Applied Biochemistry and Microbiology最新文献

Sugarcane molasses is a byproduct of the sugar industry. Its low cost and high remnant sugar content make it an ideal carbon source for bioethanol fermentation using the yeast Saccharomyces cerevisiae as a brewer. After long-term domestication, industrial S. cerevisiae became strongly adaptable to sugarcane molasses. To understand the related underlying mechanisms, we sequenced and analyzed the whole genome of the sugarcane-isolated diploid industrial S. cerevisiae A1015 strain. Compared to the S288c strain and two other wild isolates collected from the same environment, we observed that the A1015 strain possesses several specific genomic characteristics such as high heterozygous nucleotide variations (including single nucleotide polymorphisms and insertion/deletions). This result indicates that uneven distribution across all chromosomes appears through the outcrossing of compatible lineages and asexual reproduction-resulted relevant heterozygosity loss. In addition, we revealed a pericentric inversion caused by microhomology-mediated end joining in chromosome 16, potentially involving the positive selection of the SSU1 gene in ORF/promoter. The presence of genes such as the biotin prototrophic biosynthesis genes BIO1 and BIO6 or molasses toxicity resistance-related gene RTM1, as well as two copies of invertases, etc. reveals a phenotypic impact on industrial fermentation. Moreover, we identified numerous truncated ORFs in A1015 strain caused by non-triple insertions from tandem duplications, suggesting a unique genome evolution in the present industrial strain for molasses. Taken together, this study helps better understanding the genomic evolution of industrial S. cerevisiae for molasses fermentation.

TnpB is a protein encoded by a transposon and serves as a key component in the prokaryotic OMEGA system. It is predicted to be the “ancestor” of the Cas12 protein in the CRISPR system. TnpB is a programmable RNA-guided DNA endonuclease, which uses ωRNA molecules to guide the binding and cleavage of target DNA. Compared to proteins like Cas9 and Cas12, TnpB is smaller in size, consisting of approximately 400 amino acids. This smaller size offers an advantage in cellular delivery efficiency, as a single viral particle can carry it and facilitate its entry into the cell nucleus, where the genomic DNA is located. This article provides a detailed discussion of TnpB’s structure, function, its relationship with other gene-editing systems, and its potential applications in gene editing, offering a comprehensive reference for further research and application of TnpB.

According to the information available today, all types of microorganisms have common mechanisms for regulating the activity of virulence factors by the secondary messenger cAMP. They have been studied best in human and animal pathogens. At the same time, microorganisms that differ in specialization and habitat conditions, such as phytopathogens and mutualists, have mechanisms controlled by cAMP and adenylate cyclases that are fundamentally different from those in animal pathogens. The level of study of these processes in microorganisms of different specializations is uneven. This review attempts to systematize the available literature data and conduct a comparative analysis.

Alternative splicing (AS) is a non-canonical gene splicing process that allows a single gene to synthesise multiple protein isoforms and enhance a variety of protein functions. In this study, the involvement of AS in the generation of plant resistance to abiotic stresses was investigated using the VaCPK26 calcium-dependent protein kinase (CPK) gene, which is responsible for the resistance of Vitis amurensis Rupr. grapes to soil salinity and drought. The level of VaCPK26 transcription in grape leaves was studied under the influence of different environmental factors. Under low temperature exposure, in addition to the full-length VaCPK26 transcript, a short-spliced VaCPK26s1 transcript was obtained that lacked the 2nd exon out of the 7 exons that make up the full-length VaCPK26. Recombinant VaCPK26 increased the resistance of grape cells to salt stress and drought, and overexpression of the spliced VaCPK26s1 transcript in V. amurensis grape cell cultures had no effect on resistance to the stresses tested. These results show that AS can lead to the loss of properties of spliced transcripts characteristic of the original full-length form, which is important for complete understanding of the biological functions of CPK and alternative splicing.

In recent decades, the interest in Emericellopsis genus as producers of bioactive molecules has increased significantly due to the isolation of new compounds with potential pharmaceutical applications. Evaluation of the spectrum of antibiotic activity has allowed us to choose a promising producer of a new antibacterial compound, the strain Emericellopsis sp. E102 derived from saline soils. Strain E102, based on molecular and phylogenetic constructions, is allocated to a separate clade within the marine clade of Emericellopsis and is presumably a new species. The ethyl acetate extract of the E102 strain demonstrated significant efficacy at a concentration of 1000 μg/mL, resulting in the inhibition zones of 20.3–30.0 mm in size against Escherichia coli ATCC 25922; Escherichia coli ATCC 25922, Klebsiella pneumoniae ATCC 700603, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 29213 and Enterococcus faecalis ATCC 29212. The high-performance liquid chromatography analysis identified a compound with monoisotopic mass of the substance 724.5 g/mol. Using the Chemcalc.org service, the most probable gross formulas of the required component were determined. Based on the presented calculations, there is a high probability that the substance has a sterane framework.

The effects of the neurotransmitters serotonin (5-НТ), histamine, dopamine (DA), norepinephrine (NE), and acetylcholine (ACh) at concentrations of 0.1–10 μM on the contents of chlorophylls (а and b) and carotenoids in strains IPPAS B-239 and BM-1 of the microalga Haematococcus lacustris are considered. In the strain H. lacustris BM-1, all tested neurotransmitters except serotonin were found to stimulate carotenoid formation with an increase in the carotenoid content in the cells. The stimulatory effect was quite significant with acetylcholine and especially histamine and was manifested less with dopamine and norepinephrine. Carotenoid formation by strain IPPAS H-239 was only stimulated by acetylcholine and, to a lesser extent, by norepinephrine. The other neurotransmitters inhibited carotenoid formation. The total chlorophyll a and b content increased in the presence of all tested neurotransmitters except serotonin in strain BM-1. As for strain IPPAS H-239, its chlorophyll content was increased by acetylcholine and norepinephrine, whereas histamine and serotonin lowered the chlorophyll content. It is suggested that the tested neurotransmitters influence the vegetative cell—palmelloid cell—encysted cell transition, fixing it at the intermediate brown palmelloid stage characterized by significant chlorophyll and carotenoid contents.

The possibility of combining recognizing (sensitive) biological components with various converters creates a huge variety of biosensor systems. One promising area belongs to biosensor systems based on microwave resonators. The principle of operation of microwave sensors is based on a change in the resonant frequency of an electromagnetic resonator upon contact with the studied biological object. This review shows the possibilities of using microwave sensor systems and discusses the various options of conducting analysis when determining biomolecules (using antibiotics and disease markers, including glucose and antibodies, as an example). The presented results demonstrate the prospects of using microwave sensor systems to determine biomolecules and their further implementation for biomedical applications.

The content of negative allelopathic substances, N-phenyl-2-naphthylamine (N-PNA) and phthalates, was studied in morphologically and physiologically different root sites, in the epicotile of etiolated pea seedlings (Pisum sativum L.) and in the callus obtained from their epicotiles. The detection of N-PNA, o-phthalic acid, and phthalates in callus cells is evidence of the independent biosynthesis of these compounds in pea plant cells. Based on the changes in the content of N-PNA and phthalates caused by 10^–4 M naphthalene, it was shown that the main loci of biosynthesis of these compounds in pea seedlings include the growing apical part of the root and the epicotyle. It has been suggested that legumes, characterized by the ability to metabolize these substances with the participation of endophytic bacteria capable of degrading PAHs, can be used for remediation of soils contaminated with PAH pollutants.

Nonenzymatic glycation is an irreversible posttranslational protein modification, which leads to a violation of physicochemical properties and functions. Glycation most often affects lysine and arginine residues. Since hemoglobins contain many lysine residues (average 9%), they are often targets for the glycating agents glyoxal and methylglyoxal (MG). A comparative study of the susceptibility for glycation of leghemoglobin (Lb) from bean nodules (Vicia faba L.), myoglobins (Mb) from sperm whale muscles and horse hearts, and hemoglobins (Hb) from bovine and human erythrocytes was carried out. The level of glycation was defined by the autofluorescence of protein-bound advanced glycation end products (AGEs). The glycation level of Lb was 2.5 times higher than that of sperm whale Mb and human Hb and five times higher than that of horse Mb and bovine Hb. The Lb glycation level depended on the presence of oxygen in the medium. Under microaerobic conditions, the amount of AGEs formed was three times lower than in an oxygen-containing environment, and the degradation of the heme group was also slower. Glycation also affected the peroxidase activity of hemoproteins. The initial rate of Lb peroxidase reaction was six times higher than that of myoglobins and 10–13 times higher than that of hemoglobins. Glycation decreased the rate of the Lb and hemoglobin peroxidase reaction, while for myoglobins it did not change or increased depending on thte incubation time with MG.

Efficient transformation of mycobacteria, in particular, M. abscessus, is significantly complicated by the specific structure of their cell wall. The most widely used and effective method of introducing plasmid and phage DNA into mycobacterial cells is electroporation. The efficiency of electroporation is significantly affected by many factors, such as the nature of the DNA, the selective marker, growth supplements, the parameters of the electrical impulse, the species and the strain of the recipient mycobacterium. Although conditions for efficient electroporation for the slow-growing pathogen M. tuberculosis and the fast-growing saprophyte M. smegmatis have been described in details, recommendations for M. abscessus are scattered and even contradictory. Here it was established that efficient transformation of M. abscessus ATCC 19977 with the replicative vector pMV261 by electroporation is possible when using a logarithmic growth phase culture in a fairly wide range of optical density values OD₆₀₀ = 0.8–4.2, while cooling has little effect on the transformation frequency. A critical parameter is the mass of the introduced DNA. It has been established that the number of transformants obtained per 1 µg of DNA increases proportionally to the square of its mass. In case of introducing less than 0.5 μg of plasmid DNA the efficiency of electroporation is insufficient.