3- and 4-phosphorylated phosphatidylinositols in the aquatic plant Spirodela polyrhiza L.
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ABSTRACT:
SUBMITTER: Brearley CA
PROVIDER: S-EPMC1131022 | biostudies-other | 1992 Apr
REPOSITORIES: biostudies-other
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Project description:BackgroundSpirodela polyrhiza is a species of the order Alismatales, which represent the basal lineage of monocots with more ancestral features than the Poales. Its complete sequence of the mitochondrial (mt) genome could provide clues for the understanding of the evolution of mt genomes in plant.MethodsSpirodela polyrhiza mt genome was sequenced from total genomic DNA without physical separation of chloroplast and nuclear DNA using the SOLiD platform. Using a genome copy number sensitive assembly algorithm, the mt genome was successfully assembled. Gap closure and accuracy was determined with PCR products sequenced with the dideoxy method.ConclusionsThis is the most compact monocot mitochondrial genome with 228,493 bp. A total of 57 genes encode 35 known proteins, 3 ribosomal RNAs, and 19 tRNAs that recognize 15 amino acids. There are about 600 RNA editing sites predicted and three lineage specific protein-coding-gene losses. The mitochondrial genes, pseudogenes, and other hypothetical genes (ORFs) cover 71,783 bp (31.0%) of the genome. Imported plastid DNA accounts for an additional 9,295 bp (4.1%) of the mitochondrial DNA. Absence of transposable element sequences suggests that very few nuclear sequences have migrated into Spirodela mtDNA. Phylogenetic analysis of conserved protein-coding genes suggests that Spirodela shares the common ancestor with other monocots, but there is no obvious synteny between Spirodela and rice mtDNAs. After eliminating genes, introns, ORFs, and plastid-derived DNA, nearly four-fifths of the Spirodela mitochondrial genome is of unknown origin and function. Although it contains a similar chloroplast DNA content and range of RNA editing as other monocots, it is void of nuclear insertions, active gene loss, and comprises large regions of sequences of unknown origin in non-coding regions. Moreover, the lack of synteny with known mitochondrial genomic sequences shed new light on the early evolution of monocot mitochondrial genomes.
| S-EPMC3464924 | biostudies-literature
Project description:[3H]Inositol and [32P]Pi labelling of the aquatic plant Spirodela polyrhiza L. revealed the presence of PtdIns(3,4)P2, in addition to PtdIns3P, PtdIns4P and PtdIns(4,5)P2 previously identified [Brearley and Hanke (1992) Biochem. J. 283, 255-260]. PtdIns(3,4,5)P3 was not detected. Throughout a 40 min [32P]Pi-labelling period the specific radioactivity of the gamma-phosphate of ATP and of the ATP pool as a whole increased. Chemical and enzymic dissection of phosphoinositides obtained from plants labelled for 35 min with [32P]Pi showed that over 99.7% of the label in PtdIns3P and PtdIns4P was accounted for by the monoester phosphates. The 3- and 4-monoester phosphates of PtdIns(3,4)P2 accounted for 23.1% and 76.6% respectively of the label, whereas the 4- and 5-monoester phosphates of PtdIns(4,5)P2 accounted for 21.1% and 78.6% respectively. These results are consistent with the synthesis of PtdIns(4,5)P2 via PtdIns4P. The labelling of the individual phosphates of PtdIns(3,4)P2 is, however, inconsistent with synthesis from PtdIns(4,5)P2 via PtdIns(3,4,5)P3, but instead suggests that PtdIns(3,4)P2 is synthesized by 4-phosphorylation of PtdIns3P. These results afford the first evidence that in plants in vivo, synthesis of PtdIns(4,5)P2 follows the pathway described in animal cells and also that plants possess PtdIns3P 4-kinase activity similar to that reported from animal cells.
| S-EPMC1132394 | biostudies-other
Project description:RNA editing is the post-transcriptional conversion from C to U before translation, providing a unique feature in the regulation of gene expression. Here, we used a robust and efficient method based on RNA-seq from non-ribosomal total RNA to simultaneously measure chloroplast-gene expression and RNA editing efficiency in the Greater Duckweed, Spirodela polyrhiza, a species that provides a new reference for the phylogenetic studies of monocotyledonous plants. We identified 66 editing sites at the genome-wide level, with an average editing efficiency of 76%. We found that the expression levels of chloroplast genes were relatively constant, but 11 RNA editing sites show significant changes in editing efficiency, when fronds turn into turions. Thus, RNA editing efficiency contributes more to the yield of translatable transcripts than steady state mRNA levels. Comparison of RNA editing sites in coconut, Spirodela, maize, and rice suggests that RNA editing originated from a common ancestor.
| S-EPMC4627657 | biostudies-literature
Project description:The subfamily of the Lemnoideae belongs to a different order than other monocotyledonous species that have been sequenced and comprises aquatic plants that grow rapidly on the water surface. Here we select Spirodela polyrhiza for whole-genome sequencing. We show that Spirodela has a genome with no signs of recent retrotranspositions but signatures of two ancient whole-genome duplications, possibly 95 million years ago (mya), older than those in Arabidopsis and rice. Its genome has only 19,623 predicted protein-coding genes, which is 28% less than the dicotyledonous Arabidopsis thaliana and 50% less than monocotyledonous rice. We propose that at least in part, the neotenous reduction of these aquatic plants is based on readjusted copy numbers of promoters and repressors of the juvenile-to-adult transition. The Spirodela genome, along with its unique biology and physiology, will stimulate new insights into environmental adaptation, ecology, evolution and plant development, and will be instrumental for future bioenergy applications.
| S-EPMC3948053 | biostudies-literature
Project description:Short-term 32P labelling and enzymic dissection of inositol phospholipids was used to study the turnover of 3-, 3,4-, 4-, and 4,5-phosphorylated phosphatidylinositols in the plant Spirodela polyrhiza L. Analysis of label in the whole headgroup reveals that phosphatidylinositol 3- and 4-monophosphates (PtdIns3P and PtdIns4P) and phosphatidylinositol 3,4- and 4,5-bisphosphates [PtdIns(3,4)P2 and PtdIns(4,5)P2] all turn over with a half-life of approximately 2-5 h. Analysis of the labelling of individual phosphomonoesters and phosphodiesters of these lipids indicates a rapid equilibration of label between the 4- and 5-monoester phosphates of PtdIns(4,5)P2 within 5 h and largely independent of changes of labelling in the diester. We observed substantially slower equilibration of label (within approximately 27 h) between the monoester and diester of PtdIns4P. These studies therefore indicate that PtdIns4P and PtdIns(4,5)P2 participate in substrate-cycling reactions, evidence for which has been described experimentally only in erythrocytes, and give confirmation in vivo of the previous detection of inositol phospholipid phosphomonoesterase activity. Similar analyses of label in PtdIns3P and PtdIns(3,4)P2 reveal the likely participation of these molecules in substrate cycles and hence for the first time the presence of PtdIns3P 3-phosphatase and PtdIns(3,4)P2 4-phosphatase activities in plants. PtdIns3P and PtdIns(3,4)P2 undergo turnover at rates similar to those of PtdIns4P and PtdIns(4,5)P2. Estimates are made of the relative sizes of the pools of phospholipid participating in the turnover process.
| S-EPMC1136101 | biostudies-other
Project description:Aquatic plants have to adapt to the environments distinct from where land plants grow. A critical aspect of adaptation is the dynamics of sequence repeats, not resolved in older sequencing platforms due to incomplete and fragmented genome assemblies from short reads. Therefore, we used PacBio long-read sequencing of the Spirodela polyrhiza genome, reaching a 44-fold increase of contiguity with an N50 (a median of contig lengths) of 831 kb and filling 95.4% of gaps left from the previous version. Reconstruction of repeat regions indicates that sequentially nested long terminal repeat (LTR) retrotranspositions occur early in monocot evolution, featured with both prokaryote-like gene-rich regions and eukaryotic repeat islands. Protein-coding genes are reduced to 18,708 gene models supported by 492,435 high-quality full-length PacBio complementary DNA (cDNA) sequences. Different from land plants, the primitive architecture of Spirodela's adventitious roots and lack of lateral roots and root hairs are consistent with dispensable functions of nutrient absorption. Disease-resistant genes encoding antimicrobial peptides and dirigent proteins are expanded by tandem duplications. Remarkably, disease-resistant genes are not only amplified, but also highly expressed, consistent with low levels of 24-nucleotide (nt) small interfering RNA (siRNA) that silence the immune system of land plants, thereby protecting Spirodela against a wide spectrum of pathogens and pests. The long-read sequence information not only sheds light on plant evolution and adaptation to the environment, but also facilitates applications in bioenergy and phytoremediation.
| S-EPMC6754600 | biostudies-literature
Project description:Spirodela polyrhiza isolate:whole plant Genome sequencing
| PRJNA575564 | ENA
Project description:Invasive plant species are among the major threats to freshwater biodiversity. Few experimental studies have investigated whether native plant diversity can provide biotic resistance to invaders in freshwater ecosystems. At small spatial scales, invasion resistance may increase with plant species richness due to a better use of available resources, leaving less available for a potential invader (Complementarity effect) and/or the greater probability to have a highly competitive (or productive) native species in the community (Selection effect). In submerged aquatic plant communities, we tested the following hypotheses: (1) invader establishment success is greatest in the absence of a native plant community; (2) lower in plant communities with greater native species richness, due to complementary and/or selection effects; and (3) invader establishment success would be lowest in rooted plant communities, based on the limiting similarity theory as the invader is a rooted submerged species. In a greenhouse experiment, we established mesocosms planted with 0 (bare sediment), 1, 2, and 4 submerged plant species native to NW Europe and subjected these to the South African invader Lagarosiphon major (Ridl.) Moss. We used two rooted (Myriophyllum spicatum L., Potamogeton perfoliatus L.) and two non-rooted native species (Ceratophyllum demersum L., Utricularia vulgaris L.) representing two distinct functional groups considering their nutrient acquisition strategy which follows from their growth form, with, respectively, the sediment and water column as their main nutrient source. We found that the presence of native vegetation overall decreased the establishment success of an alien aquatic plant species. The strength of this observed biotic resistance increased with increasing species richness of the native community. Mainly due to a selection effect, the native biomass of mixed communities overyielded, and this further lowered the establishment success of the invader in our experiment. The strongest biotic resistance was caused by the two native plant species that were of the same functional group, i.e., functionally most similar to the invader. These results support the prediction of Elton's biotic resistance hypothesis in aquatic ecosystems and indicate that both species richness and functional group identity can play an important role in decreasing establishment success of alien plant species.
| S-EPMC5811644 | biostudies-literature
Project description:This study investigated the potential local CH4 sink in various plant parts as a boundary environment of CH4 emission and consumption. By comparing CH4 consumption activities in cultures inoculated with parts from 39 plant species, we observed significantly higher consumption of CH4 associated with aquatic plants than other emergent plant parts such as woody plant leaves, macrophytic marine algae, and sea grass. In situ activity of CH4 consumption by methanotrophs associated with different species of aquatic plants was in the range of 3.7-37 μmol·h(-1)·g(-1) dry weight, which was ca 5.7-370-fold higher than epiphytic CH4 consumption in submerged parts of emergent plants. The qPCR-estimated copy numbers of the particulate methane monooxygenase-encoding gene pmoA were variable among the aquatic plants and ranged in the order of 10(5)-10(7) copies·g(-1) dry weight, which correlated with the observed CH4 consumption activities. Phylogenetic identification of methanotrophs on aquatic plants based on the pmoA sequence analysis revealed a predominance of diverse gammaproteobacterial type-I methanotrophs, including a phylotype of a possible plant-associated methanotroph with the closest identity (86-89%) to Methylocaldum gracile.
| S-EPMC3909826 | biostudies-literature
Project description:Seedling root rot of soybeans caused by the host-specific pathogen Phytophthora sojae, and a large number of Pythium species, is an economically important disease across the Midwest United States that negatively impacts soybean yields. Research on biocontrol strategies for crop pathogens has focused on compounds produced by microbes from soil, however, recent studies suggest that aquatic bacteria express distinct compounds that efficiently inhibit a wide range of pathogens. Based on these observations, we hypothesized that freshwater strains of pseudomonads might be producing novel antagonistic compounds that inhibit the growth of oomycetes. To test this prediction, we utilized a collection of 330 Pseudomonas strains isolated from soil and freshwater habitats, and determined their activity against a panel of five oomycetes: Phytophthora sojae, Pythium heterothalicum, Pythium irregulare, Pythium sylvaticum, and Pythium ultimum, all of which are pathogenic on soybeans. Among the bacterial strains, 118 exhibited antagonistic activity against at least one oomycete species, and 16 strains were inhibitory to all pathogens. Antagonistic activity toward oomycetes was significantly more common for aquatic isolates than for soil isolates. One water-derived strain, 06C 126, was predicted to express a siderophore and exhibited diverse antagonistic profiles when tested on nutrient rich and iron depleted media suggesting that more than one compound was produced that effectively inhibited oomycetes. These results support the concept that aquatic strains are an efficient source of compounds that inhibit pathogens. We outline a strategy to identify other strains that express unique compounds that may be useful biocontrol agents.
| S-EPMC5986895 | biostudies-literature