Biotech Applications Research Articles

Clocking out and letting go to unleash green biotech applications in a photosynthetic host

Cyanobacteria are photosynthetic bacteria whose gene expression patterns are globally regulated by their circadian (daily) clocks. Due to their ability to use sunlight as their energy source, they are also attractive hosts for "green" production of pharmaceuticals, renewable fuels, and chemicals. However, despite the application of traditional genetic tools such as the identification of strong promoters to enhance the expression of heterologous genes, cyanobacteria have lagged behind other microorganisms such as Escherichia coli and yeast as economically efficient cell factories. The previous approaches have ignored large-scale constraints within cyanobacterial metabolic networks on transcription, predominantly the pervasive control of gene expression by the circadian (daily) clock. Here, we show that reprogramming gene expression by releasing circadian repressor elements in the transcriptional regulatory pathways coupled with inactivation of the central oscillating mechanism enables a dramatic enhancement of expression in cyanobacteria of heterologous genes encoding both catalytically active enzymes and polypeptides of biomedical significance.

Purification and Cryo-Electron Microscopy Analysis of Bacterial Appendages.

A number of extracellular helical protein polymers are crucial for supporting bacterial motility. The bacterial flagellum is a polymeric appendage used to support cellular motility. Historically, structural studies of flagellar and other filaments were limited to those present as or locked into straightened states. Here, we present a robust workflow that produces biologically relevant high-resolution cryo-electron microscopy (cryo-EM) structures of bacterial flagellar filaments. We highlight how a simple purification method, centered around several centrifugation steps, exploits the process of filament ejection in Caulobacter crescentus and results in isolated filaments amenable to transmission electron microscopy (TEM) studies. The quality of the sample is validated by SDS-PAGE and negative stain TEM analysis before a sample is vitrified for cryogenic electron microscopy (cryo-EM) data collection. We provide a detailed protocol for reconstructing either straight or curved flagellar filaments by cryo-EM helical reconstruction methods, followed by an overview of model building and validation. In our hands, this workflow resulted in several flagellar structures below 3 Å resolution, with one data set reaching a global resolution of 2.1 Å. The application of this workflow supports structure-function studies to better understand the molecular interactions that regulate filament architecture in biologically relevant states. Future work will not only examine interactions that regulate bacterial flagellar and other filament organization but also provide a foundation for developing new helical biopolymers for biotech applications. Key features • Rapid high-quality purification of bacterial flagella via simple bacterial culturing, centrifugation, and resuspension methods. • High-throughput cryo-EM data collection of filamentous objects. • Use of cryoSPARC implementations of helical reconstruction algorithms to generate high-resolution 3D structures of bacterial flagella or other helical polymers.

Cloning, Expression, Purification, and Characterization of a Novel β-Galactosidase/α-L-Arabinopyranosidase from Paenibacillus polymyxa KF-1.

Glycosidases are essential for the industrial production of functional oligosaccharides and many biotech applications. A novel β-galactosidase/α-L-arabinopyranosidase (PpBGal42A) of the glycoside hydrolase family 42 (GH42) from Paenibacillus polymyxa KF-1 was identified and functionally characterized. Using pNPG as a substrate, the recombinant PpBGal42A (77.16 kD) was shown to have an optimal temperature and pH of 30 °C and 6.0. Using pNPαArap as a substrate, the optimal temperature and pH were 40 °C and 7.0. PpBGal42A has good temperature and pH stability. Furthermore, Na+, K+, Li+, and Ca2+ (5 mmol/L) enhanced the enzymatic activity, whereas Mn2+, Cu2+, Zn2+, and Hg2+ significantly reduced the enzymatic activity. PpBGal42A hydrolyzed pNP-β-D-galactoside and pNP-α-L-arabinopyranoside. PpBGal42A liberated galactose from β-1,3/4/6-galactobiose and galactan. PpBGal42A hydrolyzed arabinopyranose at C20 of ginsenoside Rb2, but could not cleave arabinofuranose at C20 of ginsenoside Rc. Meanwhile, the molecular docking results revealed that PpBGal42A efficiently recognized and catalyzed lactose. PpBGal42A hydrolyzes lactose to galactose and glucose. PpBGal42A exhibits significant degradative activity towards citrus pectin when combined with pectinase. Our findings suggest that PpBGal42A is a novel bifunctional enzyme that is active as a β-galactosidase and α-L-arabinopyranosidase. This study expands on the diversity of bifunctional enzymes and provides a potentially effective tool for the food industry.

Harnessing redox power for biotechnological application in purple non-sulphur bacteria

Harnessing redox power for biotechnological application in purple non-sulphur bacteria Here we explore purple non-sulfur bacteria (PNSB) and some of its biotech applications, with a focus on how these applications have been enhanced by manipulating the flow of reducing power. Cellular metabolism refers to the sum of chemical reactions that cells use to obtain energy and material to live, grow, and make products. Many of these reactions are performed by specialized proteins called enzymes, which act on a specific substrate, or input, to produce a specific effect or product, also called a metabolite. To make metabolites, you need three major inputs: carbon, energy, and electrons. Depending on the organism, carbon can be fixed from atmospheric CO2, or can be obtained from organic compounds like carbohydrates or lipids. Energy can be generated in a variety of ways, but typically results in the formation of phosphate bonds in molecules like adenosine triphosphate (ATP) for widespread use in the cell.

Comparison of Fungal Thermophilic and Mesophilic Catalase-Peroxidases for Their Antioxidative Properties.

Catalase-peroxidases (KatGs) are unique bifunctional oxidoreductases that contain heme in their active centers allowing both the peroxidatic and catalatic reaction modes. These originally bacterial enzymes are broadly distributed among various fungi allowing them to cope with reactive oxygen species present in the environment or inside the cells. We used various biophysical, biochemical, and bioinformatics methods to investigate differences between catalase-peroxidases originating in thermophilic and mesophilic fungi from different habitats. Our results indicate that the architecture of the active center with a specific post-translational modification is highly similar in mesophilic and thermophilic KatG and also the peroxidatic acitivity with ABTS, guaiacol, and L-DOPA. However, only the thermophilic variant CthedisKatG reveals increased manganese peroxidase activity at elevated temperatures. The catalatic activity releasing molecular oxygen is comparable between CthedisKatG and mesophilic MagKatG1 over a broad temperature range. Two constructed point mutations in the active center were performed selectively blocking the formation of described post-translational modification in the active center. They exhibited a total loss of catalatic activity and changes in the peroxidatic activity. Our results indicate the capacity of bifunctional heme enzymes in the variable reactivity for potential biotech applications.

Stiffening Polymer Brush Membranes for Enhanced Organic Solvent Nanofiltration Selectivity.

Membrane-based separations allow energy-efficient purification of organic solvents which are typically carried out by energy-intensive distillation. Polymer membranes are inexpensive and have obtained widespread industrial acceptance for water and biotech applications but not organic solvent nanofiltration due to relatively low selectivities. In this work, a new class of polymer brush membranes was prepared with high selectivities for methanol-toluene separation. Stiffening the brush structure by cross-linking with aromatic trimesic acid and aliphatic itaconic acid resulted in an increase in selectivity from 1.4 to 6.5-11.5. This was achieved by graft polymerization of a primary amine monomer (aminoethyl methacrylate) using single electron transfer-living radical polymerization (SET-LRP) followed by cross-linking. Attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR), X-ray photoelectron spectroscopy (XPS), atomic force microscopy (AFM), and captive bubble contact angle measurements were used to characterize these membranes. The stiffness of the brush membranes was measured using a quartz crystal microbalance-dissipation (QCM-D) and correlated positively with selectivity for separating organic feed mixtures. This new class of membranes offers a tunable and scalable method for purification of organics.

Biotech Application of Exopolysaccharides from Curvularia brachyspora: Optimization of Production, Structural Characterization, and Biological Activity.

C. brachyspora, a widespread dematiaceous fungus, was evaluated in this study to optimize the production of exopolysaccharides (CB-EPS). Optimization was performed using response surface methodology, and the best production yielded 75.05% of total sugar at pH 7.4, with 0.1% urea, after 197 h. The obtained CB-EPS showed typical signals of polysaccharides, which was confirmed by FT-IR and NMR. The HPSEC analysis indicated a polydisperse polymer, showing a non-uniform peak, with an average molar mass (Mw) of 24,470 g/mol. The major monosaccharide was glucose (63.9 Mol%), followed by mannose (19.7 Mol%), and galactose (16.4 Mol%). Methylation analysis encountered derivatives that indicated the presence of a β-d-glucan and a highly branched glucogalactomannan. CB-EPS was tested on murine macrophages to verify its immunoactivity, and the treated cells were able to produce TNF-α, IL-6, and IL-10. However, the cells did not produce superoxide anions or nitric oxide nor stimulated phagocytosis. The results demonstrated an indirect antimicrobial activity of macrophages by stimulating cytokines, showing another biotech applicability for the exopolysaccharides produced by C. brachyspora.

A Qualitative Experimental Proof of Principle of Self-Assembly in 3D Printed Microchannels towards Embedded Wiring in Biofuel Cells

A range of biotech applications, e.g., microfluidic benthic biofuel cells, require devices with the simultaneous capabilities of embedded electrical wiring, aqueous fluidic access, 3D arrays, biocompatibility, and affordable upscalability. These are very challenging to satisfy simultaneously. As a potential solution, herein we present a qualitative experimental proof of principle of a novel self-assembly technique in 3D printed microfluidics towards embedded wiring combined with fluidic access. Our technique uses surface tension, viscous flow, microchannel geometries, and hydrophobic/hydrophilic interactions to produce self-assembly of two immiscible fluids along the length of the same 3D printed microfluidic channel. The technique demonstrates a major step towards the affordable upscaling of microfluidic biofuel cells through 3D printing. The technique would be of high utility to any application that simultaneously requires distributed wiring and fluidic access inside 3D printed devices.

MELD-DNA: Accurate structural prediction of protein-DNA interactions.

Protein-DNA interaction is one of the most important aspects of biology. It is a main step of gene regulation in all organisms and is a potential target for therapeutic and biotech applications. Protein-DNA interactions are distinct from protein-protein interactions due to several factors: 1) DNA sequence and specific interactions (base readout); 2) DNA shape and its deformability (shape readout); 3) Exploration and searching on the DNA for alternative binding states. Such factors dictate affinity and specificity of transcription factors. Traditionally, these interactions were only predicted at the sequence level (e.g. using position weight matrices) and more recently using docking and machine learning models. Here we present MELD-DNA, a too that combines cheap information from experiment (which can be noisy, ambiguous and sparse) with physics-based molecular mechanics force fields using bayesian inference. MELD will accelerate sampling of the binding process by temperature and hamiltonian replica exchanging that is guided by experimental data. We have tested the tool on a diverse set of 15 systems from various TF families and we observed native-like bound structures most of them with room for more improvements. We also compare and benchmark with the state-of-the-art in docking (HADDOCK) and ML (RosettaFold2NA). In this study we discuss several issues in the available methods and techniques that need to be addressed for more accurate predictions. We believe MELD-DNA can be an essential tool in the community from drug design, regulation and fundamental research.

Predictive Modelling in Clinical Bioinformatics: Key Concepts for Startups.

Clinical bioinformatics is a newly emerging field that applies bioinformatics techniques for facilitating the identification of diseases, discovery of biomarkers, and therapy decision. Mathematical modelling is part of bioinformatics analysis pipelines and a fundamental step to extract clinical insights from genomes, transcriptomes and proteomes of patients. Often, the chosen modelling techniques relies on either statistical, machine learning or deterministic approaches. Research that combines bioinformatics with modelling techniques have been generating innovative biomedical technology, algorithms and models with biotech applications, attracting private investment to develop new business; however, startups that emerge from these technologies have been facing difficulties to implement clinical bioinformatics pipelines, protect their technology and generate profit. In this commentary, we discuss the main concepts that startups should know for enabling a successful application of predictive modelling in clinical bioinformatics. Here we will focus on key modelling concepts, provide some successful examples and briefly discuss the modelling framework choice. We also highlight some aspects to be taken into account for a successful implementation of cost-effective bioinformatics from a business perspective.

Evolution of Heme Peroxygenases: Ancient Roots and Later Evolved Branches.

We reconstructed the molecular phylogeny of heme containing peroxygenases that are known as very versatile biocatalysts. These oxidoreductases capable of mainly oxyfunctionalizations constitute the peroxidase–peroxygenase superfamily. Our representative reconstruction revealed a high diversity but also well conserved sequence motifs within rather short protein molecules. Corresponding genes coding for heme thiolate peroxidases with peroxygenase activity were detected only among various lower eukaryotes. Most of them originate in the kingdom of fungi. However, it seems to be obvious that these htp genes are present not only among fungal Dikarya but they are distributed also in the clades of Mucoromycota and Chytridiomycota with deep ancient evolutionary origins. Moreover, there is also a distinct clade formed mainly by phytopathogenic Stramenopiles where even HTP sequences from Amoebozoa can be found. The phylogenetically older heme peroxygenases are mostly intracellular, but the later evolution gave a preference for secretory proteins mainly among pathogenic fungi. We also analyzed the conservation of typical structural features within various resolved clades of peroxygenases. The presented output of our phylogenetic analysis may be useful in the rational design of specifically modified peroxygenases for various future biotech applications.

The effectiveness of Proteolytic bacteria in the leather and detergent industry isolated waste from the Modjo tannery

Protease also called proteinase or peptidase is a digestive enzyme that is categorized under proteolytic enzymes and it has great potential in industrial application. Extracellular proteases are used in a variety of industries because they exhibit practically all of the characteristics needed for biotech applications such as detergent, bioremediation, food, and leather processing. In the synthesis of all three major types of acidic, neutral, and alkaline proteases, microbial sources have dominated an unbeatable area. Alkaline proteases are a large group of industrial enzymes formed by a wide variety of species, including animals, fungi, and bacteria. The fermentation method serves to make bacteria, fungi, and yeast alkaline proteases. Proteases are produced in large quantities by Gram-positive bacteria, especially those belonging to the Bacillus genus. Following standard procedures, the bacterial isolates PMOJ-01 and PMOJ-05 with the prominent zone of clearance and efficient enzyme development were further characterized to the genus level. Moreover, the growth conditions for the highest protease production were optimized with different pH, temperatures, and NaCl concentrations, in the results of PMOJ-01 and PMOJ- 05 pH (7 and 8), temperatures 45oC, and 1% NaCl concentrations both cases respectively. The proteases activities from PMOJ-01, Pseudomonas aeruginosa, and PMOJ-05, Bacillus subtilis were most active at pH 7.0 and pH 8.0 and temperature at 35oC and 45oC, respectively. The enzyme activity and the total solid protease sample of the crude enzyme of Pseudomonas aeruginosa and Bacillus subtilis were 0.299 U/ mL and 0.289 U/ mL, 1.37±0.14 U/mg, and 1.199 U/mg respectively. The effect on dehairing, distaining, and scum removal revealed that the purified protease enzyme of PMOJ-01 and PMOJ-05 can be used in detergent and leather industries.

Optimization of lipase production using fungal isolates from oily residues

Lipases are triacylglycerol hydrolases that catalyze hydrolysis, esterification, interesterification, and transesterification reactions. These enzymes are targets of several industrial and biotech applications, such as catalysts, detergent production, food, biofuels, wastewater treatment, and others. Microbial enzymes are preferable for large scale production due to ease of production and extraction. Several studies have reported that lipases from filamentous fungi are predominantly extracellular and highly active. However, there are many factors that interfere with enzyme production (pH, temperature, medium composition, agitation, aeration, inducer type, and concentration, etc.), making control difficult and burdening the process. This work aimed to optimize the lipase production of four fungal isolates from oily residues (Penicillium sp., Aspergillus niger, Aspergillus sp., and Aspergillus sp.). The lipase-producing fungi isolates were morphologically characterized by optical and scanning electron microscopy. The optimal lipase production time curve was previously determined, and the response variable used was the amount of total protein in the medium after cultivation by submerged fermentation. A complete factorial design 32 was performed, evaluating the temperatures (28 °C, 32 °C, and 36 °C) and soybean oil inducer concentration (2%, 6%, and 10%). Each lipase-producing isolate reacted differently to the conditions tested, the Aspergillus sp. F18 reached maximum lipase production, compared to others, under conditions of 32 °C and 2% of oil with a yield of 11,007 (µg mL−1). Penicillium sp. F04 achieved better results at 36 °C and 6% oil, although for Aspergillus niger F16 was at 36 °C and 10% oil and Aspergillus sp. F21 at 32 °C and 2% oil. These results show that microorganisms isolated from oily residues derived from environmental sanitation can be a promising alternative for the large-scale production of lipases.Graphical

Survival-related genes are diversified across cancers but generally enriched in cancer hallmark pathways

BackgroundPan-cancer studies have disclosed many commonalities and differences in mutations, copy number variations, and gene expression alterations among cancers. Some of these features are significantly associated with clinical outcomes, and many prognosis-predictive biomarkers or biosignatures have been proposed for specific cancer types. Here, we systematically explored the biological functions and the distribution of survival-related genes (SRGs) across cancers.ResultsWe carried out two different statistical survival models on the mRNA expression profiles in 33 cancer types from TCGA. We identified SRGs in each cancer type based on the Cox proportional hazards model and the log-rank test. We found a large difference in the number of SRGs among different cancer types, and most of the identified SRGs were specific to a particular cancer type. While these SRGs were unique to each cancer type, they were found mostly enriched in cancer hallmark pathways, e.g., cell proliferation, cell differentiation, DNA metabolism, and RNA metabolism. We also analyzed the association between cancer driver genes and SRGs and did not find significant over-representation amongst most cancers.ConclusionsIn summary, our work identified all the SRGs for 33 cancer types from TCGA. In addition, the pan-cancer analysis revealed the similarities and the differences in the biological functions of SRGs across cancers. Given the potential of SRGs in clinical utility, our results can serve as a resource for basic research and biotech applications.

The endophytome (plant-associated microbiome): methodological approaches, biological aspects, and biotech applications.

Similar to other organisms, plants establish interactions with a variety of microorganisms in their natural environment. The plant microbiome occupies the host plant's tissues, either internally or on its surfaces, showing interactions that can assist in its growth, development, and adaptation to face environmental stresses. The advance of metagenomics and metatranscriptomics approaches has strongly driven the study and recognition of plant microbiome impacts. Research in this regard provides comprehensive information about the taxonomic and functional aspects of microbial plant communities, contributing to a better understanding of their dynamics. Evidence of the plant microbiome's functional potential has boosted its exploitation to develop more ecological and sustainable agricultural practices that impact human health. Although microbial inoculants' development and use are promising to revolutionize crop production, interdisciplinary studies are needed to identify new candidates and promote effective practical applications. On the other hand, there are challenges in understanding and analyzing complex data generated within a plant microbiome project's scope. This review presents aspects about the complex structuring and assembly of the microbiome in the host plant's tissues, metagenomics, and metatranscriptomics approaches for its understanding, covering descriptions of recent studies concerning metagenomics to characterize the microbiome of non-model plants under different aspects. Studies involving bio-inoculants, isolated from plant microbial communities, capable of assisting in crops' productivity, are also reviewed.

Potato pectin falls to Phytophthora

Plant Science P hytophthora infestans is a plant oomycete pathogen that drove the potato famines of the 1800s and continues to afflict potato fields today. The polysaccharide pectin makes up about a third of the cell wall in potatoes. Sabbadin et al. identified a family of lytic polysaccharide monooxygenases (LMPOs) that cleave pectin and are up-regulated in P. infestans during infection. Silencing the relevant LMPO gene successfully inhibited P. infestans infections. These findings open doors for disease intervention targets and for biotech applications. Science , abj1342, this issue p. [774][1] [1]: /lookup/doi/10.1126/science.abj1342

Secreted pectin monooxygenases drive plant infection by pathogenic oomycetes.

The oomycete Phytophthora infestans is a damaging crop pathogen and a model organism to study plant-pathogen interactions. We report the discovery of a family of copper-dependent lytic polysaccharide monooxygenases (LPMOs) in plant pathogenic oomycetes and its role in plant infection by P. infestans We show that LPMO-encoding genes are up-regulated early during infection and that the secreted enzymes oxidatively cleave the backbone of pectin, a charged polysaccharide in the plant cell wall. The crystal structure of the most abundant of these LPMOs sheds light on its ability to recognize and degrade pectin, and silencing the encoding gene in P. infestans inhibits infection of potato, indicating a role in host penetration. The identification of LPMOs as virulence factors in pathogenic oomycetes opens up opportunities in crop protection and food security.

In light of evolution. Making sense of biotech applications

Evolutionary biologist Theodosius Dobzhansky refl ected on the place held by evolutionary theory in modern biology in the title of his famous article: «Nothing in biology makes sense except in the light of evolution». Published in the early seventies, at the dawn of a revolution sparked by new genetic engineering techniques, his message still holds weight; perhaps even more so.

Phage satellites and their emerging applications in biotechnology.

The arms race between (bacterio)phages and their hosts is a recognised hot spot for genome evolution. Indeed, phages and their components have historically paved the way for many molecular biology techniques and biotech applications. Further exploration into their complex lifestyles has revealed that phages are often parasitised by distinct types of hyperparasitic mobile genetic elements. These so-called phage satellites exploit phages to ensure their own propagation and horizontal transfer into new bacterial hosts, and their prevalence and peculiar lifestyle has caught the attention of many researchers. Here, we review the parasite-host dynamics of the known phage satellites, their genomic organisation and their hijacking mechanisms. Finally, we discuss how these elements can be repurposed for diverse biotech applications, kindling a new catalogue of exciting tools for microbiology and synthetic biology.

A rapid, simple and sensitive microfluidic chip electrophoresis mass spectrometry method for monitoring amino acids in cell culture media

The development and optimization of cell culture media for biotech applications is a fundamental step of process development. The composition of cell culture media requires an ideal blend of amino acids, vitamins, nucleosides, lipids, carbohydrates, trace elements and other components. The ability to monitor these constituents is required to ensure that cells receive sufficient nutrients to facilitate growth, viability and productivity. Analysis of cell culture media is challenging due to the range and diversity of compounds contained in this matrix and normally requires time consuming methods. A rapid, simple and sensitive microfluidic chip CE-MS method is described to monitor amino acids in chemically defined cell culture media from a Chinese hamster ovary cell line cultured over a period of 10 days. The described platform enabled the separation of 16 amino acids in less than 2 minutes and without the requirement for extensive sample preparation. The analytical parameters evaluated were precision, linearity, limit of detection and limit of quantification. The majority of essential amino acids were present in cell culture growth in high concentrations compared to non-essential amino acids. Over the course of the 10 days cell culture the concentration of certain amino acids declined by up to 100%. Microfluidic chip based CE-MS methods can be used effectively to obtain the consumption rates of amino acids in cell culture media during cell growth and to perform at-line monitoring and screening of cell culture status.