Markiyan Samborskyy

Saccharopolyspora erythraea is an industrially important actinobacteria and a model in polyketide biosynthesis studies. However, its genetic toolbox remains limited. Here, we evaluated the properties of integrative and replicative vectors in Sacch. erythraea DSM40517. Three actinophage-based integrative vectors (φC31, φBT1, VWB) were efficiently transferred into Sacch. erythraea . The attB sites for these vector systems were identified. In case of φBT1- and VWB-based vectors, unique integration sites exists within the chromosome of the strain. In case of pSET152 (φC31), at least four different loci were identified with different efficiency of recombination. Our data revealed that all three integrative vectors are excised from the chromosome of the strain with varying frequencies, highlighting the need for selective pressures for their stable maintenance. Commonly used replicative vectors with Streptomyces replicons (pIJ101 and pSG5) have low transfer efficiency in Sacch. erythraea . To solve this problem, we constructed a shuttle vector pYS191 based on the replicon of plasmid pJV1. This vector was efficiently transferred into Sacch. erythraea and other actinobacteria including Streptomyces , Saccharothrix and Couchioplanes species . pYS191 is maintained at a low copy number under selective conditions, and is rapidly lost without antibiotic pressure. Neither integrative nor replicative vectors significantly affected erythromycin production. This study provides a comprehensive assessment of vector system in Sacch. erythraea and reports a new replicative vector based on rarely exploited pJV1 replicon for transient gene expression and genome engineering. These results expand the genetic toolbox for Saccharopolyspora and facilitate its use in natural products research and industrial biotechnology. Key points: • Actinobacterial integrative vectors are suited for gene cloning in Sacch. erythraea. • attB sites for three integrative vectors identified within Sacch. erythraea genome. • A new replicative vector pYS191 for use in Sacch. erythraea was constructed.

A novel endophytic yeast fungus, Vitasergia svidasoma IMV F-100106 (PRJNA807518), belonging to the family Debaryomycetaceae, was isolated from the fruiting body of Tuber melanosporum. The complete genome of the species is 11.195 Mb in size and consists of eight chromosomes and one mitochondrial genome. Vitasergia svidasoma IMV F-100106 is an active component of the soil biological preparation Mykovital (Oliferchuk et al., 2022; Oliferchuk et al., 2023a; Oliferchuk et al., 2023b). Its application in tomato cultivation technologies contributed to improved plant growth, increased yield and fruit quality, accelerated fruit ripening in the absence of mineral fertilizers, and stimulated the development of mycorrhizal symbiosis. An important practical application of V. svidasoma was its use in combination with biochar to facilitate the establishment of Amaranthus tricolor in an area damaged by artillery shelling. This technology demonstrated the potential of the endophytic yeast fungus for restoring vegetation cover and regulating microbiological processes in soils degraded by military activities.The results obtained demonstrate the considerable potential of Vitasergia svidasoma IMV F-100106 as a biological agent for sustainable agriculture, soil microbiome regulation, stimulation of mycorrhizal interactions, and biological remediation of ecosystems disturbed by anthropogenic and military impacts. Keywords: Vitasergia svidasoma IMV F-100106 (PRJNA807518); mycorrhizal symbiosis; organic farming; soil mycobiome; military-degraded soils.

Actinobacteria are often involved in ecological interactions with insects. Streptomyces sp. Sce081 with notable antifungal activity was isolated from the nest of wasp Sceliphron destillatorium (Illiger, 1807). Here, we report the draft sequence and analysis of the Streptomyces sp. Sce081 genome.

Mumia are one of the rarest representatives of phylum Actinomycetota with only four species known. Here, we report the complete genome sequence of Mumia sp. Pv 4-285 isolated from a rhizosphere sample of Phyllostachys viridiglaucescens . The genome consists of a 4,649,352 bp circular chromosome with 4,361 protein-coding genes.

The rapid development of new molecular methods and approaches, sequencing technologies, has provided new insights into genetic and structural features of bacterial genomes. Information about the genetic organization of metabolic pathways and their regulatory elements has greatly contributed to the increase in the number of studies related to the construction of new bacterial strains with improved characteristics. In this study, the entire genome of the producing strain Clostridium sp. UCM В-7570 from the “Collection of producing strains of microorganisms and plant lines for food and agricultural biotechnology” of Institute of Food Biotechnology and Genomics of the National Academy of Sciences of Ukraine was sequenced and characterized. The genome was assembled into the scaffold with a total size of 4,470,321 bp and a GC content of 29.7%. The total number of genes identified was 4262, of which 4057 encoded proteins, 10 were rRNA operons, and 80 were tRNA genes. The genes of the sequenced genome encoding enzymes involved in butanol fermentation were found and analyzed. They were organized into cluster structures, and their protein sequences were found to be similar to the corresponding strains of C. acetobutylicum, C. beijerinckii, and C. pasteurianum type strains with the highest similarity to the latter. Thus, Clostridium sp. UCM В-7570 producing strain was identified as C. pasteurianum and suggested for metabolic engineering purposes.

During recent decades the importance of ecosystems management services and maintenance have became paramount. We have proposed and implemented the technology of mycocenosis regulation of the rhizosphere of walnut nursery plants. Biotechnology involves inoculation before planting the roots of tree...

Coronaviruses share conservative spike protein (S) on their enveloped membrane surface, where S1 subunit recognizes and binds the cellular receptor, and the S2 subunit mediates membrane fusion. This similarity raises the question: does coronaviral infection by one create protection to others? Convalescent SARS-CoV-2 (COVID-19) sera were tested for cross reactivity with peptides from Middle East respiratory syndrome coronavirus (MERS-CoV) which shares 74% homology. Our results showed significant cross-reactivity with a peptide of the heptad repeat 2 (HR2) domain of the MERS-CoV spike protein. Sera samples of 47 validated seropositive convalescent COVID-19 patients and 40 sera samples of control patients, collected in pre-COVID time were used to establish cross-bind reactivity with the MERS-CoV peptide. Significantly stronger binding (p < 0.0001) was observed for IgG antibodies in convalescent COVID-19 patients compared to the control group. In ELISA, MERS-CoV peptide helps to discriminate post-COVID-19 populations and non-infected ones by the presence of antibodies in blood samples. This suggests that polyclonal antibodies established during SARS-CoV-2 infection can recognize and probably decrease severity of MERS-CoV and other coronaviral infections. The high homology of the spike protein domain also suggests that the opposite effect can be true: coronaviral infections produce cross-reactive antibodies effective against SARS-CoV-2. The collected data prove that despite the core HR2 region is hidden in the native viral conformation, its exposure during cell entry makes it highly immunogenic. Since inhibitory peptides to this region were previously described, this opens new possibilities in fighting coronaviral infections and developing vaccines effective even after possible viral mutations.

Adenylate-forming enzymes (AFEs) are a mechanistic superfamily of proteins that are involved in many cellular roles. In the biosynthesis of benzoxazole antibiotics, an AFE has been reported to play a key role in the condensation of cyclic molecules. In the biosynthetic gene cluster for the benzoxazole AJI9561, AjiA1 catalyzes the condensation of two 3-hydroxyanthranilic acid (3-HAA) molecules using ATP as a co-substrate. Here, the enzymatic activity of AjiA1 is reported together with a structural analysis of its apo form. The structure of AjiA1 was solved at 2.0 Å resolution and shows a conserved fold with other AFE family members. AjiA1 exhibits activity in the presence of 3-HAA (K _m = 77.86 ± 28.36, k _cat = 0.04 ± 0.004) and also with the alternative substrate 3-hydroxybenzoic acid (3-HBA; K _m = 22.12 ± 31.35, k _cat = 0.08 ± 0.005). The structure of AjiA1 in the apo form also reveals crucial conformational changes that occur during the catalytic cycle of this enzyme which have not been described for any other AFE member. Consequently, the results shown here provide insights into this protein family and a new subgroup is proposed for enzymes that are involved in benzoxazole-ring formation.

Enzymes that catalyse remarkable Diels–Alder-like [4+2] cyclizations have been previously implicated in the biosynthesis of spirotetronate and spirotetramate antibiotics. Biosynthesis of the polyether antibiotic tetronasin is not expected to require such steps, yet the tetronasin gene cluster encodes enzymes Tsn11 and Tsn15, which are homologous to authentic [4+2] cyclases. Here, we show that deletion of Tsn11 led to accumulation of a late-stage intermediate, in which the two central rings of tetronasin and four of its twelve asymmetric centres remain unformed. In vitro reconstitution showed that Tsn11 catalyses an apparent inverse-electron-demand hetero-Diels–Alder-like [4+2] cyclization of this species to form an unexpected oxadecalin compound that is then rearranged by Tsn15 to form tetronasin. To gain structural and mechanistic insight into the activity of Tsn15, the crystal structure of a Tsn15-substrate complex has been solved at 1.7 Å resolution.