Year: 2022

A group from Molecular Plant Physiology, Institute of Botany, University of the Punjab, Lahore, Pakistan, etc. has reported about the effects of sulfonamides on soil microbial population and respiration in rhizospheric soil of wheat.
https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0264476

Sulfonamide is widely used in livestock farming and has been used to treat a variety of bacterial diseases. Due to poor management, they are excreted into the soil after treatments and these are extremely hazardous. Sulfonamides may impair the growth of plants, leaves, and roots at concentrations of several hundred mg/L. Accumulations of different antibiotics, including sulfonamides harmed the function and activity of microorganism and reduce soil enzymatic activity. Antibiotics in soil can bring constant changes in organisms and plants and exert harmful impacts on soil microbes.

This study was conducted to infer impact of four newly synthesized sulfonamides on isolated native strains from rhizosphere of wheat cultivar ‘Chakwal-50’. Furthermore, present research focused on the susceptibility of soil microbes and microbial respiration in the rhizospheric soil of wheat.

Sulfonamides: 2-(phenylsulfonyl) hydrazine carbothioamide (TSBS-1), N, 2-bis phenyl hydrazine carbothioamide (TSBS-2), aminocarbonyl benzene sulfonamide (UBS-1), and N, N’-carbonyl dibenzene sulfonamide (UBS-2) were applied on five isolated bacterial strains, i.e., AC (Actinobacter spp), RS-3a (Bacillus spp.), RS-7a (Bacillus subtilis), RS-4a (Enterobacter spp.) and RS-5a (Enterobacter spp.) isolated from the wheat rhizosphere. All sulfonamide derivatives exhibited antibacterial activity against tested bacterial strains, except for TSBS-1. In comparison of all sulfonamide derivatives, UBS-1 exhibited the highest inhibition zone (11.47 ± 0.90 mm) against RS-4a at the highest concentration (4 mg/ml).

numbers in the figure are UBS-1 concentrations (mg/mL)

Thus, sulfonamides have a negative influence on the soil microbiome, and some soil microorganisms that are unable to resist such stressors, so it is difficult to retain soil fertility and plant development as well. Soil microbial respiration changes mediated by sulfonamides were dependent on length of exposure and concentration. It is needed that antibiotics should be carefully watched and their impact on plant growth should be tested in the future studies.

A group from Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA, etc. has identified activated interstitial macrophages as a prominent site of SARS-CoV-2 viral takeover and focus of inflammation.
https://www.biorxiv.org/content/10.1101/2022.05.10.491266v1.full

Here, an experimental model of SARS-CoV-2 infection was proposed to allow systematic interrogation of the early molecular events and pathogenic mechanism of COVID-19 at cellular resolution in native human lung tissue.
To define the early events of SARS-CoV-2 infection in human lung, thick sections (~300-500 µm “slices”) of fresh lung tissue were prepared from therapeutic surgical resections or organ donors, and placed the slices in culture medium containing DMEM/F12 and 10% FBS. Then those tissue slices were infected with SARS-CoV-2 (USA-WA1/2020) at a multiplicity of infection (MOI) of 1 for two hours, and the cultures continued for 24 or 72 hours to allow infection to proceed.

To characterize viral and host gene expression during SARS-CoV-2 infection, slices were dissociated and analyzed by single-cell RNA sequencing. Multiplexed single molecule fluorescence in situ hybridization (smFISH) of the infected lung slices were also performed to simultaneously detect positive strand viral RNA (S gene probe), negative strand viral RNA (replication intermediate, Orf1ab gene probe), the canonical viral receptor ACE2, and markers of the infected cell types detected in scRNA-seq.

The results indicate that the most susceptible lung target of SARS-CoV-2 and focus of inflammation is activated interstitial macrophages. In this newly characterized lung macrophage subtype, viral RNA amplification results in host cell takeover with viral transcripts comprising up to 60% of the total cellular transcriptome. During takeover, there is cell-autonomous induction of an interferon-dominated inflammatory response, including induction of chemokines that can recruit local innate immune cells expressing the cognate receptors (CCL8, CCL2, CCL13, CXCL10). Takeover also induces expression of cytokine IL6, the potent inflammatory molecule central to cytokine storm. Thus, SARS-CoV-2 infection and takeover of interstitial macrophages and interferon-dominated induction of this suite of chemokines and cytokines forms a focus of lung inflammation and immune infiltration, which we propose initiates the transition from COVID-19 pneumonia to ARDS.

To explore the mechanism of SARS-CoV-2 entry into human lung macrophages, a modified recombinant Spike-pseudotyped lentivirus system was applied. Treatment of purified lung macrophages with hydroxychloroquine, a lysosomal protease inhibitor, or cytochalasin D did not block infection by the lentivirus across a wide range of concentrations. This indicates that Spike-mediated entry into lung macrophages does not require phagocytosis. Then, neutralization assays using three potent anti-Spike monoclonal antibodies (mAbs) were evaluated. Although each of these mAbs robustly inhibited lentivirus infection of HeLa-ACE2/TMPRSS2 at nanomolar concentrations, none reduced lentivirus infection of purified lung macrophages. Thus, this means that spike-mediated entry into lung macrophages occurs by a potentially novel mechanism that does not require phagocytosis or the ACE2-interacting receptor binding motif of the SARS-CoV-2 Spike protein.

A group from Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, San Raffaele Via Olgettina 58, 20132, Milan, Italy, etc. has reported that Chitinase-3-like protein-1 at hospital admission predicts COVID-19 outcome.
https://www.nature.com/articles/s41598-022-11532-x

It was found hat high levels of CHI3L1 were associated with an increased risk of adverse outcome, including transfer to the ICU or mortality, independently of age, sex, comorbidities, degree of respiratory insufficiency and systemic inflammation at admission, all known to be associated with COVID-19 clinical outcome.

The ideal biomarkers should not just reflect the overall inflammatory burden but disclose the events responsible for adverse disease evolution, such as vascular inflammation and lung remodeling. Moreover, since the interplay of antigen-presenting cells and T cells is crucial determinant of COVID-19 outcome, molecules involved in this process could be suitable candidates. Chitinase-3 like-protein-1 (CHI3L1), a member of the glycoside hydrolase family, meets these requirements. CHI3L1 binds to chitin, although being devoid of the ability to cleave the protein. It also binds to other substrates such as hyaluronic acid and heparin. Various signals that are activated in the early phases of COVID-19, including extracellular matrix (ECM) alterations, cell and tissue injury and response to cytokines and growth factors, elicit its synthesis by tissue cells and inflammatory leukocytes. In turn, CHI3L1 stimulates the expression of ACE-2 and viral spike protein priming proteases in pulmonary epithelial and vascular cells.

Since CHI3L1 is a recognized biomarker of kidney injury, CHI3L1 levels may at least in part reflect kidney damage, but it must be studied further.

A group from Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX USA, etc. has reported about folding structures of rotavirus spike protein VP4 and the difference in those glycan binding specificities.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9072675/

Rotaviruses are classified into ten different species or groups (A–J). Group A, B, C, and H rotaviruses infect both humans and animals. Epidemiologically, groups A, B, and C are the best characterized. Group A rotaviruses (RVA) and to a lesser extent group C rotaviruses (RVC) are the causative agents of most gastroenteric infections worldwide, the group B rotaviruses (RVB) have been associated with large epidemic outbreaks of severe gastroenteritis in China and sporadic infection in several countries.

The viral genome consists of 11 segments of double-stranded RNA that code for 6 structural viral proteins (VP) and 6 nonstructural proteins. The infectious virion is a triple-layered particle consisting of a core layer made of VP2, an intermediate layer made of VP6, and an outer shell made of glycoprotein VP7. Sixty protein spikes made of a protease-sensitive protein, VP4, extend from the VP7 shell.

The proteolytic treatment of VP4 results in two fragments, VP8* and VP5*. Sequence comparison of the structural proteins encoded by different rotavirus groups shows that the VP8* domain of the spike protein VP4 is the most variable. Extensive structural studies have shown that there is a galectin-like domain in human RVA and RVC (VP8*A and VP8*C), and recognize various cellular glycans in a genotype-dependent manner. The most typical glycan binding specificity of VP8*A and VP8*C are known to be H-antigen and A-antigen respectively.

Interestingly, the VP8*B shares no sequence identity with either VP8*A or VP8*C, which could differentially impact not only the structure but also the glycan-binding properties. Authors have found that VP8*B exhibits a fold with a twisted β-sheet clasping an α-helix that is entirely different from VP8*A or VP8*C, and glycan array screening and in silico docking analysis show VP8*B recognizes glycans containing LacNAc.

A group from Lab Microbial Ecology of the Rhizosphere (LEMiRE), CEA, CNRS, BIAM, Aix Marseille Univ, Saint-Paul-Lez-Durance, France, etc. has reported about the complexity of the multiple molecular dialogues that take place underground between microorganisms and between plants and its rhizosphere microbiota.
https://sfamjournals.onlinelibrary.wiley.com/doi/10.1111/1751-7915.14023

In this report, it was investigated the ability of the plant root-associated Pseudomonas brassicacearum NFM421 known as phytobeneficial bacteria to compete with two other rhizobacteria, Kosakonia sacchari NO9, a root-associated diazotroph and Rhizobium alamii YAS34, known for its ability to produce exopolysaccharide. Especially, the expression of the well known phytobeneficial genes phlD (production of DAPG), hcnA (production of hydrogen cyanide) and acdS (ACC deaminase activity) was evaluated in a variety of situations. The intracellular status of iron in P. brassicacearum NFM421 was also evaluated by analysing the expression of iron-regulatory RNAs prrF in this strain, because when iron is scarce, bacteria produce siderophores that may act as antifungals by depriving fungi of iron. The antagonism of P. brassicacearum NFM421 wt and the knockout mutants ∆phlD and ∆gacA against the soil-borne plant pathogens Fusarium culmorum, Fusarium graminearum and Microdochium nivale was evaluated as well, to compare the antifungal activity of DAPG and HCN.

Pseudomonads promote plant growth and produce antimicrobial secondary metabolites including HCN and DAPG. The expression of phlD was one thousand times higher than that of hcnA, indicating that even if HCN is known to be effective against pathogenic fungi, the levels of its expression by P. brassicacearum NFM421 are too low to inhibit fungal growth. Therefore, the mode of biocontrol of plant pathogenic fungi used in this study, which seems plausible in P. brassicacearum NFM421, most likely involves DAPG.

showing antifungal activity of P. brassicacearum NFM421wt, ∆phlD and ∆gacA towards Fusarium culmorum (Fc), Fusarium graminearum (Fg) or Microdochium nivale (Mn)

On in vitro conditions in CAA medium, the presence of the other two strains, N09 and YAS34, (separately or together) caused significant transcriptional changes in the expression of phlD, hcnA and acdS in P. brassicacearum NFM421 under iron-rich conditions. phlD was positively regulated by iron, an almost fourfold increase under iron-rich conditions, when the bacterium was grown alone. However, the presence of the competitors in CAA medium significantly decreased the phlD expression under iron-rich conditions (twofold), while no significant difference was observed under iron-depleted conditions. However, contrary to what was observed under in vitro conditions, phlD expression in P. brassicacearum NFM421 did not change during their interaction with B. napus root system in response to iron availability when grown alone.

As a conclusion, a scheme targeting the modulation of phl gene expression by other microorganisms and the plant was proposed, as well as the role of iron and its regulation by prrF RNAs. Anyway, the mechanisms by which one bacterial population interferes with the gene expression of another population are not yet fully understood and are future problems.

A group from Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA has reported existence of O-glycosylation unique to SARS-CoV-2 Omicron variant.
https://www.biorxiv.org/content/10.1101/2022.02.09.479776v2.full

HEK293 expressed S-RBD protein arising from WT (WA1/2020), Delta (T478K), and Omicron (BA.1) variants were analyzed by Fourier transform ion cyclotron (FTICR)-MS and trapped ion mobility spectrometry (TIMS)-MS. To elucidate the molecular sequence and O-glycans of the various S-RBDs, N-glycans from the S-RBD were removed by using a PNGase F treatment to minimize the interference posed by N-glycan heterogeneity.

Detailed top-down MS/MS analysis of the S-RBD O-glycoforms revealed the presence of a new O-glycosite (Thr376) unique to the Omicron variant. Fascinatingly, all detected S-RBD O-glycans for the WT and Delta variants were confidently assigned solely to Thr323. Given the smaller number of mutations present on Delta as compared to Omicron, it is not surprising that the O-glcyosite Thr323 was conserved between Delta and WT variants.
On the other hand, the Omicron variant yielded both the familiar Thr323 O-glycosite and a new Thr376 O-glycosite corresponding to the GalNAcGal(NeuAc)2 O-glycoform that is simultaneously occupied. This Thr376 O-glycosite is conveniently n + 3 adjacent to a proline at residue 373, which is consistent with previous reports of increased O-glycosylation frequency near proline. This particular Pro373 is a site-specific mutation unique to the Omicron variant and likely is the reason for this new O-glycosite. It might be better to note that the site occupancy of the Thr376 site was low(< 30%) relative to the Thr323. However, it is unclear at this moment if Thr376 O-glycan has any relationship with Omicron infectivity and escape from immunological protection.