Corrigendum to "Aptamer-based cell-free detection system to detect target protein" [Synth Syst Biotechnol 6 (3) (2021) 209-215].

[This corrects the article DOI: 10.1016/j.synbio.

Degradation strategies of pesticide residue: From chemicals to synthetic biology.

The past 50 years have witnessed a massive expansion in the demand and application of pesticides. However, pesticides are difficult to be completely degraded without intervention hence the pesticide residue could pose a persistent threat to non-target organisms in many aspects. To aim at the problem of the abuse of pesticide products and excessive pesticide residues in the environment, chemical and biological degradation methods are widely developed but are scaled and insufficient to solve such a pollution.

A Novel κ-Carrageenase from Marine Bacterium SM41: Heterologous Expression, Biochemical Characterization and Salt-Tolerance Mechanism Investigation.

κ-carrageenases are members of the glycoside hydrolase family 16 (GH16) that hydrolyze sulfated galactans in red algae, known as κ-carrageenans. In this study, a novel κ-carrageenase gene from the marine bacterium SM41 (RsCgk) was discovered via the genome mining approach. There are currently no reports on κ-carrageenase from the genus, and RsCgk shares a low identity (less than 65%) with κ- carrageenase from other genera.

Responses of human gut microbiota abundance and amino acid metabolism to berberine.

The intestine is a potential location for berberine (BBR) to exert its therapeutic effects, but the understanding of the influences of BBR on the gut microbiota is limited. Through fermentation of human intestinal microbiota, we investigated the effects of BBR on microbiota composition and metabolism. The result indicated that BBR reduced the production of acetic acid and propionic acid and had no effect on the content of butyric acid.

Corrigendum: Key Enzymes in Fatty Acid Synthesis Pathway for Bioactive Lipids Biosynthesis.

[This corrects the article DOI: 10.3389/fnut.2022.

Key Enzymes in Fatty Acid Synthesis Pathway for Bioactive Lipids Biosynthesis.

Dietary bioactive lipids, one of the three primary nutrients, is not only essential for growth and provides nutrients and energy for life's activities but can also help to guard against disease, such as Alzheimer's and cardiovascular diseases, which further strengthen the immune system and maintain many body functions. Many microorganisms, such as yeast, algae, and marine fungi, have been widely developed for dietary bioactive lipids production. These biosynthetic processes were not limited by the climate and ground, which are also responsible for superiority of shorter periods and high conversion rate.

Biochemical Characterization and Cold-Adaption Mechanism of a PL-17 Family Alginate Lyase Aly23 from Marine Bacterium sp. ASY5 and Its Application for Oligosaccharides Production.

As an important enzyme involved in the marine carbon cycle, alginate lyase has received extensive attention because of its excellent degradation ability on brown algae, which is widely utilized for alginate oligosaccharide preparation or bioethanol production. In comparison with endo-type alginate lyases (PL-5, PL-7, and PL-18 families), limited studies have focused on PL-17 family alginate lyases, especially for those with special characteristics. In this study, a novel PL-17 family alginate lyase, Aly23, was identified and cloned from the marine bacterium ASY5.

Applications of Synthetic Biotechnology on Carbon Neutrality Research: A Review on Electrically Driven Microbial and Enzyme Engineering.

With the advancement of science, technology, and productivity, the rapid development of industrial production, transportation, and the exploitation of fossil fuels has gradually led to the accumulation of greenhouse gases and deterioration of global warming. Carbon neutrality is a balance between absorption and emissions achieved by minimizing carbon dioxide (CO) emissions from human social productive activity through a series of initiatives, including energy substitution and energy efficiency improvement. Then CO was offset through forest carbon sequestration and captured at last.

Helical structure motifs made searchable for functional peptide design.

The systematic design of functional peptides has technological and therapeutic applications. However, there is a need for pattern-based search engines that help locate desired functional motifs in primary sequences regardless of their evolutionary conservation. Existing databases such as The Protein Secondary Structure database (PSS) no longer serves the community, while the Dictionary of Protein Secondary Structure (DSSP) annotates the secondary structures when tertiary structures of proteins are provided.

Aptamer-based cell-free detection system to detect target protein.

Biomarkers of disease, especially protein, show great potential for diagnosis and prognosis. For detecting a certain protein, a binding assay implementing antibodies is commonly performed. However, antibodies are not thermally stable and may cause false-positive when the sample composition is complicated.

Identification and antioxidant activity of bovine bone collagen-derived novel peptides prepared by recombinant collagenase from Bacillus cereus.

Millions of tons of collagen-rich bovine bone are produced as byproducts of the consumption of beef. Hydrolyzing bovine bone collagen (BBC) is an effective measure for both increasing its added value and protecting the environment. In this study, a kind of recombinant bacterial collagenase mining from Bacillus cereus was successfully performed and applied to hydrolyze BBC to collagen-soluble peptides (CPP).

Construction and characterization of a novel glucose dehydrogenase-leucine dehydrogenase fusion enzyme for the biosynthesis of L-tert-leucine.

Background: Biosynthesis of L-tert-leucine (L-tle), a significant pharmaceutical intermediate, by a cofactor regeneration system friendly and efficiently is a worthful goal all the time. The cofactor regeneration system of leucine dehydrogenase (LeuDH) and glucose dehydrogenase (GDH) has showed great coupling catalytic efficiency in the synthesis of L-tle, however the multi-enzyme complex of GDH and LeuDH has never been constructed successfully.

Results: In this work, a novel fusion enzyme (GDH-R3-LeuDH) for the efficient biosynthesis of L-tle was constructed by the fusion of LeuDH and GDH mediated with a rigid peptide linker.

Determination of Ag[I] and NADH Using Single-Molecule Conductance Ratiometric Probes.

The sensing platform based on single-molecule measurements provides a new perspective for constructing ultrasensitive systems. However, most of these sensing platforms are unavailable for the accurate determination of target analytes. Herein, we demonstrate a conductance ratiometric strategy combing with the single-molecule conductance techniques for ultrasensitive and precise determination.

Immobilization of formate dehydrogenase on polyethylenimine-grafted graphene oxide with kinetics and stability study.

Graphene oxide-based nanomaterials are promising for enzyme immobilization due to the possibilities of functionalizing surface. Polyethylenimine-grafted graphene oxide was constructed as a novel scaffold for immobilization of formate dehydrogenase. Compared with free formate dehydrogenase and graphene oxide adsorbed formate dehydrogenase, thermostability, storage stability, and reusability of polyethylenimine-grafted graphene oxide-formate dehydrogenase were enhanced.

Synthesizing Chiral Drug Intermediates by Biocatalysis.

The chiral feature is a critical factor for the efficacy and safety of many therapeutic agents. At present, about 57% of marketed drugs are chiral drugs and about 99% of purified natural products are chiral compounds. There has been a tremendous potential of functional microorganisms and biocatalysts derived from them for the bioconversion of synthetic chemicals into drugs with high enantio-, chemo-, and regio-selectivities.

Coenzyme Coupling Boosts Charge Transport through Single Bioactive Enzyme Junctions.

Oxidation of formate to CO is catalyzed via the donation of electrons from formate dehydrogenase (FDH) to nicotinamide adenine dinucleotide (NAD), and thus the charge transport characteristics of FDH become essential but remain unexplored. Here, we investigated the charge transport through single-enzyme junctions of FDH using the scanning tunneling microscope break junction technique (STM-BJ). We found that the coupling of NAD with FDH boosts the charge transport by ∼2,100%, and the single-enzyme conductance highly correlates with the enzyme activity.

Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder.

Autism spectrum disorder (ASD) is a brain-based neurodevelopmental disorder characterized by behavioral abnormalities. Accumulating studies show that the gut microbiota plays a vital role in the pathogenesis of ASD, and gut microbiota transplantation (GMT) is a promising technique for the treatment of ASD. In clinical applications of GMT, it is challenging to obtain effective transplants because of the high costs of donor selection and heterogeneity of donors' gut microbiota, which can cause different clinical responses.

Design and Application of an Artificial Hybrid PromoterPin Genetic Circuit to Achieve Lower Basal Expression Level.

Quorum quenching (QQ) enzymes, which degrade signaling molecules so as to disrupt the quorum sensing signaling process, have drawn much attention as alternative antimicrobial agents. However, the screening methods for evolution of such enzymes through constructing genetic circuits remain a challenge for its relatively high false positive rates caused by the higher basal expression level of the naturally acquired promoter. Thus, we presented an improved genetic circuit by introducing an artificial hybrid promoter P combining P originated from lactose promoter with QS regulatory promoter P to control the expression of reporter gene rfp.

Coenzyme Binding Site Analysis of an Isopropanol Dehydrogenase with Wide Substrate Spectrum and Excellent Organic Solvent Tolerance.

NAD(P)H-dependent enzymes are ideal biocatalysts for the industrial production of chiral compounds, such as chiral alcohols, chiral amino acids, and chiral amines; however, efficient strategies for the regeneration of coenzyme are expected as costly of the coenzymes. Herein, a solvent-tolerant isopropanol dehydrogenase (IDH) showing lower similarity (37%) with other proteins was obtained and characterized. The enzyme exhibits high catalysis ability of its substrates methanol, ethanol, ethylene glycol, glycerol, isopropanol, n-butanol, isobutanol, and acetone.

Evaluation of the effects of four media on human intestinal microbiota culture in vitro.

The human intestinal microbiota has an important role in the maintenance of human health and disease pathogenesis. The aim of this research was to investigate the impact of four media on human intestinal microbiota metabolite and composition changes, we performed in vitro batch culture using intestinal microbiota samples from three fecal microbiota transplantation (FMT) donors. After 48 h culture, gut microbiota medium (GMM) had the highest production of acetic acid (73.

Biosynthetic bifunctional enzyme complex with high-efficiency luciferin-recycling to enhance the bioluminescence imaging.

Firefly luciferase is a prominent reporter on molecular imaging with the advantage of longer wavelength on light emission and the ATP linear correlation, which makes it useful in most of current bioluminescence imaging model. However, the utility of this biomaterial was limited by the signal intensity and stability which are respectively affected by enzyme activity and substrate consumption. This study demonstrated a series of novel synthetic bifunctional enzyme complex of Firefly luciferase (Fluc) and Luciferin-regenerating enzyme (LRE).

Bioinspired genetic engineering of supramolecular assembled formate dehydrogenase with enhanced biocatalysis activities.

A bioinspired strategy for the synthesis of supramolecular and biocatalytical materials was developed base on protein-protein supramolecular interaction and genetic engineering. Formate dehydrogenase (FDH) and its functional fragments were separately fused to form a multi-function domain. The fusion proteins and functional fragments self-assembled into the expanded and controllable supramolecular interaction networks.

Fusion expression of bifunctional enzyme complex for luciferin-recycling to enhance the luminescence imaging.

Firefly luciferase (Fluc) has been widely used as a bioluminescent monitor. The ATP linear correlation and exogenous luciferin requirement make it useful in most of current imaging systems. However, the utility of this reporter was still limited by the intensity and decay of the luminescent signal, and the active site and structure of enzyme including the relevant substrate channeling region.

Resolution Mechanism and Characterization of an Ammonium Chloride-Tolerant, High-Thermostable, and Salt-Tolerant Phenylalanine Dehydrogenase from Bacillus halodurans.

As phenylalanine dehydrogenase (PheDH) plays an important role in the synthesis of chiral drug intermediates and detection of phenylketonuria, it is significant to obtain a PheDH with specific and high activity. Here, a PheDH gene, pdh, encoding a novel BhPheDH with 61.0% similarity to the known PheDH from Microbacterium sp.