Donald Danforth Plant Science Center

Continued growth and intensification of aquaculture production depends upon the development of sustainable protein sources to replace fish meal in aquafeeds. This document reviews various plant feedstuffs, which currently are or potentially may be incorporated into aquafeeds to support the sustainable production of various fish species in aquaculture. The plant feedstuffs considered include oilseeds, legumes and cereal grains, which traditionally have been used as protein or energy concentrates as well as novel products developed through various processing technologies. The nutritional composition of these various feedstuffs are considered along with the presence of any bioactive compounds that may positively or negatively affect the target organism. Lipid composition of these feedstuffs is not specifically considered although it is recognized that incorporating lipid supplements in aquafeeds to achieve proper fatty acid profiles to meet the metabolic requirements of fish and maximize human health benefits are important aspects. Specific strategies and techniques to optimize the nutritional composition of plant feedstuffs and limit potentially adverse effects of bioactive compounds are also described. Such information will provide a foundation for developing strategic research plans for increasing the use of plant feedstuffs in aquaculture to reduce dependence of animal feedstuffs and thereby enhance the sustainability of aquaculture.

Comparing photosynthetic and photovoltaic efficiencies is not a simple issue. Although both processes harvest the energy in sunlight, they operate in distinctly different ways and produce different types of products: biomass or chemical fuels in the case of natural photosynthesis and nonstored electrical current in the case of photovoltaics. In order to find common ground for evaluating energy-conversion efficiency, we compare natural photosynthesis with present technologies for photovoltaic-driven electrolysis of water to produce hydrogen. Photovoltaic-driven electrolysis is the more efficient process when measured on an annual basis, yet short-term yields for photosynthetic conversion under optimal conditions come within a factor of 2 or 3 of the photovoltaic benchmark. We consider opportunities in which the frontiers of synthetic biology might be used to enhance natural photosynthesis for improved solar energy conversion efficiency.

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

Bacterial blight of rice is an important disease in Asia and Africa. The pathogen, Xanthomonas oryzae pv. oryzae (Xoo), secretes one or more of six known transcription-activator-like effectors (TALes) that bind specific promoter sequences and induce, at minimum, one of the three host sucrose transporter genes SWEET11, SWEET13 and SWEET14, the expression of which is required for disease susceptibility. We used CRISPR-Cas9-mediated genome editing to introduce mutations in all three SWEET gene promoters. Editing was further informed by sequence analyses of TALe genes in 63 Xoo strains, which revealed multiple TALe variants for SWEET13 alleles. Mutations were also created in SWEET14, which is also targeted by two TALes from an African Xoo lineage. A total of five promoter mutations were simultaneously introduced into the rice line Kitaake and the elite mega varieties IR64 and Ciherang-Sub1. Paddy trials showed that genome-edited SWEET promoters endow rice lines with robust, broad-spectrum resistance.

Plant growth and development are regulated by internal signals and by external environmental conditions. One important regulator that coordinates growth and development with responses to the environment is the sesquiterpenoid hormone abscisic acid (ABA). ABA plays important roles in many cellular

Ray Ming, Robert Paull, Qingyi Yu and colleagues report the genome sequences of two cultivated pineapple varieties and one wild pineapple relative. Their analysis supports the use of the pineapple as a reference genome for monocot comparative genomics and provides insight into the evolution of crassulacean acid metabolism photosynthesis. Pineapple (Ananas comosus (L.) Merr.) is the most economically valuable crop possessing crassulacean acid metabolism (CAM), a photosynthetic carbon assimilation pathway with high water-use efficiency, and the second most important tropical fruit. We sequenced the genomes of pineapple varieties F153 and MD2 and a wild pineapple relative, Ananas bracteatus accession CB5. The pineapple genome has one fewer ancient whole-genome duplication event than sequenced grass genomes and a conserved karyotype with seven chromosomes from before the ρ duplication event. The pineapple lineage has transitioned from C3 photosynthesis to CAM, with CAM-related genes exhibiting a diel expression pattern in photosynthetic tissues. CAM pathway genes were enriched with cis-regulatory elements associated with the regulation of circadian clock genes, providing the first cis-regulatory link between CAM and circadian clock regulation. Pineapple CAM photosynthesis evolved by the reconfiguration of pathways in C3 plants, through the regulatory neofunctionalization of preexisting genes and not through the acquisition of neofunctionalized genes via whole-genome or tandem gene duplication.

Anticipated population growth, shifting demographics, and environmental variability over the next century are expected to threaten global food security. In the face of these challenges, crop yield for food and fuel must be maintained and improved using fewer input resources. In recent years, genetic tools for profiling crop germplasm has benefited from rapid advances in DNA sequencing, and now similar advances are needed to improve the throughput of plant phenotyping. We highlight recent developments in high-throughput plant phenotyping using robotic-assisted imaging platforms and computer vision-assisted analysis tools.

Plant transformation has enabled fundamental insights into plant biology and revolutionized commercial agriculture. Unfortunately, for most crops, transformation and regeneration remain arduous even after more than 30 years of technological advances. Genome editing provides novel opportunities to enhance crop productivity but relies on genetic transformation and plant regeneration, which are bottlenecks in the process. Here, we review the state of plant transformation and point to innovations needed to enable genome editing in crops. Plant tissue culture methods need optimization and simplification for efficiency and minimization of time in culture. Currently, specialized facilities exist for crop transformation. Single-cell and robotic techniques should be developed for high-throughput genomic screens. Plant genes involved in developmental reprogramming, wound response, and/or homologous recombination should be used to boost the recovery of transformed plants. Engineering universal Agrobacterium tumefaciens strains and recruiting other microbes, such as Ensifer or Rhizobium, could facilitate delivery of DNA and proteins into plant cells. Synthetic biology should be employed for de novo design of transformation systems. Genome editing is a potential game-changer in crop genetics when plant transformation systems are optimized.

Trillions of microbes inhabit the distal gut of adult humans. They have evolved to compete efficiently for nutrients, including a wide array of chemically diverse, complex glycans present in our diets, secreted by our intestinal mucosa, and displayed on the surfaces of other gut microbes. Here, we review how members of the Bacteroidetes, one of two dominant gut-associated bacterial phyla, process complex glycans using a series of similarly patterned, cell envelope-associated multiprotein systems. These systems provide insights into how gut, as well as terrestrial and aquatic, Bacteroidetes survive in highly competitive ecosystems. Trillions of microbes inhabit the distal gut of adult humans. They have evolved to compete efficiently for nutrients, including a wide array of chemically diverse, complex glycans present in our diets, secreted by our intestinal mucosa, and displayed on the surfaces of other gut microbes. Here, we review how members of the Bacteroidetes, one of two dominant gut-associated bacterial phyla, process complex glycans using a series of similarly patterned, cell envelope-associated multiprotein systems. These systems provide insights into how gut, as well as terrestrial and aquatic, Bacteroidetes survive in highly competitive ecosystems. Our distal gut is home to one of the most densely populated microbial ecosystems on Earth. Dominated by members of the domain Bacteria, the gut microbiota harbors a collection of beneficial symbionts (mutualists) that perform myriad functions, including the provision of metabolic attributes not encoded in the human genome. One such attribute is the ability to ferment otherwise indigestible complex glycans to products such as short-chain fatty acids that we can absorb (1Flint H.J. Bayer E.A. Rincon M.T. Lamed R. White B.A. Nat. Rev. Microbiol. 2008; 6: 121-131Crossref PubMed Scopus (1160) Google Scholar). This microbial process can provide up to 10% of daily caloric intake depending upon the diet (2McNeil N.I. Am. J. Clin. Nutr. 1984; 39: 338-342Crossref PubMed Scopus (509) Google Scholar). Viewed at the broadest taxonomic level, the distal gut microbiota of humans and other mammals is typically dominated by two of the ∼100 known bacterial phyla (divisions): Bacteroidetes and Firmicutes (3Ley R.E. Hamady M. Lozupone C. Turnbaugh P.J. Ramey R.R. Bircher J.S. Schlegel M.L. Tucker T.A. Schrenzel M.D. Knight R. Gordon J.I. Science. 2008; 320: 1647-1651Crossref PubMed Scopus (2398) Google Scholar). During the past 2 years, several HMPs 2The abbreviations used are:HMPhuman microbiome projectPULpolysaccharide utilization locusECF-σextracytoplasmic function-σ.2The abbreviations used are:HMPhuman microbiome projectPULpolysaccharide utilization locusECF-σextracytoplasmic function-σ.have been initiated throughout the world to better understand the assembly and composition of the microbiota in both healthy humans and those suffering from various pathophysiologic states such as obesity and inflammatory bowel diseases (4Turnbaugh P.J. Ley R.E. Hamady M. Fraser-Liggett C.M. Knight R. Gordon J.I. Nature. 2007; 449: 804-810Crossref PubMed Scopus (3600) Google Scholar). These HMPs seek to determine the organismal diversity and gene content of the gut microbiota using culture-independent (metagenomic) approaches in conjunction with sequencing of several hundred cultured representatives of gut and non-gut communities. A central challenge to the sequencing efforts of HMPs is to go beyond descriptions of “who is there” or “what genes are present” in a community by continuing to probe the mechanisms by which microbes gain access to their habitats, operate as a community, and shape the biological properties of their hosts. In the distal gut, one important area is deciphering how community members have evolved to feed off the complex glycans that constantly inundate their habitat. human microbiome project polysaccharide utilization locus extracytoplasmic function-σ. human microbiome project polysaccharide utilization locus extracytoplasmic function-σ. Individual representatives of several bacterial phyla, including the Bacteroidetes and Firmicutes, are capable of metabolizing a variety of complex carbohydrates (5Salyers A.A. West S.E. Vercellotti J.R. Wilkins T.D. Appl. Environ. Microbiol. 1977; 34: 529-533Crossref PubMed Google Scholar). Early phenotypic surveys revealed that the Gram-negative Bacteroidetes typically harbor very broad saccharolytic potential, with some species able to target dozens of different complex glycans (6Salyers A.A. Vercellotti J.R. West S.E. Wilkins T.D. Appl. Environ. Microbiol. 1977; 33: 319-322Crossref PubMed Google Scholar). Members of the genus Bacteroides are prominently represented in the intestine: some are notably aerotolerant and therefore readily cultured outside of their native habitat. Combined with the development of tools for their genetic manipulation (7Salyers A.A. Bonheyo G. Shoemaker N.B. Methods. 2000; 20: 35-46Crossref PubMed Scopus (41) Google Scholar), they have become favored models for characterizing mechanisms of glycan metabolism by gut bacteria. A number of different plant-associated glycans are common components of our diets. These include plant cell storage glycans, such as starches and fructans, and plant cell wall glycans. Among cell wall glycans, cellulose is the most abundant, followed by two heterogeneous classes of polysaccharides: hemicelluloses and pectins. Hemicelluloses include xylan, galactoglucomannans, and xyloglucan (8York W.S. O'Neill M.A. Curr. Opin. Plant Biol. 2008; 11: 258-265Crossref PubMed Scopus (153) Google Scholar). Pectin is composed of homogalacturonan and/or rhamnogalacturonan I backbones that can be decorated with additional side chains such as rhamnogalacturonan II, β-1,4- and β-1,3-galactans (each of which may contain α-arabinose branches), and α-arabinan (9Mohnen D. Curr. Opin. Plant Biol. 2008; 11: 266-277Crossref PubMed Scopus (1471) Google Scholar). These dietary plant glycans, many of which cannot be digested in the proximal gut by the host, combine with mucin O-glycans, N-glycans, and glycosaminoglycans produced by the intestinal mucosa and the diverse repertoire of polysaccharide capsules and cell walls present on other gut microbes to form a biochemically rich nutrient foundation that sustains members of the distal gut microbiota. Seminal work by members of the laboratory of Abigail Salyers provided a template for understanding how Bacteroides thetaiotaomicron, a prominent human gut Bacteroidete, is able to catabolize dietary glycans. Through their studies of starch degradation, they discovered a cell envelope-associated multiprotein system, which they named Sus (starch utilization system), that enables the bacterium to bind and degrade this carbohydrate. Subsequent microbial genome sequencing projects revealed that derivatives of this prototypic system (“Sus-like systems”) are highly represented in the genome of B. thetaiotaomicron and many other saccharolytic Bacteroidetes. A key feature of these Sus-like systems is the coordinated action of several gene products involved in substrate binding and degradation. Like other multicomponent strategies for glycan degradation (e.g. cellulosomes), this model highlights the fact that the concerted activities of multiple gene products can be more sophisticated and elaborate than their individual and isolated functions. Below, we review the current model of how the B. thetaiotaomicron Sus mediates starch utilization and then consider the breadth of different glycan substrates targeted by the many other Sus-like systems present in B. thetaiotaomicron and other related species from diverse habitats. The sus locus consists of eight adjacent genes, susRABCDEFG, that encode proteins composing the cell envelope-associated apparatus illustrated in Fig. 1. SusCDEFG localize to the outer membrane (10Shipman J.A. Berleman J.E. Salyers A.A. J. Bacteriol. 2000; 182: 5365-5372Crossref PubMed Scopus (158) Google Scholar). SusC is a member of the TonB-dependent receptor family, a group of outer membrane-spanning β-barrel proteins that transport solutes and macromolecules via energy derived from the proton-motive force and the TonB-ExbBD complex (11Ferguson A.D. Deisenhofer J. Biochim. Biophys. Acta. 2002; 1565: 318-332Crossref PubMed Scopus (119) Google Scholar, 12Schauer K. Rodionov D.A. de Reuse H. Trends Biochem. Sci. 2008; 33: 330-338Abstract Full Text Full Text PDF PubMed Scopus (255) Google Scholar). SusDEFG are predicted lipoproteins that contain a bacterial signal peptidase II recognition motif. Following cleavage of their signal peptides, an N-acyl-S-diacylglyceryl moiety is covalently linked to their N-terminal cysteines (13Bos M.P. Robert V. Tommassen J. Annu. Rev. Microbiol. 2007; 61: 191-214Crossref PubMed Scopus (352) Google Scholar). Immunohistochemical studies of intact and disrupted B. thetaiotaomicron cells suggest that all four Sus lipoproteins are exposed to the external environment, consistent with the notion that they are trafficked to and remain at the outer leaflet of the plasma membrane (10Shipman J.A. Berleman J.E. Salyers A.A. J. Bacteriol. 2000; 182: 5365-5372Crossref PubMed Scopus (158) Google Scholar). The three remaining Sus products (SusRAB) contain signal peptidase I recognition motifs. SusA and SusB remain in the periplasm (10Shipman J.A. Berleman J.E. Salyers A.A. J. Bacteriol. 2000; 182: 5365-5372Crossref PubMed Scopus (158) Google Scholar), whereas SusR contains a single internal transmembrane region that allows it to span the cytoplasmic membrane and extend domains into both the periplasm and cytoplasm (see below). Initial genetic experiments suggested that Sus function was required only for catabolism of starch-derived glycans containing four or more glucose units and was dispensable during growth on glucose, maltose, and maltotriose (14Tancula E. Feldhaus M.J. Bedzyk L.A. Salyers A.A. J. Bacteriol. 1992; 174: 5609-5616Crossref PubMed Scopus (66) Google Scholar). A requisite step in starch utilization is binding of the glycan to the cell surface (15Anderson K.L. Salyers A.A. J. Bacteriol. 1989; 171: 3192-3198Crossref PubMed Scopus (105) Google Scholar). Before this can occur, extracellular starch must transit a polysaccharide capsule that may be several hundred nanometers thick (Fig. 1, upper left inset). Intriguingly, B. thetaiotaomicron coordinates expression of some of its eight capsular polysaccharide synthesis loci via transcriptional regulators that also mediate expression of a subset of its Sus-like systems (16Martens E.C. Roth R. Heuser J.E. Gordon J.I. J. Biol. Chem. 2009; 284: 18445-18457Abstract Full Text Full Text PDF PubMed Scopus (129) Google Scholar). Thus, B. thetaiotaomicron may alter the chemical composition of its surface capsule to facilitate utilization of extracellular glycans. Starch binding at the cell surface is accomplished through the concerted efforts of SusCDEF (10Shipman J.A. Berleman J.E. Salyers A.A. J. Bacteriol. 2000; 182: 5365-5372Crossref PubMed Scopus (158) Google Scholar, 17Reeves A.R. Wang G.R. Salyers A.A. J. Bacteriol. 1997; 179: 643-649Crossref PubMed Scopus (148) Google Scholar). Recent biochemical and structural characterizations of SusD revealed that each SusD monomer has a single oligosaccharide-binding pocket that interacts with up to three individual glucose units in the target glycan (18Koropatkin N.M. Martens E.C. Gordon J.I. Smith T.J. Structure. 2008; 16: 1105-1115Abstract Full Text Full Text PDF PubMed Scopus (224) Google Scholar). This pocket is composed of an arc of aromatic residues that conforms to the characteristic helical shape of amylose (Fig. 1, upper right inset) (19Boraston A.B. Bolam D.N. Gilbert H.J. Davies G.J. Biochem. J. 2004; 382: 769-781Crossref PubMed Scopus (1505) Google Scholar). Purified SusD binds to linear malto-oligosaccharides with relatively low affinity compared with cyclic oligosaccharides of the same length. For example, binding of linear maltoheptaose is almost 10-fold weaker than that of the cyclized form (18Koropatkin N.M. Martens E.C. Gordon J.I. Smith T.J. Structure. 2008; 16: 1105-1115Abstract Full Text Full Text PDF PubMed Scopus (224) Google Scholar). In addition, the nature of the contacts between protein and ligand suggests that starch binding to SusD is driven by recognition of the backbone of the starch helices rather than by the stereochemistry of the individual glucose units. Thus, at least part of the substrate recognition mechanism of the Sus system depends on identifying the three-dimensional structure of the target substrate. This feature has also been observed for other carbohydrate-binding proteins that are not homologous to SusD, such as the carbohydrate-binding modules of numerous plant glycan-degrading glycoside hydrolases (19Boraston A.B. Bolam D.N. Gilbert H.J. Davies G.J. Biochem. J. 2004; 382: 769-781Crossref PubMed Scopus (1505) Google Scholar). Genetic experiments revealed that SusD is required not only for utilization of larger starch-derived molecules with more than six glucose units but also for optimal growth on maltotetraose and maltopentaose, for which SusD has little to no detectable affinity (18Koropatkin N.M. Martens E.C. Gordon J.I. Smith T.J. Structure. 2008; 16: 1105-1115Abstract Full Text Full Text PDF PubMed Scopus (224) Google Scholar). This suggests that SusD plays additional roles beyond polysaccharide binding, such as channeling malto-oligosaccharides to other Sus proteins or maintaining the structural integrity of a Sus protein complex. Previous work in the Salyers laboratory indicated that both SusC and SusD are required for starch binding to the cell surface and interact with each other. Studies of isogenic mutants indicated that SusC and SusD alone contribute ∼60% of the starch binding affinity observed in wild-type B. thetaiotaomicron. Inclusion of SusE with SusC and SusD increases affinity for starch to >80% of the wild type. SusF contributes the remaining ∼20% (10Shipman J.A. Berleman J.E. Salyers A.A. J. Bacteriol. 2000; 182: 5365-5372Crossref PubMed Scopus (158) Google Scholar). Recent experiments with purified SusE and SusF, which share ∼38% amino acid homology at their C termini, demonstrated that each interacts directly with starch and its oligosaccharides and that their affinity for starch-derived oligosaccharides is greater than that of M. and J. experiments in which B. thetaiotaomicron was in on highly purified and of starch indicated that SusE and SusF are not for growth Salyers A.A. J. Bacteriol. PubMed Scopus Google Scholar). These affinity proteins may function to facilitate access to the more of starch that the distal they may malto-oligosaccharides at the cell to microbes. starch is through the action of an outer membrane of alone not growth on starch but is for starch utilization A.R. Wang G.R. Salyers A.A. J. Bacteriol. 1997; 179: 643-649Crossref PubMed Scopus (148) Google Scholar). all Sus are dispensable on substrates than it is that an internal in a starch oligosaccharides larger than which are then by SusC into the (Fig. In the oligosaccharides are into their to transport to the This is accomplished via two additional glycoside SusA and which and Salyers A.A. J. Bacteriol. PubMed Scopus Google Scholar, M. M. H. M. J. Biol. Chem. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar). Genetic of or alone not growth on starch Salyers A.A. J. Bacteriol. PubMed Scopus Google Scholar), that is to it is that this function may be by other Salyers A.A. J. Bacteriol. PubMed Scopus Google Scholar). The structure and of SusB have been M. M. H. M. J. Biol. Chem. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar). This substrates such as to the notion that SusA the larger oligosaccharides through SusC and that SusB from SusA (Fig. SusB substrates with different and This may the substrate for the Sus system, of substrates such as highly of sus genes is accomplished via a in the of The of SusR is to extend into the whereas its C containing a predicted Salyers A.A. J. Bacteriol. PubMed Scopus Google Scholar), in the cytoplasm (Fig. The of starch that sus expression is the Salyers A.A. J. Bacteriol. PubMed Scopus Google Scholar). of SusR must this directly or this recognition is most by its therefore to of malto-oligosaccharides to glucose and may provide additional to B. thetaiotaomicron, content and a the by a more the substrate. The B. thetaiotaomicron genome contains glycoside hydrolases and polysaccharide in the C. V. B. 2009; PubMed Scopus Google Scholar). this genome also contains of and that the for starch utilization has been to target other J. M.A. Ley R.E. Lozupone Hamady M. Martens E.C. B. H. K. L.A. Knight Gordon J.I. Biol. 2007; PubMed Scopus Google Scholar). are individual of and genes, with the of the Fig. These are components of larger gene known as that contain of those in the prototypic including glycan-degrading and regulators J. J. Gordon J.I. Science. PubMed Scopus Google Scholar, Martens E.C. Gordon J.I. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, E.C. Gordon J.I. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar). Individual genes share little or no homology with the prototypic sus locus beyond that of and B. thetaiotaomicron contains of these genes and composing of its genome E.C. Gordon J.I. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar). the feature used to each Sus-like is a single of of these gene in B. thetaiotaomicron the prototypic sus locus in that they encode both glycan-degrading and a in B. thetaiotaomicron not have regulators related to SusR but system or Like these regulators in to glycans but through different mechanisms Fig. A and E.C. Gordon J.I. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar). A that system and regulators share with SusR is that each the cytoplasmic membrane and the cell to both the content and of they are (16Martens E.C. Roth R. Heuser J.E. Gordon J.I. J. Biol. Chem. 2009; 284: 18445-18457Abstract Full Text Full Text PDF PubMed Scopus (129) Google Scholar, Gordon J.I. Sci. PubMed Scopus Google Scholar). This may be through with the or may be and on substrate recognition by other of by of a with is the of several different B. thetaiotaomicron by through a mechanism (16Martens E.C. Roth R. Heuser J.E. Gordon J.I. J. Biol. Chem. 2009; 284: 18445-18457Abstract Full Text Full Text PDF PubMed Scopus (129) Google Scholar, R. Trends Microbiol. Full Text Full Text PDF PubMed Scopus Google Scholar). In this an membrane-spanning interacts with a receptor in the outer membrane to the of extracellular glycans to a cytoplasmic The protein both cell and a transcriptional the glycan is present the receptor (see Fig. and for (16Martens E.C. Roth R. Heuser J.E. Gordon J.I. J. Biol. Chem. 2009; 284: 18445-18457Abstract Full Text Full Text PDF PubMed Scopus (129) Google Scholar). The to glycans by regulators is in the adjacent genes, which encode the required to degrade the substrate. The predicted activities of the glycan-degrading in B. thetaiotaomicron the that different have evolved to glycans transcriptional of B. thetaiotaomicron in on purified glycans and in the distal gut of different Fig. have revealed of the that individual substrates to the of Sus-like Martens E.C. Gordon J.I. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, E.C. Gordon J.I. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar, J. J. Gordon J.I. Science. PubMed Scopus Google Scholar). For example, B. thetaiotaomicron Sus-like to target various glycans, rhamnogalacturonan and α-arabinan in C. D. and J. dietary plant glycans are not glycans O-glycans, N-glycans, and can as nutrient Martens E.C. Gordon J.I. J. Biol. Chem. Full Text Full Text PDF PubMed Scopus Google Scholar, E.C. Gordon J.I. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar). In to involved in some also encode for of glycan (e.g. the and in Fig. which is a step in the The Bacteroidetes are a diverse and and include members represented in both and (e.g. gut, and both and ecosystems (3Ley R.E. Hamady M. Lozupone C. Turnbaugh P.J. Ramey R.R. Bircher J.S. Schlegel M.L. Tucker T.A. Schrenzel M.D. Knight R. Gordon J.I. Science. 2008; 320: 1647-1651Crossref PubMed Scopus (2398) Google Scholar, M. C. Appl. Environ. Microbiol. PubMed Scopus Google Scholar, G. M. R. B. M.J. Appl. Environ. Microbiol. 2007; PubMed Scopus Google Scholar, M. M. H. M. E. C. H. D. K. M. R. Environ. Microbiol. PubMed Scopus Google Scholar). They can be or and include N.M. Appl. Environ. Microbiol. PubMed Scopus Google Scholar, J. B. M. Structure. 2004; Full Text Full Text PDF PubMed Scopus Google Scholar). Like their in a common feature with Bacteroidetes is their ability to degrade complex glycans. or genome are for Bacteroidetes isolated from the gut or the of these encode E.C. Gordon J.I. 2008; Full Text Full Text PDF PubMed Scopus Google Scholar). The only to is an of with a genome its N.M. Appl. Environ. Microbiol. PubMed Scopus Google Scholar). The diversity of Bacteroidetes Sus-like systems this suggests that they have been to degrade numerous substrates in diverse with this many Bacteroidetes species that harbor these systems additional substrates to B. and (6Salyers A.A. Vercellotti J.R. West S.E. Wilkins T.D. Appl. Environ. Microbiol. 1977; 33: 319-322Crossref PubMed Google Scholar, G. M. R. B. M.J. Appl. Environ. Microbiol. 2007; PubMed Scopus Google Scholar, M. M. H. M. E. C. H. D. K. M. R. Environ. Microbiol. PubMed Scopus Google Scholar, J. B. M. Structure. 2004; Full Text Full Text PDF PubMed Scopus Google Scholar). diversity Sus-like systems can be observed in both and of B. thetaiotaomicron. For example, B. thetaiotaomicron, the human gut Bacteroides on all known plant hemicelluloses (6Salyers A.A. Vercellotti J.R. West S.E. Wilkins T.D. Appl. Environ. Microbiol. 1977; 33: 319-322Crossref PubMed Google Scholar). This is to the of additional that target at least two of these target and Fig. P.J. Salyers A.A. Appl. Environ. Microbiol. 1992; PubMed Google Scholar, Biochim. Biophys. Acta. PubMed Scopus Google Scholar). The proteins encoded in these as well as lipoproteins of function encoded by genes of these Fig. bind directly to their the lipoproteins encoded by these genes no homology to SusE and SusF to a in glycan with signal peptidase II are encoded in most and are of the Fig. that they important roles in the of Sus-like systems. for substrate diversity can also be observed outside of the Bacteroides For example, the contains multiple of and and these are also components of A feature of this is its ability to degrade the glycan M.J. J. Bacteriol. PubMed Scopus Google Scholar). with this the genome harbors a three predicted Fig. this locus is to be for it the Sus-like system that a highly Bacteroidetes Sus-like system is a group of cell envelope-associated proteins that degrade a Like other microbial involved in nutrient degradation and (e.g. cellulosomes), Sus-like systems two key multiple proteins work during and the genes these concerted are linked into The of different present in Bacteroidetes an diverse group of genes involved in and glycan of the genes in these share little or no homology with genes in other and a (e.g. of the genes in B. are not homologous to genes of known the breadth of substrates targeted by different Bacteroidetes suggests that the Sus-like has evolved to include a very broad of including those important to such as cellulose and individual with glycan substrates be a step in the of these genes and to of proteins involved in glycan how these systems function to provide important insights into the of our gut microbiota and the of our The also be to other ecosystems that our for with with

Small GTP-binding proteins regulate diverse processes in eukaryotic cells such as signal transduction, cell proliferation, cytoskeletal organization, and intracellular membrane trafficking. These proteins function as molecular switches that cycle between "active" and "inactive" states, and this cycle is linked to the binding and hydrolysis of GTP. The Arabidopsis genome contains 93 genes that encode small GTP-binding protein homologs. Phylogenetic analysis of these genes shows that plants contain Rab, Rho, Arf, and Ran GTPases, but no Ras GTPases. We have assembled complete lists of these small GTPases families, as well as accessory proteins that control their activity, and review what is known of the functions of individual members of these families in Arabidopsis. We also discuss the possible roles of these GTPases in relation to their similarity to orthologs with known functions and localizations in yeast and/or animal systems.

Potassium (K(+)) is an essential nutrient required by plants in large quantities, but changes in soil concentrations may limit K(+) acquisition by roots. It is not known how plant root cells sense or signal the changes that occur after the onset of K(+) deficiency. Changes in the kinetics of Rb(+) uptake in Arabidopsis roots occur within 6 h after K(+) deprivation. Reactive oxygen species (ROS) and ethylene increased when the plants were deprived of K(+). ROS accumulated in a discrete region of roots that has been shown to be active in K(+) uptake and translocation. Suppression of an NADPH oxidase in Arabidopsis (rhd2), which is involved in ROS production, prevented the up-regulation of genes that are normally induced by K(+) deficiency, but the induction of high-affinity K(+) transport activity was unchanged. Application of H(2)O(2) restored the expression of genes induced by K(+) deficiency in rhd2 and was also sufficient to induce high-affinity K(+) transport activity in roots grown under K(+)-sufficient conditions. ROS production is an early root response to K(+) deficiency that modulates gene expression and physiological changes in the kinetics of K(+) uptake.

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

We determined the role of Phospholipase Dalpha1 (PLDalpha1) and its lipid product phosphatidic acid (PA) in abscisic acid (ABA)-induced production of reactive oxygen species (ROS) in Arabidopsis thaliana guard cells. The pldalpha1 mutant failed to produce ROS in guard cells in response to ABA. ABA stimulated NADPH oxidase activity in wild-type guard cells but not in pldalpha1 cells, whereas PA stimulated NADPH oxidase activity in both genotypes. PA bound to recombinant Arabidopsis NADPH oxidase RbohD (respiratory burst oxidase homolog D) and RbohF. The PA binding motifs were identified, and mutation of the Arg residues 149, 150, 156, and 157 in RbohD resulted in the loss of PA binding and the loss of PA activation of RbohD. The rbohD mutant expressing non-PA-binding RbohD was compromised in ABA-mediated ROS production and stomatal closure. Furthermore, ABA-induced production of nitric oxide (NO) was impaired in pldalpha1 guard cells. Disruption of PA binding to ABI1 protein phosphatase 2C did not affect ABA-induced production of ROS or NO, but the PA-ABI1 interaction was required for stomatal closure induced by ABA, H(2)O(2), or NO. Thus, PA is as a central lipid signaling molecule that links different components in the ABA signaling network in guard cells.

BACKGROUND: Although it is agreed that a major polyploidy event, gamma, occurred within the eudicots, the phylogenetic placement of the event remains unclear. RESULTS: To determine when this polyploidization occurred relative to speciation events in angiosperm history, we employed a phylogenomic approach to investigate the timing of gene set duplications located on syntenic gamma blocks. We populated 769 putative gene families with large sets of homologs obtained from public transcriptomes of basal angiosperms, magnoliids, asterids, and more than 91.8 gigabases of new next-generation transcriptome sequences of non-grass monocots and basal eudicots. The overwhelming majority (95%) of well-resolved gamma duplications was placed before the separation of rosids and asterids and after the split of monocots and eudicots, providing strong evidence that the gamma polyploidy event occurred early in eudicot evolution. Further, the majority of gene duplications was placed after the divergence of the Ranunculales and core eudicots, indicating that the gamma appears to be restricted to core eudicots. Molecular dating estimates indicate that the duplication events were intensely concentrated around 117 million years ago. CONCLUSIONS: The rapid radiation of core eudicot lineages that gave rise to nearly 75% of angiosperm species appears to have occurred coincidentally or shortly following the gamma triplication event. Reconciliation of gene trees with a species phylogeny can elucidate the timing of major events in genome evolution, even when genome sequences are only available for a subset of species represented in the gene trees. Comprehensive transcriptome datasets are valuable complements to genome sequences for high-resolution phylogenomic analysis.

Vitamin C (ascorbic acid) is essential to prevent disease associated with connective tissue (e.g., scurvy), improves cardiovascular and immune cell functions, and is used to regenerate alpha-tocopherol (vitamin E). In contrast to most animals, humans lack the ability to synthesize ascorbic acid as a result of a mutation in the last enzyme required for ascorbate biosynthesis. Vitamin C, therefore, must be obtained from dietary sources and, because it cannot be stored in the body, it must be obtained regularly. Once used, ascorbic acid can be regenerated from its oxidized form in a reaction catalyzed by dehydroascorbate reductase (DHAR). To examine whether overexpression of DHAR in plants would increase the level of ascorbic acid through improved ascorbate recycling, a DHAR cDNA from wheat was isolated and expressed in tobacco and maize, where DHAR expression was increased up to 32- and 100-fold, respectively. The increase in DHAR expression increased foliar and kernel ascorbic acid levels 2- to 4-fold and significantly increased the ascorbate redox state in both tobacco and maize. In addition, the level of glutathione, the reductant used by DHAR, also increased, as did its redox state. These results demonstrate that the vitamin C content of plants can be elevated by increasing expression of the enzyme responsible for recycling ascorbate.

We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.

Plants often grow in soils that contain very low concentrations of the macronutrients nitrogen, phosphorus, potassium, and sulfur. To adapt and grow in nutrient-deprived environments plants must sense changes in external and internal mineral nutrient concentrations and adjust growth to match resource availability. The sensing and signal transduction networks that control plant responses to nutrient deprivation are not well characterized for nitrogen, potassium, and sulfur deprivation. One branch of the signal transduction cascade related to phosphorus-deprivation response has been defined through the identification of a transcription factor that is regulated by sumoylation. Two different microRNAs play roles in regulating gene expression under phosphorus and sulfur deprivation. Reactive oxygen species increase rapidly after mineral nutrient deprivation and may be one upstream mediator of nutrient signaling. A number of molecular analyses suggest that both short-term and longer-term responses will be important in understanding the progression of signaling events when the external, then internal, supplies of nutrients become depleted.

Plant root sensing and adaptation to changes in the nutrient status of soils is vital for long-term productivity and growth. Reactive oxygen species (ROS) have been shown to play a role in root response to potassium deprivation. To determine the role of ROS in plant response to nitrogen and phosphorus deficiency, studies were conducted using wild-type Arabidopsis and several root hair mutants. The expression of several nutrient-responsive genes was determined by Northern blot, and ROS were quantified and localized in roots. The monitored genes varied in intensity and timing of expression depending on which nutrient was deficient. In response to nutrient deprivation, ROS concentrations increased in specific regions of the Arabidopsis root. Changes in ROS localization in Arabidopsis and in a set of root hair mutants suggest that the root hair cells are important for response to nitrogen and potassium. In contrast, the response to phosphorus deprivation occurs in the cortex where an increase in ROS was measured. Based on these results, we put forward the hypothesis that root hair cells in Arabidopsis contain a sensing system for nitrogen and potassium deprivation.

Lettuce (Lactuca sativa) is a major crop and a member of the large, highly successful Compositae family of flowering plants. Here we present a reference assembly for the species and family. This was generated using whole-genome shotgun Illumina reads plus in vitro proximity ligation data to create large superscaffolds; it was validated genetically and superscaffolds were oriented in genetic bins ordered along nine chromosomal pseudomolecules. We identify several genomic features that may have contributed to the success of the family, including genes encoding Cycloidea-like transcription factors, kinases, enzymes involved in rubber biosynthesis and disease resistance proteins that are expanded in the genome. We characterize 21 novel microRNAs, one of which may trigger phasiRNAs from numerous kinase transcripts. We provide evidence for a whole-genome triplication event specific but basal to the Compositae. We detect 26% of the genome in triplicated regions containing 30% of all genes that are enriched for regulatory sequences and depleted for genes involved in defence.

Drought stress is a common adverse environmental condition that seriously affects crop productivity worldwide. Due to the complexity of drought as a stress signal, deciphering drought tolerance mechanisms has remained a major challenge to plant biologists. To develop new approaches to study plant drought tolerance, we searched for phenotypes conferred by drought stress and identified the inhibition of lateral root development by drought stress as an adaptive response to the stress. This drought response is partly mediated by the phytohormone abscisic acid. Genetic screens using Arabidopsis (Arabidopsis thaliana) were devised, and drought inhibition of lateral root growth (dig) mutants with altered responses to drought or abscisic acid in lateral root development were isolated. Characterization of these dig mutants revealed that they also exhibit altered drought stress tolerance, indicating that this root response to drought stress is intimately linked to drought adaptation of the entire plant and can be used as a trait to access the elusive drought tolerance machinery. Our study also revealed that multiple mechanisms coexist and together contribute to whole-plant drought tolerance.