The impacts of metal-based engineered nanomaterial mixtures on microbial systems: A review

Next-generation sequencing (NGS) technology has revolutionized sequence-based research. In recent years, high-throughput sequencing has become the method of choice in studying the toxicity of chemical agents through observing and measuring changes in transcript levels. Engineered nanomaterial (ENM)-toxicity has become a major field of research and has adopted microarray and newer RNA-Seq methods. Recently, nanotechnology has become a promising tool in the diagnosis and treatment of several diseases in humans. However, due to their high stability, they are likely capable of remaining in the body and environment for long periods of time. Their mechanisms of toxicity and long-lasting effects on our health is still poorly understood. This review explores the effects of three ENMs including carbon nanotubes (CNTs), quantum dots (QDs), and Ag nanoparticles (AgNPs) by cross examining publications on transcriptomic changes induced by these nanomaterials.

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High-throughput microbioreactor provides a capable tool for early stage bioprocess development

Scientific Reports ◽

10.1038/s41598-021-81633-6 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Mathias Fink ◽

Monika Cserjan-Puschmann ◽

Daniela Reinisch ◽

Gerald Striedner

Keyword(s):

High Throughput ◽

Process Development ◽

Early Stage ◽

Explanatory Power ◽

Batch Mode ◽

E Coli ◽

Speed Up ◽

Bioreactor System ◽

Cell Densities ◽

Microbial Systems

AbstractTremendous advancements in cell and protein engineering methodologies and bioinformatics have led to a vast increase in bacterial production clones and recombinant protein variants to be screened and evaluated. Consequently, an urgent need exists for efficient high-throughput (HTP) screening approaches to improve the efficiency in early process development as a basis to speed-up all subsequent steps in the course of process design and engineering. In this study, we selected the BioLector micro-bioreactor (µ-bioreactor) system as an HTP cultivation platform to screen E. coli expression clones producing representative protein candidates for biopharmaceutical applications. We evaluated the extent to which generated clones and condition screening results were transferable and comparable to results from fully controlled bioreactor systems operated in fed-batch mode at moderate or high cell densities. Direct comparison of 22 different production clones showed great transferability. We observed the same growth and expression characteristics, and identical clone rankings except one host-Fab-leader combination. This outcome demonstrates the explanatory power of HTP µ-bioreactor data and the suitability of this platform as a screening tool in upstream development of microbial systems. Fast, reliable, and transferable screening data significantly reduce experiments in fully controlled bioreactor systems and accelerate process development at lower cost.

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Control engineering and synthetic biology: working in synergy for the analysis and control of microbial systems

Current Opinion in Microbiology ◽

10.1016/j.mib.2021.05.004 ◽

2021 ◽

Vol 62 ◽

pp. 68-75

Author(s):

Giansimone Perrino ◽

Andreas Hadjimitsis ◽

Rodrigo Ledesma-Amaro ◽

Guy-Bart Stan

Keyword(s):

Synthetic Biology ◽

Control Engineering ◽

And Control ◽

Microbial Systems

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Rational design strategies for functional reconstitution of plant cytochrome P450s in microbial systems

Current Opinion in Plant Biology ◽

10.1016/j.pbi.2021.102005 ◽

2021 ◽

Vol 60 ◽

pp. 102005

Author(s):

Anqi Zhou ◽

Kang Zhou ◽

Yanran Li

Keyword(s):

Rational Design ◽

Cytochrome P450s ◽

Design Strategies ◽

Microbial Systems

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Disulfide bond engineering of AppA phytase for increased thermostability requires co-expression of protein disulfide isomerase in Pichia pastoris

Biotechnology for Biofuels ◽

10.1186/s13068-021-01936-8 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Laura Navone ◽

Thomas Vogl ◽

Pawarisa Luangthongkam ◽

Jo-Anne Blinco ◽

Carlos H. Luna-Flores ◽

...

Keyword(s):

Pichia Pastoris ◽

Phytic Acid ◽

Disulfide Bond ◽

Wild Type ◽

Wild Type Enzyme ◽

E Coli ◽

Biochemical Characterisation ◽

Disulfide Bond Isomerase ◽

Microbial Systems ◽

Protein Disulfide

Abstract Background Phytases are widely used commercially as dietary supplements for swine and poultry to increase the digestibility of phytic acid. Enzyme development has focused on increasing thermostability to withstand the high temperatures during industrial steam pelleting. Increasing thermostability often reduces activity at gut temperatures and there remains a demand for improved phyases for a growing market. Results In this work, we present a thermostable variant of the E. coli AppA phytase, ApV1, that contains an extra non-consecutive disulfide bond. Detailed biochemical characterisation of ApV1 showed similar activity to the wild type, with no statistical differences in kcat and KM for phytic acid or in the pH and temperature activity optima. Yet, it retained approximately 50% activity after incubations for 20 min at 65, 75 and 85 °C compared to almost full inactivation of the wild-type enzyme. Production of ApV1 in Pichia pastoris (Komagataella phaffi) was much lower than the wild-type enzyme due to the presence of the extra non-consecutive disulfide bond. Production bottlenecks were explored using bidirectional promoters for co-expression of folding chaperones. Co-expression of protein disulfide bond isomerase (Pdi) increased production of ApV1 by ~ 12-fold compared to expression without this folding catalyst and restored yields to similar levels seen with the wild-type enzyme. Conclusions Overall, the results show that protein engineering for enhanced enzymatic properties like thermostability may result in folding complexity and decreased production in microbial systems. Hence parallel development of improved production strains is imperative to achieve the desirable levels of recombinant protein for industrial processes.

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Identification of an N-acetylneuraminic acid-presenting bacteria isolated from a human microbiome

Scientific Reports ◽

10.1038/s41598-021-83875-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zhen Han ◽

Peter S. Thuy-Boun ◽

Wayne Pfeiffer ◽

Vincent F. Vartabedian ◽

Ali Torkamani ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Human Microbiome ◽

Host Immunity ◽

Rrna Gene ◽

Metabolic Labeling ◽

Selective Labeling ◽

Fecal Microbiome ◽

Acetylneuraminic Acid ◽

Intestinal Mucus ◽

Microbial Systems

AbstractN-Acetylneuraminic acid is the most abundant sialic acid (SA) in humans and is expressed as the terminal sugar on intestinal mucus glycans. Several pathogenic bacteria harvest and display host SA on their own surfaces to evade Siglec-mediated host immunity. While previous studies have identified bacterial enzymes associated with SA catabolism, no reported methods permit the selective labeling, tracking, and quantitation of SA-presenting microbes within complex multi-microbial systems. We combined metabolic labeling, click chemistry, 16S rRNA gene, and whole-genome sequencing to track and identify SA-presenting microbes from a cultured human fecal microbiome. We isolated a new strain of Escherichia coli that incorporates SA onto its own surface and encodes for the nanT, neuA, and neuS genes necessary for harvesting and presenting SA. Our method is applicable to the identification of SA-presenting bacteria from human, animal, and environmental microbiomes, as well as providing an entry point for the investigation of surface-expressed SA-associated structures.

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