Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) transcription factors are key regulators of auxin responses in plants. We identified the suites of genes in the two gene families ...in Populus and performed comparative genomic analysis with Arabidopsis and rice.
A total of 35 Aux/IAA and 39 ARF genes were identified in the Populus genome. Comparative phylogenetic analysis revealed that several Aux/IAA and ARF subgroups have differentially expanded or contracted between the two dicotyledonous plants. Activator ARF genes were found to be two fold-overrepresented in the Populus genome. PoptrIAA and PoptrARF gene families appear to have expanded due to high segmental and low tandem duplication events. Furthermore, expression studies showed that genes in the expanded PoptrIAA3 subgroup display differential expression.
The present study examines the extent of conservation and divergence in the structure and evolution of Populus Aux/IAA and ARF gene families with respect to Arabidopsis and rice. The gene-family analysis reported here will be useful in conducting future functional genomics studies to understand how the molecular roles of these large gene families translate into a diversity of biologically meaningful auxin effects.
The community of researchers studying molecular plant‐microbe interactions under the banners of fundamental plant science, biofuel‐bioenergy, and crop productivity and sustainability research is ...expanding rapidly. The review summarizes multiple, separate lines of evidences linking auxin transport, signaling, and synthesis pathways to beneficial plant‐microbe interactions and modulations in host root architecture. Compelling physiology and functional genomics‐based evidence was found in support of a delicate and precise orchestration of distinct root phenotypic effects achieved via a shared auxin biosynthesis and signaling machinery involving signaling crosstalk. A hypothetical and simplified model on role of auxin in beneficial plant‐microbe interactions is presented, and outstanding research challenges and potential future directions are discussed.
A wide variety of microorganisms known to produce auxin and auxin precursors form beneficial relationships with plants and alter host root development. Moreover, other signals produced by microorganisms affect auxin pathways in host plants. However, the precise role of auxin and auxin‐signalling pathways in modulating plant–microbe interactions is unknown. Dissecting out the auxin synthesis, transport and signalling pathways resulting in the characteristic molecular, physiological and developmental response in plants will further illuminate upon how these intriguing inter‐species interactions of environmental, ecological and economic significance occur. The present review seeks to survey and summarize the scattered evidence in support of known host root modifications brought about by beneficial microorganisms and implicate the role of auxin synthesis, transport and signal transduction in modulating beneficial effects in plants. Finally, through a synthesis of the current body of work, we present outstanding challenges and potential future research directions on studies related to auxin signalling in plant–microbe interactions.
Transgenic Poplar Designed for Biofuels Bryant, Nathan D.; Pu, Yunqiao; Tschaplinski, Timothy J. ...
Trends in plant science,
September 2020, 2020-09-00, 20200901, 2020-09-01, Letnik:
25, Številka:
9
Journal Article
Recenzirano
Odprti dostop
Members of the genus Populus (i.e., cottonwood, hybrid poplar) represent a promising source of lignocellulosic biomass for biofuels. However, one of the major factors negatively affecting poplar’s ...efficient conversion to biofuel is the inherent recalcitrance to enzymatic saccharification due to cell wall components such as lignin. To this effect, there have been efforts to modify gene expression to reduce biomass recalcitrance by changing cell wall properties. Here, we review recent genetic modifications of poplar that led to change cell wall properties and the resulting effects on subsequent pretreatment efficacy and saccharification. Although genetic engineering’s impacts on cell wall properties are not fully predictable, recent studies have shown promising improvement in the biological conversion of transgenic poplar to biofuels.
The cell wall properties of poplar can be altered by modifying gene expression. Modifying the expression of lignin, hemicellulose, and cellulose biosynthesis genes have both been demonstrated to have an impact on poplar’s natural recalcitrance to enzymatic saccharification.Lignin is typically cited as the primary contributor to recalcitrance. However, as modifying gene expression usually results in multifaceted effects on cell wall chemistry, it is difficult to attribute improved saccharification to any single factor.As examined in this review, the effects (or interaction of effects) from genetic engineering on poplar have, in some cases, resulted in drastic improvements in saccharification efficiency.
Aims
The aim of this study is to develop and test the applicability of a rapid in situ plant chemistry profiling technique to determine elemental composition of small-volume plant and soil samples ...obtained from a woody bioenergy crop species,
Populus trichocarpa
. Expanding the research tools available to characterize the nutrient element correlations among plant tissue types and soil depths is a critical need in the path of understanding productivity and adaptation of plants to variations in external abiotic and biotic factors and developing sustainable perennial bioenergy crops that are co-optimized for biomass valorization aboveground and carbon sequestration belowground.
Methods
Several plant root, stem, and soil samples were tested using laser-induced breakdown spectroscopy (LIBS) to evaluate the presence and distribution of nutrient elements. Samples were tested as collected and after being dried and cross sectioned to evaluate the effectiveness of using LIBS for in situ analysis on plant samples.
Results
The collected LIBS spectra show the elemental peaks were the same in both the as collected and prepared samples for roots and stems. Qualitative amounts of elements such as H, C, N, O, Li, Na, Mg, K, Ca, Fe, Al, and Si were able to be identified rapidly in raw samples.
Conclusion
Here we demonstrate suitability of LIBS in obtaining rapid, in situ, elemental distribution in plant and soil samples, utilizing only small sample volumes and minimal sample preparation. This demonstration opens up a new rapid phenotyping avenue necessary to fill the asymmetrical knowledge gaps in belowground performance of plant systems.
Populus is a model woody plant and a promising feedstock for lignocellulosic biofuel production. However, its lengthy life cycle impedes rapid characterization of gene function.
We optimized a ...Populus leaf mesophyll protoplast isolation protocol and established a Populus protoplast transient expression system. We demonstrated that Populus protoplasts are able to respond to hormonal stimuli and that a series of organelle markers are correctly localized in the Populus protoplasts. Furthermore, we showed that the Populus protoplast transient expression system is suitable for studying protein-protein interaction, gene activation, and cellular signaling events.
This study established a method for efficient isolation of protoplasts from Populus leaf and demonstrated the efficacy of using Populus protoplast transient expression assays as an in vivo system to characterize genes and pathways.
Metabolite genome-wide association studies (mGWASs) are increasingly used to discover the genetic basis of target phenotypes in plants such as
, a biofuel feedstock and model woody plant species. ...Despite their growing importance in plant genetics and metabolomics, few mGWASs are experimentally validated. Here, we present a functional genomics workflow for validating mGWAS-predicted enzyme-substrate relationships. We focus on uridine diphosphate-glycosyltransferases (UGTs), a large family of enzymes that catalyze sugar transfer to a variety of plant secondary metabolites involved in defense, signaling, and lignification. Glycosylation influences physiological roles, localization within cells and tissues, and metabolic fates of these metabolites. UGTs have substantially expanded in
, presenting a challenge for large-scale characterization. Using a high-throughput assay, we produced substrate acceptance profiles for 40 previously uncharacterized candidate enzymes. Assays confirmed 10 of 13 leaf mGWAS associations, and a focused metabolite screen demonstrated varying levels of substrate specificity among UGTs. A substrate binding model case study of UGT-23 rationalized observed enzyme activities and mGWAS associations, including glycosylation of trichocarpinene to produce trichocarpin, a major higher-order salicylate in
We identified UGTs putatively involved in lignan, flavonoid, salicylate, and phytohormone metabolism, with potential implications for cell wall biosynthesis, nitrogen uptake, and biotic and abiotic stress response that determine sustainable biomass crop production. Our results provide new support for
analyses and evidence-based guidance for
functional characterization.
Photosynthetic assimilation of atmospheric carbon dioxide by land plants offers the underpinnings for terrestrial carbon (C) sequestration. A proportion of the C captured in plant biomass is ...partitioned to roots, where it enters the pools of soil organic C and soil inorganic C and can be sequestered for millennia. Bioenergy crops serve the dual role of providing biofuel that offsets fossil-fuel greenhouse gas (GHG) emissions and sequestering C in the soil through extensive root systems. Carbon captured in plant biomass can also contribute to C sequestration through the deliberate addition of biochar to soil, wood burial, or the use of durable plant products. Increasing our understanding of plant, microbial, and soil biology, and harnessing the benefits of traditional genetics and genetic engineering, will help us fully realize the GHG mitigation potential of phytosequestration.
Summary
Fine‐tuning plant cell wall properties to render plant biomass more amenable to biofuel conversion is a colossal challenge. A deep knowledge of the biosynthesis and regulation of plant cell ...wall and a high‐precision genome engineering toolset are the two essential pillars of efforts to alter plant cell walls and reduce biomass recalcitrance. The past decade has seen a meteoric rise in use of transcriptomics and high‐resolution imaging methods resulting in fresh insights into composition, structure, formation and deconstruction of plant cell walls. Subsequent gene manipulation approaches, however, commonly include ubiquitous mis‐expression of a single candidate gene in a host that carries an intact copy of the native gene. The challenges posed by pleiotropic and unintended changes resulting from such an approach are moving the field towards synthetic biology approaches. Synthetic biology builds on a systems biology knowledge base and leverages high‐precision tools for high‐throughput assembly of multigene constructs and pathways, precision genome editing and site‐specific gene stacking, silencing and/or removal. Here, we summarize the recent breakthroughs in biosynthesis and remodelling of major secondary cell wall components, assess the impediments in obtaining a systems‐level understanding and explore the potential opportunities in leveraging synthetic biology approaches to reduce biomass recalcitrance.
Plant endo‐β‐1,4‐glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)‐β‐d‐glucosidic linkages. ...Modification of cell wall chemistry via RNA interference (RNAi)‐mediated downregulation of Populus deltoides KORRIGAN (PdKOR), an endo‐β‐1,4‐glucanase familygene was shown to have functional consequences on the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood. Here a liquid chromatography (LC)‐tandem mass spectrometry (MS/MS)‐based proteome profiling approach is used to survey the molecular remodeling in root tissues of PdKOR and control plants. A total of 14316 peptides are identified and these mapped to 7139 P. deltoides proteins. Based on 90% sequence identity, the measured protein accessions represent 1187 functional protein groups. Analysis of Gene Ontology (GO) categories and specific individual proteins show differential expression of proteins relevant to plant‐microbe interactions, cell wall chemistry, and metabolism. The new proteome dataset serves as a useful resource for deriving new hypotheses and empirical testing pertaining to functional roles of proteins and pathways in differential priming of plant roots to interactions with microbes.
A cellulose synthesis complex with a "rosette" shape is responsible for synthesis of cellulose chains and their assembly into microfibrils within the cell walls of land plants and their charophyte ...algal progenitors. The number of cellulose synthase proteins in this large multisubunit transmembrane protein complex and the number of cellulose chains in a microfibril have been debated for many years. This work reports a low resolution structure of the catalytic domain of CESA1 from Arabidopsis (Arabidopsis thaliana; AtCESA1CatD) determined by small-angle scattering techniques and provides the first experimental evidence for the self-assembly of CESA into a stable trimer in solution. The catalytic domain was overexpressed in Escherichia coli, and using a two-step procedure, it was possible to isolate monomeric and trimeric forms of AtCESA1CatD. The conformation of monomeric and trimeric AtCESA1CatD proteins were studied using small-angle neutron scattering and small-angle x-ray scattering. A series of AtCESA1CatD trimer computational models were compared with the small-angle x-ray scattering trimer profile to explore the possible arrangement of the monomers in the trimers. Several candidate trimers were identified with monomers oriented such that the newly synthesized cellulose chains project toward the cell membrane. In these models, the class-specific region is found at the periphery of the complex, and the plant-conserved region forms the base of the trimer. This study strongly supports the "hexamer of trimers" model for the rosette cellulose synthesis complex that synthesizes an 18-chain cellulose microfibril as its fundamental product.
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