Anton A. Nizhnikov

Crystal (Cry) toxins produced by Bacillus thuringiensis are highly specific insecticidal proteins that are widely used as biological insecticides and function through proteolytic activation in insect midguts, which generates a three-domain toxic core responsible for membrane disruption as well as cleaved N- and C-terminal domains. While the structure and function of this core have been extensively characterized, the fate of the cleaved C-terminal region remains poorly understood. Amyloids are protein fibrils with a characteristic cross-β structure that participate in a wide range of functions in bacteria. Here, using bioinformatic approaches, we demonstrated that the C-terminal domains of Cry are rich in potentially amyloidogenic regions. We investigated the aggregation behavior of C-terminal domains from Cry1Ea11 and Cry1Ab12 proteins using a combination of biochemical and structural approaches. We found that the C-terminal domains of Cry1Ea11 and Cry1Ab12 undergo self-assembly in vitro, forming aggregates with fibrillar morphology. These assemblies bind amyloid-associated dyes, exhibit partial resistance to ionic detergents and proteolytic digestion, and display X-ray diffraction patterns confirming their amyloid properties. Functional assessment in insect cells showed that although these amyloids do not induce detectable cytotoxicity, amyloids of the C-terminal domains of Cry1Ea11 alter the readouts of the MTT assay in a manner consistent with previously described amyloid-associated effects on cellular formazan handling. Together, our findings demonstrate that the C-terminal domains of Cry toxins, which are released in the insect midgut as a result of proteolytic cleavage, are able to form bona fide amyloids that affect the metabolism of insect cells.

The development of eco-friendly multifunctional biopreparations based on microorganisms is a fundamental challenge in modern agriculture. Bacillus thuringiensis (Bt) strains are widely used for development of biopreparations, and a deeper understanding of their genomic makeup is required. Here, we used the Illumina platform and sequenced the genome of Bt strain 25, patented as an efficient biocontrol agent against coleopteran pests, including Leptinotarsa decemlineata, and fungal phytopathogens Fusarium oxysporum and Botrytis cinerea. The genome was 6,104,178 bp in length, with a low contamination (0.04 %) and a high completeness (99.01 %) level. Out of 6409 genes, 1030 loci were related to functionally important activities. The genome harboured 9 genes encoding well-known insecticidal toxins, such as InhA1/2, Bmp1, Spp1Aa, and Cry1Ea, 89 insecticidal minor virulence factors, and 560 putative proteases. It was predicted to be active against nematodes and lepidopteran pests. The genome contained a total of 24 biosynthetic gene clusters (BGCs), 11 of which are probably related to bactericidal activities, while 5 are known clusters, synthesising, e. g., lipopeptide fengycin and siderophores petrobactin and bacillibactin. The genome was enriched with mobile genetic elements and horizontally transferred regions. Our results elucidate the composition of genetic determinants controlling beneficial features of Bt strain 25.

Automatic prediction of metabolic activities of bacterial isolates directly from genomic data is both an essential task and a daunting challenge. The most widely used algorithm bundled into current tools is a gap-filling algorithm aimed to complement the patchy genome-derived data. We examined the most accurate available software, qapseq, and assessed its applicability to revealing chemotaxonomic properties of bacterial species. Using 11 genomes of experimentally studied Megasphaera spp., we compared the computational findings with the experimental results based on 18 utilized and 11 produced substanc es. Two modes were considered: medium prediction and filling procedure. Correlation analysis showed that the “medium” mode reflected the metabolized compounds better than the “fill” mode, with correlation estimates of 0.64 and 0.33, respectively. The true positive rate (TPR) in the “medium” mode reached 0.97. In “fill” mode, TPR estimates were 0.42 for characterizing utilization and 0.21 for production of substances. The worst performance of the gapseq utility was found when reporting the biosynthesis of organic acids such as isovaleric and isobutyric acid. Having shown the strengths and limitations of the gap-filling-based approach, we propose using taxonomic studies to refine metabolic reconstruction and to devise robust methods.

The Fourth scientific forum "Genetic Resources of Russia" was held in St. Petersburg from May 12-15, 2026, at the St. Petersburg Branch of the Russian Academy of Sciences and under the auspices of the Vavilov Society of Geneticists and Breeders. The Forum included six plenary sessions and roundtables, as well as two parallel scientific events and poster sessions. A meeting of the Scientific Council of the Division of Biological Sciences of the Russian Academy of Sciences on biological (bioresource) collections was also held in the framwework of the Forum. More than 300 researchers from St. Petersburg, Moscow, Novosibirsk, Vladivostok, Tyumen, Ufa, Yakutsk, Petrozavodsk, Kursk, Yalta, Saratov, Krasnoyarsk, Sochi, Minsk, and other cities participated in the Forum. Over the course of four days, scientists from 29 regions of Russia, as well as the Republic of Belarus, presented more than a hundred oral reports to the scientific community, covering a wide range of topics – from genetic resources management technologies to their role in active longevity and bioeconomics. The Forum events included detailed discussions of research results and topical issues in the following areas: biodiversity conservation, genetic resources for active longevity, genetic resources for the bioeconomy, legal and ethical issues related to working with biological collections, training personnel for working with biological collections, and herbarium and museum genomics. The results of these discussions are presented in this publication as a Forum resolution.

Members of the genus Psychrobacillus are widely distributed across diverse environments, and novel representatives continue to be identified. Here, we describe the strain nc5.1 ^T , isolated from soil near Lake Syltran-Kel in the Kabardino-Balkarian Republic, Russia. Phylogenomic analysis indicated that P. glaciei PB01 ^T was its closest relative, placing the isolate within the genus Psychrobacillus . The average nucleotide identity (84.3%) and digital DNA–DNA hybridization (31%) values compared with PB01 ^T suggested that the isolate represents a novel species. The strain nc5.1 ^T was a Gram-negative, motile, rod-shaped bacterium forming circular, smooth, beige-brown colonies. No morphologically detectable endospores were observed under sporulation-inducing conditions. Optimal growth conditions were pH 6.5, 0.5% NaCl, and 30°C; however, a minor but reproducible viable fraction persisted after exposure to 80°C. Biochemical profiling revealed that the strain assimilated 46 carbon sources spanning carbohydrates, amino acids, and organic acids and exhibited growth in the presence of aztreonam, nalidixic acid, and potassium tellurite. The dominant cellular fatty acids were C _14:1 (52.8%), C _14:0 (16.0%), and C _16:0 (7.7%), which distinguished the isolate from P. glaciei . Genomic analysis identified biosynthetic gene clusters associated with the synthesis of iturin and a streptozotocin-like moiety, suggesting the capacity for biosynthesis of secondary metabolites with beneficial properties. MTT assays showed that culture supernatants did not reduce mammalian cell viability but, conversely, moderately stimulated the proliferation of PANC-1 cells. Together, the phenotypic, chemotaxonomic, and genomic data indicate that strain nc5.1 ^T represents a novel species with the proposed name Psychrobacillus syltrankelensis sp. nov. The type strain is nc5.1 ^T (=RCAM 07221). IMPORTANCE: The discovery of the P. syltrankelensis species extends our understanding of diversity within Bacillaceae and reveals traits that challenge the established views of the family. Based on genomic thresholds, nc5.1ᵀ clearly represents a novel species while also displaying atypical morphological features, such as Gram-negative staining and absence of sporulation. Despite the lack of morphologically detectable endospores, the strain retained viability after exposure to elevated temperatures, further emphasizing its unusual physiological profile. These characteristics underscore the limitations of morphology-based taxonomy and the necessity of genome-guided classification. Genome analysis revealed two adaptive groups within Psychrobacillus , distinguished by mutually exclusive biosynthetic clusters responsible for the synthesis of either iturin or bacillomycin D, with nc5.1ᵀ belonging to the iturin-producing lineage. The nc5.1ᵀ isolate also harbored a highly divergent streptozotocin-like locus, indicating unexplored secondary metabolism with potential biotechnological relevance. At the same time, culture supernatants unexpectedly stimulated the growth of human pancreatic carcinoma cells, underlining the complexity of functional predictions based solely on genomic data. Together, these findings highlight the importance of combining phenotypic, ecological, and genomic approaches for accurate species delineation and provide new insights into the hidden metabolic potential of Psychrobacillus .

The article describes the scientific and pedagogical career of Lyudmila Alekseevna Lutova, Doctor of Biological Sciences, and Professor of the Department of Genetics and Biotechnology at St. Petersburg State University (SPbU), who celebrated her anniversary in October 2025. It highlights key areas of her research in biotechnology and plant developmental genetics, including the development of the genetic bases of plant regeneration and the creation of pest-resistant forms and plants producing bioactive compounds. Particular attention is paid to her teaching activities, contributions to personnel training, and the popularization of advances in genetics. Colleagues from the Vavilov Society of Geneticists and Breeders (VOGiS) cordially congratulated Lyudmila Alekseevna on her anniversary and wished further creative success in her research and teaching, lots of energy, good health, and successful development of plant genetics and biotechnology at St. Petersburg University!

Oxydifficidin is a natural polyketide antibiotic that has long been recognized as a ribosome-targeting agent that inhibits protein synthesis. In this paper, we describe Bacillus velezensis strain EV17 and compare its complete genome sequence with that of the previously characterized B. velezensis strain K-3618 and the difficidin biosynthetic gene cluster (BGC) combined with mass spectrometry to elucidate the production of oxydifficidin by these strains. Toeprinting and small fluorescent peptide assays showed that isolated oxydifficidin induces a generalized inhibition of translation at every step of elongation in protein biosynthesis. In previous studies, it has been demonstrated that oxydifficidin targets bL12 protein. Although spontaneous mutations conferring resistance to oxydifficidin in ribosomal protein bL12 located relatively close to the thiostrepton binding site on uL11, our data show that oxydifficidin binding does not interfere with thiostrepton, thereby refining previous findings about its putative ribosomal target. We are the first to show that this compound does not affect eukaryotic translation and has two orders of magnitude lower effect on eukaryotic cells compared to bacteria. These facts are important to further investigate its potential as a bioprotectant against phytopathogens or even as a therapeutic agent.

Amyloids are protein aggregates with fibrillar morphology and a characteristic spatial structure called “cross-β.” Amyloids have been known for over 150 years, and many of them are associated with the development of predominantly incurable human diseases called amyloidoses, some of which, including Alzheimer’s disease, are of high social significance. At the turn of the 21st century, it was established that amyloids not only result from protein misfolding disorders but are involved in performing biological functions in all three domains of the living world: archaea, bacteria, and eukaryotes, including humans. The greatest diversity of functional amyloids has been described in bacteria in which these protein aggregates are involved mainly in the processes of formation of biofilms that play an important role in the development of bacterial infections and antibiotic resistance. Amyloid fibrils represent an important structural component of the biofilm matrix in various groups of bacteria. Although some bacterial amyloids are formed by specific secretion and assembly systems, the mechanisms of formation of another group of bacterial amyloids, including amyloid states of outer membrane proteins and components of the translation apparatus, are unclear. Current evidence suggests that more general, “nonspecific” mechanisms, including regulated cell death during biofilm development, may be involved in the formation of such amyloids.

The transition to organic farming is one of the most desirable achievements of our time. Rational use of organic farming approaches not only enables a reduction in costs and increased yields but also limits the risks associated with the use of pesticides and chemicals. Despite the widest practical application of numerous biocontrol agents based on Bacillus strains, their metabolome, including the main active substances, often remains unknown. In order to understand the basic principles of the functioning of the Bacillus velezensis K-3618 strain, widely used in organic farming, we studied its spectrum of antimicrobial metabolites in detail. It was shown that the main antimicrobial agents of B. velezensis K-3618 are representatives of the macrolactin family. The identified macrolactin A (MLN A) and its acylated analogs 7-O-malonyl macrolactin A (mal-MLN A) and 7-O-succinyl macrolactin A (suc-MLN A) are active against Gram-positive bacterial pathogens, including multidrug-resistant strains. Among them, suc-MLN A is the most potent antimicrobial, highly active (MIC = 0.1 μg/mL) against the common human pathogen methicillin-resistant Staphylococcus aureus (MRSA). It was revealed that the primary mechanism of action of MLN A-based macrolactins is protein translation inhibition. Acylated macrolactins outperform MLN A in the prokaryotic cell-free system, displaying high efficiency in low micromolar concentrations. We observed that acylated MLN A analogs undergo pathogen-mediated biotransformation into MLN F analogs, having their antimicrobial activity reduced by two orders of magnitude. Hence, both acylation of MLNs and stabilization of the MLN A core are essential for the creation of new synthetic MLNs with improved antimicrobial activity and stability. However, we speculate that these degradability modes are of prime importance for bacterial ecology, and they are highly conserved in Bacillus species from various ecological niches.