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1. Xyloglucan Xylosyltransferase 1 Displays Promiscuity Toward Donor Substrates During In vitro Reactions

   https://doi.org/10.1093/pcp/pcab114  

   Ehrlich, Jacqueline J; Weerts, Richard M; Shome, Sayane; Culbertson, Alan T; Honzatko, Richard B; Jernigan, Robert L; Zabotina, Olga A (July 2021, Plant and Cell Physiology)

   null (Ed.)

   Abstract Glycosyltransferases (GTs) are a large family of enzymes that add sugars to a broad range of acceptor substrates, including polysaccharides, proteins, and lipids, by utilizing a wide variety of donor substrates in the form of activated sugars. Individual GTs have generally been considered to exhibit a high level of substrate specificity, but this has not been thoroughly investigated across the extremely large set of GTs. Here we investigate Xyloglucan Xylosyltransferase 1 (XXT1), a GT involved in synthesis of the plant cell wall polysaccharide, xyloglucan. Xyloglucan has a glucan backbone, with initial side chain substitutions exclusively composed of xylose from UDP-Xylose. While this conserved substitution pattern suggests a high substrate specificity for XXT1, our in vitro kinetic studies elucidate a more complex set of behavior. Kinetic studies demonstrate comparable kcat values for reactions with UDP-Xylose and UDP-Glucose, while reactions with UDP-Arabinose and UDP-Galactose are over 10-fold slower. Using kcat/Km as a measure of efficiency, UDP-Xylose is 8-fold more efficient as a substrate than the next best alternative, UDP-Glucose. To the best of our knowledge, we are the first to demonstrate that not all plant XXTs are highly substrate specific, and some do show significant promiscuity in their in vitro reactions. Kinetic parameters alone likely do not explain the high substrate selectivity in planta, suggesting there are additional control mechanisms operating during polysaccharide biosynthesis. Improved understanding of substrate specificity of the GTs will aid in protein engineering, development of diagnostic tools, and understanding of biological systems. 

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2. Cell wall polymers in the Phaeoceros placenta reflect developmental and functional differences across generations

   https://doi.org/10.11646/bde.43.1.19  

   HENRY, JASON S.; LIGRONE, ROBERTO; VAUGHN, KEVIN C.; LOPEZ, RENEE A.; RENZAGLIA, KAREN S. (June 2021, Bryophyte Diversity and Evolution)

   null (Ed.)

   The placenta of hornworts is unique among bryophytes in the restriction of transfer cells that are characterized by elaborate wall labyrinths to the gametophyte generation. During development, cells around the periphery of the sporophyte foot elongate, forming smooth-walled haustorial cells that interdigitate with gametophyte cells. Using immunogold labeling with 22 antibodies to diverse cell wall polymers, we examined compositional differences in the developmentally and morphologically distinct cell walls of gametophyte transfer cells and sporophyte haustorial cells in the placenta of Phaeoceros. As detected by Calcofluor White fluorescence, cellulose forms the cell wall scaffolding in cells on both sides of the placenta. Homogalacturonan (HG) and rhamnogalacturonan I (RG-I) pectins are abundant in both cell types, and haustorial cells are further enriched in methyl-esterified HGs. The abundance of pectins in placental cell walls is consistent with the postulated roles of these polymers in cell wall porosity and in maintaining an acidic apoplastic pH favorable to solute transport. Xyloglucan hemicellulose, but not mannans or glucuronoxylans, are present in cell walls at the interface between the two generations with a lower density in gametophytic wall ingrowths. Arabinogalactan proteins (AGPs) are diverse along the plasmalemma of placental cells and are absent in surrounding cells in both generations. AGPs in placental cell walls may play a role in calcium binding and release associated with signal transduction as has been speculated for these glycoproteins in other plants. Callose is restricted to thin areas in cell walls of gametophyte transfer cells. In contrast to studies of transfer cells in other systems, no reaction to the JIM12 antibody against extensin was observed in Phaeoceros. 

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3. Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae

   https://doi.org/10.1093/plcell/koac166  

   Palos, Kyle; Nelson Dittrich, Anna C; Yu, Li’ang; Brock, Jordan R; Railey, Caylyn E; Wu, Hsin-Yen Larry; Sokolowska, Ewelina; Skirycz, Aleksandra; Hsu, Polly Yingshan; Gregory, Brian D; et al (June 2022, The Plant Cell)

   Abstract Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth of RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement a harmonized identification and annotation effort for lincRNAs that enables cross-species functional and genomic comparisons as well as prioritization of functional candidates. In this study, we processed >24 Tera base pairs of RNA-seq data from >16,000 experiments to identify ∼130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify conserved motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our data set with sequence or transcriptional conservation. Finally, we used guilt-by-association analyses to assign putative functions to lincRNAs within our data set. We tested this approach on a subset of lincRNAs associated with germination and seed development, observing germination defects for Arabidopsis lines harboring T-DNA insertions at these loci. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, small open reading frames, or abiotic-stress modulated expression are a few of the annotations that will guide functional analyses into this cryptic portion of the transcriptome. 

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4. Functional diversity of leaf litter mixtures slows decomposition of labile but not recalcitrant carbon over two years

   https://doi.org/10.1002/ecm.1407  

   Grossman, Jake J.; Cavender‐Bares, Jeannine; Hobbie, Sarah E. (April 2020, Ecological Monographs)

   Abstract The decomposition of leaf litter constitutes a major pathway of carbon and nutrient cycling in terrestrial ecosystems. Though it is well established that litter decomposition varies among species, most leaf litter decomposes not alone, but in mixture with litter from heterospecifics. The consequences of this mixing, and of the role of multiple dimensions of plant biodiversity, for litter decomposition are ambiguous, with past research suggesting that mixing diverse litter can speed up, slow down, or have no effect on decomposition. Furthermore, different chemical constituents of litter decompose at different rates, and the consequences of diversity for each of these rates are not completely understood. We created litterbags corresponding to 49 different litter mixtures ranging from one to 12 temperate forest species and allowed them to decompose over 2 yr in a common garden in temperate eastern Minnesota, USA. Following collections at 2, 4, 12, and 24 months, we assessed total mass loss and changes in four classes of litter carbon (soluble cell contents, hemicellulose and bound proteins, cellulose, and lignin/acid unhydrolyzable recalcitrants). Species varied in litter decomposition rate (losing from 8% to 41% of total mass) and they lost soluble cell contents (up to 64% of ash‐free mass) and hemicellulose and bound proteins (69%) much more rapidly over 2 yr than they lost cellulose (40%) and acid‐unhydrolyzable residues (12%). A variety of macro‐ and micronutrients supported litter decomposition, with calcium, in particular, promoting it. In mixtures of litter from 2, 5, or 12 species, neither species richness nor phylogenetic diversity was associated with deviations from expected decomposition rates based on monocultures. Yet more functionally diverse litter mixtures lost labile carbon (soluble cell contents and hemicellulose) significantly more slowly than expected. This novel finding of the effect of litter diversity not on total litter decomposition, but on the decomposition of a particular class of litter compounds elucidates potential consequences of biodiversity for cycling of nutrients and energy in forest ecosystems. 

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5. The nuclear lamina is required for proper development and nuclear shape distortion in tomato

   https://doi.org/10.1093/jxb/erad294  

   Blunt, Endia L.; Choi, Junsik; Sussman, Hayley; Christopherson, Rachel C.; Keen, Patricia; Rahmati Ishka, Maryam; Li, Linda Y.; Idrovo, Joanna M.; Julkowska, Magdalena M.; Van Eck, Joyce; et al (July 2023, Journal of Experimental Botany)

   Abstract The nuclear lamina in plant cells is composed of plant-specific proteins, including nuclear matrix constituent proteins (NMCPs), which have been postulated to be functional analogs of lamin proteins that provide structural integrity to the organelle and help stabilize the three-dimensional organization of the genome. Using genomic editing, we generated alleles for the three genes encoding NMCPs in cultivated tomato (Solanum lycopersicum) to determine if the consequences of perturbing the nuclear lamina in this crop species were similar to or distinct from those observed in the model Arabidopsis thaliana. Loss of the sole NMCP2-class protein was lethal in tomato but is tolerated in Arabidopsis. Moreover, depletion of NMCP1-type nuclear lamina proteins leads to distinct developmental phenotypes in tomato, including leaf morphology defects and reduced root growth rate (in nmcp1b mutants), compared with cognate mutants in Arabidopsis. These findings suggest that the nuclear lamina interfaces with different developmental and signaling pathways in tomato compared with Arabidopsis. At the subcellular level, however, tomato nmcp mutants resembled their Arabidopsis counterparts in displaying smaller and more spherical nuclei in differentiated cells. This result argues that the plant nuclear lamina facilitates nuclear shape distortion in response to forces exerted on the organelle within the cell. 

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