O-methylated N-glycans Distinguish Mosses from Vascular Plants

In the animal kingdom, a stunning variety of N-glycan structures have emerged with phylogenetic specificities of various kinds. In the plant kingdom, however, N-glycosylation appears to be strictly conservative and uniform. From mosses to all kinds of gymno- and angiosperms, land plants mainly express structures with the common pentasaccharide core substituted with xylose, core α1,3-fucose, maybe terminal GlcNAc residues and Lewis A determinants. In contrast, green algae biosynthesise unique and unusual N-glycan structures with uncommon monosaccharides, a plethora of different structures and various kinds of O-methylation. Mosses, a group of plants that are separated by at least 400 million years of evolution from vascular plants, have hitherto been seen as harbouring an N-glycosylation machinery identical to that of vascular plants. To challenge this view, we analysed the N-glycomes of several moss species using MALDI-TOF/TOF, PGC-MS/MS and GC-MS. While all species contained the plant-typical heptasaccharide with no, one or two terminal GlcNAc residues (MMXF, MGnXF and GnGnXF, respectively), many species exhibited MS signals with 14.02 Da increments as characteristic for O-methylation. Throughout all analysed moss N-glycans, the level of methylation differed strongly even within the same family. In some species, methylated glycans dominated, while others had no methylation at all. GC-MS revealed the main glycan from Funaria hygrometrica to contain 2,6-O-methylated terminal mannose. Some mosses additionally presented very large, likewise methylated complex-type N-glycans. This first finding of the methylation of N-glycans in land plants mirrors the presumable phylogenetic relation of mosses to green algae, where the O-methylation of mannose and many other monosaccharides is a common trait.

Molecular Genetic Analysis with Microsatellite-like Loci Reveals Specific Dairy-Associated and Environmental Populations of the Yeast Geotrichum candidum

Geotrichum candidum is an environmental yeast, also found as part of the cheese surface microbiota, where it is important in the ripening of many traditional cheeses, such as Camembert. We have previously developed a Multi Locus Sequence Typing (MLST) scheme, which differentiated five clades, of which one contained only environmental isolates, two were composed almost entirely of dairy isolates, and two others contained a mixture of dairy, environmental, and miscellaneous food isolates. In order to provide a simple method to uniquely type G. candidum strains, and in addition to permit investigation of the population structure at a fine level, we describe here a molecular analysis using a set of twelve highly discriminating microsatellite-like markers. The present study consolidates the previously suggested division between dairy and environmental strains, and in addition distinguishes a specifically European group of environmental strains. This analysis permitted the discrimination of 72 genotypes from the collection of 80 isolates, while retaining the underlying meaningful phylogenetic relation between groups of strains.

O-methylated N-glycans Distinguish Mosses from Vascular Plants

In the animal kingdom, a stunning variety of N-glycan structures has emerged with phylogenetic specificities of various kinds. In the plant kingdom, however, N-glycosylation appears as strictly conservative and uniform. From mosses to all kinds of gymno- and angiosperms, land plants mainly express structures with the common pentasaccharide core substituted with xylose, core α1,3-fucose, maybe terminal GlcNAc residues and Lewis A determinants. In contrast, green algae biosynthesize unique and unusual N-glycan structures with uncommon monosaccharides, a plethora of different structures and various kinds of O-methylation. Mosses, a group of plants that are separated by at least 400 million years of evolution from vascular plants, were hitherto seen as harbouring an N-glycosylation machinery identical to that of vascular plants. To challenge this view, we have analysed the N-glycomes of several moss species using MALDI-TOF/TOF, PGC-MS/MS and GC-MS. While all species contained the plant-typical heptasaccharide with no, one or two terminal GlcNAc residues (MMXF, MGnXF and GnGnXF, respectively), many species exhibited MS signals with 14.02 Da increments as characteristic for O-methylation. Throughout all analysed moss N-glycans the level of methylation differed strongly even in the same family. In some species, methylated glycans dominated, while others had no methylation at all. GC-MS revealed the main glycan from Funaria hygrometrica to contain 2,6-O-methylated terminal mannose. Some mosses additionally presented very large, likewise methylated complex-type N-glycans. This first finding of methylation of N-glycans in land plants mirrors the presumable phylogenetic relation of mosses to green algae, where O-methylation of mannose and many other monosaccharides is a common trait.

Comparative Analysis of The Kinomes of Plasmodium Falciparum, Plasmodium Vivax And Their Host Homo Sapiens

Background: Novel antimalarials should be effective across all species of malaria parasites that infect humans, especially the two species that bear the most impact, Plasmodium falciparum and Plasmodium vivax. Protein kinases encoded by pathogens, as well as host kinases required for survival of intracellular pathogens, carry considerable potential as targets for antimalarial intervention 1,2. To date, no comprehensive P. vivax kinome assembly has been conducted; and the P. falciparum kinome, first assembled in 2004, requires an update. The present study, aimed to fill these gaps, utilises a recently published structurally-validated multiple sequence alignment (MSA) of the human kinome 3. This MSA is used as a scaffold to assist the alignment of all protein kinase sequences from P. falciparum and P. vivax, and (where possible) their assignment to specific kinase groups/families.Results: We were able to assign six P. falciparum previously classified as OPK or ‘orphans’ (i.e. with no clear phylogenetic relation to any of the established ePK groups) to one of the aforementioned ePK groups. Direct phylogenetic comparison established that despite an overall high level of similarity between the P. falciparum and P. vivax kinomes, which will help in selecting targets for intervention, there are differences that may underlie the biological specificities of these species. Furthermore, we highlight a number of Plasmodium kinases that have a surprisingly high level of homology with their human counterparts and therefore not well suited as targets for drug discovery.Conclusions: Direct comparison of the kinomes of Homo sapiens, P. falciparum and P. vivax sheds additional light on the previously documented divergence of many P. falciparum and P. vivax kinases from those of their human host. We provide the first direct kinome comparison between the phylogenetically distinct species of P. falciparum and P. vivax, illustrating the key similarities and differences which must be considered in the context of kinase-directed antimalarial drug discovery, and discuss the divergences and similarities between the human and Plasmodium kinomes to inform future searches for selective antimalarial intervention.

Plasmepsin-Like Aspartyl Proteases in Babesia

Apicomplexan genomes encode multiple pepsin-family aspartyl proteases (APs) that phylogenetically cluster to six independent clades (A to F). Such diversification has been powered by the function-driven evolution of the ancestral apicomplexan AP gene and is associated with the adaptation of various apicomplexan species to different strategies of host infection and transmission through various invertebrate vectors. To estimate the potential roles of Babesia APs, we performed qRT-PCR-based expressional profiling of Babesia microti APs (BmASP2, 3, 5, 6), which revealed the dynamically changing mRNA levels and indicated the specific roles of individual BmASP isoenzymes throughout the life cycle of this parasite. To expand on the current knowledge on piroplasmid APs, we searched the EuPathDB and NCBI GenBank databases to identify and phylogenetically analyse the complete sets of APs encoded by the genomes of selected Babesia and Theileria species. Our results clearly determine the potential roles of identified APs by their phylogenetic relation to their homologues of known function—Plasmodium falciparum plasmepsins (PfPM I–X) and Toxoplasma gondii aspartyl proteases (TgASP1–7). Due to the analogies with plasmodial plasmepsins, piroplasmid APs represent valuable enzymatic targets that are druggable by small molecule inhibitors—candidate molecules for the yet-missing specific therapy for babesiosis.

DIVERSITY AND PHENETIC STUDY ON SYCONIUM OF FICUS L. (MORACEAE) FROM KERALA, INDIA REVEALING NATURAL CLASSIFICATION ALONG WITH AN IDENTIFICATION KEY

NAIR, S. S., BACHAN, K. H. A. & EBIN, P. J. 2021. Diversity and phenetic study on syconium of Ficus L. (Moraceae) from Kerala, India revealing natural classification along with an identification key. Reinwardtia 20(1): 27–36. — Ficus L. commonly called ‘figs’ is one of the most complex genera among the angiosperms with its specialised inflorescence called syconium that looks like a fruit. Syconium of 33 species of Ficus reported from Kerala were observed here to develop a novel key, solely based on syconium morphology. Numerical taxonomic methodology for syconium morphological characters were standardised, considering 22 characters with 104 character states and analysed using similarity clustering. The floral features of the genus are very much complex and all the existing keys for the species identification relays on both vegetative as well as floral features. Hence, the present key will be practical in use when syconium is the only available part. The numerical analysis of the syconium features well clustered and separated the trees with cauliflorous inflorescence, hemi epiphytic -epiphytic life forms and independent trees similar to the natural classification of the figs as “Atthi, Itthi and Aal”, indicating that phenetic analysis using the syconium characters alone provided a grouping similar to the natural grouping based on the habit. Preliminary phylogenetic analysis of figs also provided a similar clustering. This gives an insight into the fact that the separation of figs into these natural groups is reflecting phylogenetic trait. Detailed studies including more morphological traits and molecular analysis could establish the phylogenetic relation of figs in relation to the evolutionary history of climate and vegetation.

Functional metagenomics of the Thioredoxin superfamily

Environmental sequence data of microbial communities now makes up the majority of public genomic information. The assignment of a function to sequences from these metagenomic sources is challenging, because organisms associated with the data are often uncharacterized and not cultivable. To overcome these challenges, we created a rationally designed expression library of metagenomic proteins covering the sequence space of the thioredoxin superfamily. This library of 100 individual proteins represents more than 22’000 thioredoxins found in the Global Ocean Sampling dataset. We screened this library for the functional rescue of Escherichia coli mutants lacking the thioredoxin-type reductase (∆trxA), isomerase (∆dsbC), or oxidase (∆dsbA). We were able to assign functions to more than a quarter of our representative proteins. The in vivo function of a given representative could not be predicted by phylogenetic relation but did correlate with the predicted isoelectric surface potential of the protein. Selected proteins were then purified and we determined their activity using a standard insulin reduction assay and measured their redox potential. An unexpected gel shift of protein E5 during the redox potential determination revealed a redox cycle distinct from that of typical thioredoxin-superfamily oxidoreductases. Instead of the intramolecular disulfide bond formation typical for thioredoxins, this protein forms an intermolecular disulfide between the attacking cysteines of two separate subunits during its catalytic cycle. Our functional metagenomic approach proved not only useful to assign in vivo functions to representatives of thousands of proteins, but also uncovered a novel reaction mechanism in a seemingly well-known protein superfamily.

Repositioning of drugs to counter COVID-19 pandemic - An Insight

: COVID-19 is a coronavirus pandemic, caused by the novel coronavirus 2 (SARS-CoV-2) severe acute respiratory syndrome. The devastating impact of this novel coronavirus outbreak has necessitated the need for rapid and effective anti-viral therapies against SARS-CoV-2, to contain the spread of disease and importantly, alleviate the severe life-threatening symptoms and disorders. Drug repurposing strategy offers an attractive, immediate and realistic approach to tackle this growing pandemic of COVID-19. Due to the similarities with SARS-CoV-1 virus and phylogenetic relation to MERS-CoV virus, accelerated screening of approved drugs and development of repositioning strategies have proved to be critical in the survival of many COVID-19 patients. Numerous scientific investigations from the initial years of coronavirus outbreak along with upcoming advances of immunotherapy and vaccines may prove to be beneficial. Currently, several repurposing strategies are under different phases of clinical trials and provide with definitive framework for the development of future therapies for the effective treatment of COVID-19. This review article summarizes the latest developments and trends in drug repurposing strategy for COVID-19 treatment.

Phylogenetic Analysis of Phenylalanine Hydroxylase Enzyme and Its Future Aspect in Treatment of Phenylalanine Hydroxylase Enzyme Deficiency (Phenylketonuria)

PAH enzyme is one of the most vital enzymes in protein metabolism of the body. The enzyme has been found in various organisms and thus proves it has evolved along with speciation.PAH catalyses hydroxylation of the aromatic side of the phenylalanine to generate Tyrosine (4-hydroxyphenylalanine), one of the 20 standard amino acids that exist. The buildup of excess phenylalanine in the body due to deficiency of PAH causes a condition called Phenylketonuria which causes significant nerve damage. The condition Phenylketonuria is caused due to genetic mutation in PAH gene (Cr.12 )in an individual which can cause PAH enzyme deficiency. The purpose of this analysis was to use the existing Bioinformatics databases to draw relevant similarities of PAH of Homo sapiens and other organism using BLAST , MSA(Multiple Sequence Alignment) and phylogenetic relation while proposing the use of gene therapy using the data derived to cure Phenylketonuria