Novel plant and fungal AGP-like proteins in the Medicago truncatula-Glomus intraradices arbuscular mycorrhizal symbiosis

Loss of function of the bHLH transcription factor Nrd1 in tomato enhances resistance to Pseudomonas syringae

Basic helix-loop-helix (bHLH) transcription factors constitute a superfamily in eukaryotes, but their roles in plant immunity remain largely uncharacterized. We found that the transcript abundance in tomato (Solanum lycopersicum) leaves of one bHLH transcription factor-encoding gene, negative regulator of resistance to DC3000 1 (Nrd1), increased significantly after treatment with the immunity-inducing flgII-28 peptide. Plants carrying a loss-of-function mutation in Nrd1 (Δnrd1) showed enhanced resistance to Pseudomonas syringae pv. tomato (Pst) DC3000 although early pattern-triggered immunity responses, such as generation of reactive oxygen species and activation of mitogen-activated protein kinases after treatment with flagellin-derived flg22 and flgII-28 peptides, were unaltered compared to wild-type plants. RNA-sequencing (RNA-seq) analysis identified a gene, Arabinogalactan protein 1 (Agp1), whose expression is strongly suppressed in an Nrd1-dependent manner. Agp1 encodes an arabinogalactan protein, and overexpression of the Agp1 gene in Nicotiana benthamiana led to ∼10-fold less Pst growth compared to the control. These results suggest that the Nrd1 protein promotes tomato susceptibility to Pst by suppressing the defense gene Agp1. RNA-seq also revealed that the loss of Nrd1 function has no effect on the transcript abundance of immunity-associated genes, including AvrPtoB tomato-interacting 9 (Bti9), Cold-shock protein receptor (Core), Flagellin sensing 2 (Fls2), Flagellin sensing (Fls3), and Wall-associated kinase 1 (Wak1) upon Pst inoculation, suggesting that the enhanced immunity observed in the Δnrd1 mutants is due to the activation of key PRR signaling components as well as the loss of Nrd1-regulated suppression of Agp1.

A targeted bioinformatics approach identifies highly variable cell surface proteins that are unique to Glomeromycotina

Diversity in arbuscular mycorrhizal fungi (AMF) contributes to biodiversity and resilience in natural environments and healthy agricultural systems. Functional complementarity exists among species of AMF in symbiosis with their plant hosts, but the molecular basis of this is not known. We hypothesise this is in part due to the difficulties that current sequence assembly methodologies have assembling sequences for intrinsically disordered proteins (IDPs) due to their low sequence complexity. IDPs are potential candidates for functional complementarity because they often exist as extended (non-globular) proteins providing additional amino acids for molecular interactions. Rhizophagus irregularis arabinogalactan-protein-like proteins (AGLs) are small secreted IDPs with no known orthologues in AMF or other fungi. We developed a targeted bioinformatics approach to identify highly variable AGLs/IDPs in RNA-sequence datasets. The approach includes a modified multiple k-mer assembly approach (Oases) to identify candidate sequences, followed by targeted sequence capture and assembly (mirabait-mira). All AMF species analysed, including the ancestral family Paraglomeraceae, have small families of proteins rich in disorder promoting amino acids such as proline and glycine, or glycine and asparagine. Glycine- and asparagine-rich proteins also were found in Geosiphon pyriformis (an obligate symbiont of a cyanobacterium), from the same subphylum (Glomeromycotina) as AMF. The sequence diversity of AGLs likely translates to functional diversity, based on predicted physical properties of tandem repeats (elastic, amyloid, or interchangeable) and their broad pI ranges. We envisage that AGLs/IDPs could contribute to functional complementarity in AMF through processes such as self-recognition, retention of nutrients, soil stability, and water movement.

Arabinogalactan Proteins in Plant Roots - An Update on Possible Functions

Responsiveness to environmental conditions and developmental plasticity of root systems are crucial determinants of plant fitness. These processes are interconnected at a cellular level with cell wall properties and cell surface signaling, which involve arabinogalactan proteins (AGPs) as essential components. AGPs are cell-wall localized glycoproteins, often GPI-anchored, which participate in root functions at many levels. They are involved in cell expansion and differentiation, regulation of root growth, interactions with other organisms, and environmental response. Due to the complexity of cell wall functional and regulatory networks, and despite the large amount of experimental data, the exact molecular mechanisms of AGP-action are still largely unknown. This dynamically evolving field of root biology is summarized in the present review.

Evolution of Sequence-Diverse Disordered Regions in a Protein Family: Order within the Chaos

Approaches for studying the evolution of globular proteins are now well established yet are unsuitable for disordered sequences. Our understanding of the evolution of proteins containing disordered regions therefore lags that of globular proteins, limiting our capacity to estimate their evolutionary history, classify paralogs, and identify potential sequence–function relationships. Here, we overcome these limitations by using new analytical approaches that project representations of sequence space to dissect the evolution of proteins with both ordered and disordered regions, and the correlated changes between these. We use the fasciclin-like arabinogalactan proteins (FLAs) as a model family, since they contain a variable number of globular fasciclin domains as well as several distinct types of disordered regions: proline (Pro)-rich arabinogalactan (AG) regions and longer Pro-depleted regions.

Sequence space projections of fasciclin domains from 2019 FLAs from 78 species identified distinct clusters corresponding to different types of fasciclin domains. Clusters can be similarly identified in the seemingly random Pro-rich AG and Pro-depleted disordered regions. Sequence features of the globular and disordered regions clearly correlate with one another, implying coevolution of these distinct regions, as well as with the N-linked and O-linked glycosylation motifs. We reconstruct the overall evolutionary history of the FLAs, annotated with the changing domain architectures, glycosylation motifs, number and length of AG regions, and disordered region sequence features. Mapping these features onto the functionally characterized FLAs therefore enables their sequence–function relationships to be interrogated. These findings will inform research on the abundant disordered regions in protein families from all kingdoms of life.

PRPs localized to the middle lamellae are required for cortical tissue integrity in Medicago truncatula roots

A family of repetitive proline-rich proteins interact with acidic pectins and play distinct roles in legume root cell walls affecting cortical and vascular structure. A proline-rich protein (PRP) family, composed of tandemly repeated Pro-Hyp-Val-X-Lys pentapeptide motifs, is found primarily in the Leguminosae. Four distinct size classes within this family are encoded by seven tightly linked genes: MtPRP1, MtPRP2 and MtPRP3, and four nearly identical MtPRP4 genes. Promoter fusions to β-glucuronidase showed strong expression in the stele of hairy roots for all 4 PRP genes tested, with additional expression in the cortex for PRP1, PRP2 and PRP4. All except MtPRP4 are strongly expressed in non-tumorous roots, and secreted and ionically bound to root cell walls. These PRPs are absent from root epidermal cell walls, and PRP accumulation is highly localized within the walls of root cortical and vascular tissues. Within xylem tissue, PRPs are deposited in secondary thickenings where it is spatially exclusive to lignin. In newly differentiating xylem, PRPs are deposited in the regularly spaced paired-pits and pit membranes that hydraulically connect neighboring xylem elements. Hairpin-RNA knock-down constructs reducing PRP expression in Medicago truncatula hairy root tumors disrupted cortical and vascular patterning. Immunoblots showed that the knockdown tumors had potentially compensating increases in the non-targeted PRPs, all of which cross-react with the anti-PRP antibodies. However, PRP3 knockdown differed from knockdown of PRP1 and PRP2 in that it greatly reduced viability of hairy root tumors. We hypothesize that repetitive PRPs interact with acidic pectins to form block-copolymer gels that can play distinct roles in legume root cell walls.

Adhesion molecules from the diatom Phaeodactylum tricornutum (Bacillariophyceae): genomic identification by amino-acid profiling and in vivo analysis

Cell adhesion molecules (CAMs) are important in prokaryotes and eukaryotes for cell-cell and cell-substratum interactions. The characteristics of adhesive proteins in the model diatom Phaeodactylum tricornutum were investigated by bioinformatic analysis and in vivo characterization. Bioinformatic analysis of the protein coding potential of the P. tricornutum genome used an amino-acid profile that we developed as a new system to identify uncharacterized or novel CAMs. Putative diatom CAMs were identified and seven were characterized in vivo, by generation of transgenic diatom lines overexpressing genes encoding C-terminal yellow fluorescent protein (YFP) fusion proteins. Three of these selected genes encode proteins with weak similarity to characterized proteins, a c-type lectin and two fasciclins, whereas the others are novel. The resultant cell lines were investigated for alterations in their adhesive ability. Whole cell-substratum adhesion strength was measured in a fully turbulent flow chamber, while atomic force microscopy was used to quantify the relative frequency of adhesion, as well as the length and strength of single molecules in the secreted mucilage. Finally, quartz crystal microbalance analysis characterized the visco-elastic properties and interaction of the mucilage-substratum interface. These combined studies revealed a range of phenotypes affecting adhesion, and led to the identification of candidate proteins involved in diatom adhesion. In summary, our study has for the first time combined bioinformatics and molecular physiological studies to provide new insights into diatom adhesive molecules.

Arabinogalactan proteins in root-microbe interactions

Arabinogalactan proteins (AGPs) are among the most intriguing sets of macromolecules, specific to plants, structurally complex, and found abundantly in all plant organs including roots, as well as in root exudates. AGPs have been implicated in several fundamental plant processes such as development and reproduction. Recently, they have emerged as interesting actors of root-microbe interactions in the rhizosphere. Indeed, recent findings indicate that AGPs play key roles at various levels of interaction between roots and soil-borne microbes, either beneficial or pathogenic. Therefore, the focus of this review is the role of AGPs in the interactions between root cells and microbes. Understanding this facet of AGP function will undoubtedly improve plant health and crop protection.

Arabinogalactan proteins occur in the free-living cyanobacterium genus Nostoc and in plant-Nostoc symbioses

Arabinogalactan proteins (AGP) are a diverse family of proteoglycans associated with the cell surfaces of plants. AGP have been implicated in a wide variety of plant cell processes, including signaling in symbioses. This study investigates the existence of putative AGP in free-living cyanobacterial cultures of the nitrogen-fixing, filamentous cyanobacteria Nostoc punctiforme and Nostoc sp. strain LBG1 and at the symbiotic interface in the symbioses between Nostoc spp. and two host plants, the angiosperm Gunnera manicata (in which the cyanobacterium is intracellular) and the liverwort Blasia pusilla (in which the cyanobacterium is extracellular). Enzyme-linked immunosorbent assay, immunoblotting, and immunofluorescence analyses demonstrated that three AGP glycan epitopes (recognized by monoclonal antibodies LM14, MAC207, and LM2) are present in free-living Nostoc cyanobacterial species. The same three AGP glycan epitopes are present at the Gunnera-Nostoc symbiotic interface and the LM2 epitope is detected during the establishment of the Blasia-Nostoc symbiosis. Bioinformatic analysis of the N. punctiforme genome identified five putative AGP core proteins that are representative of AGP classes found in plants. These results suggest a possible involvement of AGP in cyanobacterial-plant symbioses and are also suggestive of a cyanobacterial origin of AGP.

Arabinogalactan proteins in root and pollen-tube cells: distribution and functional aspects

BACKGROUND

Arabinogalactan proteins (AGPs) are complex proteoglycans of the cell wall found in the entire plant kingdom and in almost all plant organs. AGPs encompass a large group of heavily glycosylated cell-wall proteins which share common features, including the presence of glycan chains especially enriched in arabinose and galactose and a protein backbone particularly rich in hydroxyproline residues. However, AGPs also exhibit strong heterogeneities among their members in various plant species. AGP ubiquity in plants suggests these proteoglycans are fundamental players for plant survival and development.

SCOPE

In this review, we first present an overview of current knowledge and specific features of AGPs. A section devoted to major tools used to study AGPs is also presented. We then discuss the distribution of AGPs as well as various aspects of their functional properties in root tissues and pollen tubes. This review also suggests novel directions of research on the role of AGPs in the biology of roots and pollen tubes.

Investigation of self-assembling proline- and glycine-rich recombinant proteins and peptides inspired by proteins from a symbiotic fungus using atomic force microscopy and circular dichroism spectroscopy

Fiber-forming proteins and peptides are being scrutinized as a promising source of building blocks for new nanomaterials. Arabinogalactan-like (AGL) proteins expressed at the symbiotic interface between plant roots and arbuscular mycorrhizal fungi have novel sequences, hypothesized to form polyproline II (PPII) helix structures. The functional nature of these proteins is unknown but they may form structures for the establishment and maintenance of fungal hyphae. Here we show that recombinant AGL1 (rAGL1) and recombinant AGL3 (rAGL3) are extended proteins based upon secondary structural characteristics determined by electronic circular dichroism (CD) spectroscopy and can self-assemble into fibers and microtubes as observed by atomic force microscopy (AFM) and scanning electron microscopy (SEM). CD spectroscopy results of synthetic peptides based on repeat regions in AGL1, AGL2 and AGL3 suggest that the synthetic peptides contain significant amounts of extended PPII helices and that these structures are influenced by ionic strength and, at least in one case, by concentration. Point mutations of a single residue of the repeat region of AGL3 resulted in altered secondary structures. Self-assembly of these repeats was observed by means of AFM and optical microscopy. Peptide (APADGK)(6) forms structures with similar morphology to rAGL1 suggesting that these repeats are crucial for the morphology of rAGL1 fibers. These novel self-assembling sequences may find applications as precursors for bioinspired nanomaterials.