Applied Biochemistry and Microbiology最新文献

{"title":"Molecular Cloning and Biochemical Characterization of a Novel Disulfide Bond-Reductase from Feather-Degrading Stenotrophomonas sp. Yang-5","authors":"M. Jiang,&nbsp;X. Qiao,&nbsp;E. Zhu,&nbsp;Y. Gu,&nbsp;Z. Chen,&nbsp;X. Ju,&nbsp;L. Li,&nbsp;X. Zhong,&nbsp;Z. Chen","doi":"10.1134/S0003683824606619","DOIUrl":"10.1134/S0003683824606619","url":null,"abstract":"<p>Disulfide bond-reductase (DSBR) exerts an initial role in the enzymatic degradation of feather waste. However, despite its significance, there are currently very few reports on the heterologous expression and enzymatic properties of this type of enzyme. This study focuses on a novel DSBR derived from the strain <i>Stenotrophomonas</i> sp. Yang-5 (Yang-5-DSBR), which was previously found to efficiently degrade feathers. The target band of the DSBR was cloned by PCR, with a size of 687 bp. Domain prediction revealed that the enzyme consists of two distinct parts: N-terminal domain similar to glutathione-S-transferase, spanning amino acids from 1 to 92, and C-terminal domain spanning amino acids from 110 to 204. Subsequently, recombinant expression was carried out using a prokaryotic expression host, followed by nickel column purification of the protein. SDS-PAGE analysis showed that the size of the target protein was approximately 26 kDa, which was in line with our expectations. Enzymatic property assays indicated that the optimal reaction temperature and pH for the Yang-5-DSBR were 35 °C and pH 7.0, respectively. It maintained over 80% enzymatic activity at pH levels ranging from 6.0 to 8.0 and at 40 °C, demonstrating moderate tolerance with significant potential for further improvement. Notably, most metal ions and chemicals inhibited the activity of Yang-5-DSBR, but among them, Al³⁺, Mg²⁺ and Mn²⁺ at a concentration of 0.025 mM could enhance enzymatic activity by 20–50%. Additionally, the presence of 2.5% reducing reagent DTT increased enzymatic activity by 20%, akin to enzymes with Cys as a catalytic key amino acid, such as keratinase and nitrilase. Substrate specificity studies revealed that Yang-5-DSBR had a preference for GSSG and soluble keratin but exhibited lower activity towards other feather substrates. Kinetic parameter assays determined the <i>V</i>_max and K_M of DSBR to be 7.4 and 6.7 mg/mL, respectively. Overall, these insights enhance understanding of DSBR’s role in feather degradation and facilitate its potential applications in biochemical processes and industry.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 1","pages":"49 - 57"},"PeriodicalIF":1.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The ABC Transport Protein PotC Plays a Crucial Role in Antibiotic Resistance in Escherichia coli","authors":"Q. Zhao,&nbsp;Y. Wu,&nbsp;J. Sun,&nbsp;J. Zhang,&nbsp;X. Li,&nbsp;X. Pang,&nbsp;S. Gu","doi":"10.1134/S0003683824603706","DOIUrl":"10.1134/S0003683824603706","url":null,"abstract":"<p>The phenomenon of microbial resistance is becoming increasingly serious. The efflux pump system plays a key role in bacterial resistance to antibiotics. The transcriptional profile of <i>Escherichia</i> <i>coli</i> treated with antibiotics revealed the pathways and response mechanisms of up- or down-regulation of efflux pump-related genes. In this study, 104 of all 2548 genes, efflux pump-related differentially significantly expressed genes were screened. The most significant spermidine transport in the Gene Ontology functional enrichment analysis was the most likely important pathway for the <i>E. coli</i> species to respond to antibiotics. The functional enrichment results of Kyoto Encyclopedia of Genes and Genomes showed that most of the antibiotic-induced transport proteins belong to the “ABC family efflux pumps”. The results of the protein-protein interaction network indicated that <i>potC</i> might act as a key gene for <i>E. coli</i> to respond to antibiotics. Finally, overexpressing strains of <i>potC</i> were constructed, and the survival rates of overexpressing strains of <i>potC</i> were improved by 18.9, 14.0, 43.3, and 31.7% after treatment with four antibiotics: gentamicin, norfloxacin, chloramphenicol, and cefotaxime sodium, respectively. This further suggested the role of PotC in the resistance of <i>E. coli</i> to antibiotics, providing scientific support for the study of bacterial resistance mechanisms.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 1","pages":"58 - 67"},"PeriodicalIF":1.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Colorimetric Assessment of Extracellular Electron Transfer in Bacteria: a Novel Approach for Evaluating Antibiotic Efficacy","authors":"M. Khedri","doi":"10.1134/S000368382460547X","DOIUrl":"10.1134/S000368382460547X","url":null,"abstract":"<p>A need exists for a rapid and straightforward method to measure antibiotic susceptibility in bacteria to optimize antibiotic usage and mitigate the emergence of antimicrobial resistance. In this study, we investigated a novel, facile, and rapid colorimetric method for assessing bacterial antibiotic susceptibility via the extracellular electron transfer (EET) assay. This method relies on the colorimetric detection of EET from bacterial respiratory metabolism to an EET reagent containing an electron transfer mediator (riboflavin) and a detectable electron acceptor (methylene blue). The minimum inhibitory concentration (MIC) values obtained for three real clinical nosocomial pathogens <i>(Staphylococcus aureus, Pseudomonas aeruginosa, and Klebsiella pneumoniae</i>) using our technique align closely with those derived from the gold standard micro-dilution broth assay. Employed riboflavin as an external mediator for electron transfer, enables to screen antibiotic susceptibility of bacterial strains with different capabilities of EET. Our innovative approach offers a rapid assay for identifying EET, and strain-specific effectiveness of antibiotics with diverse mechanisms of action. As we employed simple and cost-effective equipment, there is potential for this method to evolve into a practical approach for simplified antibiotic susceptibility testing.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 1","pages":"68 - 75"},"PeriodicalIF":1.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793220","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Amphotericin B-conjugated Silica-Capped Gold Nanoparticles as Antifungal Agents with improved Cellular Uptake","authors":"S. Nagaraj,&nbsp;S. Narayan","doi":"10.1134/S0003683824604153","DOIUrl":"10.1134/S0003683824604153","url":null,"abstract":"<p>Multidrug resistance is a serious menace that has resulted in several drugs or antibiotics becoming ineffective resulting in triggering toxic responses which has led to the use of nano-based carrier systems to delivery drugs or antibiotics. The broad-spectrum antifungal agent Amphotericin B (Amb) is used for treating invasive fungal infections. The conventional surfactant formulation releases Amb in a fast manner and elicits toxicity through surfactant-related mechanisms. To overcome this lacuna of the present formulations, amine-functionalized silica-capped gold nanoparticles conjugated with Amb have been designed. The structure, functionalization, size, and shape of the conjugated nanoformulation have been assessed through appropriate techniques. Around 70% Amb was found to be conjugated to the nanoparticles and they had a decent stability as indicated by the zeta potential value of –9.65 mV. Haemolysis assay confirmed the biocompatible character of the composite, possibly related to the silica capping. The cytotoxicity assays revealed that toxicity of the drug reduced confirming the hypothesis that a gradual release of Amb could overcome the lacunae of the conventional formulations. The uptake of the drug conjugate was also improved as evidenced from fluorescence microscopic and spectroscopic studies, which again can be attributed to the controlled release of Amb from the conjugate. The study suggests that the use of stable nanoparticles can improve the delivery of Amb, and can prevent biofilm formation of <i>Candida albicans</i> through improved uptake of Amb.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 1","pages":"137 - 155"},"PeriodicalIF":1.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793225","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Feeding Impact on the Gut Microbiome of Hermetia illucens Larvae","authors":"M. V. Vecherskii,&nbsp;T. A. Kuznetsova,&nbsp;D. R. Khairullin,&nbsp;I. A. Chaporov,&nbsp;A. I. Bastrakov,&nbsp;N. A. Ushakova","doi":"10.1134/S0003683824606851","DOIUrl":"10.1134/S0003683824606851","url":null,"abstract":"<p>The microbiome of the black soldier fly larvae (BSFL) formed in real rearing substrates in close to industrial conditions was studied. The used substrates, dairy waste and feeding yeasts, differed in the sources of protein, which are available in commercial rearing of the black soldier fly (BSF). Amplicon 16S rRNA sequencing of the BSFL gut metagenome reveals high variability in the microbiome composition. The only bacteria genus found in all the studied developmental stages of BSFL was <i>Enterococcus</i>. We identified typical microorganisms for the initial and final stages of the experiment, as well as typical patterns in changes of the abundance of the main groups of microorganisms. It has been noted that many microorganisms previously believed to be members of the core microbiome of BSFL gut (such as <i>Dysgonomonas</i>) may be completely absent. It is important that the change of rearing conditions influences also the BSFL microbiome: opportunistic pathogen microorganisms, as well as unwanted histamine-poisoning bacteria can appear. Most of them belong to the families Enterobacteriaceae, Morganelliaceae, and Campylobacteriaceae. Other conditions prompt development of spore-forming bacilli, the presence of which may prevent successful heat sterilization of the final product (larva biomass). However, various modifications of substrate composition and the duration of the larva rearing lead to a reduction or complete elimination of unwanted microorganisms.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 1","pages":"200 - 210"},"PeriodicalIF":1.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chlordimeform Degradation by a Mixed Culture of Bacillus sp., Acinetobacter sp. and Rhodococcus rhodochrous","authors":"H. D. Duc,&nbsp;N. T. Thanh,&nbsp;N. T. Thuy,&nbsp;H. H. Hong Vu,&nbsp;T. T. Xuan","doi":"10.1134/S0003683824605043","DOIUrl":"10.1134/S0003683824605043","url":null,"abstract":"<p>Chlordimeform is an insecticide extensively applied causing serious environmental pollution. In this study, some bacterial strains, i.e., <i>Bacillus</i> sp. Cd1, <i>Acinetobacter</i> sp. Ca3 and <i>Rhodococcus rhodochrous</i> Ct2 isolated from soil were determined for their degradability towards the compound. <i>Bacillus</i> sp. Cd1 first transformed the substrate into 4-chloro-2-methylaniline and 3-chlorotoluene, and then slowly degraded the metabolites mainly via meta-cleavage pathway. By contrast, <i>Acinetobacter</i> sp. Ca3 slowly transformed chlordimeform but quickly degraded 4-chloro-2-methylaniline through ortho-cleavage pathway, while <i>R. rhodochrous</i> Ct2 showed rapid degradation of 3-chlorotoluene through the meta-cleavage pathway. The degradation kinetics for chlordimeform of the mixed culture followed the Edwards model with the maximum degradation rate being 10.49 ± 0.11 mM/day. Immobilization of the mixed culture in rice straw showed effective degradation, with almost complete degradation at the 6-th cycle using a pack-packed bed bioreactor. The cultivation with peanut and water spinach association with inoculation of the mixed culture enhanced the degradation of the compound in soil. This study elucidates the synergistic interaction among isolated bacteria to enhance degradation of chlordimeform and its metabolites. The cooperation among isolated bacteria, plant cultivation and indigenous microorganisms also increased the insecticide degradation in soil.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 1","pages":"92 - 100"},"PeriodicalIF":1.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793222","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simultaneous Production of Hydrophobic Bioactive Compounds from Biomass of Purple Non-sulfur Bacterium Cereibacter sphaeroides","authors":"O. O. Ashikhmina,&nbsp;A. A. Ashikhmin,&nbsp;P. A. Starygina,&nbsp;A. V. Pashintseva,&nbsp;A. A. Tsygankov","doi":"10.1134/S0003683824606437","DOIUrl":"10.1134/S0003683824606437","url":null,"abstract":"<p>This paper presents a method for simultaneous extraction and separation of a number of valuable biologically active compounds (bacteriochlorophyll <i>a</i>, carotenoids, ubiquinone, fatty acids and lipids) from the biomass of purple non-sulfur bacteria using <i>Cereibacter sphaeroides</i> as an example. The hexane:isopropanol extraction method was demonstrated to isolate the most complete range of hydrophobic compounds and to preserve the stability of bacteriochlorophyll <i>a</i> to air oxygen and diffused light. Preliminary cell disruption did not significantly improve the extraction quality. It was also found that the use of low-pressure column chromatography did not provide the separation of the carotenoid fraction from the coenzyme Q10. Losses of target substances in this case amounted to 74 and 70% for bacteriochlorophyll <i>a</i> and carotenoids, respectively, relative to their content in the biomass. The HPLC method was applied for the separation and qualitative and quantitative determination of the carotenoid content in bacterial biomass. Losses of target substances in this case were also strongly reduced to 40 and 14% for bacteriochlorophyll <i>a</i> and carotenoids, respectively. The developed method of complex production of hydrophobic compounds using biomass of <i>C. sphaeroides</i> grown in fed-batch mode under chemoheterotrophic conditions allowed to obtain 4.4 mg of bacteriochlorophyll <i>a</i>, 1.5 mg of carotenoids and 2.1 mg of coenzyme Q10 per 1 g of dry biomass. The possibilities of further utilization of the residual biomass and supernatant are considered.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"61 1","pages":"101 - 109"},"PeriodicalIF":1.0,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143793223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Lipoxygenase in Adaptation of the Neurospora crassa Cells to Temperature Stress","authors":"S. Yu. Filippovich,&nbsp;G. P. Bachurina","doi":"10.1134/S0003683824604864","DOIUrl":"10.1134/S0003683824604864","url":null,"abstract":"<p>The adaptation of the <i>N. crassa</i> lipoxygenase (LOX) in response to heat (45°C) and cold (4°C) shock was studied. The difference was revealed in the dynamics of the LOX activity depending on the growing conditions of the mycelium. After incubation of the surface culture at 45°C, a gradual increase in the specific activity of the enzyme was observed with maximum at 2–3 h, followed by a subsequent decrease to the initial level. Under the same conditions, in a submerged culture, a decrease in the LOX activity was observed after 5 min; however, after 1 h of incubation, the enzyme activity also reached the initial level. The sensitivity of the <i>N. crassa</i> LOX to elevated temperatures is very high, since it is noted only in a narrow temperature range: the effect was detected at 45^oC; however, the enzymatic activity did not change in the culture incubated at 42°C, but, on the other hand, LOX was completely inactivated in the mycelium at 48°C. When the fungal cells were exposed to cold, the specific LOX activity increased after 1 h, then decreased to the initial level (2–3 h) and increased again, reaching a maximum after 18 h. When two stress factors, cold and starvation, acted simultaneously on the <i>N. crassa</i> cells, the treatment with cold had a decisive effect on the LOX activity, which was especially noticeable after 8 h of incubation.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"60 6","pages":"1171 - 1176"},"PeriodicalIF":1.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844884","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characteristics of Growth and Metabolism of Lacticaseibacillus casei in Model Milk Media and Semi-Hard Cheeses","authors":"G. M. Sviridenko,&nbsp;D. S. Vakhrusheva,&nbsp;O. M. Shukhalova,&nbsp;D. S. Mamykin,&nbsp;V. A. Mordvinova","doi":"10.1134/S0003683824604980","DOIUrl":"10.1134/S0003683824604980","url":null,"abstract":"<p>This paper presents the results of a study of the dynamics of growth and metabolism of <i>Lacticaseibacillus casei</i> production strains in model milk media and semi-hard cheeses. In dairy media under optimal conditions, the maximum number of viable cells of the studied <i>Lacticaseibacillus casei</i> strains was achieved on day 3; an increase in titratable acidity continued for up to 7‒10 days. In model dairy media simulating cheese ripening conditions, the growth and metabolism (glycolysis, proteolysis, and production of volatile aroma compounds) of <i>Lacticaseibacillus casei</i> slowed down. In semi-hard cheeses, the <i>Lacticaseibacillus</i> <i>casei</i> culture (as an independent acid-generating starter component), did not provide the required intensity of acid formation during the production process. However, as an adjunct culture, it intensified proteolysis and the processes of gas and aroma formation during ripening, thus, improving the organoleptic characteristics of cheeses.</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"60 6","pages":"1351 - 1362"},"PeriodicalIF":1.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic Composition of Microbial Communities from Fouling of Titanium Plates in the Coastal Zone of the Black and White Seas","authors":"A. L. Bryukhanov,&nbsp;A. S. Shutova,&nbsp;K. A. Komarova,&nbsp;T. A. Semenova,&nbsp;A. A. Semenov,&nbsp;V. A. Karpov","doi":"10.1134/S0003683824605195","DOIUrl":"10.1134/S0003683824605195","url":null,"abstract":"<p>With high-throughput sequencing of the variable region V3–V4 of the 16S rRNA gene, the study of the full phylogenetic composition of microbial communities developed on the surface of titanium plates exposed in the water column of the coastal zone of the Black and White Seas was carried out. The presence of potentially corrosive microorganisms from various physiological groups, such as sulfate-reducing bacteria, acidophilic iron-oxidizing bacteria and archaea, sulfur-oxidizing and nitrifying bacteria, was shown in the fouling. In the fouling of titanium plates exposed in the Black Sea, the most common microorganisms were uncultivated sulfate-reducing bacteria of the order <i>Desulfotomaculales</i>, which accounted for 8.13% of all 16S rRNA gene sequence reads, as well as acidophilic iron-oxidizing bacteria of the genera <i>Acidiferrobacter</i> (5.47%), <i>Acidithiobacillus</i> (4.52%), and <i>Acidiphilium</i> (2.55%). Acidophilic archaea accounted for up to 7.97% of all reads. In the fouling of titanium plates exposed in the White Sea, the most common were also acidophilic bacteria from the orders <i>Acidiferrobacterales</i> and <i>Acidithiobacillales</i> (7.68%), as well as acidophilic archaea from the order <i>Thermoplasmatales</i> (7.43%). Uncultivated sulfate-reducing bacteria of the order <i>Desulfotomaculales</i> were also represented in relatively high numbers (6.61% of all reads).</p>","PeriodicalId":466,"journal":{"name":"Applied Biochemistry and Microbiology","volume":"60 6","pages":"1259 - 1265"},"PeriodicalIF":1.0,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142844949","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}