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1.
Plant Biotechnol J ; 14(2): 567-80, 2016 Feb.
Article in English | MEDLINE | ID: mdl-26015295

ABSTRACT

In planta production of the bioplastic polyhydroxybutyrate (PHB) is one important way in which plant biotechnology can address environmental problems and emerging issues related to peak oil. However, high biomass C4 plants such as maize, switch grass and sugarcane develop adverse phenotypes including stunting, chlorosis and reduced biomass as PHB levels in leaves increase. In this study, we explore limitations to PHB accumulation in sugarcane chloroplasts using a systems biology approach, coupled with a metabolic model of C4 photosynthesis. Decreased assimilation was evident in high PHB-producing sugarcane plants, which also showed a dramatic decrease in sucrose and starch content of leaves. A subtle decrease in the C/N ratio was found which was not associated with a decrease in total protein content. An increase in amino acids used for nitrogen recapture was also observed. Based on the accumulation of substrates of ATP-dependent reactions, we hypothesized ATP starvation in bundle sheath chloroplasts. This was supported by mRNA differential expression patterns. The disruption in ATP supply in bundle sheath cells appears to be linked to the physical presence of the PHB polymer which may disrupt photosynthesis by scattering photosynthetically active radiation and/or physically disrupting thylakoid membranes.


Subject(s)
Carbon/metabolism , Metabolic Engineering/methods , Models, Biological , Plant Leaves/metabolism , Saccharum/metabolism , Systems Biology/methods , Chloroplasts/metabolism , Chloroplasts/ultrastructure , Circadian Rhythm , Gene Expression Regulation, Plant , Hydroxybutyrates/metabolism , Metabolome , Nitrogen/metabolism , Photosynthesis , Plants, Genetically Modified , RNA, Messenger/genetics , RNA, Messenger/metabolism , Saccharum/genetics
2.
Curr Opin Biotechnol ; 32: 68-75, 2015 Apr.
Article in English | MEDLINE | ID: mdl-25437636

ABSTRACT

The production of novel biopolymers in plants has the potential to provide renewable sources of industrial materials through agriculture. In this review we will highlight recent progress with plant-based production of polyhydroxyalkanoates (PHAs), silk, elastin, collagen, and cyanophycin with an emphasis on the synthesis of poly[(R)-3-hydroxybutyrate] (PHB), a renewable biodegradable PHA polymer with potential commercial applications in plastics, chemicals, and feed markets. Improved production of PHB has required manipulation of promoters driving expression of transgenes, reduction in activity of endogenous enzymes in competing metabolic pathways, insertion of genes to increase carbon flow to polymer, and basic plant biochemistry to understand metabolic limitations. These experiments have increased our understanding of carbon availability and partitioning in different plant organelles, cell types, and organs, information that is useful for the production of other novel molecules in plants.


Subject(s)
Biopolymers/biosynthesis , Plants/metabolism , Amino Acids/metabolism , Animals , Biotechnology/methods , Humans , Plants/genetics , Prohibitins , Recombinant Proteins/genetics , Recombinant Proteins/metabolism
3.
Plant Biotechnol J ; 13(5): 700-7, 2015 Jun.
Article in English | MEDLINE | ID: mdl-25532451

ABSTRACT

Engineering the production of polyhydroxyalkanoates (PHAs) into high biomass bioenergy crops has the potential to provide a sustainable supply of bioplastics and energy from a single plant feedstock. One of the major challenges in engineering C4 plants for the production of poly[(R)-3-hydroxybutyrate] (PHB) is the significantly lower level of polymer produced in the chloroplasts of mesophyll (M) cells compared to bundle sheath (BS) cells, thereby limiting the full PHB yield-potential of the plant. In this study, we provide evidence that the access to substrate for PHB synthesis may limit polymer production in M chloroplasts. Production of PHB in M cells of sugarcane is significantly increased by replacing ß-ketothiolase, the first enzyme in the bacterial PHA pathway, with acetoacetyl-CoA synthase. This novel pathway enabled the production of PHB reaching an average of 6.3% of the dry weight of total leaf biomass, with levels ranging from 3.6 to 11.8% of the dry weight (DW) of individual leaves. These yields are more than twice the level reported in PHB-producing sugarcane containing the ß-ketothiolase and illustrate the importance of producing polymer in mesophyll plastids to maximize yield. The molecular weight of the polymer produced was greater than 2 × 10(6)  Da. These results are a major step forward in engineering a high biomass C4 grass for the commercial production of PHB.


Subject(s)
Acetyl-CoA C-Acyltransferase/metabolism , Hydroxybutyrates/metabolism , Polyesters/metabolism , Polyhydroxyalkanoates/metabolism , Saccharum/enzymology , Acetyl-CoA C-Acyltransferase/genetics , Acyl Coenzyme A/metabolism , Biomass , Biosynthetic Pathways , Chloroplasts/genetics , Crops, Agricultural , Mesophyll Cells/metabolism , Plant Leaves/enzymology , Plant Leaves/genetics , Plant Leaves/growth & development , Plant Proteins/genetics , Plant Proteins/metabolism , Plants, Genetically Modified , Plastids/metabolism , Saccharum/genetics , Saccharum/growth & development
4.
BMC Biotechnol ; 14: 83, 2014 Sep 10.
Article in English | MEDLINE | ID: mdl-25209261

ABSTRACT

BACKGROUND: Polyhydroxyalkanoates are linear biodegradable polyesters produced by bacteria as a carbon store and used to produce a range of bioplastics. Widespread polyhydroxyalkanoate production in C4 crops would decrease petroleum dependency by producing a renewable supply of biodegradable plastics along with residual biomass that could be converted into biofuels or energy. Increasing yields to commercial levels in biomass crops however remains a challenge. Previously, lower accumulation levels of the short side chain polyhydroxyalkanoate, polyhydroxybutyrate (PHB), were observed in the chloroplasts of mesophyll (M) cells compared to bundle sheath (BS) cells in transgenic maize (Zea mays), sugarcane (Saccharum sp.), and switchgrass (Panicum virgatum L.) leading to a significant decrease in the theoretical yield potential. Here we explore various factors which might affect polymer accumulation in mesophyll cells, including targeting of the PHB pathway enzymes to the mesophyll plastid and their access to substrate. RESULTS: The small subunit of Rubisco from pea effectively targeted the PHB biosynthesis enzymes to both M and BS chloroplasts of sugarcane and switchgrass. PHB enzyme activity was retained following targeting to M plastids and was equivalent to that found in the BS plastids. Leaf total fatty acid content was not affected by PHB production. However, when fatty acid synthesis was chemically inhibited, polymer accumulated in M cells. CONCLUSIONS: In this study, we provide evidence that access to substrate and neither poor targeting nor insufficient activity of the PHB biosynthetic enzymes may be the limiting factor for polymer production in mesophyll chloroplasts of C4 plants.


Subject(s)
Hydroxybutyrates/metabolism , Mesophyll Cells/chemistry , Panicum/metabolism , Polyesters/metabolism , Saccharum/metabolism , Chloroplasts/chemistry , Panicum/genetics , Plants, Genetically Modified/metabolism , Saccharum/genetics
5.
Plant Biotechnol J ; 12(8): 1044-52, 2014 Oct.
Article in English | MEDLINE | ID: mdl-24944109

ABSTRACT

Polyhydroxyalkanoates (PHAs) are bacterial carbon storage polymers used as renewable, biodegradable plastics. PHA production in plants may be a way to reduce industrial PHA production costs. We recently demonstrated a promising level of peroxisomal PHA production in the high biomass crop species sugarcane. However, further production strategies are needed to boost PHA accumulation closer to commercial targets. Through exogenous fatty acid feeding of Arabidopsis thaliana plants that contain peroxisome-targeted PhaA, PhaB and PhaC enzymes from Cupriavidus necator, we show here that the availability of substrates derived from the ß-oxidation cycle limits peroxisomal polyhydroxybutyrate (PHB) biosynthesis. Knockdown of peroxisomal citrate synthase activity using artificial microRNA increased PHB production levels approximately threefold. This work demonstrates that reduction of peroxisomal citrate synthase activity may be a valid metabolic engineering strategy for increasing PHA production in other plant species.


Subject(s)
Arabidopsis/enzymology , Citrate (si)-Synthase/genetics , Peroxisomes/enzymology , Polyhydroxyalkanoates/metabolism , Arabidopsis/genetics , Arabidopsis Proteins/genetics , Arabidopsis Proteins/metabolism , Biosynthetic Pathways , Citrate (si)-Synthase/metabolism , Fatty Acids/metabolism , Gene Knockdown Techniques , Metabolic Engineering , Oxidation-Reduction , Plants, Genetically Modified , Substrate Specificity
6.
Plant Biotechnol J ; 11(9): 1146-51, 2013 Dec.
Article in English | MEDLINE | ID: mdl-24112832

ABSTRACT

Polyhydroxybutyrate (PHB) is a naturally occurring bacterial polymer that can be used as a biodegradable replacement for some petrochemical-derived plastics. Polyhydroxybutyrate is produced commercially by fermentation, but to reduce production costs, efforts are underway to produce it in engineered plants, including sugarcane. However, PHB levels in this high-biomass crop are not yet commercially viable. Chemical ripening with herbicides is a strategy used to enhance sucrose production in sugarcane and was investigated here as a tool to increase PHB production. Class A herbicides inhibit ACCase activity and thus reduce fatty acid biosynthesis, with which PHB production competes directly for substrate. Treatment of PHB-producing transgenic sugarcane plants with 100 µM of the class A herbicide fluazifop resulted in a fourfold increase in PHB content in the leaves, which peaked ten days post-treatment. The minimum effective concentration of herbicide required to maximize PHB production was 30 µM for fluazifop and 70 µM for butroxydim when applied to saturation. Application of a range of class A herbicides from the DIM and FOP groups consistently resulted in increased PHB yields, particularly in immature leaf tissue. Butroxydim or fluazifop treatment of mature transgenic sugarcane grown under glasshouse conditions increased the total leaf biomass yield of PHB by 50%-60%. Application of an ACCase inhibitor in the form of a class A herbicide to mature sugarcane plants prior to harvest is a promising strategy for improving overall PHB yield. Further testing is required on field-grown transgenic sugarcane to more precisely determine the effectiveness of this strategy.


Subject(s)
Acetyl-CoA Carboxylase/antagonists & inhibitors , Herbicides/pharmacology , Hydroxybutyrates/metabolism , Saccharum/enzymology , Acetyl-CoA Carboxylase/metabolism , Biomass , Gene Expression Regulation, Plant , Genetic Engineering , Plant Leaves/drug effects , Plant Leaves/enzymology , Plant Leaves/genetics , Plant Leaves/metabolism , Plants, Genetically Modified , Saccharum/drug effects , Saccharum/genetics , Saccharum/metabolism , Time Factors
7.
Biosci Biotechnol Biochem ; 77(3): 487-96, 2013.
Article in English | MEDLINE | ID: mdl-23470752

ABSTRACT

Because sucrose stored in mature stalks (in excess of 40% of stalk dry weight) can be wholly mobilized to supply carbon for the growth of heterotrophic tissues, we propose that sucrose mobilization requires a net sink-to-source transition that acts in toto within sett internode storage parenchyma. Based on our data we propose that mobilization of sucrose from culm storage parenchyma requires minimal investment of metabolic resources, and that the mechanism of sucrose mobilization is metabolically neutral. By magnetic resonance spectroscopy and phloem-specific tracer dyes, strong evidence was found that sucrose is mobilized from sett storage parenchyma via phloem to the growing shoot tissue. An analysis of the enzyme activities involved in sucrose metabolism and glycolysis suggested that sucrose synthase activity is downregulated due to the effects of sucrose mobilization. Overall, metabolism in storage parenchyma shifts from futile cycling to a more quiescent state during sucrose mobilization.


Subject(s)
Movement , Plant Stems/metabolism , Saccharum/metabolism , Sucrose/metabolism , Coloring Agents/metabolism , Glycolysis , Magnetic Resonance Spectroscopy , Phloem/cytology , Phloem/metabolism , Plant Shoots/growth & development , Plant Stems/cytology , Saccharum/cytology , Saccharum/enzymology , Spatio-Temporal Analysis , Xylem/cytology , Xylem/metabolism
8.
J Plant Physiol ; 169(8): 830-3, 2012 May 15.
Article in English | MEDLINE | ID: mdl-22386008

ABSTRACT

Peroxisomes are functionally diverse organelles that are wholly dependent on import of nuclear-encoded proteins. The signals that direct proteins into these organelles are either found at the C-terminus (type 1 peroxisomal targeting signal; PTS1) or N-terminus (type 2 peroxisomal targeting signal; PTS2) of the protein. Based on a limited number of tests in heterologous systems, PTS1 signals appear to be conserved across species. To further test the generality of this conclusion and to establish the extent to which the PTS1 signals can be relied on for biotechnological purposes across species, we tested two PTS1 signals for their ability to target fluorescent proteins in diverse plant species. Transient assays following microprojectile bombardment showed that the six amino acid PTS1 sequence (RAVARL) from spinach glycolate oxidase effectively targets green fluorescent fusion protein to the leaf peroxisomes in all 20 crops tested, including four monocots (sugarcane, wheat, corn and onion) and 16 dicots (carrot, cucumber, broccoli, tomato, lettuce, turnip, radish, cauliflower, cabbage, capsicum, celery, tobacco, petunia, beetroot, eggplant and coriander). Similarly, results indicated that the 10 amino acid PTS1 sequence (IHHPRELSRL) from pumpkin malate synthase effectively targets red fluorescent fusion protein to the leaf peroxisomes in all four crops tested including monocot (sugarcane) and dicot (cabbage, celery and pumpkin) species. These signal sequences should be useful metabolic engineering tools to direct recombinant proteins to the leaf peroxisomes in diverse plant species of biotechnological interest.


Subject(s)
Alcohol Oxidoreductases/metabolism , Crops, Agricultural/metabolism , Green Fluorescent Proteins/metabolism , Peroxisomes/metabolism , Plant Leaves/metabolism , Alcohol Oxidoreductases/chemistry , Amino Acid Sequence , Malate Synthase/chemistry , Malate Synthase/metabolism , Microscopy, Confocal , Molecular Sequence Data , Plant Growth Regulators/metabolism , Plant Leaves/cytology , Protein Sorting Signals , Protein Transport , Spinacia oleracea/metabolism
9.
Plant Biotechnol J ; 10(5): 569-78, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22369516

ABSTRACT

Polyhydroxybutyrate (PHB) is a bacterial polyester that has properties similar to some petrochemically produced plastics. Plant-based production has the potential to make this biorenewable plastic highly competitive with petrochemical-based plastics. We previously reported that transgenic sugarcane produced PHB at levels as high as 1.8% leaf dry weight without penalty to biomass accumulation, suggesting scope for improving PHB production in this species. In this study, we used different plant and viral promoters, in combination with multigene or single-gene constructs to increase PHB levels. Promoters tested included the maize and rice polyubiquitin promoters, the maize chlorophyll A/B-binding protein promoter and a Cavendish banana streak badnavirus promoter. At the seedling stage, the highest levels of polymer were produced in sugarcane plants when the Cavendish banana streak badnavirus promoter was used. However, in all cases, this promoter underwent silencing as the plants matured. The rice Ubi promoter enabled the production of PHB at levels similar to the maize Ubi promoter. The maize chlorophyll A/B-binding protein promoter enabled the production of PHB to levels as high as 4.8% of the leaf dry weight, which is approximately 2.5 times higher than previously reported levels in sugarcane. This is the first time that this promoter has been tested in sugarcane. The highest PHB-producing lines showed phenotypic differences to the wild-type parent, including reduced biomass and slight chlorosis.


Subject(s)
Hydroxybutyrates/metabolism , Plants, Genetically Modified/metabolism , Polyesters/metabolism , Saccharum/metabolism , Badnavirus/genetics , Biomass , Gene Expression Regulation, Plant , Plants, Genetically Modified/genetics , Promoter Regions, Genetic , Saccharum/genetics , Transformation, Genetic , Zea mays/genetics
10.
Springerplus ; 1(1): 74, 2012 Dec.
Article in English | MEDLINE | ID: mdl-23539210

ABSTRACT

To engineer trehalose metabolism in sugarcane (Saccharum spp. hybrids) two transgenes were introduced to the genome: trehalose-6-phosphate synthase- phosphatase (TPSP), to increase trehalose biosynthesis and an RNAi transgene specific for trehalase, to abrogate trehalose catabolism. In RNAi-expressing lines trehalase expression was abrogated in many plants however no decrease in trehalase activity was observed. In TPSP lines trehalase activity was significantly higher. No events of co-integration of TPSP and RNAi transgenes were observed. We suggest trehalase activity is essential to mitigate embryonic lethal effects of trehalose metabolism and discuss the implications for engineering trehalose metabolism.

11.
Curr Microbiol ; 63(4): 392-401, 2011 Oct.
Article in English | MEDLINE | ID: mdl-21850475

ABSTRACT

Yeasts associate with numerous insects, and they can assist the metabolic processes within their hosts. Two distinct yeasts were identified by PCR within the planthopper Perkinsiella saccharicida, the vector of Fiji disease virus to sugarcane. The utility of both microbes for potential paratransgenic approaches to control Fiji leaf gall (FLG) was assessed. Phylogenetic analysis showed one of the microbes is related to yeast-like symbionts from the planthoppers: Laodelphax striatellus, Nilaparvata lugens, and Sogetella furcifera. The second yeast was a member of the Candida genus, a group that has been identified in beetles and recently described in planthoppers. Microscopy revealed the presence of yeast in the fat body of P. saccharicida. The Candida yeast was cultured, and transformation was accomplished by electroporation of Candida albicans codon optimized plasmids, designed to integrate into the genome via homologous recombination. Transgenic lines conferred resistance to the antibiotic nourseothricin and expression of green fluorescent protein was observed in a proportion of the yeast cells. Stably transformed yeast lines could not be isolated as the integrative plasmids presumably replicated within the yeast without integration into the genome. If stable transformation can be achieved, then this yeast may be useful as an agent for a paratransgenic control of FLG.


Subject(s)
Hemiptera/microbiology , Plant Diseases/prevention & control , Plant Diseases/virology , Reoviridae/physiology , Saccharum/virology , Yeasts/isolation & purification , Animals , Hemiptera/physiology , Hemiptera/virology , Insect Vectors/microbiology , Insect Vectors/physiology , Insect Vectors/virology , Molecular Sequence Data , Pest Control, Biological , Phylogeny , Plant Leaves/virology , Reoviridae/genetics , Symbiosis , Yeasts/classification , Yeasts/genetics , Yeasts/physiology
12.
Plant Biotechnol J ; 9(9): 958-69, 2011 Dec.
Article in English | MEDLINE | ID: mdl-21447054

ABSTRACT

Polyhydroxyalkanoates (PHAs) are bacterial carbon storage polymers with diverse plastic-like properties. PHA biosynthesis in transgenic plants is being developed as a way to reduce the cost and increase the sustainability of industrial PHA production. The homopolymer polyhydroxybutyrate (PHB) is the simplest form of these biodegradable polyesters. Plant peroxisomes contain the substrate molecules and necessary reducing power for PHB biosynthesis, but peroxisomal PHB production has not been explored in whole soil-grown transgenic plants to date. We generated transgenic sugarcane (Saccharum sp.) with the three-enzyme Ralstonia eutropha PHA biosynthetic pathway targeted to peroxisomes. We also introduced the pathway into Arabidopsis thaliana, as a model system for studying and manipulating peroxisomal PHB production. PHB, at levels up to 1.6%-1.8% dry weight, accumulated in sugarcane leaves and A. thaliana seedlings, respectively. In sugarcane, PHB accumulated throughout most leaf cell types in both peroxisomes and vacuoles. A small percentage of total polymer was also identified as the copolymer poly (3-hydroxybutyrate-co-3-hydroxyvalerate) in both plant species. No obvious deleterious effect was observed on plant growth because of peroxisomal PHA biosynthesis at these levels. This study highlights how using peroxisomal metabolism for PHA biosynthesis could significantly contribute to reaching commercial production levels of PHAs in crop plants.


Subject(s)
Peroxisomes/metabolism , Polyhydroxyalkanoates/biosynthesis , Saccharum/metabolism , Acetyl-CoA C-Acyltransferase/metabolism , Arabidopsis/genetics , Arabidopsis/growth & development , Arabidopsis/metabolism , Cloning, Molecular , Cupriavidus necator/genetics , Cupriavidus necator/metabolism , Enzyme Assays , Gene Dosage , Gene Expression Regulation, Plant , Genetic Vectors/genetics , Genetic Vectors/metabolism , Plant Leaves/genetics , Plant Leaves/metabolism , Plants, Genetically Modified/genetics , Plants, Genetically Modified/growth & development , Plants, Genetically Modified/metabolism , Polyesters/metabolism , Saccharum/genetics , Saccharum/growth & development , Seedlings/genetics , Seedlings/metabolism , Transformation, Genetic , Vacuoles/metabolism , Zea mays/genetics
13.
Plant Physiol ; 154(4): 1871-85, 2010 Dec.
Article in English | MEDLINE | ID: mdl-20974891

ABSTRACT

Leaves of C(4) grasses (such as maize [Zea mays], sugarcane [Saccharum officinarum], and sorghum [Sorghum bicolor]) form a classical Kranz leaf anatomy. Unlike C(3) plants, where photosynthetic CO(2) fixation proceeds in the mesophyll (M), the fixation process in C(4) plants is distributed between two cell types, the M cell and the bundle sheath (BS) cell. Here, we develop a C(4) genome-scale model (C4GEM) for the investigation of flux distribution in M and BS cells during C(4) photosynthesis. C4GEM, to our knowledge, is the first large-scale metabolic model that encapsulates metabolic interactions between two different cell types. C4GEM is based on the Arabidopsis (Arabidopsis thaliana) model (AraGEM) but has been extended by adding reactions and transporters responsible to represent three different C(4) subtypes (NADP-ME [for malic enzyme], NAD-ME, and phosphoenolpyruvate carboxykinase). C4GEM has been validated for its ability to synthesize 47 biomass components and consists of 1,588 unique reactions, 1,755 metabolites, 83 interorganelle transporters, and 29 external transporters (including transport through plasmodesmata). Reactions in the common C(4) model have been associated with well-annotated C(4) species (NADP-ME subtypes): 3,557 genes in sorghum, 11,623 genes in maize, and 3,881 genes in sugarcane. The number of essential reactions not assigned to genes is 131, 135, and 156 in sorghum, maize, and sugarcane, respectively. Flux balance analysis was used to assess the metabolic activity in M and BS cells during C(4) photosynthesis. Our simulations were consistent with chloroplast proteomic studies, and C4GEM predicted the classical C(4) photosynthesis pathway and its major effect in organelle function in M and BS. The model also highlights differences in metabolic activities around photosystem I and photosystem II for three different C(4) subtypes. Effects of CO(2) leakage were also explored. C4GEM is a viable framework for in silico analysis of cell cooperation between M and BS cells during photosynthesis and can be used to explore C(4) plant metabolism.


Subject(s)
Arabidopsis/genetics , Genome, Plant , Models, Biological
14.
Phytochemistry ; 71(7): 736-41, 2010 May.
Article in English | MEDLINE | ID: mdl-20193955

ABSTRACT

Sugarcane (a Saccharum spp. interspecific hybrid) was previously engineered to synthesize sorbitol (designated as sorbitolcane). Motivated by the atypical development of the leaves in some sorbitolcane, the polar metabolite profiles in the leaves of those plants were compared against a group of control sugarcane plants. Eighty-six polar metabolites were detected in leaf extracts by GC-MS. Principal component analysis of the metabolites indicated that three compounds were strongly associated with sorbitolcane. Two were identified as sorbitol and gentiobiose and the third was unknown. Gentiobiose and the unknown compound were positively correlated with sorbitol accumulation. The unknown compound was only abundant in sorbitolcane. This compound was structurally characterized and found to be a sorbitol-glucose conjugate. (13)C NMR analysis indicated that the glucopyranose and glucitol moieties were 1,6-linked. Ligand exchange chromatography confirmed that the compound was a beta-anomer, thus identifying the compound as 6-O-beta-d-glucopyranosyl-D-glucitol, or gentiobiitol.


Subject(s)
Saccharum/metabolism , Sorbitol/analogs & derivatives , Sorbitol/metabolism , Chromatography, High Pressure Liquid , Chromatography, Ion Exchange , Gas Chromatography-Mass Spectrometry , Glycosylation , Magnetic Resonance Spectroscopy , Plant Leaves/chemistry , Plants, Genetically Modified , Saccharum/genetics , Sorbitol/chemical synthesis
15.
Plant Physiol ; 152(2): 579-89, 2010 Feb.
Article in English | MEDLINE | ID: mdl-20044452

ABSTRACT

Genome-scale metabolic network models have been successfully used to describe metabolism in a variety of microbial organisms as well as specific mammalian cell types and organelles. This systems-based framework enables the exploration of global phenotypic effects of gene knockouts, gene insertion, and up-regulation of gene expression. We have developed a genome-scale metabolic network model (AraGEM) covering primary metabolism for a compartmentalized plant cell based on the Arabidopsis (Arabidopsis thaliana) genome. AraGEM is a comprehensive literature-based, genome-scale metabolic reconstruction that accounts for the functions of 1,419 unique open reading frames, 1,748 metabolites, 5,253 gene-enzyme reaction-association entries, and 1,567 unique reactions compartmentalized into the cytoplasm, mitochondrion, plastid, peroxisome, and vacuole. The curation process identified 75 essential reactions with respective enzyme associations not assigned to any particular gene in the Kyoto Encyclopedia of Genes and Genomes or AraCyc. With the addition of these reactions, AraGEM describes a functional primary metabolism of Arabidopsis. The reconstructed network was transformed into an in silico metabolic flux model of plant metabolism and validated through the simulation of plant metabolic functions inferred from the literature. Using efficient resource utilization as the optimality criterion, AraGEM predicted the classical photorespiratory cycle as well as known key differences between redox metabolism in photosynthetic and nonphotosynthetic plant cells. AraGEM is a viable framework for in silico functional analysis and can be used to derive new, nontrivial hypotheses for exploring plant metabolism.


Subject(s)
Arabidopsis/metabolism , Computational Biology/methods , Metabolic Networks and Pathways , Models, Genetic , Arabidopsis/genetics , Computer Simulation , Genome, Plant
16.
J Plant Physiol ; 167(4): 329-32, 2010 Mar 01.
Article in English | MEDLINE | ID: mdl-19879015

ABSTRACT

Metabolic engineering of plant peroxisomes for biotechnological purposes typically requires efficient peroxisomal targeting of heterologous proteins. Type I peroxisomal targeting signals (PTS1) consist of three uncleaved amino acids (SKL or a conserved variant) at the carboxyl terminus and direct nuclear-encoded proteins into the peroxisomes of eukaryotic cells. PTS1 fusion with a heterologous protein results in peroxisomal targeting of that protein, but the minimal length of PTS1 required for efficient targeting in plants is vague. Here, we determine short effective PTS1 sequences derived from plant peroxisomal proteins to target four heterologous proteins, namely the green fluorescent protein (GFP) and the three enzymes required for polyhydroxybutyrate (PHB) production, PhaA, PhaB and PhaC, each fused to the C-terminus of GFP. Transient expression analysis in leaf cells of Saccharum sp. (sugarcane interspecific hybrids) indicated that a three amino acid (ARL) PTS1 effectively targeted only GFP and PhaB to peroxisomes. The same signal was not sufficient to target PhaA and only inefficiently targeted PhaC. An alternative, prototypic three amino acid (SKL) PTS1 was also insufficient to target PhaA and inefficient in targeting PhaC, whilst a six amino acid (RAVARL) PTS1 efficiently targeted both of these enzymes. This study highlights the need for more than a three amino acid PTS1 to target some heterologous proteins to plant peroxisomes.


Subject(s)
Amino Acids/metabolism , Peroxisomes/enzymology , Polyesters/metabolism , Protein Sorting Signals , Green Fluorescent Proteins/metabolism , Microscopy, Confocal , Plant Leaves/cytology , Plant Leaves/metabolism , Saccharum/cytology , Saccharum/metabolism , Structure-Activity Relationship
17.
Curr Genet ; 55(5): 571-81, 2009 Oct.
Article in English | MEDLINE | ID: mdl-19730866

ABSTRACT

Metarhizium anisopliae is a naturally occurring cosmopolitan fungus infecting greyback canegrubs (Dermolepida albohirtum). The main molecular factors involved in the complex interactions occurring between the greyback canegrubs and M. anisopliae (FI-1045) were investigated by comparing the proteomes of healthy canegrubs, canegrubs infected with Metarhizium and fungus only. Differentially expressed proteins from the infected canegrubs were subjected to mass spectrometry to search for pathogenicity related proteins. Immune-related proteins of canegrubs identified in this study include cytoskeletal proteins (actin), cell communication proteins, proteases and peptidases. Fungal proteins identified include metalloproteins, acyl-CoA, cyclin proteins and chorismate mutase. Comparative proteome analysis provided a view into the cellular reactions triggered in the canegrub in response to the fungal infection at the onset of biological control.


Subject(s)
Coleoptera/microbiology , Metarhizium/physiology , Proteome , Animals , Coleoptera/growth & development , Electrophoresis, Polyacrylamide Gel , Insect Proteins/metabolism , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
18.
Appl Environ Microbiol ; 74(13): 4036-43, 2008 Jul.
Article in English | MEDLINE | ID: mdl-18456847

ABSTRACT

Bacteria from the hindguts of Dermolepida albohirtum larvae were assessed for their potential to be used in paratransgenic strategies that target scarab pests of sugarcane. Bacteria isolated in pure culture from the hindguts of D. albohirtum larvae were from the Proteobacteria, Firmicutes, and Actinobacteria phyla and matched closely with taxa from intestinal and rhizosphere environments. However, these isolates were not the most common gut-associated bacteria identified in denaturing gradient gel electrophoresis (DGGE) hindgut profiles. Subsequently, eight species of gut bacteria were fed to larvae, and RNA-based DGGE analysis of 16S rRNA was used to detect the persistence of these isolates in the hindgut environment. One of these isolates (Da-11) remained metabolically active in the hindgut for 19 days postconsumption. Da-11 most likely forms a new genus within the Burkholderiales order, along with taxa independently identified from larvae of the European scarab pest, Melolontha melolontha. Using the EZ::Tn5 transposon system, a kanamycin resistance gene was inserted into the chromosome of Da-11, thus establishing a stable transformation technique for this species. A second feeding trial that included inoculating approximately 400 transgenic Da-11 cells onto a food source resulted in a density of 1 x 10(6) transgenic Da-11 cells/ml in the hindguts of larvae at 9 days postconsumption. These populations were maintained in the hindgut for at least another 12 days. The successful isolation, genetic transformation, and establishment of transgenic Da-11 cells in the hindguts of D. albohirtum larvae fulfill fundamental requirements for the future development of a paratransgenic approach to control scarab pests of sugarcane.


Subject(s)
Bacteria/isolation & purification , Coleoptera/growth & development , Intestines/microbiology , Transformation, Bacterial , Transgenes , Animals , Bacteria/classification , Bacteria/genetics , Bacteria/growth & development , Behavior, Animal , Coleoptera/microbiology , Coleoptera/physiology , DNA Transposable Elements/genetics , Feeding Behavior , Larva/microbiology , Larva/physiology , Molecular Sequence Data , Phylogeny , Plasmids/genetics , Sequence Analysis, DNA
19.
Funct Plant Biol ; 35(2): 166-170, 2008 Apr.
Article in English | MEDLINE | ID: mdl-32688768

ABSTRACT

Approximately 10-15% of plant nuclear genes appear to encode mitochondrial proteins that are directed to mitochondria by specific targeting signals. Reports on the heterologous function of these targeting signals are generally limited to one or a few species, with an emphasis on model plants such as tobacco and Arabidopsis. Given their sequence diversity and their insufficient testing in commercially important crops (including monocotyledonous crops), the extent to which these signals can be relied on for biotechnological purposes across species remains to be established. This study provides the experimental verification of a mitochondrial signal that is functional across diverse crop species, including five monocots (sugarcane, wheat, corn, sorghum and onion) and seven dicots (cucumber, cauliflower, tomato, capsicum, pumpkin, coriander and sunflower). In all 12 crops, transient assays following microprojectile bombardment showed that the N-terminal mitochondrial presequence from F1-ATPase ß-subunit (ATPase-ß) of Nicotiana plumbaginifolia Viv. targeted green fluorescent fusion protein to the mitochondria. The transient assay results in sugarcane were confirmed in stably transformed root cells. The ATPase-ß signal should be a useful metabolic engineering tool for directing recombinant proteins to the mitochondrial matrix in diverse plant species of commercial interest.

20.
Appl Environ Microbiol ; 74(3): 762-7, 2008 Feb.
Article in English | MEDLINE | ID: mdl-18083861

ABSTRACT

Symbiotic bacteria residing in the hindgut chambers of scarab beetle larvae may be useful in paratransgenic approaches to reduce larval root-feeding activities on agricultural crops. We compared the bacterial community profiles associated with the hindgut walls of individual Dermolepida albohirtum third-instar larvae over 2 years and those associated with their plant root food source among different geographic regions. Denaturing gradient gel electrophoresis analysis was used with universal and Actinobacteria-specific 16S rRNA primers to reveal a number of taxa that were found consistently in all D. albohirtum larvae but not in samples from their food source, sugarcane roots. These taxa included representatives from the "Endomicrobia," Firmicutes, Proteobacteria, and Actinobacteria and were related to previously described bacteria from the intestines of other scarab larvae and termites. These universally distributed taxa have the potential to form vertically transmitted symbiotic associations with these insects.


Subject(s)
Bacteria/classification , Bacteria/isolation & purification , Coleoptera/growth & development , Coleoptera/microbiology , Intestines/microbiology , Actinobacteria/classification , Actinobacteria/genetics , Actinobacteria/isolation & purification , Animals , Bacteria/genetics , DNA, Bacterial/analysis , DNA, Bacterial/isolation & purification , Larva/microbiology , Molecular Sequence Data , Phylogeny , Plant Roots/microbiology , Saccharum/microbiology , Sequence Analysis, DNA , Soil Microbiology
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