. patens. The protonema was more sensitive to Ag NPs than the leafy gametophyte. Ag NPs inhibited the growth of the protonema following the trend of AgNPs-B > AgNPs-Cit > AgNPs-PVP. Ag NPs changed the thylakoid and chlorophyll contents, but did not affect the contents of essential elements in the protonema. At the leafy gametophyte stage, Ag NPs inhibited the growth of P. patens following a different order: AgNPs-Cit > AgNPs-B ≈ AgNPs-PVP. Ag NPs decreased the chlorophyll b content and disturbed the balance of some important essential elements in the leafy gametophytes. Both the dissolved fraction of Ag NPs and Ag NPs per se contributed to the toxicity. This study for the first time reveals the effects of Ag NPs on bryophytes at different growth stages, which calls for more attention to the nanoecotoxicology of Ag NPs. Highlights • Ag NPs inhibited the growth of P. patens. • The protonema was more sensitive to Ag NPs than the leafy germetophyte. • Ag NPs inhibited the growth of the protonema: AgNPs-B > AgNPs-Cit > AgNPs-PVP. • Ag NPs inhibited the growth of the leafy germetophyte: AgNPs-Cit > AgNPs-B≈AgNPs-PVP. • Both dissolution and particulate of Ag NPs contributed to the toxicity. [ABSTRACT FROM AUTHOR]

Traditionally, protein structures have been described by the secondary structure architecture and fold arrangement. However, the relatively novel method of 3D confocal microscopy of fluorescent-protein-tagged networks in living cells allows resolving the detailed spatial organization of these networks. This provides new possibilities to predict network functionality, as structure and function seem to be linked at various scales. Here, we propose a quantitative approach using 3D confocal microscopy image data to describe protein networks based on their nano-structural characteristics. This analysis is constructed in four steps: (i) Segmentation of the microscopic raw data into a volume model and extraction of a spatial graph representing the protein network. (ii) Quantifying protein network gross morphology using the volume model. (iii) Quantifying protein network components using the spatial graph. (iv) Linking these two scales to obtain insights into network assembly. Here, we quantitatively describe the filamentous temperature sensitive Z protein network of the moss Physcomitrella patens and elucidate relations between network size and assembly details. Future applications will link network structure and functionality by tracking dynamic structural changes over time and comparing different states or types of networks, possibly allowing more precise identification of (mal) functions or the design of protein-engineered biomaterials for applications in regenerative medicine. Statement of Significance Protein networks are highly complex and dynamic structures that play various roles in biological environments. Analyzing the detailed spatial structure of these networks may lead to new insight into biological functions and malfunctions. Here, we propose a tool set that extracts structural information at two scales of the protein network and allows therefore to address questions such as “how is the network built?” or “how networks grow?”. [ABSTRACT FROM AUTHOR]

Plant chitinases play diverse roles including defense against pathogenic fungi. Using reverse-transcription quantitative PCR analysis, we found that six chitinase (PpChi) genes and two genes for chitin elicitor receptor kinases (PpCERKs) are expressed at considerable levels in the mossPhyscomitrella patenssubsp.patens. The expressed PpChis belonged to glycoside hydrolase family 19 (class I: PpChi-Ia and -Ib; class II: PpChi-IIa and -IIc; and class IV: PpChi-IV) and to glycoside hydrolase family 18 (class V: PpChi-Vb). Treatment with chitin tetramer or hexamer increased the expression of class I and IV PpChi genes and decreased that of class II PpChi genes. Recombinant PpChi-Ia, PpChi-IV, and PpChi-Vb were characterized. PpChi-IV exhibited higher activity against chitin tetramer and pentamer than PpChi-Ia did. PpChi-Vb showed transglycosylation activity and PpChi-Ia inhibited fungal growth. These results suggest that chitinases of different classes play different roles in defense mechanism of moss plant against fungal pathogens. Possible roles of each class of chitinase and chitin elicitor receptor kinase (CERK) for self-defense against pathogenic fungi in moss plant. [ABSTRACT FROM AUTHOR]

12-Oxo-phytodienoic acid (OPDA) is induced by mechanical wounding and suppresses the growth ofPhyscomitrella patens; OPDA is considered as a signal compound in this moss species. In this study, a proteomic analysis ofP. patensprotonemata treated with OPDA was performed. The abundance levels of 41 proteins were significantly altered by OPDA, with decreased levels for 40 proteins. The proteins for which abundance decreased in response to OPDA at the protonema developmental stage were mainly involved in the metabolism of proteins and carbohydrates. The effects of inhibition on protein abundance are likely a major physiological function of OPDA inP. patens. OPDA also suppressed the expression of histones at the protein level and gene transcription level. Suppression of histone expression might be an OPDA-specific function inP. patensprotonemata. InP. patens,a subset of the physiological responses caused by OPDA is shown to differ between protonema and gametophore developmental stages. Classification of OPDA-regulated proteins inPhyscomitrella patensprotonema according to their functions. [ABSTRACT FROM AUTHOR]

Packaging of eukaryotic DNA largely depends on histone modifications that affect the accessibility of DNA to transcriptional regulators, thus controlling gene expression. The Polycomb group (PcG) chromatin remodeling complex deposits a methyl group on lysine 27 of histone 3 leading to repressed gene expression. Plants encode homologs of the Enhancer of zeste (E(z)), a component of the PcG complex from Drosophila , one of which is a SET domain protein designated CURLY LEAF (CLF). Although this SET domain protein exhibits a strong correlation with the presence of the H3K27me3 mark in plants, the methyl-transferase activity and specificity of its SET domain have not been directly tested in-vivo . Using the evolutionary early-diverged land plant model species Physcomitrella patens we show that abolishment of a single copy gene PpCLF , as well as an additional member of the PcG complex, FERTILIZATION-INDEPENDENT ENDOSPERM ( PpFIE ), results in a specific loss of tri-methylation of H3K27. Using site-directed mutagenesis of key residues, we revealed that H3K27 tri-methylation is mediated by the SET domain of the CLF protein. Moreover, the abolishment of H3K27me3 led to enhanced expression of transcription factor genes. This in turn led to the development of fertilization-independent sporophyte-like structures, as observed in PpCLF and PpFIE null mutants. Overall, our results demonstrate the role of PpCLF as a SET protein in tri-methylation of H3K27 in-vivo and the importance of this modification in regulating the expression of transcription factor genes involved in developmental programs of P. patens . [ABSTRACT FROM AUTHOR]

The effects of iron nanoparticles on bryophytes ( Physcomitrella patens ) were studied following foliar exposure. We used iron nanoparticles (Fe–NP) representative of industrial emissions from the metallurgical industries. After a characterization of iron nanoparticles and the validation of nanoparticle internalization in cells, the effects (cytotoxicity, oxidative stress, lipid peroxidation of membrane) of iron nanoparticles were determined through the axenic culturing of Physcomitrella patens exposed at five different concentrations (5 ng, 50 ng, 500 ng, 5 µg and 50 µg per plant). Following exposure, the plant health, measured as ATP concentrations, was not impacted. Moreover, we studied oxidative stress in three ways: through the measure of reactive oxygen species (ROS) production, through malondialdehyde (MDA) production and also through glutathione regulation. At concentrations tested over a short period, the level of ROS, MDA and glutathione were not significantly disturbed. [ABSTRACT FROM AUTHOR]

The article discusses research which investigates growth suppression of the moss Physcomitrella patens induced from overexpression of protein coding genes RelA/SpoT homologs PpRSH2a and PpRSH2b. Topics discussed include isolation of RelA/SpoT homologs from Physcomitrella patens, analysis of PpRSH2a and PpRSH2b in bacteria Escherichia coli, and impact on expression of the PpRSH genes from treatment with abscisic acid or abiotic stresses like dehydration and UV (ultra violet) irradiation.

The article presents a study focusing on proteomic analysis of Physcomitrella patens moss treated with 12-oxo-phytodienoic acid which is a vital oxylipin molecule in plants. The findings of the study include the inducement of 12-Oxo-phytodienoic acid (OPDA) by bacterial infection and mechanical stress, the change in expression of 82 proteins, and the involvement of proteins in photosynthesis, metabolism, and protein synthesis.

To comprehensively understand the major processes in plant biology, it is necessary to study a diverse set of species that represent the complexity of plants. This research will help to comprehend common conserved mechanisms and principles, as well as to elucidate those mechanisms that are specific to a particular plant clade. Thereby, we will gain knowledge about the invention and loss of mechanisms and their biological impact causing the distinct specifications throughout the plant kingdom. Since the establishment of transgenic plants, these studies concentrate on the elucidation of gene functions applying an increasing repertoire of molecular techniques. In the last two decades, the moss Physcomitrella patens joined the established set of plant models based on its evolutionary position bridging unicellular algae and vascular plants and a number of specific features alleviating gene function analysis. Here, we want to provide an overview of the specific features of P. patens making it an interesting model for many research fields in plant biology, to present the major achievements in P. patens genetic engineering, and to introduce common techniques to scientists who intend to use P. patens as a model in their research activities. [ABSTRACT FROM AUTHOR]

The article focuses on a study that focuses on the putative COP1-target, B-box-containing transcriptional factor (BBX) in Physcomitrella patens. It notes that an Arabidopsis thaliana, a sub-family of B-box, has been used as model seed plant that has demonstrated the mediation of light sensors to numerous adaptive responses. Furthermore, results confirmed the difference of P. patens and A. thaliana, including the period of haploid generation.

The article presents a study regarding the functional characterization of HY5-family of transcription factors associated in early light-signaling in Physcomitrella patens. The study retrieved two HY5-homologs named PpHY5b and PpHY5a from the whole genome database of P. patens. The study has found that the function of HY5-homologs in P. patens is implicated in a process of caulonema development and evolutionarily conserved.

The article presents a study on the heterologous expression and functional characterization of the moss PpPRR2 gene, a pseudo-response regulator homolog of Physcomitrella patens, in Arabidopsis. The phenotype of the transformants with reference to the clock-related gene expression and photoperiodic responses was analyzed. It notes that the heterologous expression alters the intrinsic mechanism in the circadian clock which indicates that PpPRR2 is a clock component in Physcomitrella patens.

The article discusses a study which examines the function of CYP78, a subfamily of cytochrome P450 monooxygenases, in the moss Physcomitrella patens. It states that single and double mutants were produced, along with the overexpression lines for CYP78A27 and CYP78A28, to investigate CYP78's involvement in the moss. Findings reveal that CYP78As engage in the synthesis of Physcomitrella patens' critical development.

The article presents a study which classifies the genes linked in the moss Physcomitrella patens' (P. patens) two-component system (TCS), a signal transduction mechanism. The study explored a P. patens genome database to identify coding-sequences that are associated with cyotikinin signal transduction in comparison to that of Arabidopsis thaliana including hiskinases (HKs) genes and type-A and B RR genes. Result show that ethylene regulates the HK mechanism of an ethylene-receptor homolog.

The PpCCA1a and PpCCA1b genes of the moss Physcomitrella patens are functional homologs of the Arabidopsis thaliana circadian clock genes CCA1/ LHY. We made use of disruptant lines for PpCCA1a and/or PpCCA1b to elucidate the physiological significance of these genes in the growth of moss protonemal tissue under alternating day/night cycles. Protonemal cells of the double disruptant line, carrying neither of the two genes, grew faster than those of the wild-type plant (WT) in long days (LD), whereas no difference in the growth rate was detected between them in short days (SD). The double disruptant line also showed day length-dependent phenotypic changes in the PpCCA1b promoter activity: the diurnal profile of bioluminescence from the PCCA1b::LUC+ reporter strain was more significantly affected in LD than in SD. These observations are the first demonstration of a physiological function of the circadian clock in non-angiosperm land plants, and are consistent with recent findings that the clock controls hypocotyl elongation of A. thaliana in a photoperiod-dependent manner. [ABSTRACT FROM AUTHOR]

The article presents the study that examines allene oxide synthase (AOS), an enzyme of jasmonic acid (JA) biosynthesis, found in Physcomitrella patens. Presence of Jasmonic acid (JA) was observed in P. patens which are much higher than in flowering plants. The lipoxygenase activity and AOS activity indicates presence of octadecanoid pathway in P. patens. Moreover, it states that JA can act a signal molecule in bryophytes.

The article presents a study on expression and complementation analyses of chloroplast-localized homolog of bacterial RecA protein in the moss Physcomitrella patens. The researchers have identified two bacterial-types in moss wherein the mutational analysis results showed that first codon acts as initiation codon. Moreover, the researchers determined the genomic deoxyribonucleic acid (DNA) encompassing and compared it with the complementary DNA (cDNA).

Green roofs play an important role for cities in mediating some problems caused by urbanization. Mosses are ecologically important plants and capable of tolerating harsh conditions, and thus their use for greening building surfaces has become more common. There is only a little information concerning moss-associated microbes, especially those found in green roof environments. Moss-associated microbes might have significant role on the welfare of green roofs as they might induce both beneficial as well as adverse effects on mosses. In this study, the occurrence of fungal populations was studied on green roofs in Finland. A total of 94 samples were collected from nine different green roofs, and 64 fungal isolates and one oomycete were obtained from the brown, necrotic parts of the collected green roof mosses. The most general isolated fungal genus was Trichoderma , comprising 25 different fungal isolates. The second most common genus was Fusarium , with 15 fungal isolates. The third most common genus was Mucor , with nine fungal isolates. Most of the Trichoderma isolates were described as T. harzianum , whereas most of the Fusarium isolates were described as F. acuminatium. In addition, the genera Phoma and Mortierella were frequently present. Fifty-two of 65 isolates caused symptoms in the model plant Physcomitrella patens. The most harmful Trichoderma isolates were described as T. atroviride , T. viride , T. koningiopsis and T. hamatum , all of which caused severe damage to the protonema, stem and leaves. The most harmful Fusarium isolates were F. acuminatium , F. avenaceum and F. tricinctum. The genera Mucor and Mortierella were isolated but they did not cause detectable symptoms in P. patens. These results indicate that many fungal isolates belonging to different genera are able to colonize mosses on green roofs and some of them cause severe damage to the mosses. [ABSTRACT FROM AUTHOR]

Antioxidative responses of axenic protonema cultures of the moss Physcomitrella patens exposed to 10 μM Cd over 40 d were studied. Cd treatment suppressed growth by ca. 75% with concomitant browning of some filaments and suppression of chlorophyll autofluorescence but had no impact on tissue water content. Despite this negative growth responses which could be related to enhanced ROS formation (as detected using fluorescence staining reagents for total ROS, hydroperoxides and lipid peroxidation), some metabolites revealed strong elevation by Cd which could contribute to attenuation of long-term Cd stress (elevation of ascorbic, malic and citric acids). Molar ratio of malate to Cd was 12.7 and citrate to Cd 2.5, thus potentially contributing to Cd chelation. Interestingly, GSH/GSSG pool and nitric oxide formation remained unaltered by Cd. Accumulation of Cd reached 82 μg/g DW with bioaccumulation factor of 73. Data indicate that Cd induces elevation of potentially protective metabolites even after prolonged exposure though they do not prevent oxidative stress sufficiently. Image 1 • Axenic protonema cultures of Physcomitrella patens were exposed to 10 μM Cd over 40 d. • Cd amount reached 82 μg/g DW with BAF 73 and suppressed growth by ca. 75%. • Signs of oxidative stress were elevated but NO formation remained unchanged by Cd. • Amount of ascorbate and main Krebs acids increased but GSH/GSSG remained unchanged. • Data indicate that Cd-induced metabolites do not prevent oxidative stress sufficiently. [ABSTRACT FROM AUTHOR]