Metabolic and genetic perturbations accompany the modification of galactomannan in seeds of Medicago truncatula expressing mannan synthase from guar (Cyamopsis tetragonoloba L.)

De novo sequencing allows genome-wide identification of genes involved in galactomannan synthesis in locust bean (Ceratonia siliqua)

Locust bean (Ceratonia siliqua) accumulates the galactomannan (GM) locust bean gum (LBG) in its seeds. LBG is a major industrial raw material used as a food thickener and gelling agent, whose unique properties mean that it cannot be readily replaced by other GMs. Whereas much is known about GM accumulation and the genes associated with GM biosynthesis in legumes, the genes involved in GM biosynthesis in C. siliqua are largely unknown. Here, we present a genome-wide list of genes predicted to be associated with the GM biosynthesis pathway in C. siliqua. We confirmed high GM accumulation in endosperm using a newly established GM quantification method involving LC-MS/MS. Through de novo draft genome assembly, we comprehensively identified genes predicted to be related to the GM biosynthesis pathway in C. siliqua by identifying orthologous groups. In particular, we identified all genes predicted to encode mannan synthase (ManS) and galactomannan galactosyltransferase (GMGT), enzymes functioning in the final step of GM biosynthesis, from the C. siliqua draft genome. ManS and the GMGT paralogs were predominantly expressed in endosperm. The genome and transcriptome produced in this study should facilitate research examining why C. siliqua produces LBG, unlike other legumes.

Elucidation of Galactomannan Biosynthesis Pathway Genes through Transcriptome Sequencing of Seeds Collected at Different Developmental Stages of Commercially Important Indian Varieties of Cluster Bean (Cyamopsis tetragonoloba L.)

Cyamopsis tetragonoloba (L) endosperm predominantly contains guar gum a polysaccharide, which has tremendous industrial applications in food, textile, paper, oil drilling and water treatment. In order to understand the genes controlling galactomannan biosynthesis, mRNA was isolated from seeds collected at different developmental stages; young pods, mature pods and young leaf from two guar varieties, HG365 and HG870 and subjected to Illumina sequencing. De novo assembly of fourteen individual read files from two varieties of guar representing seven developmental stages gave a total of 1,13,607 contigs with an N50 of 1,244 bases. Annotation of assemblies with GO mapping revealed three levels of distribution, namely, Biological Processes, Molecular Functions and Cellular Components. GO studies identified major genes involved in galactomannan biosynthesis: Cellulose synthase D1 (CS D1) and GAUT-like gene families. Among the polysaccharide biosynthetic process (GO:0000271) genes the transcript abundance for CS was found to be predominantly more in leaf samples, whereas, the transcript abundance for GAUT-like steadily increased from 65% to 90% and above from stage1 to stage5 indicating accumulation of galactomannan in developing seeds; and validated by qRT-PCR analysis. Galactomannan quantification by HPLC showed HG365 (12.98–20.66%) and HG870 (7.035–41.2%) gradually increasing from stage1 to stage 5 (10–50 DAA) and highest accumulation occurred in mature and dry seeds with 3.8 to 7.1 fold increase, respectively. This is the first report of transcriptome sequencing and complete profiling of guar seeds at different developmental stages, young pods, mature pods and young leaf material from two commercially important Indian varieties and elucidation of galactomannan biosynthesis pathway. It is envisaged that the data presented herein will be very useful for improvement of guar through biotechnological interventions in future.

Regulation of Carbon Partitioning in the Seed of the Model Legume Medicago truncatula and Medicago orbicularis: A Comparative Approach

The proportion of starch, protein and oil in legume seeds is species dependent. The model legume, Medicago truncatula, has predominantly oil and protein stores. To investigate the regulation of seed oil production we compared M. truncatula with M. orbicularis, which has less oil and protein. The types of protein and fatty acids are similar between the two species. Electron microscopy indicated that the size and distribution of the oil bodies in M. orbicularis, is consistent with reduced oil production. M. orbicularis has more extruded endosperm mucilage compared to M. truncatula. The cotyledons have a greater cell wall content, visualized as thicker cell walls. The reduced oil content in M. orbicularis is associated with increased expression of the MtGLABRA2-like (MtGL2) transcription factor, linked to an inverse relationship between mucilage and oil content in Arabidopsis. The expression of the pectin biosynthesis GALACTURONOSYLTRANSFERASE (GAUT) genes, is also increased in M. orbicularis. These increases in extruded mucilage and cell wall storage components in M. orbicularis are accompanied by reduced expression of transcriptional regulators of oil biosynthesis, MtLEAFY COTYLEDON1-LIKE (MtL1L), MtABSCISIC ACID-INSENSITIVE3 (MtABI3), and MtWRINKLED-like (MtWRI), in M. orbicularis. The reduced oil in M. orbicularis, is consistent with increased synthesis of cell wall polysaccharides and decreased expression of master transcription factors regulating oil biosynthesis and embryo maturation. Comparative investigations between these two Medicago species is a useful system to investigate the regulation of oil content and carbon partitioning in legumes.

Oil body biogenesis and biotechnology in legume seeds

The seeds of many legume species including soybean, Pongamia pinnata and the model legume Medicago truncatula store considerable oil, apart from protein, in their cotyledons. However, as a group, legume storage strategies are quite variable and provide opportunities for better understanding of carbon partitioning into different storage products. Legumes with their ability to fix nitrogen can also increase the sustainability of agricultural systems. This review integrates the cell biology, biochemistry and molecular biology of oil body biogenesis before considering biotechnology strategies to enhance oil body biosynthesis. Cellular aspects of packaging triacylglycerol (TAG) into oil bodies are emphasized. Enhancing seed oil content has successfully focused on the up-regulation of the TAG biosynthesis pathways using overexpression of enzymes such as diacylglycerol acyltransferase1 and transcription factors such as WRINKLE1 and LEAFY COTYLEDON1. While these strategies are central, decreasing carbon flow into other storage products and maximizing the packaging of oil bodies into the cytoplasm are other strategies that need further examination. Overall there is much potential for integrating carbon partitioning, up-regulation of fatty acid and TAG synthesis and oil body packaging, for enhancing oil levels. In addition to the potential for integrated strategies to improving oil yields, the capacity to modify fatty acid composition and use of oil bodies as platforms for the production of recombinant proteins in seed of transgenic legumes provide other opportunities for legume biotechnology.

Are designer plant cell walls a realistic aspiration or will the plasticity of the plant's metabolism win out?

Plants have been redesigned by humans since the advent of modern agriculture some 10000 years ago, to provide ever increasing benefits to society. The phenomenal success of the green revolution in converting biomass from vegetative tissues into grain yield has sustained a growing population. At the dawn of the 21st century the need to further optimise plant biomass (largely plant walls) for a sustainable future is increasingly evident as our supply of fossil fuels is finite and the quality of our crop-based foods (functional foods; also determined by the composition of walls) are critical to maintaining a healthy lifestyle. Our capacity to engineer 'designer walls' suited to particular purposes is challenging plant breeders and biotechnologists in unprecedented ways. In this review we provide an overview of the critical steps in the assembly and remodelling of walls, the success (or otherwise) of such approaches and highlight another complex network, the cell surface, as a cell wall integrity (CWI) sensor that exerts control over wall composition and will need to be considered in any future modification of walls for agro-industrial purposes.

Deep EST profiling of developing fenugreek endosperm to investigate galactomannan biosynthesis and its regulation

Galactomannans are hemicellulosic polysaccharides composed of a (1 → 4)-linked β-D-mannan backbone substituted with single-unit (1 → 6)-α-linked D-galactosyl residues. Developing fenugreek (Trigonella foenum-graecum) seeds are known to accumulate large quantities of galactomannans in the endosperm, and were thus used here as a model system to better understand galactomannan biosynthesis and its regulation. We first verified the specific deposition of galactomannans in developing endosperms and determined that active accumulation occurred from 25 to 38 days post anthesis (DPA) under our growth conditions. We then examined the expression levels during seed development of ManS and GMGT, two genes encoding backbone and side chain synthetic enzymes. Based on transcript accumulation dynamics for ManS and GMGT, cDNA libraries were constructed using RNA isolated from endosperms at four ages corresponding to before, at the beginning of, and during active galactomannan deposition. DNA from these libraries was sequenced using the 454 sequencing technology to yield a total of 1.5 million expressed sequence tags (ESTs). Through analysis of the EST profiling data, we identified genes known to be involved in galactomannan biosynthesis, as well as new genes that may be involved in this process, and proposed a model for the flow of carbon from sucrose to galactomannans. Measurement of in vitro ManS and GMGT activities and analysis of sugar phosphate and nucleotide sugar levels in the endosperms of developing fenugreek seeds provided data consistent with this model. In vitro enzymatic assays also revealed that the ManS enzyme from fenugreek endosperm preferentially used GDP-mannose as the substrate for the backbone synthesis.

Modifying crops to increase cell wall digestibility

Improving digestibility of roughage cell walls will improve ruminant animal performance and reduce loss of nutrients to the environment. The main digestibility impediment for dicotyledonous plants is highly lignified secondary cell walls, notably in stem secondary xylem, which become almost non-digestible. Digestibility of grasses is slowed severely by lignification of most tissues, but these cell walls remain largely digestible. Cell wall lignification creates an access barrier to potentially digestible wall material by rumen bacteria if cells have not been physically ruptured. Traditional breeding has focused on increasing total dry matter digestibility rather than cell wall digestibility, which has resulted in minimal reductions in cell wall lignification. Brown midrib mutants in some annual grasses exhibit small reductions in lignin concentration and improved cell wall digestibility. Similarly, transgenic approaches down-regulating genes in monolignol synthesis have produced plants with reduced lignin content and improved cell wall digestibility. While major reductions in lignin concentration have been associated with poor plant fitness, smaller reductions in lignin provided measurable improvements in digestibility without significantly impacting agronomic fitness. Additional targets for genetic modification to enhance digestibility and improve roughages for use as biofuel feedstocks are discussed; including manipulating cell wall polysaccharide composition, novel lignin structures, reduced lignin/polysaccharide cross-linking, smaller lignin polymers, enhanced development of non-lignified tissues, and targeting specific cell types. Greater tissue specificity of transgene expression will be needed to maximize benefits while avoiding negative impacts on plant fitness.cauliflower mosiac virus (CaMV) 35S promoter.

Characterization of the mannan synthase promoter from guar (Cyamopsis tetragonoloba)

Guar seed gum, consisting primarily of a high molecular weight galactomannan, is the most cost effective natural thickener, having broad applications in the food, cosmetics, paper, pharmaceutical and petroleum industries. The properties of the polymer can potentially be enhanced by genetic modification. Development of suitable endosperm-specific promoters for use in guar is desirable for metabolic engineering of the seed gum. A ~1.6 kb guar mannan synthase (MS) promoter region has been isolated. The MS promoter sequence was fused with the GUS reporter gene and overexpressed in the heterologous species alfalfa (Medicago sativa). The potential strength and specificity of the MS promoter was compared with those of the constitutive 35S promoter and the seed specific β-phaseolin promoter. Quantitative GUS assays revealed that the MS promoter directs GUS expression specifically in endosperm in transgenic alfalfa. Thus, the guar MS promoter could prove generally useful for directing endosperm-specific expression of transgenes in legume species.

The Medicago truncatula gene expression atlas web server

BACKGROUND

Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose.

DESCRIPTION

The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip(R) Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/.

CONCLUSIONS

The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view.

The Medicago truncatula gene expression atlas web server

Background

Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of legume genes. With the rapid growth of publically available Affymetrix GeneChip Medicago Genome Array GeneChip data from a great range of tissues, cell types, growth conditions, and stress treatments, the legume research community desires an effective bioinformatics system to aid efforts to interpret the Medicago genome through functional genomics. We developed the Medicago truncatula Gene Expression Atlas (MtGEA) web server for this purpose.

Description

The Medicago truncatula Gene Expression Atlas (MtGEA) web server is a centralized platform for analyzing the Medicago transcriptome. Currently, the web server hosts gene expression data from 156 Affymetrix GeneChip^® Medicago genome arrays in 64 different experiments, covering a broad range of developmental and environmental conditions. The server enables flexible, multifaceted analyses of transcript data and provides a range of additional information about genes, including different types of annotation and links to the genome sequence, which help users formulate hypotheses about gene function. Transcript data can be accessed using Affymetrix probe identification number, DNA sequence, gene name, functional description in natural language, GO and KEGG annotation terms, and InterPro domain number. Transcripts can also be discovered through co-expression or differential expression analysis. Flexible tools to select a subset of experiments and to visualize and compare expression profiles of multiple genes have been implemented. Data can be downloaded, in part or full, in a tabular form compatible with common analytical and visualization software. The web server will be updated on a regular basis to incorporate new gene expression data and genome annotation, and is accessible at: http://bioinfo.noble.org/gene-atlas/.

Conclusions

The MtGEA web server has a well managed rich data set, and offers data retrieval and analysis tools provided in the web platform. It's proven to be a powerful resource for plant biologists to effectively and efficiently identify Medicago transcripts of interest from a multitude of aspects, formulate hypothesis about gene function, and overall interpret the Medicago genome from a systematic point of view.

Solutions for dissolution--engineering cell walls for deconstruction

Photosynthetic carbon capture by terrestrial plants represents a major sink for atmospheric CO(2), ultimately terminating in the synthesis of a secondary plant cell wall-a complex matrix of polysaccharides intricately linked to lignin. The production and co-ordinated deposition of this lignocellulosic composite confers both protective and structural properties to the plant cell. The inherent properties of this complex cell wall also represent a major obstacle for its effective industrial utilization, as operationally effective mechanisms for the removal of lignin and the consequential release of carbohydrate constituents remain elusive. Perturbing plants by mis-regulating key genes/enzymes integral to major cell wall pathways can provide both rich insights into cell wall development and architecture, and concurrently provide significant opportunities for improved lignocellulose utilization.