Making Roots, Shoots, and Seeds: IDD Gene Family Diversification in Plants
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Coelho, Carla P.↗
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Cellulose synthase gene expression profiling of Physcomitrella patens
Abstract The cellulose synthase ( CESA ) gene family of seed plants comprises six clades that encode isoforms with conserved expression patterns and distinct functions in cellulose synthesis complex ( CSC ) formation and primary and secondary cell wall synthesis. In mosses, which have rosette CSC s like those of seed plants but lack lignified secondary cell walls, the CESA gene family diversified independently and includes no members of the six functionally distinct seed plant clades. There are seven CESA isoforms encoded in the genome of the moss Physcomitrella patens . However, only Pp CESA 5 has been characterised functionally, and little information is available on the expression of other Pp CESA family members. We have profiled Pp CESA expression through quantitative RT ‐ PCR , analysis of promoter‐reporter lines, and cluster analysis of public microarray data in an effort to identify expression and co‐expression patterns that could help reveal the functions of Pp CESA isoforms in protein complex formation and development of specific tissues. In contrast to the tissue‐specific expression observed for seed plant CESA s, each of the Pp CESA s was broadly expressed throughout most developing tissues. Although a few statistically significant differences in expression of Pp CESA s were noted when some tissues and hormone treatments were compared, no strong co‐expression patterns were observed. Along with CESA phylogenies and lack of single Pp CESA mutant phenotypes reported elsewhere, broad overlapping expression of the Pp CESA s indicates a high degree of inter‐changeability and is consistent with a different pattern of functional specialisation in the evolution of the seed plant and moss CESA families.
Tran, M. L.↗
Non-TZF Protein AtC3H59/ZFWD3 Is Involved in Seed Germination, Seedling Development, and Seed Development, Interacting with PPPDE Family Protein Desi1 in Arabidopsis
Despite increasing reports on the function of CCCH zinc finger proteins in plant development and stress response, the functions and molecular aspects of many non-tandem CCCH zinc finger (non-TZF) proteins remain uncharacterized. AtC3H59/ZFWD3 is an Arabidopsis non-TZF protein and belongs to the ZFWD subfamily harboring a CCCH zinc finger motif and a WD40 domain. In this study, we characterized the biological and molecular functions of AtC3H59, which is subcellularly localized in the nucleus. The seeds of AtC3H59-overexpressing transgenic plants (OXs) germinated faster than those of wild type (WT), whereas atc3h59 mutant seeds germinated slower than WT seeds. AtC3H59 OX seedlings were larger and heavier than WT seedlings, whereas atc3h59 mutant seedlings were smaller and lighter than WT seedlings. Moreover, AtC3H59 OX seedlings had longer primary root length than WT seedlings, whereas atc3h59 mutant seedlings had shorter primary root length than WT seedlings, owing to altered cell division activity in the root meristem. During seed development, AtC3H59 OXs formed larger and heavier seeds than WT. Using yeast two-hybrid screening, we isolated Desi1, a PPPDE family protein, as an interacting partner of AtC3H59. AtC3H59 and Desi1 interacted via their WD40 domain and C-terminal region, respectively, in the nucleus. Taken together, our results indicate that AtC3H59 has pleiotropic effects on seed germination, seedling development, and seed development, and interacts with Desi1 in the nucleus via its entire WD40 domain. To our knowledge, this is the first report to describe the biological functions of the ZFWD protein and Desi1 in Arabidopsis.
59 BASIC BIOLOGICAL SCIENCES↗
Metabolic and transcriptomic study of pennycress natural variation identifies targets for oil improvement
Pennycress (Thlaspi arvense L.), a member of the Brassicaceae family, produces seed oil high in erucic acid, suitable for biodiesel and aviation fuel. Although pennycress, a winter annual, could be grown as a dedicated bioenergy crop, an increase in its seed oil content is required to improve its economic competitiveness. The success of crop improvement relies upon finding the right combination of biomarkers and targets, and the best genetic engineering and/or breeding strategies. In this work, we combined biomass composition with metabolomic and transcriptomic studies of developing embryos from 22 pennycress natural variants to identify targets for oil improvement. The selected accession collection presented diverse levels of fatty acids at maturity ranging from 29% to 41%. Pearson correlation analyses, weighted gene co‐expression network analysis and biomarker identifications were used as complementary approaches to detect associations between metabolite level or gene expression and oil content at maturity. The results indicated that improving seed oil content can lead to a concomitant increase in the proportion of erucic acid without affecting the weight of embryos. Processes, such as carbon partitioning towards the chloroplast, lipid metabolism, photosynthesis, and a tight control of nitrogen availability, were found to be key for oil improvement in pennycress. Besides identifying specific targets, our results also provide guidance regarding the best timing for their modification, early or middle maturation. Thus, this work lays out promising strategies, specific for pennycress, to accelerate the successful development of lines with increased seed oil content for biofuel applications.
59 BASIC BIOLOGICAL SCIENCES↗
Accessing the SEED Genome Databases via Web Services API: Tools for Programmers
Background: The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. Results: The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. Conclusions: We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.
59 BASIC BIOLOGICAL SCIENCES↗
Redundant roles of four ZIP family members in zinc homeostasis and seed development in Arabidopsis thaliana
Zinc (Zn) is essential for normal plant growth and development. The Zn-regulated transporter, iron-regulated transporter (IRT)-like protein (ZIP) family members are involved in Zn transport and cellular Zn homeostasis throughout the domains of life. In this study, we have characterized four ZIP transporters from Arabidopsis thaliana (IRT3, ZIP4, ZIP6, and ZIP9) to better understand their functional roles. The four ZIP proteins can restore the growth defect of a yeast Zn uptake mutant and are upregulated under Zn deficiency. Single and double mutants show no phenotypes under Zn-sufficient or Zn-limited growth conditions. In contrast, triple and quadruple mutants show impaired growth irrespective of external Zn supply due to reduced Zn translocation from root to shoot. All four ZIP genes are highly expressed during seed development, and siliques from all single and higher-order mutants exhibited an increased number of abnormal seeds and decreased Zn levels in mature seeds relative to wild type. The seed phenotypes could be reversed by supplementing the soil with Zn. Finally, our data demonstrate that IRT3, ZIP4, ZIP6, and ZIP9 function redundantly in maintaining Zn homeostasis and seed development in A. thaliana.
59 BASIC BIOLOGICAL SCIENCES↗
Species diversity driven by morphological and ecological disparity: a case study of comparative seed morphology and anatomy across a large monocot order
Phenotypic variation can be attributed to genetic heritability as well as biotic and abiotic factors. Across Zingiberales, there is a high variation in the number of species per clade and in phenotypic diversity. Factors contributing to this phenotypic variation have never been studied in a phylogenetic or ecological context. Seeds of 166 species from all eight families in Zingiberales were analyzed for 51 characters using synchrotron based 3D X-ray tomographic microscopy to determine phylogenetically informative characters and to understand the distribution of morphological disparity within the order. All families are distinguishable based on seed characters. Non-metric multidimensional scaling analyses show Zingiberaceae occupy the largest seed morphospace relative to the other families, and environmental analyses demonstrate that Zingiberaceae inhabit both temperate and tropical regions, while other Zingiberales are almost exclusively tropical. Temperate species do not cluster in morphospace nor do they share a common suite of character states. This suggests that the diversity seen is not driven by adaptation to temperate niches; rather, the morphological disparity seen likely reflects an underlying genetic plasticity that allowed Zingiberaceae to repeatedly colonize temperate environments. The notable morphoanatomical variety in Zingiberaceae seeds may account for their extraordinary ecological success and high species diversity as compared to other Zingiberales.
Cannaceae↗
Microbiomes of commercially-available pine nuts and sesame seeds
Metagenomic analysis of food is becoming more routine and can provide important information pertaining to the shelf life potential and the safety of these products. However, less information is available on the microbiomes associated with low water activity foods. Pine nuts and sesame seeds, and food products which contain these ingredients, have been associated with recalls due to contamination with bacterial foodborne pathogens. The objective of this study was to identify the microbial community of pine nuts and sesame seeds using targeted 16S rRNA sequencing technology. Ten different brands of each seed type were assessed, and core microbiomes were determined. A total of 21 and 16 unique taxa with proportional abundances >1% in at least one brand were identified in the pine nuts and sesame seeds, respectively. Members of the core pine nut microbiome included the genera Alishewanella, Aminivibrio, Mycoplasma, Streptococcus, and unassigned OTUs in the families of Desulfobacteraceae and Xanthomonadaceae. For sesame seeds, the core microbiome included Aminivibrio, Chryseolina, Okibacterium, and unassigned OTUs in the family Flavobacteriaceae. The microbiomes of these seeds revealed that these products are dominated by environmental bacterial genera commonly isolated from soil, water, and plants; bacterial genera containing species known as commensal organisms were also identified. Understanding these microbiomes can aid in the risk assessment of these products by identifying food spoilage potential and community members which may co-enrich with foodborne bacterial pathogens.
59 BASIC BIOLOGICAL SCIENCES↗
Secondary metallicity in analytic models of chemical evolution of galaxies
Analytic models of the chemical evolution of galactic regions that grow in mass owing to the continuous infall of matter are characterized, emphasizing the solutions for secondary nuclei (defined as those nuclei whose stellar yields are proportional to the abundance of a primary seed nucleus) in the families of models described by Clayton (1984 and 1985). Wide variations in time dependence of both primary and secondary nuclei as well as in the ratio of secondary to primary are displayed by these model families, confirming again the usefulness of these families as interpretive guides if galaxies do in fact evolve with substantial infall. Additionally, analytic solutions are presented for two other possible interesting systems: the evolution of abundances if the primary metallicity in the infall is increasing in time, and the evolution of abundances if the primary yield changes linearly with time owing to continuous changes in the stellar mass function, the opacity, or other astrophysical agents. Finally, test evaluations of the instantaneous recycling approximation on which these analytic models rely are presented.
Clayton, D. D.↗
Accumulation of medium-chain, saturated fatty acyl moieties in seed oils of transgenic Camelina sativa
With its high seed oil content, the mustard family plant Camelina sativa has gained attention as a potential biofuel source. As a bioenergy crop, camelina has many advantages. It grows on marginal land with low demand for water and fertilizer, has a relatively short life cycle, and is stress tolerant. As most other crop seed oils, camelina seed triacylglycerols (TAGs) consist of mostly long, unsaturated fatty acyl moieties, which is not desirable for biofuel processing. In our efforts to produce shorter, saturated chain fatty acyl moieties in camelina seed oil for conversion to jet fuel, a 12:0-acyl-carrier thioesterase gene, UcFATB1, from California bay (Umbellularia californica Nutt.) was expressed in camelina seeds. Up to 40% of short chain laurate (C12:0) and myristate (C14:0) were present in TAGs of the seed oil of the transgenics. The total oil content and germination rate of the transgenic seeds were not affected. Analysis of positions of these two fatty acyl moieties in TAGs indicated that they were present at the sn-1 and sn-3 positions, but not sn-2, on the TAGs. Suppression of the camelina KASII genes by RNAi constructs led to higher accumulation of palmitate (C16:0), from 7.5% up to 28.5%, and further reduction of longer, unsaturated fatty acids in seed TAGs. Co-transformation of camelina with both constructs resulted in enhanced accumulation of all three medium-chain, saturated fatty acids in camelina seed oils. Our results show that a California bay gene can be successfully used to modify the oil composition in camelina seed and present a new biological alternative for jet fuel production.
09 BIOMASS FUELS↗
Identification of Key Enzymes for Pectin Synthesis in Seed Mucilage
Pectin is a vital component of the plant cell wall, and provides the molecular glue that maintains cell-cell adhesion, among other functions. As the most complex wall polysaccharide, pectin is composed of several covalently-linked domains, such as homogalacturonan (HG) and rhamnogalacturonan I (RG I). Pectin has widespread uses in the food industry and has emerging biomedical applications, but its synthesis remains poorly understood. For instance, the enzymes that catalyze RG I elongation remain unknown. Recently, a co-expression and sequence-based MUCILAGE-RELATED (MUCI) reverse genetic screen uncovered hemicellulose biosynthetic enzymes in the Arabidopsis thaliana seed coat. Here, we use an extension of this strategy to identify MUCI70 as the founding member of a glycosyltransferase family essential for the accumulation of seed mucilage, a gelatinous wall rich in unbranched RG I. Detailed biochemical and histological characterization of two muci70 mutants and two gaut11 mutants identified MUCI70 and GAUT11 as required for two distinct RG I domains in seed mucilage. We demonstrate that, unlike MUCI70, GAUT11 catalyzes HG elongation in vitro, and is thus likely required for the synthesis of an HG region important for RG I elongation. Analysis of a muci70 gaut11 double mutant confirmed that MUCI70 and GAUT11 are indispensable for the production and release of the bulk of mucilage RG I, and for shaping the surface morphology of seeds. In addition, we uncover relationships between pectin and hemicelluloses and show that xylan is essential for the elongation of at least one RG I domain.
54 ENVIRONMENTAL SCIENCES↗
Organ-delimited gene regulatory networks provide high accuracy in candidate transcription factor selection across diverse processes
Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana . A GRN inference approach was used to determine the: i. influential transcription factors (TFs) in each organ and, ii. most influential TFs for specific biological processes in that organ. These genome-wide, organ-delimited GRNs (OD-GRNs), recalled many known regulators of organ development and processes operating in those organs. Importantly, many previously unknown TF regulators were uncovered as potential regulators of these processes. As a proof-of-concept, we focused on experimentally validating the predicted TF regulators of lipid biosynthesis in seeds, an important food and biofuel trait. Of the top 20 predicted TFs, eight are known regulators of seed oil content, e.g., WRI1, LEC1, FUS3. Importantly, we validated our prediction of MybS2, TGA4, SPL12, AGL18, and DiV2 as regulators of seed lipid biosynthesis. We elucidated the molecular mechanism of MybS2 and show that it induces purple acid phosphatase family genes and lipid synthesis genes to enhance seed lipid content. This general approach has the potential to be extended to any species with sufficiently large gene expression datasets to find unique regulators of any trait-of-interest.
09 BIOMASS FUELS↗
HuMiChip: Development of a Functional Gene Array for the Study of Human Microbiomes
Microbiomes play very important roles in terms of nutrition, health and disease by interacting with their hosts. Based on sequence data currently available in public domains, we have developed a functional gene array to monitor both organismal and functional gene profiles of normal microbiota in human and mouse hosts, and such an array is called human and mouse microbiota array, HMM-Chip. First, seed sequences were identified from KEGG databases, and used to construct a seed database (seedDB) containing 136 gene families in 19 metabolic pathways closely related to human and mouse microbiomes. Second, a mother database (motherDB) was constructed with 81 genomes of bacterial strains with 54 from gut and 27 from oral environments, and 16 metagenomes, and used for selection of genes and probe design. Gene prediction was performed by Glimmer3 for bacterial genomes, and by the Metagene program for metagenomes. In total, 228,240 and 801,599 genes were identified for bacterial genomes and metagenomes, respectively. Then the motherDB was searched against the seedDB using the HMMer program, and gene sequences in the motherDB that were highly homologous with seed sequences in the seedDB were used for probe design by the CommOligo software. Different degrees of specific probes, including gene-specific, inclusive and exclusive group-specific probes were selected. All candidate probes were checked against the motherDB and NCBI databases for specificity. Finally, 7,763 probes covering 91.2percent (12,601 out of 13,814) HMMer confirmed sequences from 75 bacterial genomes and 16 metagenomes were selected. This developed HMM-Chip is able to detect the diversity and abundance of functional genes, the gene expression of microbial communities, and potentially, the interactions of microorganisms and their hosts.
54 ENVIRONMENTAL SCIENCES↗
Seeds in space experiment results
Two million seeds of 120 different varieties representing 106 species, 97 genera, and 55 plant families were flown aboard the Long Duration Exposure Facility (LDEF). The seeds were housed on the space exposed experiment developed for students (SEEDS) tray in sealed canister number six and in two small vented canisters. The tray was in the F-2 position. The seeds were germinated and the germination rates and development of the resulting plants compared to the control seed that stayed in Park Seed's seed storage facility. The initial results are presented. There was a better survival rate in the sealed canister in space than in the storage facility at Park Seed. At least some of the seeds in each of the vented canisters survived the exposure to vacuum for almost six years. The number of observed apparent mutations was very low.
Alston, Jim A.↗
Seeds in space experiment
Two million seeds of 120 different varieties representing 106 species, 97 genera, and 55 plant families were flown aboard the Long Duration Exposure Facility (LDEF). The seeds were housed in one sealed canister and in two small vented canisters. After being returned to earth, the seeds were germinated and the germination rates and development of the resulting plants were compared to the performance of the control seeds that stayed in the Park Seed's seed storage facility. There was a better survival rate in the sealed canister in space than at the storage facility at Park Seed. At least some of the seeds in each of the vented canisters survived the exposure to vacuum for almost six years. The number of observed apparent mutations was very low.
Jim A Alston↗
Continued results of the seeds in space experiment
Two million seeds of 120 different varieties representing 106 species, 97 genera, and 55 plant families were flown aboard the Long Duration Exposure Facility (LDEF). The seeds were housed on the Space Exposed Experiment Developed for Students (SEEDS) tray in the sealed canister number 6 and in two small vented canisters. The seeds were germinated and the germination rates and development of the resulting plants compared to the control seed that stayed in the storage facility. There was a better survival rate in the sealed canister in space than in the storage facility. At least some of the seed in the vented canisters survived the exposure to vacuum for almost six years. The number of observed mutations was very low. In the initial testing, the small seeded crops were not grown to maturity to check for mutation and obtain a second generation seed. These small seeded crops are now being grown for evaluation.
Alston, Jim A.↗
Continued results of the seeds in space experiment
Two million seeds of 120 different varieties representing 106 species, 97 genera, and 55 plant families were flown aboard the Long Duration Exposure Facility (LDEF). The seed were housed on the Space Exposed Experiment Developed for Students (SEEDS) tray in the sealed canister number 6 and in two small vented canisters. The tray was in the F-2 position. The seed were germinated and the germination rates and the development of the resulting plants were compared to the performance of the control seed that stayed in Park Seed's seed storage facility. The initial results were presented in a paper at the First LDEF Post-Retrieval Symposium. There was a better survival rate of the seed in the sealed canister in space than in the storage facility at Park Seed. At least some of the seed in each of the vented canisters survived the exposure to vacuum for almost six years. The number of observed apparent mutations was very low. In the initial testing, the small seeded crops were not grown to maturity to check for mutations and obtain second generation seed. These small seeded crops have now been grown for evaluation and second generation seed collected.
Alston, Jim A.↗
Dynamic genome evolution in a model fern
The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.
59 BASIC BIOLOGICAL SCIENCES↗