Category: Nature

Nature

Differences in maize rhizosphere microbiome due to drought and flooding stress

A group from Nanjing Agricultural University, China, etc. has reported about differences in maize rhizosphere microbiome due to drought and flooding stress.
https://www.frontiersin.org/articles/10.3389/fmicb.2023.1295376/full

The results showed that
(1) the sum of the two phylums, Actinobacteria and Proteobacteri, accounted for nearly 50% existance, and
(2) Actinobacteria was the most dominant phylum in the two drought-flood abrupt alternation (DFAA) groups during the drought period and the rewatering period, and Proteobacteria was the most dominant phylum during the flooding period and the harvest period.
For your info., DFAA1 group means a trace rainfall to heavy rain condition and DFAA2 means a continuous drought to flooding condition.

where, A: during the drought period, and B:flooding period

Nature

Structure and Characteristics of a Lectin named ”Cvill” isolated from Canavalia villosa seeds

A group from Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, Belgium, etc. has reported about a ConA-like mannose-specific lectin, Cvill, isolated from Canavalia villosa seeds.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10649158/

Cvill is a ConA-like mannose-specific lectin isolated from Canavalia villosa seeds.

The lectin structure is composed of 237 amino acid residues, similar to other ConA-like lectins .

Cvill exhibits the typical legume lectin fold, also known as a β-sandwich, characterized by the presence of two superimposed beta sheets, resembling a sandwich. These beta sheets consist of antiparallel strands, with one beta sheet formed by six long, flat beta strands and the other by seven curved strands.The arrangement of dimers and tetramers in the quaternary structure was predicted.

Glycan array experiments indicated that Cvill exhibits affinity for terminal α-mannosyl residues and the tri-mannosidic core of N-glycans.

Cvill demonstrated dose-dependent cytotoxicity against all tested cell lines and this toxicity was carbohydrate-mediated. Cvill presented IC50 values of 97.0 μg/mL after 48 h incubation period for HeLa ells. Cvill also affected the viability of the fibrosarcoma (HT1080 cells) and the NHDF cells with IC50 values of 116.08 μg/mL and 108.34 μg/mL after a 48 h incubation period.

Nature

Gal modification of laminin receptor integrin α6β1 is reduced in hepatocellular carcinoma, and thereby accelerates cancer cell invasion

A group from Graduate Institute of Anatomy and Cell Biology, College of Medicine, National Taiwan University, Taipei, Taiwan, etc. has reported that Beta1,4-galactosyltransferases (B4GALTs) downregulation upregurates agalacto N-glycans and enhances the laminin-binding activity of integrin α6 and integrin β1 to promote invasiveness of Hepatocellular carcinoma (HCC) cells.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10618527/

Nature

Increase in high mannosylation prevents decidualization of the endometrium and causes pregnancy failure

A group from Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, Department of Biochemistry and Molecular Biology, Dalian Medical University, China, etc. has found increased high-mannose glycans and concomitant reduction of mannosidase MAN1A1 in the decidual tissues of miscarriage patients compared with early pregnant women using lectin microarrays. Among lectins, mannose binding lerctins, NPA, HHL, LCHA, CALSEPA, and GNA, showed significant changes.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10616321/

The abnormally elevated high mannosylation by MAN1A1 downregulation inhibited decidualization.
Screening of Long noncoding RNAs (LncRNAs) revealed that LncNEAT1 was increased in the decidual tissues of miscarriage patients.
Furthermore, it was found that LncNEAT1 interacted with NPM1-SP1 transcription complex and inhibited MAN1A1 expression, thereby hampering endometrial decidualization and embryo implantation.

Nature

SARS-CoV-2 suppresses TLR4 expressed on human DCs

A group from Department of Experimental Immunology, Amsterdam UMC location University of Amsterdam, The Netherlands, etc. has identified a novel pathway activated by SARS-CoV-2 that suppresses TLR4, the major bacterial TLR on human dendritic cells (DCs).
https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1011735

It was strongly suggested that SARS-CoV-2 interacts with the C-type lectin receptor DC-SIGN leading to Raf-1-mediated suppression of TLR4 signaling. As a result, SARS-CoV-2 actively suppresses DC function via DC-SIGN, and causes the higher mortality rates observed in patients with COVID-19 and bacterial superinfections.

Nature, Technology

Methods to promote colonization and activation of Bacillu. in the rhizosphere: SynCom and Prebiotics

A group from College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China etc. has reviewed about plant biocontrol mechanisms of Bacillus.
https://ami-journals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.14348

As is well known, species of the genus Bacillus have been widely used for the biocontrol of plant diseases in the demand for sustainable agricultural development.

The “cry for help” mechanism in plant means that plants fight pathogen attack by assembling health-promoting beneficial microbes by releaseing specific signals. This mechanism is very similar to human’s immunity that immune cells secrete cytokines/chemokines, and thereby recruit immune cells further and activate immunity.
The root exudates are extremely crucial for recruiting biocontrol agents (i.e., beneficial microbes like Bacillus) in response to plant diseases, and it has been known that L-malic acid, citric acid, fumaric acid, and tryptophan, threonic acid, lysine, pectin, xylan, and arabinogalactan are key exudates.

The use of Bacillus strains for the biocontrol of plant disease has achieved certain benefits worldwide. However, practical utilization of Bacillus is usually confronted with unstable disease suppression efficacy under field conditions. That is because complicated and dynamic factors, such as soil characteristics, plant genotypes, and indigenous microbiota, can all influence the colonization and functional efficacy of inoculated Bacillus agents.

To overcome this issue, two types of methods have been proposed.
One is to use a method called “SynCom” which is to use a bacterial consortium constructed by using some keystone strains from the genus of Bacillus, Burkholderia, Enterobacter, Lysobacter, Stenotrophomonas, Pseudoxanthomonas, Pseudomonas, and Acinetobacter.
The other is to use “Prebiotics”. As mentioed above, specific signals released from root exudates recruit Bacillus strains and induce their activities. Therefore, relevant compounds can be developed as prebiotics for enhancing root colonization and biocontrol performance, similar to those widely applied for stimulating beneficial bacteria in the human gut. So, exogenous addition of sucrose, L-glutamic acid, riboflavin could be used as prebiotics to promote rhizosphere colonization by beneficial Bacullus strains.

Nature

Averrant glycosylation (reduced fucosylation) of Mesoderm-specific transcript (MEST) is related to pregnancy failure.

A group from Liaoning Provincial Core Lab of Glycobiology and Glycoengineering, College of Basic Medical Science, Dalian Medical University, Dalian, China, etc. has reported that averrant glycosylation (reduced fucosylation) of Mesoderm-specific transcript (MEST) is related to pregnancy failure.
https://www.nature.com/articles/s41419-023-06166-4

By using Lectin microarray, it was discovered that the α1,3-fucosylation, especially difucosylated Lewis Y (LeY: Fuc α1–2 Gal-β1–4[Fuc α1–3]GlcNAcβ1) glycan, in the villus tissues of miscarriage patients decreased comparing with normal pregnancy women. And a novel evidence was shown that decreasing LeY on MEST hampers the binding of MEST and eukaryotic initiation factor (eIF4E2) and inhibits implantation-related gene translation, which leads to pregnancy failure.

MEST, also named as PEG1, belongs to the alpha/beta hydrolase superfamily. MEST is a single chain glycoprotein composed of 335 amino acids. As a maternal imprint gene, MEST is widely expressed throughout the embryonic developmental period. MEST plays a crucial role in the development of embryo and placenta, as well as fetal growth. Inappropriate MEST expression is linked to the increased probability of early spontaneous miscarriage and severe fetal defects, such as growth abnormality, low birth weight, or metabolic disorders in human.

Nature, Technology

Recognition of N-glycans of the porcine whipworm by the immune system

A group from Institut für Biochemie, Department für Chemie, Universität für Bodenkultur, Wien, Austria, etc. has reported about recognition of N-glycans of the porcine whipworm by the immune system.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10542551/

In this work, a natural glycan microarray using N-glycans (27 species) from porcine nematode parasite Trichuris suis was developed, and the interactions of these glycans with C-type lectins (DC-SIGN, Dectin-2, MGL), etc. were explored. Obtained N-glycans were fucosylated LacdiNAc motifs (bi/tri/tetra-antennary) with and without phosphorylcholine moieties and phosphorylcholine-modified oligomannose structures.

DC-SIGN recognises a rather wide range of oligomannosidic and fucosylated ligands, in the present study, its binding correlated generally with the occurrence of Man5-9GlcNAc2 in the relevant fractions.
Dectin-2 binding was lower on the array relativeto other innate immune system lectins.
MGL bound the majority of fractions, regardless of the presence of phosphorylcholine-modifications of the putative LacdiNAc-containing ligands.

Nature

Exosomes secreted from ST3G5-high cancer cells mediate peritoneal dissemination

A group from Department of Molecular Medicine and Biochemistry, Akita University Graduate School of Medicine, Akita, Japan, etc. has reported that lactosylceramide alpha-2,3-sialyltransferase (ST3G5) would be a suitable therapeutic target for preventing peritoneal dissemination mediated by exosomes secreted from ST3G5-high cancer cells.
https://pubmed.ncbi.nlm.nih.gov/37716915/

In this paper, the roles of lactosylceramide alpha-2,3-sialyltransferase (ST3G5; also known as ST3GAL5 and GM3 synthase) in the exosome-mediated pre-metastatic niche in peritoneal milky spots (MSs)was investigated.

It was demonstrated that exosomes secreted from ST3G5-high cancer cells (ST3G5high-cExos) were found to contain high levels of h ypoxia-inducible factor 1-alpha (HIF1α) and glycolytic enzymes, and accumulated in MSs via uptake in macrophages owing to increased expression of sialic acid binding GM3 receptor (CD169; also known as Siglec1). The upreguration of CD169 further promotes the incorporation of exosomes via positive-feedback loop.
As is known, GM3 is the first molecule in ganglioside family biosynthesisformed by the transfer of sialic acid to lactosylceramide by ST3G5 and regulates cell adhesion, proliferation, and migration, and it was shown that HIF1α increases the expression of immune checkpoint molecules, PD-L1, and T cell exhaustion in MSs

This results suggest that ST3G5 would be a promising target for preventing peritoneal dissemination in some cancers.

Nature, Technology

Multi-omics evaluation was performed using a model in which Arabidopsis was inoculated with Trichoderma spp.

A group from Department for Sustainable Food Process, CRAST Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy, etc. has reported about investigation of Trichoderma-mediated impact of heat, drought, and their combined stress on Arabidopsis thaliana, considering physiological responses, molecular implications at metabolome level, as well as the root and rhizosphere bacterial microbiota.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10484583/#B19

Plants treated with Trichodelma spp. were characterized by an increment of the fresh biomass even during drought and heat stress, suggesting that the increase in fresh weight observed was mainly due to an accumulation of water inside plant tissues.

The inoculation with Trichoderma spp. leaded to increased production of N-containing metabolites (including alkaloids and polyamines), phenylpropanoids, phytoalexins, tarpens, glucosinolates. It was also found that phytoholmons such as auxin-related substances (i.e., indole-3-acetaldehyde, indole-3-carboxaldehyde, and indole-3-ethanol), small peptides, and volatile organic compounds are upregulated by the inoculation with Trichoderma. And also, the soil microbiomes shifted in abundance and composition in response to environmental factors and Trichoderma treatments. Proteobacteria were the most predominant in roots and soil, on average, 89.6% of roots and 59.4 % of soil. Besides Proteobacteria in soil samples, one of the most abundant phyla were Bacteroides and Actinobacteroides.

They concluded that a holobiont approach, in other words, an multi-omics approach, is needed to understand the coordinated and complex dynamic interactions between the plant and its rhizosphere bacteria.