Cloning, expression and characterization of β- and γ‑carbonic anhydrase from Bacillus sp. SS105 for biomimetic sequestration of CO2

Characterization of fungal carbonyl sulfide hydrolase belonging to clade D β-carbonic anhydrase

Carbonyl sulfide hydrolase (COSase) is a unique enzyme that exhibits high activity towards carbonyl sulfide (COS) but low carbonic anhydrase (CA) activity, despite belonging to the CA family. COSase was initially identified in a sulfur-oxidizing bacterium and later discovered in the ascomycete Trichoderma harzianum strain THIF08. The COSase from T. harzianum has been recognized as a key enzyme in the assimilation of gaseous COS, and homologous genes are widely present not only in Ascomycota but also in Basidiomycota. Here, we characterized the COSases from the basidiomycete Gloeophyllum trabeum NBRC 6430 and T. harzianum to obtain detailed characteristics of fungal COSase. This study contributes to a better understanding of COS metabolism in fungi.

Four Decades of Bacillus Biofertilizers: Advances and Future Prospects in Agriculture

Over the past four decades, Bacillus biofertilizers, which are microbial formulations based on Bacillus species, have significantly contributed to sustainable agriculture by enhancing crop growth, improving soil health, and reducing the dependency on chemical fertilizers. Bacillus species, particularly known for their ability to promote plant growth, fix nitrogen, solubilize phosphorus, and produce growth-promoting substances such as phytohormones and antibiotics, have emerged as key players in the development of eco-friendly agricultural solutions. This research utilizes bibliometric analysis based on 3,242 documents sourced from the Web of Science database to map the development, key contributions, and innovation within the field from 1985 to 2023. This study identifies exponential growth in research output, particularly from 2003 onwards, indicating a robust interest and expanding research base predominantly in China, India, and the United States. We segmented the research timeline into three distinct phases, each marked by varying growth rates and research foci. This paper presents novel insights into the geographical and institutional distributions of research, highlighting the predominant role of developing countries in advancing Bacillus-based technologies. Key research hotspots have evolved from basic applications to complex interactions involving synthetic microbial communities and advanced multi-omics techniques. Our findings demonstrate a trend towards more strategic and technologically integrated approaches to developing Bacillus biofertilizers, reflecting broader shifts towards more sustainable agricultural systems. This study not only charts historical progress, but also proposes future research trajectories aimed at enhancing the application and effectiveness of microbial fertilizers across diverse ecosystems.

Polyurethane degradation by extracellular urethanase producing bacterial isolate Moraxella catarrhalis strain BMPPS3

Plastic waste has become a global issue and a threat to the ecosystem. The present study isolated polyurethane (PU) degrading bacterial species from soil dumped with plastic wastes. Four bacterial isolates, RS1, RS6, RS9 and RS13 were obtained and their ability to degrade PU in a synthetic medium with PU as a sole source of carbon was assessed individually. After thirty days of incubation, the highest PU weight loss of 67.36 ± 0.32% was recorded in the medium containing RS13 isolate. The results of FTIR revealed the occurrence of carbonyl peaks. The putative isolate RS13 confirmed with the genus Moraxella according to 16S rRNA gene sequencing and the isolate was specified as Moraxella catarrhalis strain BMPPS3. The restriction analysis of Moraxella catarrhalis strain BMPPS3 revealed that the GCAT content to 51% and 49% correspondingly. Moraxella catarrhalis strain BMPPS3 was able to colonize on PU surface and form a biofilm as revealed by SEM investigation. Fatty acids and alkanes were found to be the degradation products by GC-MS analysis. The presence of these metabolites facilitated the growth of strain RS13 and suggested that ester hydrolysis products had been mineralized into CO2 and H2O. Extracellular biosurfactant synthesis has also been found in Moraxella catarrhalis strain BMPPS13 inoculated with synthetic media and mineral salt media containing PU and glucose as carbon sources, respectively with a significant level of cell-surface hydrophobicity (32%). The production and activity of extracellular esterase showed consistent increase from day 1-15 which peaked (1.029 mM/min/mg) on day 24 significantly at P < 0.001. Crude biosurfactants were lipopeptide-based, according to the characteristic investigation. According to this study findings, Moraxella catarrhalis produces biosurfactants of the esterase, urethanase and lipase (lipopeptide) types when carbon source PU is present.

Pore size and organic carbon of biochar limit the carbon sequestration potential of Bacillus cereus SR

Carbon-fixing functional strain-loaded biochar may have significant potential in carbon sequestration given the global warming situation. The carbon-fixing functional strain Bacillus cereus SR was loaded onto rice straw biochar pyrolyzed at different temperatures with the anticipation of clarifying the carbon sequestration performance of this strain on biochar and the interaction effects with biochar. During the culture period, the content of dissolved organic carbon (DOC), easily oxidizable organic carbon, and microbial biomass carbon in biochar changed. This finding indicated that B. cereus SR utilized organic carbon for survival and enhanced carbon sequestration on biochar to increase organic carbon, manifested by changes in CO2 emissions and ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) enzyme activity. Linear regression analysis showed that the strain was likely to consume DOC on 300 °C biochar, although the Rubisco enzyme activity was higher. In contrast, the strain had a higher carbon sequestration potential on 500 °C biochar. Correlation analysis showed that Rubisco enzyme activity was controlled by the physical structure of the biochar. Our results highlight the differences in the survival mode and carbon sequestration potential of B. cereus SR on biochar pyrolyzed at different temperatures.

Pyrimidines: Molecular docking and inhibition studies on carbonic anhydrase and cholinesterases

Alzheimer's disease (AD) is a neurodegenerative disorder. The disease is characterized by dementia, memory impairment, cognitive impairment, and speech impairment. Cholinesterases (ChEs; AChE, acetylcholinesterase and BChE, butyrylcholinesterase) inhibitors and their benefits of cholinergic replacement in the treatment of AD have been researched and documented by scientists in various ways to date. Recent studies prove that human carbonic anhydrases (hCAs) are also one of the important targets in the treatment of AD. Therefore, the development of new agents that can simultaneously modulate the various mechanisms or targets involved in the AD pathway may be a powerful strategy to treat AD, the current disease. Considering these data, the effects of the pyrimidines (1-7) were investigated in this study for the discovery and development of multitargeted ChEs and hCAs inhibitors associated with AD. In addition, the molecular docking analysis of the 4-amino-2-choloropyrimidine (2) was performed to understand the binding interactions on the active site of the enzyme. All compounds (1-7) showed satisfactory enzyme inhibitory potency in micromolar concentrations against AChE, BChE, hCAI, and hCAII with K_I values ranging from 0.099 to 0.241 μM, from 1.324 to 3.418 μM, from 0.201 to 0.884 μM, from 1.867 to 3.913 μM, respectively. Due to their ChEs and hCAs inhibition, these compounds (1-7) may be considered as leads for investigations in neurodegenerative diseases. All these results revealed that the 4-amino-5,6-dichloropyrimidine (7) (K_I value of 0.201 ± 0.041 μM for hCA I), the 4-amino-6-hydroxypyrimidine (4) (K_I value of 1.867 ± 0.296 μM for hCA II), the 4-amino-5,6-dichloropyrimidine (7) (K_I value of 0.099 ± 0.008 μM for AChE), and the 4-amino-2-chloropyrimidine (2) (K_I value of 1.324 ± 0.273 μM for BChE) from the pyrimidines in this series were the most promising derivatives, as they exhibited a good multifunctional inhibition at all experimental levels and in the in silico validation against these enzymes, for the treatment of AD.

Recombinant human carbonic anhydrase VII: Purification, characterization, inhibition, and molecular docking studies

Human carbonic anhydrase VII (hCA VII), a cytosolic enzyme, defends against oxidative stress by preventing reactive oxygen species from forming. In our study, first, hCA VII was cloned into Escherichia coli (One Shot Mach1-T1R) strain by using cDNA of the human brain and successfully expressed. The integrity of the plasmid generated by colony PCR was checked, and after, for protein expression, the plasmid was transformed into E. coli BL21 (DE-3) strain. hCA VII expression was observed after 6 h of isopropyl-D-1-thiogalactopyranoside (IPTG) induction. The fusion protein containing hexahistidine (6xHis) was purified with 7.02 EU/mg of specific activity, had 48.07% of purification yield, and approximately 21-folds using a ProbondTM nickel chelating resin affinity column. Then, both molecular mass determination and purity control of the purified recombinant enzyme was done by SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis). The mass of the SUMO-hCA VII fusion protein was calculated as 46.77 kDa. As a result of Western blot analysis using anti-His G-HRP antibody, the fusion protein was detected as approximately 45 kDa. Furthermore, the characterization assays and in vitro inhibition studies were done for the recombinant enzyme. K_I values of these agents were found between 0.29 μM and 157.6 mM. Finally, molecular docking investigations of these antibiotics were undertaken to understand further the binding interactions on the active site of this recombinant enzyme.

Enzyme mediated transformation of CO2 into calcium carbonate using purified microbial carbonic anhydrase

In this study, a bacterial carbonic anhydrase (CA) was purified from Corynebacterium flavescens for the CO₂ conversion into CaCO₃. The synthesized CaCO₃ can be utilized in the papermaking industry as filler material, construction material and in steel industry. Herein, the CA was purified by using a Sephadex G-100 column chromatography having 29.00 kDa molecular mass in SDS-PAGE analysis. The purified CA showed an optimal temperature of 35 °C and pH 7.5. In addition, a kinetic study of CA using p-NPA as substrate showed V_max (166.66 μmoL/mL/min), K_m (5.12 mM), and K_cat (80.56 sec^-1) using Lineweaver Burk plot. The major inhibitors of CA activity were Na²⁺, K⁺, Mn²⁺, and Al³⁺, whereas Zn²⁺ and Fe²⁺ slightly enhanced it. The purified CA showed a good efficacy to convert the CO₂ into CaCO₃ with a total conversion rate of 65.05 mg CaCO₃/mg of protein. In silico analysis suggested that the purified CA has conserved Zn²⁺ coordinating residues such as His 111, His 113, and His 130 in the active site center. Further analysis of the CO₂ binding site showed conserved residues such as Val 132, Val 142, Leu 196, Thr 197, and Val 205. However, a substitution has been observed where Trp 208 of its closest structural homolog T. ammonificans CA is replaced with Arg 207 of C. flavescens. The presence of a hydrophilic mutation in the CO₂ binding hydrophobic region is a further subject of investigation.

Carbonic anhydrase to boost CO2 sequestration: Improving carbon capture utilization and storage (CCUS)

CO₂ Capture Utilization and Storage (CCUS) is a fundamental strategy to mitigate climate change, and carbon sequestration, through absorption, can be one of the solutions to achieving this goal. In nature, carbonic anhydrase (CA) catalyzes the CO₂ hydration to bicarbonates. Targeting the development of novel biotechnological routes which can compete with traditional CO₂ absorption methods, CA utilization has presented a potential to expand as a promising catalyst for CCUS applications. Driven by this feature, the search for novel CAs as biocatalysts and the utilization of enzyme improvement techniques, such as protein engineering and immobilization methods, has resulted in suitable variants able to catalyze CO₂ absorption at relevant industrial conditions. Limitations related to enzyme recovery and recyclability are still a concern in the field, affecting cost efficiency. Under different absorption approaches, CA enhances both kinetics and CO₂ absorption yields, besides reduced energy consumption. However, efforts directed to process optimization and demonstrative plants are still limited. A recent topic with great potential for development is the CA utilization in accelerated weathering, where industrial residues could be re-purposed towards becoming carbon sequestrating agents. Furthermore, research of new solvents has identified potential candidates for integration with CA in CO₂ capture, and through techno-economic assessments, CA can be a path to increase the competitiveness of alternative CO₂ absorption systems, offering lower environmental costs. This review provides a favorable scenario combining the enzyme and CO₂ capture, with possibilities in reaching an industrial-like stage in the future.

Role of carbon-dioxide sequestering bacteria for clean air environment and prospective production of biomaterials: a sustainable approach

The increase in demand of fossil fuel uses for developmental activity and manufacturing of goods have resulted a huge emission of global warming gases (GWGs) in the atmosphere. Among all GWGs, CO₂ is the major contributor that inevitably causes global warming and climate change. Mitigation strategies like biological CO₂ capture through sequestration and their storage into biological organic form are used to minimize the concentration of atmospheric CO₂ with the goal to control climate change. Since increasing atmospheric CO₂ level supports microbial growth and productivity thus microbial-based CO₂ sequestration has remarkable advantages as compared to plant-based sequestration. This review focuses on CO₂ sequestration mechanism in bacteria through different carbon fixation pathways, involved enzymes, their role in calcite, and other environmentally friendly biomaterials such as biofuel, bioplastic, and biosurfactant.

Emerging trends in environmental and industrial applications of marine carbonic anhydrase: a review

Biocatalytic conversion of greenhouse gases such as carbon dioxide into commercial products is one of the promising key approaches to solve the problem of climate change. Microbial enzymes, including carbonic anhydrase, NAD-dependent formate dehydrogenase, ribulose bisphosphate carboxylase, and methane monooxygenase, have been exploited to convert atmospheric gases into industrial products. Carbonic anhydrases are Zn²⁺-dependent metalloenzymes that catalyze the reversible conversion of CO₂ into bicarbonate. They are widespread in bacteria, algae, plants, and higher organisms. In higher organisms, they regulate the physiological pH and contribute to CO₂ transport in the blood. In plants, algae, and photosynthetic bacteria carbonic anhydrases are involved in photosynthesis. Converting CO₂ into bicarbonate by carbonic anhydrases can solidify gaseous CO2, thereby reducing global warming due to the burning of fossil fuels. This review discusses the three-dimensional structures of carbonic anhydrases, their physiological role in marine life, their catalytic mechanism, the types of inhibitors, and their medicine and industry applications.

Bacillus subtilis Impact on Plant Growth, Soil Health and Environment: Dr. Jekyll and Mr. Hyde

The increased dependence of farmers on chemical fertilizers poses a risk to soil fertility and ecosystem stability. Plant growth-promoting rhizobacteria (PGPR) are at the forefront of sustainable agriculture, providing multiple benefits for the enhancement of crop production and soil health. Bacillus subtilis is a common PGPR in soil that plays a key role in conferring biotic and abiotic stress tolerance to plants by induced systemic resistance (ISR), biofilm formation, and lipopeptide production. As a part of bioremediating technologies, Bacillus spp. can purify metal contaminated soil. It acts as a potent denitrifying agent in agroecosystems while improving the carbon sequestration process when applied in a regulated concentration. Although it harbors several antibiotic resistance genes (ARGs), it can reduce the horizontal transfer of ARGs during manure composting by modifying the genetic makeup of existing microbiota. In some instances, it affects the beneficial microbes of the rhizosphere. External inoculation of B. subtilis has both positive and negative impacts on the endophytic and semi-synthetic microbial community. Soil texture, type, pH, and bacterial concentration play a crucial role in the regulation of all these processes. Soil amendments and microbial consortia of Bacillus produced by microbial engineering could be used to lessen the negative effect on soil microbial diversity. The complex plant-microbe interactions could be decoded using transcriptomics, proteomics, metabolomics, and epigenomics strategies which would be beneficial for both crop productivity and the well-being of soil microbiota. Bacillus subtilis has more positive attributes similar to the character of Dr. Jekyll and some negative attributes on plant growth, soil health, and the environment akin to the character of Mr. Hyde.

Integrated analysis of Whole genome sequencing and life cycle assessment for polyhydroxyalkanoates production by Cupriavidus sp. ISTL7

The current study demonstrates the enhanced production capability of strain Cupriavidus sp. ISTL7 for polyhydroxyalkanoates (PHA) using acetate and glucose (4.93 ± 0.4571 g L^-1) which was characterised analytically by GC-MS, FTIR and NMR analysis. Whole genome sequencing of strain ISTL7 unveiled an array of PHA metabolism genes which included phaA, phaB and phaC. Life cycle assessment of the protocol established that the production was most sustainable with the carbon source acetate. + Glucose as compared to acetate/glucose alone. It also concluded that solvent extraction of PHA and energy consumption during the process requires optimization to sustain the production on ecological fronts. Additionally, acetoacetyl-CoA reductase (phaB) gene was molecularly cloned, expressed and purified (27 KDa, 2.63 mg/ml). Conclusively, Cupriavidus sp. ISTL7 is a potential strain for PHA production with a scope of improvement on energy fronts which would transform the production environmentally and economically appealing.

Production and characterization of psychrophilic α-amylase from a psychrophilic bacterium, Shewanella sp. ISTPL2

A psychrophilic and halophilic bacterial isolate, Shewanella sp. ISTPL2, procured from the pristine Pangong Lake, Ladakh, Jammu and Kashmir, India, was used for the production and characterization of the psychrophilic and alkalophilic α-amylase enzyme. The α-amylase is a critical enzyme that catalyses the hydrolysis of α-1,4-glycosidic bonds of starch molecules and is predominately utilized in biotechnological applications. The highest enzyme activity of partially purified extracellular α-amylase was 10,064.20 U/mL after 12 h of incubation in a shake flask at pH 6.9 and 10 °C. Moreover, the maximum intracellular α-amylase enzyme activity (259.62 U/mL) was also observed at 6 h of incubation. The extracellular α-amylase was refined to the homogeneity with the specific enzyme activity of 36,690.47 U/mg protein corresponding to 6.87-fold purification. The optimized pH and temperature for the α-amylase were found to be pH 8 and 4 °C, respectively, suggesting its stability at alkaline conditions and low or higher temperatures. The amylase activity was highly activated by Cu2+, Fe2+ and Ca2+, while inhibited by Cd2+, Co2+ and Na2+. As per our knowledge, the current study reports the highest activity of a psychrophilic α-amylase enzyme providing prominent biotechnological potential.