Month: October 2022

Nature, Technology

Interactions between galectins and O-mannosylated core M1 glycopeptides of α-dystroglycan

A group from Frontier Research Center for Advanced Material and Life Science, Hokkaido University, Sapporo, Japan, etc. has reported about interactions between galectins and O-mannosylated glycopeptides of α-dystroglycan, especially focusing on its core M1 structure.
https://www.nature.com/articles/s41598-022-22758-0

The O-linked mannose (O-Man) exists in a limited number of proteins that are required for normal development and have vital functions in muscle and neural physiology. The α-dystroglycan (α-DG) is the extracellular component of dystroglycan (DG), and is the most extensively studied mammalian O-Man glycoprotein. It is ubiquitously expressed in the skeletal muscles and the brain and is associated with cell adhesion, muscle integrity, and neurological development. α-DG possesses unique glycans, LacNac-terminated three kind of core structures (M1, M2, and M3), in its mucin (MUC)–like domain.

In this study, it was shown that Human Gal-1, -4, and -9 (except -3) can strongly recognize O-Man LacNAc-terminated glycoconjugates, and the presence of an α2,3-sialylated terminus led to a major reduction in the affinity of galectin, suggesting that this type of extension can fine-tune galectin activity towards this type of O-Man glycans. These interactions were significantly inhibited by lactose, establishing that the α-DG core M1-type glycans bind to the canonical sugar-binding site (S-face) of galectin, thus serving as a receptor for galectins.

And further, it was shown in microarray experiments that Gal-1 revealed trans-bridging capabilities, linking laminin-111, -121, -211, and -221 (but little -511) and core M1 α-DG glycopeptides as shown below, providing a new insight on the therapeutic application of this galectin in muscular dystrophy.


Fluorescence images of M1 glycoconjugates microarrays with laminins plus galectins

Nature, Technology

Affects of AM fungi inoculation on soybean yield and the composition of microbial communities

A group from Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Heilongjiang University, Harbin, China, etc. has reported about effects of inoculation of AM fungi (Rhizophagus intraradices) on soybean yield and the composition of microbial communities.
https://www.nature.com/articles/s41598-022-22473-w

The field experiment was done in triplicate with AM fungal treatments (non-inoculated and inoculated with Rhizophagus intraradices) and continuous cropping regimes (0 and 1 year of continuous cropping for soybean) as factors, i.e., there were four conditions, In0, In1, Non0, and Non1.

The effect of AM fungal inoculation was seen greatly in the composition of fungal communities rather than the composition of bacterial communities. As shown below, the most dominant genus was Subulicystidium in In1YSF and Non1YSF. However, Fusarium was the most dominant genus in In0YSF and Non0YSF. Interestingly, the relative abundance of Fusarium decreased significantly  from 15.72% in Non0YSF to 1.58% in In0YSF.

In response to this, the disease index of soybean root rot was significantly decreased by the inoculation of AM fungi. For example, the disease index with the AM fungal inoculation decreased to 66%. The growth/yield indexes of soybean increased by the AM fungal inoculation, and it was the highest in the inoculated soybean plants under non-continuous cropping.

Technology

Modification of Glycan binding Specificity of E-selectin from sLex to 6′-sulfo-sLex with double mutations E92A/E107A

A group from Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, etc. has reported that the specificity of E-selectin could be modified from sLex to 6′-sulfo-sialyl Lewis X with introducing double mutations.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9564326/

Although lectins are often used to detect glycans, their application to sulfated glycans is challenging due to the paucity of sulfate-recognizing lectins as well as their broad or mixed specificities.

In this work, the binding specificity of E-selectin was modified by removing destabilizing steric and electrostatic interactions between the 6′-sulfate and E92 and E107 with E92A/E107A mutations, to show binding specificity to 6′-sulfo-sialyl Lewis X (6′-sulfo-sLex). As is known, E-selectin shows specific binding to non-sulfated ligand, sLex.
This new specificity mimics that of the unrelated protein Siglec-8, for which 6′-sulfo-sLex is its preferred ligand.

Nature

There are Correlations between host genetic variation and microbiota abundance

A group from State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China, etc. has reported about numerous potential genes associated with the root microbiota formation, which were identified by microbiome genome-wide association studies (mGWAS) based on 827 foxtail millet cultivars in a single environment.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9546826/

A total of 644 taxonomically different bacterial strains from root microbiota of foxtail millet were collected, and 257 bacterial isolates were retained. From these isolates, representative cultivated strains of six positive marker OTUs and four negative marker OTUs with top beta estimation in the regression model were selected for the plant growth validation experiments.

where, Positive marker OTUs were (Acidovorax OTU_46, Bacillaceae OTU_22228, Kitasatospora OTU_8, Bacillus OTU_19414, Bacillus OTU_25704 and Bacillales OTU_381), and negative marker OTUs were (Shinella OTU_37, Bacillus OTU_54, Bacillaceae OTU_19835 and Bacillaceae OTU_28133).

These 10 biomarker strains were co-cultivated with foxtail millet Huagu12 (a bred cultivar of foxtail millet (Setaria italica) for 7-days in sterilized plates, and observed altered root lengths and plant heights compared with the control. The positive biomarker strains representing OTUs with top beta estimation showed significant growth-promoting abilities. Specifically, positive biomarker strain  (Kitasatospora OTU_8) promoted both root and stem growth, whereas  (Bacillus OTU_22228) and  (Acidovorax OTU_46) only promoted shoot growth compared to the control. The negative marker strain (Bacillaceae OTU_19835) and (Bacillaceae OTU_28133) suppressed the shoot and root growth of Huagu12.

Through this study, it would be quite interesting to know that there are correlations between host genetic variation and microbiota abundance, indicating that microbiota changes with plant genotypes.

Technology

New Plant Breeding: Utilizing SynCom (Formula of Core Species in Rhizospheric Microbiota)

A turning point is approaching for classical breeding methods. One of the major trends is a breeding method using genome editing, which can change only a specific target DNA sequence. As a result, the time required for breeding can be significantly shortened compared to conventional methods. But a bigger wave is also approaching. It is the idea of ​​actively using rhizospheric microorganisms to improve plant traits. The great advantage of this method is that the plants retain their original genotype and do not require specific safety assessments compared to transgenic or genome-edited products.

I have already written a number of  blogs about the symbiotic relationship between rhizobacteria and plants (in other words, it means there are many papers published), and I would not like to emphasize its importance again here. However, I would like to emphasize in this blog that the term SynCom is beginning to be used as a methodology. Through the analysis of accumulated data on the overall composition of rhizosphere microbiota, SynCom is a formula of “a few selected core species” that are most likely to significantly influence the structure of the rhizosphere microbiota.

The efficacy of SynCom applications in real agriculture has been evaluated, but often appears to be inconsistent. The main reason for this failure is because the plant-associated rhizosphere microbes can not exert their beneficial effects as expected. To solve this problem, we must consider the host plant genotype and root secretion from it, the compatibility of the bacterial species with the environment, and the spatial competition with native soil bacteria. SynCom’s ecological interaction with naturally occurring bacterial community is likely to be one of the most important aspects that must be considered seriously when applying SynComs in a real environment. Furthermore, in order to establish SynCom in the rhizosphere and expand its territory, it may be possible to apply biostimulants designed for the SynCom.

Microbiome sensors (MBS) and biostimulants should become more and more hot topics in the near future.

Ref.)  https://www.cell.com/trends/plant-science/fulltext/S1360-1385(22)00156-X

Technology

Examples of existing Biostimulants

Biostimulants are new technologies that reduce plant damage caused by climate and soil conditions and increase plant yields. In particular, effects such as suppression of pathogenic bacteria by regulation of rhizospheric microbiome, secretion of plant growth hormone, and solubilization of plant nutrients in soil are attracting attention.
https://www.japanbsa.com/biostimulant/definition_and_significance.html

In this respect, there are already several products on the market. I would like to introduce some of them.
Rice Toreru (called KODA, contains α-linolenic acid collected from duckweed that grows in paddy fields, and exhibits a plant growth-regulating effect)
Dr. Kinkon (Contains arbuscular mycorrhizal fungi and promotes symbiotic effects with plants)
Dr. Actinomycetes (Contains actinomycetes, Gram-positive bacteria, suppressing pathogenic bacteria)
Trichodesoyl (contains the ascomycete Trichoderma and inhibits pathogenic bacteria)
Chitin (N-GlcNAc activates plant immunity and serves as food for actinomycetes)

AgroHolobiont is developing novel microbiome sensors (MBS) to improve the effects of these existing biostimulants, as well as developing new biostimulants.
Activities of AgroHolobiont

Nature, Technology

Glycobiologist, Prof. Caroline Bertozzi, Stanford Univ. has won the 2022 Nobel Prize in Chemistry

In June 2021, I blogged about an unbelievable paper published by Prof. Caroline Bertozzi, Stanford University, et. al., that RNA is glycosylated.
small noncoding RNA is glycosylated

She has won the 2022 Nobel Prize in Chemistry.
The content of the award is not glycobiology itself, but the research on the biosynthesis of sialic acid led to the development of bio-orthogonal chemistry.

By the way, Caroline talks about sialic acid modification on cancer cell surface and immunity in an easy-to-understand manner. Please for your reference!
Sialylation of cancer cell surface and immunity: TED Youtube

Nature

Effects of N-Glycosylation in FcγRIIIa interaction with IgG

A group from Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Denmark, etc. has reported about the effects of N-Glycosylation in FcγRIIIa interaction with IgG.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9524020/

The FcγRIIIa receptor is an activating IgG receptor, mainly expressed on NK cells, macrophages, and monocytes. In this work, the effects of N-glycosylation of FcγRIIa onto affinity between FcγRIIIa and IgG1.

The highest affinity of all FcγRIIIa receptors was observed to afucosylated IgG, both IgG1-G0 and the IgG1-Oligomannose, as is expected.
Interestingly, the N-glycosylation state of the FcγRIIIa had minimal effect on the binding affinity when probed with afucosylated IgG, except for oligomannosylated FcγRIIIa where binding affinity is increased by a factor of two.
The highest KD, i.e., lowest affinity, was seen for IgG1-Hybrid and IgG1-Monoantennae to all FcγRIIIa.
On the other hand, the lowest KD, i.e., highest affinity, was seen for afucosylated IgG1 and oligomannosylated FcγRIIIa.

Nature

Continuous cropping of Sugar beet changed rhizospheric fungi significantly than non-cropping

A group from National Sugar Crop Improvement Centre, Heilongjiang University, Harbin, China, etc. has reported about difference of rhizosphere between continuous and non-continuous cropping groups of sugar beet rhizosphere.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9490479/

There were significant differences in fungal community composition between continuous and non-continuous cropping groups of sugar beet rhizosphere.
Compared with non-continuous cropping, continuous cropping increased the relative abundance of potentially pathogenic fungi such as Tausonia, Gilbellulopsis, and Fusarium, but decreased the relative abundance of Olpidium.


Left figure＝rhizospheric bacteria, Right figure=rhizospheric fungi
where, Sc, continuous cropping bulk soil; Sn, non-continuous cropping bulk soil; Rc, continuous cropping rhizosphere soil; Rn, non-continuous cropping rhizosphere soil; Bc, continuous cropping sugar beetroot; Bn, non-continuous cropping sugar beetroot.

Nature

OsRMC binding to CBM1 of a blast fungal xylanase blocks access to cellulose and inhibits infection of pathogenic fungi

A group from Iwate Biotechnology Research Center, Kitakami, Iwate, Japan, etc. has reported that OsRMC binding to CBM1 of a blast fungal xylanase blocks access to cellulose, resulting in the inhibition of xylanase enzymatic activity.
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1010792

The plant apoplastic space is filled with the primary cell wall, mainly composed of the polysaccharides cellulose, hemicellulose, and pectin. Hemicellulosic polysaccharides play an important role in controlling the physical properties of the cell wall. Xyloglucan in dicotyledonous and xylan in monocotyledonous plants are the major hemicellulosic polysaccharides by quantity and strengthen the cell wall by forming cross-bridges between cellulose microfibrils. A cell wall composed of heteropolysaccharides also provides a physical barrier against plant pathogen invasion.

Plant pathogenic fungi secrete a battery of cell wall-degrading enzymes (CWDEs) that catalyze hydrolytic and oxidative degradation of plant cell wall polysaccharides, assisting fungal penetration and colonization.

Plants have evolved various activity-inhibiting proteins as a defense against fungal cell wall-degrading enzymes (CWDEs), but how plants counteract the function of fungal enzymes containing carbohydrate binding modules (CBMs) remains unknown. Here, it was demonstrated that OsRMC, a CBM1-interacting protein (CBMIP) of rice (Oryza sativa), binding to CBM1 of a blast fungal xylanase blocks access to cellulose, resulting in the inhibition of xylanase enzymatic activity. Where, OsRMC is a member of the Cysteine-rich repeat secretion proteins (CRRSPs) containing two DUF26, and binds mannose as well as CBM1.


(LEFT)Rice leaves of wild-type (Hitomebore) control (Con) and OsRMC-overexpressing (OsRMC-OX) lines 4 days after inoculation of M. oryzae inoculation.
(RIGHT)The amount of M. oryzae fungal mass in rice leaf was monitored by quantifying the ratio of M. oryzae genomic DNA to rice genomic DNA obtained by PCR.